Special topic: Metagenomics - Genome Sciences

MetaGenomics<br />

Carlos Araya | 2.6.08<br />

Life on Earth<br />

What is metagenomics? (And why now?)<br />

DNA-based identification of species<br />

diversity<br />

Sorcerer II: Global Ocean Sampling<br />

Protein prediction: A primer<br />

Human gut metagenomics<br />

Technological challenges<br />

Bioprospecting: Green Chemistry

---

Life on Earth: The cultured vs. the uncultured<br />

Prokaryotic abundance & biomass:<br />

• 4-5x10^30 cells<br />

• 5 Trillion tonnes<br />

Large population size and rapid<br />

growth imply an enormous<br />

capacity for genetic diversity.<br />

We’re missing out: Cultured<br />

microorganisms represent ≤1% of<br />

the total microbial community<br />

(from soil).<br />

Whitman et al., 1998 / Gillespie et al., 2002

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What is metagenomics?<br />

(and why now?)<br />

“…the study of genetic material<br />

recovered directly from<br />

environmental samples…”<br />

Environmental sample<br />

Gentle lysis,<br />

extraction, DNA<br />

size separation<br />

BAC/fosmid<br />

cloning<br />

(40–100 kb)<br />

Sequencing of<br />

entire BAC insert<br />

BAC single-insert sequence<br />

DeLong et al., 2005

---

Faster, cheaper<br />

DNA sequencing<br />

Today, DNA sequencing costs<br />

1/10,000th of what it used to.<br />

Impact on biology:<br />

• Human genetic variation<br />

• <strong>Metagenomics</strong>:<br />

• Environmental<br />

• Organismal<br />

transistors per chip<br />

bp sequenced per person/day<br />

Bio-ERA, 2007

---

16s rRNA: Molecular clocks & evolutionary trajectories<br />

DNA sequence similarity provides evolutionary<br />

relationships between organisms (phylogeny).<br />

What makes a good molecular clock?<br />

‣ No strong selective forces.<br />

‣ Ubiquitous<br />

‣ Large: provides sufficient information.<br />

‣ 16s rRNA sequence similarity of 97% is generally<br />

defined as a species (ribotype or phylotype).<br />

1<br />

E ~~~~~~~~~~~~~~~~~~~~~<br />

1:<br />

2:<br />

3:<br />

4:<br />

2<br />

3<br />

A A C C G G T T<br />

A A C C G G T G<br />

A C C C G G T C<br />

A C C C G G T A<br />

4<br />

Woese, 1987

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Bacillus coagulans<br />

Staphylococcus aureus<br />

Enterococcus sulfureus<br />

Streptococcus bovis<br />

Lactobacillus acidophilus<br />

Spiroplasma tiawanense<br />

Clostridium butyricum<br />

Heliobacterium gestii<br />

Thermoanaerobacter lacticus<br />

Deinococcus radiodurans<br />

Flavobacterium odoratum<br />

Chlamydia pneumoniae<br />

Fusobacterium perfoetens<br />

Escherichia coli<br />

Salmonella agona<br />

Vibrio aestuarianus<br />

Pseudomonas mendocina<br />

Legionella pneumophila<br />

Neisseria gonorrhoeae<br />

Burkholderia solanacearum<br />

Agrobacterium vitis<br />

Rhizobium leguminosarum<br />

Rickettsia montana<br />

Campylobacter hyointestinalis<br />

Helicobacter cholecystus<br />

Desulfoacinum infernum<br />

Myxococcus coralloides<br />

Spirochaeta alkalica<br />

Spirulina subsalsa<br />

Chlorobium phaeovibrioides<br />

Trichotomospora caesia<br />

Streptomyces lavendulae<br />

Microbacterium lacticum<br />

Nocardia calcarea<br />

Corynebacterium acetoacidophilum<br />

Kineococcus aurantiacus<br />

Geodermatophilus obscurus<br />

Bifidobacterium catenulatum<br />

Chloroflexus aurantiacus<br />

Aquifex pyrophilus<br />

Thermotoga maritima<br />

Pyrodictium occultum<br />

Thermoproteus tenax<br />

Thermococcus stetteri<br />

Thermococcus fumicolans<br />

Methanococcus jannaschii A<br />

Methanococcus maripaludis<br />

Methanobacterium bryantii<br />

Methanobacterium subterraneum<br />

Methanosarcina siciliae<br />

Thermoplasma acidophilum<br />

Halobacterium marismortui<br />

Haloferax denitrificans<br />

Coemansia reversa<br />

Spirodactylon aureum<br />

Coemansia braziliensis<br />

Dipsacomyces acuminosporus<br />

Linderina pennispora<br />

Kickxella alabastrina<br />

Martensiomyces pterosporus<br />

Smittium culisetae<br />

Capniomyces stellatus<br />

Furculomyces boomerangus<br />

Genistelloides hibernus<br />

Spiromyces aspiralis<br />

Spiromyces minutus<br />

Conidiobolus thromboides<br />

Macrobiotophthora vermicola<br />

Strongwellsea castrans<br />

Pandora neoaphidis<br />

Zoophthora culisetae<br />

Zoophthora radicans<br />

Eryniopsis ptycopterae<br />

Entomophaga aulicae<br />

Entomophthora muscae<br />

Entomophthora schizophora<br />

Conidiobolus coronatus<br />

Mucor ramannianus<br />

Mucor mucedo<br />

Mucor racemosus<br />

Syncephalastrum racemosum<br />

Basidiobolus ranarum<br />

Endogone pisiformis<br />

Mortierella polycephala<br />

Acaulospora rugosa<br />

Acaulospora spinosa<br />

Entrophospora columbiana<br />

Glomus mosseae<br />

Glomus cf geosporum<br />

Glomus mossae<br />

Glomus manihotis<br />

Glomus intraradices<br />

Glomus etunicatum<br />

Glomus claroideum<br />

Glomus versiforme<br />

Scuttellospora pellucida<br />

Scutellospora castanea<br />

Scutellospora heterogama<br />

Scuttellospora dipapillosa<br />

Gigaspora albida<br />

Gigaspora margarita<br />

Gigaspora decipiens<br />

Gigaspora gigantea<br />

Acaulospora gerdemannii<br />

Geosiphon pyriforme<br />

Aleurodiscus botryosus<br />

Stereum hirsutum<br />

Gloeocystidiellum leucoxantha<br />

Stereum annosum<br />

Heterobasidion annosum<br />

Laxitextum bicolor<br />

Hericium ramosum<br />

Hericium erinaceum<br />

Lentinellus ursinus<br />

Lentinellus omphalodes<br />

Clavicorona pyxidata<br />

Auriscalpium vulgare<br />

Bondarzewia berkeleyi<br />

Scytinostroma alutum<br />

Peniophora nuda<br />

Echinodontium tinctorium<br />

Russula compacta<br />

Inonotus hispidus<br />

Phellinus igniarius<br />

Trichaptum biforme<br />

Trichaptum abietinum<br />

Trichaptum fusco violaceum<br />

Trichaptum laricinum<br />

Basidioradulum radula<br />

Coltricia perennis<br />

Schizopora paradoxa<br />

Hyphodontia alutaria<br />

Sphaerobolus stellatus<br />

Geastrum saccatum<br />

Ramaria stricta<br />

Clavariadelphus pistillaris<br />

Gomphus floccosus<br />

Pseudocolus fusiformis<br />

Auricularia polytricha<br />

Auricularia auricula<br />

Pseudohydnum gelatinosum<br />

Boletus satanas<br />

Xerocomus chrysenteron<br />

Calostoma ravenelii<br />

Calostoma cinnabarinum<br />

Scleroderma citrina<br />

Paxillus panuoides<br />

Leucoagaricus gongylophorus<br />

Basid symb of Atta cephalotes<br />

Basid symb of Sericomyrmex bond<br />

Basid symb of Trachymyrmex bugn<br />

Basid symb of Cyphomyrmex rimos<br />

Basid symb of Apterostigma coll<br />

Athelia bombacina<br />

Panellus stipticus<br />

Typhula phacorrhiza<br />

Panellus serotinus<br />

Tricholoma matsutake<br />

Omphalina umbellifera<br />

Pleurotus ostreatus<br />

Coprinus cinereus<br />

Cortinarius iodes<br />

Lepiota procera<br />

Crucibulum laeve<br />

Stropharia rugosoannulata<br />

Calvatia gigantea<br />

Cyathus striatus<br />

Lentinula lateritia<br />

Amanita muscaria<br />

Cantharellus tubaeformis<br />

Dictyonema pavonia<br />

Schizophyllum commune<br />

Fistulina hepatica<br />

Pleurotus tuberregium<br />

Agaricus bisporus<br />

Tulostoma macrocephala<br />

Pluteus petasatus<br />

Termitomyces cartilagineus<br />

Termitomyces albuminosus<br />

Ceriporia purpurea<br />

Bjerkandera adusta<br />

Phlebia radiata<br />

Phanerochaete chrysosporium<br />

Rhizoctonia zeae<br />

Tretopileus sphaerophorus<br />

Dentocorticium sulphurellum<br />

Fomes fomentarius<br />

Lentinus tigrinus<br />

Ganoderma australe<br />

Trametes suaveolens<br />

Polyporus squamosus<br />

Laetiporus sulphureus<br />

Phaeolus schweinitzii<br />

Sparassis spathulata<br />

Antrodia carbonica<br />

Daedalea quercina<br />

Fomitopsis pinicola<br />

Spongipellis unicolor<br />

Panus rudis<br />

Meripilus giganteus<br />

Albatrellus syringae<br />

Gloeophyllum sepiarium<br />

Hydnum repandum<br />

Multiclavula mucida<br />

Clavulina cristata<br />

Botryobasidium subcoronatum<br />

Botryobasidium isabellinum<br />

Thanatephorus cucumeris<br />

Thanatephorus praticola<br />

Heterotextus alpinus<br />

Calocera cornea<br />

Dacrymyces chrysospermus<br />

Dacrymyces stillatus<br />

Tsuchiaea wingfieldii<br />

Cryptococcus neoformans<br />

Filobasidiella neoformans<br />

Bullera dendrophila<br />

Trimorphomyces papilionaceus<br />

Bullera miyagiana<br />

Bullera globospora<br />

Tremella globospora<br />

Bullera pseudoalba<br />

Bullera penniseticola<br />

Bullera hannae<br />

Bullera alba<br />

Bullera unica<br />

Tremella moriformis<br />

Fellomyces distylii<br />

Kockovaella schimae<br />

Fellomyces ogasawarensis<br />

Kockovaella phaffii<br />

Kockovaella machilophila<br />

Kockovaella imperatae<br />

Kockovaella sacchari<br />

Kockovaella thailandica<br />

Fellomyces fuzhouensis<br />

Fellomyces penicillatus<br />

Fellomyces polyborus<br />

Fellomyces horovitziae<br />

Sterigmatosporidium polymorphum<br />

Fibulobasidium inconspicuum<br />

Sirobasidium magnum<br />

Bullera coprosmaensis<br />

Bullera oryzae<br />

Bullera derxii<br />

Bullera sinensis<br />

Bullera mrakii<br />

Bullera huiaensis<br />

Bullera crocea<br />

Bullera armeniaca<br />

Bullera variabilis<br />

Trichosporon cutaneum<br />

Trichosporon japonicum<br />

Tremella foliacea<br />

Holtermannia corniformis<br />

Filobasidium floriforme<br />

Mrakia psychrophilia<br />

Mrakia frigida<br />

Udeniomyces megalosporus<br />

Udeniomyces puniceus<br />

Udeniomyces piricola<br />

Bullera grandispora<br />

Leucosporidium lari marini<br />

Cystofilobasidium capitatum<br />

Phaffia rhodozyma<br />

Tilletia caries<br />

Tilletiaria anomala<br />

Tilletiopsis fulvescens<br />

Tilletiopsis flava<br />

Tilletiopsis minor<br />

Tilletiopsis albescens<br />

Tilletiopsis washingtonensis<br />

Tilletiopsis pallescens<br />

Ustilago hordei<br />

Ustilago maydis<br />

Ustilago shiraiana<br />

Graphiola cylindrica<br />

Graphiola phoenicis<br />

Camptobasidium hydrophilum<br />

Sympodiomycopsis paphiopedili<br />

Kondoa malvinella<br />

Bensingtonia miscanthi<br />

Bensingtonia subrosea<br />

Bensingtonia yuccicola<br />

Bensingtonia phylladus<br />

Mycogloea macrospora<br />

Sterigmatomyces halophilus<br />

Agaricostilbum hyphaenes<br />

Bensingtonia ingoldii<br />

Bensingtonia musae<br />

Kurtzmanomyces nectairei<br />

Chionosphaera apobasidialis<br />

Sporobolomyces xanthus<br />

Bensingtonia naganoensis<br />

Bensingtonia ciliata<br />

Mixia osmundae<br />

Rhodosporidium toruloides<br />

Rhodotorula glutinis<br />

Rhodotorula graminis<br />

Rhodotorula mucilaginosa<br />

Rhodosporidium fluviale<br />

Sporidiobolus johnsonii<br />

Sporobolomyces roseus<br />

Bensingtonia yamatoana<br />

Zymoxenogloea eriophori<br />

Microbotryum violaceum<br />

Leucosporidium scottii<br />

Bensingtonia intermedia<br />

Heterogastridium pycnidioideum<br />

Hyalopsora polypodii<br />

Peridermium harknessii<br />

Cronartium ribicola<br />

Uredinopsis intermedia<br />

Physopella ampelopsidis<br />

Gymnoconia nitens<br />

Puccinia suzutake<br />

Nyssopsora echinata<br />

Aecidium epimedii<br />

Rhodotorula minuta<br />

Erythrobasidium hasegawianum<br />

Rhodotorula lactosa<br />

Rhodosporidium dacryoidum<br />

Helicobasidium purpureum<br />

Helicobasidium mompa<br />

Helicobasidium corticioides<br />

Helicogloea variabilis<br />

Graphium putredinis<br />

Graphium tectonae<br />

Petriella setifera<br />

Lomentospora prolificans<br />

Pseudallescheria boydii<br />

Pseudallescheria ellipsoidea<br />

Lignincola laevis<br />

Nais inornata<br />

Aniptodera chesapeakensis<br />

Halosarpheia retorquens<br />

Microascus cirrosus<br />

Graphium penicillioides<br />

Ceratocystis fimbriata<br />

Fusarium culmorum<br />

Gibberella pulicaris<br />

Fusarium cerealis<br />

Fusarium equiseti<br />

Nectria haematococca<br />

Fusarium oxysporum<br />

Gibberella avenacea<br />

Fusarium merismoides<br />

Paecilomyces tenuipes<br />

Cordycepioideus bisporus<br />

Hamiltonaphis styraci symb<br />

Geosmithia putterillii<br />

Geosmithia lavendula<br />

Spicellum roseum<br />

Mycoarachis inversa<br />

Nectria ochroleuca<br />

Nectria aureofulva<br />

Chaetopsina fulva<br />

Hypocrea lutea<br />

Hypomyces chrysospermus<br />

Glomerella cingulata<br />

Verticillium dahliae<br />

Hypoxylon fragiforme<br />

Xylaria carpophila<br />

Xylaria polymorpha<br />

Rosellinia necatrix<br />

Obolarina dryophila<br />

Kionochaeta ivoriensis<br />

Kionochaeta spissa<br />

Kionochaeta ramifera<br />

Meliola juddiana<br />

Meliola niessleana<br />

Podospora anserina<br />

Neurospora crassa<br />

Sordaria fimicola<br />

Chaetomium elatum<br />

Camarops microspora<br />

Ascovaginospora stellipala<br />

Cryphonectria parasitica<br />

Cryphonectria radicalis<br />

Cryphonectria havanensis<br />

Cryphonectria cubensis<br />

Endothia gyrosa<br />

Leucostoma persoonii<br />

Ophiostoma europhioides<br />

Ophiostoma cucullatum<br />

Ophiostoma ainoae<br />

Ophiostoma stenoceras<br />

Sporothrix schenckii<br />

Ophiostoma ulmi<br />

Ophiostoma penicillatum<br />

Pesotum fragrans<br />

Ophiostoma bicolor<br />

Ophiostoma piceae<br />

Pseudohalonectria falcata<br />

Ophioceras leptosporum<br />

Magnaporthe grisea<br />

Lulworthia fucicola<br />

Spathularia flavida<br />

Cudonia confusa<br />

Rhytisma salicinum<br />

Monilinia laxa<br />

Monilinia fructicola<br />

Sclerotinia sclerotiorum<br />

Amylocarpus encephaloides<br />

Neobulgaria premnophila<br />

Blumeria graminis<br />

Phyllactinia guttata<br />

Cyttaria darwinii<br />

Thelebolus stercoreus<br />

Ascozonus woolhopensis<br />

Leotia lubrica<br />

Microglossum viride<br />

Geomyces pannorum<br />

Geomyces pannorum var asperula<br />

Bulgaria inquinans<br />

Leptosphaeria bicolor<br />

Cucurbidothis pityophila<br />

Kirschsteiniothelia elaterascus<br />

Helicascus kanaloanus<br />

Pyrenophora trichostoma<br />

Pyrenophora tritici repentis<br />

Cochliobolus sativus<br />

Alternaria brassicae<br />

Clathrospora diplospora<br />

Alternaria alternata<br />

Alternaria brassicicola<br />

Alternaria raphani<br />

Pleospora herbarum<br />

Setosphaeria rostrata<br />

Pleospora betae<br />

Leptosphaeria doliolum<br />

Leptosphaeria maculans<br />

Cucurbitaria elongata<br />

Leptosphaeria microscopica<br />

Ophiobolus herpotrichus<br />

Phaeosphaeria nodorum<br />

Cucurbitaria berberidis<br />

Pleospora rudis<br />

Westerdykella dispersa<br />

Lophiostoma crenatum<br />

Sporomia lignicola<br />

Monodictys castaneae<br />

Kirschsteiniothelia maritima<br />

Herpotrichia juniperi<br />

Mycosphaerella mycopappi<br />

Herpotrichia diffusa<br />

Dendryphiopsis atra<br />

Botryosphaeria rhodina<br />

Botryosphaeria ribis<br />

Phaeosclera dematioides<br />

Dothidea insculpta<br />

Dothidea hippophaeos<br />

Aureobasidium pullulans<br />

Coccodinium bartschii<br />

Sarcinomyces crustaceus<br />

Siphula ceratites<br />

Pertusaria trachythallina<br />

Diploschistes ocellatus var al<br />

Anamylopsora pulcherrima<br />

Trapelia placodioides<br />

Trapelia involuta<br />

Placopsis gelida<br />

Conotrema populorum<br />

Cyanodermella viridula<br />

Gyalecta ulmi<br />

Nephroma arcticum<br />

Peltigera neopolydactyla<br />

Solorina crocea<br />

Pseudevernia cladoniae<br />

Pilophorus acicularis<br />

Cladia aggregata<br />

Cladonia bellidiflora<br />

Stereocaulon ramulosum<br />

Lecanora dispersa<br />

Squamarina lentigera<br />

Rhizocarpon geographicum<br />

Sphaerophorus globosus<br />

Leifidium tenerum<br />

Bunodophoron scrobiculatum<br />

Xanthoria elegans<br />

Megalospora sulphurata<br />

Lecidea fuscoatra<br />

Porpidia crustulata<br />

Calicium adspersum<br />

Texosporium sancti jacobi<br />

Thelomma mammosum<br />

Cyphelium inquinans<br />

Chromocleista malachitea<br />

Penicillium notatum<br />

Eupenicillium crustaceum<br />

Penicillium freii<br />

Penicillium namyslowskii<br />

Geosmithia namyslowskii<br />

Eupenicillium javanicum<br />

Merimbla ingelheimense<br />

Hamigera avellanea<br />

Hemicarpenteles ornatus<br />

Aspergillus flavus<br />

Aspergillus oryzae<br />

Aspergillus nomius<br />

Aspergillus parasiticus<br />

Aspergillus tamarii<br />

Aspergillus sojae<br />

Aspergillus avenaceus<br />

Monascus purpureus<br />

Eurotium herbariorum<br />

Eurotium rubrum<br />

Aspergillus restrictus<br />

Aspergillus ustus<br />

Aspergillus versicolor<br />

Emericella nidulans<br />

Aspergillus nidulans<br />

Fennellia flavipes<br />

Aspergillus terreus<br />

Aspergillus wentii<br />

Chaetosartorya cremea<br />

Neosartorya fischeri<br />

Aspergillus fumigatus<br />

Aspergillus clavatus<br />

Aspergillus ochraceus<br />

Aspergillus niger<br />

Aspergillus awamorii<br />

Aspergillus cervinus<br />

Aspergillus candidus<br />

Aspergillus zonatus<br />

Aspergillus sparsus<br />

Byssochlamys nivea<br />

Paecilomyces variotii<br />

Thermoascus crustaceus<br />

Geosmithia cylindrospora<br />

Talaromyces eburneus<br />

Talaromyces emersonii<br />

Talaromyces flavus<br />

Talaromyces bacillisporus<br />

Elaphomyces leveillei<br />

Elaphomyces maculatus<br />

Auxarthron zuffianum<br />

Malbranchea filamentosa<br />

Malbranchea dendritica<br />

Malbranchea albolutea<br />

Uncinocarpus reesii<br />

Coccidioides immitis<br />

Onygena equina<br />

Renispora flavissima<br />

Ctenomyces serratus<br />

Trichophyton rubrum<br />

Gymnoascoideus petalosporus<br />

Chrysosporium parvum<br />

Blastomyces dermatitidis<br />

Histoplasma capsulatum<br />

Histoplasma capsulatum ssp farci<br />

Histoplasma capsulatum ssp duboi<br />

Ascosphaera apis<br />

Eremascus albus<br />

Malbranchea gypsea<br />

Phaeoannellomyces elegans<br />

Nadsoniella nigra<br />

Exophiala jeanselmei<br />

Phaeococcomyces exophialae<br />

Capronia pilosella<br />

Exophiala mansonii<br />

Pullularia prototropha<br />

Exophiala dermatitidis<br />

Sarcinomyces phaeomuriformis<br />

Capronia mansonii<br />

Graphium calicioides<br />

Ceramothyrium linnaeae<br />

Coniosporium apollinis<br />

Coniosporium perforans<br />

Chaenothecopsis savonica<br />

Sphinctrina turbinata<br />

Stenocybe pullatula<br />

Mycocalicium albonigrum<br />

Lasallia rossica<br />

Umbilicaria subglabra<br />

Stegobium paniceum yeast like sym<br />

Lasioderma serricorne yeast like<br />

Monacrosporium ellipsospora<br />

Orbilia auricolor<br />

Arthrobotrys conoides<br />

Duddingtonia flagrans<br />

Monacrosporium gephyropaga<br />

Monacrosporium haptotylum<br />

Arthrobotrys robusta<br />

Dactylella oxyspora<br />

Dactylella rhopalota<br />

Arthrobotrys dactyloides<br />

Orbilia delicatula<br />

Choiromyces meandriformis<br />

Choiromyces venosus<br />

Tuber magnatum<br />

Tuber panniferum<br />

Tuber excavatum<br />

Tuber rapaeodorum<br />

Tuber gibbosum<br />

Tuber borchii<br />

Dingleya verrucosa<br />

Labyrinthomyces varius<br />

Reddellomyces donkii<br />

Wynnella silvicolor<br />

Barssia oregonensis<br />

Balsamia vulgaris<br />

Balsamia magnata<br />

Helvella lacunosa<br />

Helvella terrestris<br />

Underwoodia columnaris<br />

Caloscypha fulgens<br />

Pulvinula archeri<br />

Chalazion helveticum<br />

Ascodesmis sphaerospora<br />

Glaziella aurantiaca<br />

Aleuria aurantia<br />

Inermisia aggregata<br />

Trichophaea hybrida<br />

Wilcoxina mikolae<br />

Scutellinia scutellata<br />

Leucoscypha oroarctica<br />

Pyronema domesticum<br />

Otidea leporina<br />

Neottiella rutilans<br />

Paurocotylis pila<br />

Geopyxis carbonaria<br />

Tarzetta catinus<br />

Cookeina sulcipes<br />

Sarcoscypha austriaca<br />

Microstoma protracta<br />

Desmazierella acicola<br />

Plectania rhytidia<br />

Sarcosoma globosum<br />

Urnula hiemalis<br />

Morchella esculenta<br />

Morchella elata<br />

Verpa conica<br />

Verpa bohemica<br />

Leucangium carthusianum<br />

Fischerula subcaulis<br />

Disciotis venosa<br />

Hydnotrya tulasnei<br />

Gyromitra esculenta<br />

Gyromitra melaleucoides<br />

Pseudorhizina californica<br />

Gyromitra montana<br />

Discina macrospora<br />

Hydnotrya cerebriformis<br />

Rhizina undulata<br />

Cazia flexiascus<br />

Terfezia arenaria<br />

Peziza succosa<br />

Peziza quelepidotia<br />

Terfezia terfezioides<br />

Pachyphloeus melanoxanthus<br />

Boudiera acanthospora<br />

Peziza badia<br />

Thecotheus holmskjoldii<br />

Ascobolus lineolatus<br />

Pichia mexicana<br />

Candida conglobata<br />

Candida aaseri<br />

Candida butyri<br />

Candida insectorum<br />

Candida dendronema<br />

Candida tenuis<br />

Candida naeodendra<br />

Candida diddensiae<br />

Candida atlantica<br />

Candida atmosphaerica<br />

Candida buinensis<br />

Candida friedrichii<br />

Candida membranifaciens<br />

Pichia triangularis<br />

Candida multigemmis<br />

Candida oleophila<br />

Candida boleticola<br />

Candida schatavii<br />

Candida laureliae<br />

Candida krissii<br />

Candida santamariae var membra<br />

Candida ralunensis<br />

Candida santamariae var santam<br />

Candida beechii<br />

Candida zeylanoides<br />

Candida sophiae reginae<br />

Candida quercitrusa<br />

Candida natalensis<br />

Candida fragi<br />

Candida psychrophila<br />

Candida glucosophila<br />

Candida xestobii<br />

Candida fukuyamaensis<br />

Candida fermenticarens<br />

Pichia guilliermondii<br />

Debaryomyces hansenii var hans<br />

Debaryomyces hansenii var fabr<br />

Taphrina farlowii<br />

Yamadazyma guilliermondii<br />

Pichia farinosa<br />

Debaryomyces udenii<br />

Debaryomyces castellii<br />

Debaryomyces hansenii<br />

Candida sojae<br />

Candida tropicalis<br />

Candida albicans<br />

Candida dubliniensis<br />

Candida maltosa<br />

Candida viswanathii<br />

Candida lodderae<br />

Candida parapsilosis<br />

Lodderomyces elongisporus<br />

Candida shehatae var insectosa<br />

Candida shehatae var lignosa<br />

Candida shehatae var shehatae<br />

Candida palmioleophila<br />

Candida fluviatilis<br />

Candida saitoana<br />

Candida pseudoglaebosa<br />

Candida glaebosa<br />

Candida insectamans<br />

Candida lyxosophila<br />

Candida kruisii<br />

Candida tanzawaensis<br />

Candida sake<br />

Candida austromarina<br />

Candida coipomoensis<br />

Candida ergastensis<br />

Pichia angusta<br />

Williopsis salicorniae<br />

Endomyces fibuliger<br />

Saccharomycopsis fibuligera<br />

Saccharomycopsis capsularis<br />

Kluyveromyces nonfermentati<br />

Kluyveromyces aestuarii<br />

Kluyveromyces marxianus<br />

Kluyveromyces lactis<br />

Kluyveromyces dobzhanskii<br />

Kluyveromyces wickerhamii<br />

Holleya sinecauda<br />

Zygosaccharomyces mellis<br />

Zygosaccharomyces rouxii<br />

Zygosaccharomyces bisporus<br />

Zygosaccharomyces lentus<br />

Zygosaccharomyces bailii<br />

Arxiozyma telluris<br />

Saccharomyces dairensis<br />

Saccharomyces servazzii<br />

Saccharomyces unisporus<br />

Saccharomyces transvaalensis<br />

Zygosaccharomyces mrakii<br />

Torulaspora globosa<br />

Torulaspora delbrueckii<br />

Torulaspora pretoriensis<br />

Zygosaccharomyces microellipsoide<br />

Candida colliculosa<br />

Kazachstania viticola<br />

Kluyveromyces blattae<br />

Kluyveromyces phaffii<br />

Zygosaccharomyces florentinus<br />

Candida glabrata<br />

Kluyveromyces delphensis<br />

Saccharomyces pastorianus<br />

Saccharomyces cerevisiae<br />

Saccharomyces cerevisiae 2<br />

Saccharomyces bayanus<br />

Saccharomyces paradoxus<br />

Kluyveromyces polysporus<br />

Kluyveromyces yarrowii<br />

Kluyveromyces lodderae<br />

Saccharomyces rosinii<br />

Kluyveromyces africanus<br />

Saccharomyces spencerorum<br />

Saccharomyces exiguus<br />

Saccharomyces barnettii<br />

Saccharomyces castellii<br />

Zygosaccharomyces fermentati<br />

Saccharomyces kluyveri<br />

Kluyveromyces thermotolerans<br />

Kluyveromyces waltii<br />

Saccharomycodes ludwigii<br />

Hanseniaspora uvarum<br />

Williopsis pratensis<br />

Williopsis californica<br />

Starmera amethionina var pachy<br />

Starmera amethionina var ameth<br />

Starmera caribaea<br />

Pichia anomala<br />

Williopsis saturnus<br />

Williopsis saturnus var mrakii<br />

Williopsis mucosa<br />

Pachysolen tannophilus<br />

Candida chilensis<br />

Candida cylindracea<br />

Candida savonica<br />

Candida mesenterica<br />

Candida suecica<br />

Phaffomyces antillensis<br />

Phaffomyces opuntiae<br />

Phaffomyces thermotolerans<br />

Yarrowia lipolytica<br />

Candida rugosa<br />

Candida catenulata<br />

Candida pseudointermedia<br />

Candida intermedia<br />

Candida akabanensis<br />

Candida oregonensis<br />

Candida haemulonii<br />

Candida tsuchiyae<br />

Clavispora lusitaniae<br />

Candida melibiosica<br />

Candida torresii<br />

Metschnikowia bicuspidata<br />

Candida agrestis<br />

Metschnikowia reukaufii<br />

Metschnikowia pulcherrima<br />

Candida mogii<br />

Brettanomyces bruxellensis<br />

Dekkera bruxellensis<br />

Dekkera anomala<br />

Brettanomyces anomalus<br />

Dekkera custersiana<br />

Dekkera naardenensis<br />

Candida insectalens<br />

Candida silvatica<br />

Issatchenkia orientalis<br />

Pichia membranaefaciens<br />

Candida spandovensis<br />

Candida apicola<br />

Candida bombi<br />

Starmerella bombicola<br />

Candida geochares<br />

Candida vaccinii<br />

Endomyces geotrichum<br />

Galactomyces geotrichum<br />

Dipodascus albidus<br />

Candida chiropterorum<br />

Candida valdiviana<br />

Candida drimydis<br />

Waltomyces lipofer<br />

Dipodascopsis uninucleata<br />

Protomyces macrosporus<br />

Protomyces pachydermus<br />

Protomyces inouyei<br />

Protomyces lactucae<br />

Taphrina virginica<br />

Taphrina carnea<br />

Taphrina pruni subcordatae<br />

Taphrina mirabilis<br />

Taphrina nana<br />

Taphrina pruni<br />

Taphrina ulmi<br />

Taphrina communis<br />

Taphrina flavorubra<br />

Taphrina populina<br />

Taphrina deformans<br />

Taphrina wiesneri<br />

Taphrina robinsoniana<br />

Taphrina letifera<br />

Neolecta vitellina<br />

Neolecta irregularis<br />

Saitoella complicata<br />

Schizosaccharomyces pombe<br />

Schizosaccharomyces japonicus<br />

Pneumocystis carinii<br />

Calicium tricolor<br />

Taphrina maculans<br />

Taphrina californica<br />

Chytridium confervae<br />

Neocallimastix frontalis<br />

Neocallimastix joyonii<br />

Piromonas communis<br />

Spizellomyces acuminatus<br />

Allomyces macrogynus<br />

Blastocladiella emersonii<br />

Chrysops niger<br />

Drosophila melanogaster<br />

Ceratitis capitata<br />

Ornithoica vicina<br />

Nephrotoma altissima<br />

Lutzomyia shannoni<br />

Aedes albopictus<br />

Aedes aegypti<br />

Aedes punctor<br />

Toxorhynchites ambionensis<br />

Culex tritaeniorhynchus<br />

Anopheles psuedopunctipennis<br />

Anopheles albimanus<br />

Eucorethra underwoodi<br />

Dixella cornuta<br />

Culicoides variipennis<br />

Amblabesmia rhamphe<br />

Simulium vittatum<br />

Xenos vesparum<br />

Stylops melittae<br />

Mengenilla chobauti<br />

Galleria mellonella<br />

Archaeopsylla erinacei<br />

Panorpa germanica<br />

Anisochrysa carnea<br />

Oliarces clara<br />

Monolobus ovalipennis<br />

Antarctonomus complanatus<br />

Loricera foveata<br />

Loricera pilicornis pilicornis<br />

Amarotypus edwardsi<br />

Bembidion mexicanum<br />

Bembidion levettei carrianum<br />

Asaphidion curtum<br />

Diplous californicus<br />

Patrobus longicornis<br />

Pericompsus laetulus<br />

Diplochaetus planatus<br />

Zolus helmsi<br />

Merizodus angusticollis<br />

Sloaneana tasmaniae<br />

Batesiana hilaris<br />

Schizogenius falli<br />

Clivina ferrea<br />

Dyschirius sphaericollis<br />

Melisodera picipennis<br />

Mecyclothorax vulcans<br />

Amblytelus curtus<br />

Apotomus rufithorax<br />

Broscosoma relictum<br />

Creobius eydouxi<br />

Galerita lecontei lecontei<br />

Pseudaptinus rufulus<br />

Aptinus displosor<br />

Pterostichus melanarius<br />

Tetragonoderus latipennis<br />

Discoderus cordicollis<br />

Chlaenius ruficauda<br />

Calybe laetula<br />

Amara apricaria<br />

Agonum extensicolle<br />

Cymindis punctigera<br />

Loxandrus n sp nr amplithora<br />

Cnemalobus sulciferus<br />

Catapiesis brasiliensis<br />

Morion aridus<br />

Brachinus armiger<br />

Brachinus hirsutus<br />

Pheropsophus aequinoctialis<br />

Pasimachus atronitens<br />

Scarites subterraneus<br />

Carenum interruptum<br />

Siagona europaea<br />

Siagona jennisoni<br />

Clinidium calcaratum<br />

Omoglymmius hamatus<br />

Omus californicus<br />

Cicindela sedecimpunctata<br />

Metrius contractus<br />

Pachyteles striola<br />

Cymbionotum semelederi<br />

Cymbionotum pictulum<br />

Gehringia olympica<br />

Promecognathus crassus<br />

Laccocenus ambiguus<br />

Omophron obliteratum<br />

Psydrus piceus<br />

Ceroglossus chilensis<br />

Pamborus guerinii<br />

Calosoma scrutator<br />

Carabus nemoralis<br />

Scaphinotus petersi catalinae<br />

Cychrus italicus<br />

Opisthius richardsoni<br />

Leistus ferruginosus<br />

Nebria hudsonica<br />

Notiophilus semiopacus<br />

Trachypachus gibbsii<br />

Trachypachus holmbergi<br />

Systolosoma lateritium<br />

Elaphrus californicus<br />

Elaphrus clairvillei<br />

Blethisa multipunctata aurata<br />

Mecodema fulgidum<br />

Oregus aereus<br />

Suphis inflatus<br />

Copelatus chevrolati renovatus<br />

Hydroscapha natans<br />

Xanthopyga cacti<br />

Dynastes granti<br />

Tenebrio molitor<br />

Meloe proscarabaeus<br />

Clambus arnetti<br />

Phaeostigma notata<br />

Leptothorax acervorum<br />

Polistes dominulus<br />

Graphosoma lineatum<br />

Raphigaster nebulosa<br />

Lygus hesperus<br />

Hemiowoodwardia wilsoni<br />

Hackeriella veitchi<br />

Spissistilus festinus<br />

Prokelisia marginata<br />

Philaenus spumarius<br />

Okanagana utahensis<br />

Trioza eugeniae<br />

Pealius kelloggii<br />

Acyrthosiphon pisum<br />

Aonidiella aurantii<br />

Batrachideidae gen sp<br />

Carausius morosus<br />

Acheta domesticus<br />

Mesoperlina pecircai<br />

Aeschna cyanea<br />

Lepisma saccharina<br />

Lepidocyrtus paradoxus<br />

Crossodonthina koreana<br />

Hypogastrura dolsana<br />

Podura aquatica<br />

Theatops erythrocephala<br />

Scolopendra cingulata<br />

Cryptops trisulcatus<br />

Craterostigmus tasmanianus<br />

Lithobius variegatus<br />

Scutigera coleoptrata<br />

Pseudohimantarium mediterraneum<br />

Clinopodes poseidonis<br />

Cylindroiulus punctatus<br />

Polydesmus coriaceus<br />

Rhipicephalus appendiculatus<br />

Hyalomma lusitanicum<br />

Hyalomma rufipes<br />

Hyalomma dromedarii<br />

Rhipicephalus sanguineus<br />

Boophilus microplus<br />

Rhipicephalus zambeziensis<br />

Rhipicephalus bursa<br />

Boophilus annulatus<br />

Rhipicephalus pusillus<br />

Dermacentor andersoni<br />

Dermacentor marginatus<br />

Amblyomma triguttatum triguttat<br />

Amblyomma vikirri<br />

Aponomma fimbriatum<br />

Aponomma latum<br />

Amblyomma variegatum<br />

Amblyomma tuberculatum<br />

Amblyomma americanum<br />

Amblyomma maculatum<br />

Haemaphysalis inermis<br />

Haemaphysalis punctata<br />

Haemaphysalis leporispalustris<br />

Haemaphysalis humerosa<br />

Haemaphysalis petrogalis<br />

Haemaphysalis leachi<br />

Aponomma undatum<br />

Aponomma concolor<br />

Ixodes auritulus<br />

Ixodes ricinus<br />

Ixodes affinis<br />

Ixodes pilosus<br />

Ixodes cookei<br />

Ixodes simplex simplex<br />

Ixodes kopsteini<br />

Ixodes holocyclus<br />

Carios puertoricensis<br />

Ornithodoros moubata<br />

Ornithodoros coriaceus<br />

Otobius megnini<br />

Argas lahorensis<br />

Argas persicus<br />

Megisthanus floridanus<br />

Cosmolaelaps trifidus<br />

Hypochthonius rufulus<br />

Lohmannia banksi<br />

Nothrus sylvestris<br />

Xenillus tegeocranus<br />

Euzetes globulosus<br />

Allonothrus russeolus<br />

Archegozetes longisetosus<br />

Trhypochthonius tectorum<br />

Nehypochthonius porosus<br />

Steganacarus magnus<br />

Gehypochthonius urticinus<br />

Chortoglyphus arcuatus<br />

Acarus siro<br />

Eusimonia wunderlichi<br />

Androctonus australis<br />

Liphistius bicoloripes<br />

Eurypelma californica<br />

Odiellus troguloides<br />

Pseudocellus pearsei<br />

Limulus polyphemus<br />

Callipallene gen sp<br />

Berndtia purpurea<br />

Trypetesa lampas<br />

Octolasmis lowei<br />

Paralepas palinuri<br />

Lepas anatifera<br />

Balanus eburneus<br />

Chelonibia patula<br />

Tetraclita stalactifera<br />

Chthamalus fragilis<br />

Verruca spengleri<br />

Ibla cumingi<br />

Calantica villosa<br />

Loxothylacus texanus<br />

Dendrogaster asterinae<br />

Ulophysema oeresundense<br />

Palaemonetes kadiakensis<br />

Helice tridens<br />

Philyra pisum<br />

Callinectes sapidus<br />

Pugettia quadridens<br />

Raninoides louisianensis<br />

Procambarus leonensis<br />

Astacus astacus<br />

Nephrops norvegicus<br />

Panulirus argus<br />

Oedignathus inermis<br />

Penaeus aztecus<br />

Stenopus hispidus<br />

Artemia salina<br />

Branchinecta packardi<br />

Daphnia pulex<br />

Bosmina longirostris<br />

Daphnia galeata<br />

Stenocypris major<br />

Argulus nobilis<br />

Porocephalus crotali<br />

Milnesium tardigradum<br />

Macrobiotus hufelandi<br />

Thulinia stephaniae<br />

Echiniscus viridissimus<br />

Euperipatoides leuckarti<br />

Priapulus caudatus<br />

Pycnophyes kielensis<br />

Helix aspersa<br />

Balea biplicata<br />

Limicolaria kambeul<br />

Laevicaulis alte<br />

Onchidella celtica<br />

Siphonaria algesirae<br />

Anthosiphonaria sirius<br />

Lymnaea glabra<br />

Stagnicola palustris<br />

Lymnaea stagnalis<br />

Radix peregra<br />

Lymnaea auricularia<br />

Fossaria truncatula<br />

Bakerilymnaea cubensis<br />

Biomphalaria glabrata<br />

Littorina obtusata<br />

Littorina littorea<br />

Fasciolaria lignaria<br />

Nassarius singuinjorensis<br />

Pisania striata<br />

Reishia bronni<br />

Thais clavigera<br />

Rapana venosa<br />

Bursa rana<br />

Monodonta labio<br />

Antalis vulgaris<br />

Scutopus ventrolineatus<br />

Arctica islandica<br />

Mercenaria mercenaria<br />

Spisula subtruncata<br />

Mulinia lateralis<br />

Spisula solida<br />

Spisula solidissima<br />

Tresus nuttali<br />

Tresus capax<br />

Mactromeris polynyma<br />

Hippopus hippopus<br />

Hippopus porcellanus<br />

Tridacna squamosa<br />

Tridacna crocea<br />

Tridacna maxima<br />

Tridacna derasa<br />

Tridacna gigas<br />

Vasticardium flavum<br />

Fulvia mutica<br />

Fragum unedo<br />

Fragum fragum<br />

Corculum cardissa<br />

Galeomma takii<br />

Ostrea edulis<br />

Crassostrea virginica<br />

Nerita albicilla<br />

Mytilus edulis<br />

Mytilus trossulus<br />

Mytilus galloprovincialis<br />

Mytilus californianus<br />

Geukensia demissa<br />

Mimachlamys varia<br />

Chlamys hastata<br />

Crassadoma gigantea<br />

Pecten maximus<br />

Argopecten gibbus<br />

Argopecten irradians<br />

Placopecten magellanicus<br />

Chlamys islandica<br />

Atrina pectinata<br />

Arca noae<br />

Barbatia virescens<br />

Acanthopleura japonica<br />

Lepidochitona corrugata<br />

Lepidozona coreanica<br />

Eohemithyris grayii<br />

Platidia anomioides<br />

Stenosarina crosnieri<br />

Gryphus vitreus<br />

Thecidellina blochmanii<br />

Cancellothyris hedleyi<br />

Terebratulina retusa<br />

Liothyrella neozelanica<br />

Liothyrella uva<br />

Gwynia capsula<br />

Calloria inconspicua<br />

Gyrothyris mawsoni<br />

Neothyris parva<br />

Terebratalia transversa<br />

Macandrevia cranium<br />

Fallax neocaledonensis<br />

Laqueus californianus<br />

Megerlia truncata<br />

Terebratella sanguinea<br />

Notosaria nigricans<br />

Hemithyris psittaceae<br />

Neocrania anomala<br />

Neocrania huttoni<br />

Discina striata<br />

Glottidia pyramidata<br />

Lingula lingua<br />

Lingula anatina<br />

Phoronis architecta<br />

Phoronis psammophila<br />

Phoronis vancouverensis<br />

Alboglossiphonia heteroclita<br />

Hirudo medicinalis<br />

Haemopis sanguisuga<br />

Barbronia weberi<br />

Eisenia fetida<br />

Lumbricus rubellus<br />

Dero digitata<br />

Xironogiton victoriensis<br />

Sathodrilus attenuatus<br />

Nereis virens<br />

Aphrodita aculeata<br />

Nereis limbata<br />

Capitella capitata<br />

Harmothoe impar<br />

Sabella pavonina<br />

Magelona mirabilis<br />

Scoloplos armiger<br />

Polydora ciliata<br />

Pygospio elegans<br />

Lanice conchilega<br />

Nephtys hombergii<br />

Glycera americana<br />

Dodecaceria concharum<br />

Chaetopterus variopedatus<br />

Siboglinum fiordicum<br />

Ridgeia piscesae<br />

Ochetostoma erythrogrammon<br />

Pedicellina cernua<br />

Barentsia hildegardae<br />

Barentsia benedeni<br />

Symbion pandora<br />

Plumatella repens<br />

Alcyonidium gelatinosum<br />

Porania pulvillus<br />

Asterias amurensis<br />

Astropecten irregularis<br />

Stomopneustes variolaris<br />

Mespilia globulus<br />

Temnopleurus hardwickii<br />

Salmacis sphaeroides<br />

Tripneustes gratilla<br />

Ophiopholis aculeta<br />

Strongylocentrotus intermedius<br />

Colobocentrotus atratus<br />

Echinus esculentus<br />

Sphaerechinus granularis<br />

Psammechinus miliaris<br />

Diadema setosum<br />

Centrostephanus coronatus<br />

Eucidaris tribuloides<br />

Fellaster zelandiae<br />

Cassidulus mitis<br />

Echinodiscus bisperforatus<br />

Encope aberrans<br />

Echinocardium cordatum<br />

Brissopsis lyrifera<br />

Meoma ventricosa<br />

Arbacia lixula<br />

Asthenosoma owstoni<br />

Psychropotes longicauda<br />

Cucumaria sykion<br />

Lipotrapeza vestiens<br />

Stichopus japonicus<br />

Ophiocanops fugiens<br />

Amphipholis squamata<br />

Strongylocentrotus purpuratus<br />

Ophiomyxa brevirima<br />

Ophioplocus japonicus<br />

Astrobrachion constrictum<br />

Antedon serrata<br />

Endoxocrinus parrae<br />

Eptatretus stouti<br />

Myxine glutinosa atlantic hagfis<br />

Petromyzon marinus<br />

Lampetra aepyptera<br />

Plethodon yonhalossee<br />

Amphiuma tridactylum<br />

Siren intermedia<br />

Ambystoma mexicanum<br />

Eleutherodactylus cuneatus<br />

Hyla cinerea<br />

Bufo valliceps<br />

Nesomantis thomasseti<br />

Gastrophryne carolinensis<br />

Xenopus laevis<br />

Scaphiopus holbrooki<br />

Discoglossus pictus<br />

Grandisonia alternans<br />

Hypogeophis rostratus<br />

Ichthyophis bannanicus<br />

Typhlonectes natans<br />

Homo sapiens<br />

Mus musculus<br />

Rattus norvegicus<br />

Oryctolagus cuniculus<br />

Alligator mississippiensis<br />

Turdus migratorius<br />

Gallus gallus<br />

Heterodon platyrhinos<br />

Sceloporus undulatus<br />

Sphenodon punctatus<br />

Pseudemys scripta<br />

Latimeria chalumnae<br />

Elops hawaiiensis<br />

Megalops atlanticus<br />

Ophichthus rex<br />

Echiophis punctifer<br />

Hiodon alosoides<br />

Albula vulpes<br />

Salmo trutta<br />

Oncorhynchus kisutch<br />

Cyprinus carpio<br />

Ictalurus punctatus<br />

Clupea harengus<br />

Fundulus heteroclitus<br />

Amia calva<br />

Lepisosteus osseus<br />

Polyodon spathula<br />

Sebastolobus altivelis<br />

Rhinobatos lentiginosus<br />

Echinorhinus cookei<br />

Squalus acanthias<br />

Notorynchus cepedianus<br />

Branchiostoma floridae<br />

Halocynthia roretzi<br />

Styela plicata<br />

Herdmania momus<br />

Oikopleura dioica<br />

Doliolum nationalis<br />

Thalia democratica<br />

Pyrosoma atlanticum<br />

Ciona intestinalis<br />

Saccoglossus kowalevskii<br />

Balanoglossus carnosus<br />

Dicyema acuticephalum<br />

Dicyema orientale<br />

Sagitta elegans<br />

Sagitta crassa<br />

Paraspadella gotoi<br />

Phascolosoma granulatum<br />

Prostoma eilhardi<br />

Haplogonaria syltensis<br />

Atriofonta polyvacuola<br />

Actinoposthia beklemischevi<br />

Aphanastoma virescens<br />

Convoluta pulchra<br />

Anaperus tvaerminnensis<br />

Symsagittifera psammophila<br />

Convoluta roscoffensis<br />

Convoluta naikaiensis<br />

Anaperus biaculeatus<br />

Paedomecynostomum bruneum<br />

Postmecynostomum pictum<br />

Childia groenlandica<br />

Philomecynostomum lapillum<br />

Simplicomorpha gigantorhabditis<br />

Paratomella rubra<br />

Dugesia subtentaculata<br />

Dugesia ryukyuensis<br />

Girardia tigrina<br />

Microplana scharfii<br />

Caenoplana caerulea<br />

Australoplana sanguinea<br />

Arthiopostia triangulata<br />

Dugesia japonica<br />

Dugesia iberica<br />

Dugesia mediterranea<br />

Dugesia polychroa<br />

Cura pinguis<br />

Neppia montana<br />

Microplana nana<br />

Bipalium kewense<br />

Platydemus manokwari<br />

Artioposthia triangulata<br />

Dendrocoelopsis lactea<br />

Crenobia alpina<br />

Polycelis nigra<br />

Phagocata ullala<br />

Ectoplana limuli<br />

Bipalium trilineatum<br />

Heronimus mollis<br />

Prosorhynchoides gracilescens<br />

Stephanostomum baccatum<br />

Zalophotrema hepaticum<br />

Nasitrema globicephalae<br />

Tetracerasta blepta<br />

Fasciola gigantica<br />

Dicrocoelium dendriticum<br />

Fasciola hepatica<br />

Fasciolopsis buski<br />

Echinostoma caproni<br />

Opisthorchis viverrini<br />

Calicophoron calicophorum<br />

Schistosoma japonicum<br />

Schistosoma mansoni<br />

Schistosoma spindale<br />

Schistosoma haematobium<br />

Multicotyle purvisi<br />

Lobatostoma manteri<br />

Zeuxapta seriolae<br />

Plectanocotyle gurnardi<br />

Diclidophora denticulata<br />

Kuhnia scombri<br />

Bivagina pagrosomi<br />

Neomicrocotyle pacifica<br />

Pseudohexabothrium taeniurae<br />

Neopolystoma spratti<br />

Polystomoides malayi<br />

Grillotia erinaceus<br />

Abothrium gadi<br />

Bothriocephalus scorpii<br />

Proteocephalus exiguus<br />

Gyrocotyle urna<br />

Dictyocotyle coeliaca<br />

Calicotyle affinis<br />

Troglocephalus rhinobatidis<br />

Leptocotyle minor<br />

Pseudomurraytrema ardens<br />

Gyrodactylus salaris<br />

Udonella caligorum<br />

Encotyllabe chironemi<br />

Bothromesostoma personatum<br />

Plagiostomum cinctum<br />

Plagiostomum striatum<br />

Plicastoma cuticulata<br />

Vorticeros ijimai<br />

Plagiostomum vittatum<br />

Plagiostomum ochroleucum<br />

Pseudostomum klostermanni<br />

Pseudostomum quadrioculatum<br />

Cylindrostoma fingalianum<br />

Cylindrostoma gracilis<br />

Pseudostomum gracilis<br />

Ulianinia mollissima<br />

Reisingeria hexaoculata<br />

Urastoma cyprinae<br />

Archiloa rivularis<br />

Nemertinoides elongatus<br />

Planocera multitentaculata<br />

Notoplana koreana<br />

Notoplana australis<br />

Discocelis tigrina<br />

Pseudoceros tritriatus<br />

Thysanozoon brocchii<br />

Geocentrophora sphyrocephala<br />

Geocentrophora baltica<br />

Microstomum lineare<br />

Macrostomum tuba<br />

Stenostomum leucops aquariorum<br />

Stenostomum leucops<br />

Eubostrichus parasitiferus<br />

Eubostrichus topiarius<br />

Eubostrichus dianae<br />

Chromadoropsis vivipara<br />

Desmodora ovigera<br />

Laxus oneistus<br />

Laxus cosmopolitus<br />

Stilbonema majum<br />

Robbea hypermnestra<br />

Acanthopharynx micans<br />

Plectus aquatilis<br />

Plectus acuminatus<br />

Cruznema tripartitum<br />

Rhabditella axei<br />

Pellioditis typica<br />

Rhabditis blumi<br />

Rhabditis myriophila<br />

Haemonchus placei<br />

Haemonchus similis<br />

Haemonchus contortus<br />

Nematodirus battus<br />

Ostertagia ostertagi<br />

Nippostrongylus brasiliensis<br />

Syngamus trachea<br />

Heterorhabditis bacteriophora<br />

Caenorhabditis briggsae<br />

Caenorhabditis elegans<br />

Caenorhabditis vulgaris<br />

Pelodera strongyloides<br />

Panagrellus redivivus<br />

Teratorhabditis palmarum<br />

Aduncospiculum halicti<br />

Pristionchus lheritieri<br />

Diplogaster lethieri<br />

Strongyloides stercoralis<br />

Strongyloides ratti<br />

Steinernema carpocapsae<br />

Zeldia punctata<br />

Cephalobus oryzae<br />

Meloidogyne arenaria<br />

Globodera pallida<br />

Aphelenchus avenae<br />

Pseudoterranova decipiens<br />

Terranova caballeroi<br />

Toxocara canis<br />

Contracaecum multipapillatum<br />

Baylisascaris transfuga<br />

Ascaris suum<br />

Parascaris equorum<br />

Ascaris lumbricoides<br />

Baylisascaris procyonis<br />

Toxascaris leonina<br />

Porrocaecum depressum<br />

Goezia pelagia<br />

Iheringascaris inquies<br />

Hysterothylacium pelagicum<br />

Hysterothylacium fortalezae<br />

Hysterothylacium reliquens<br />

Heterocheilus tunicatus<br />

Cruzia americana<br />

Brumptaemilius justini<br />

Brugia malayi<br />

Dirofilaria immitis<br />

Gnathostoma neoprocyonis<br />

Gnathostoma binucleatum<br />

Gnathostoma turgidum<br />

Teratocephalus lirellus<br />

Daptonema procerus<br />

Diplolaimelloides meyli<br />

Paracanthonchus caecus<br />

Pontonema vulgare<br />

Enoplus brevis<br />

Enoplus meridionalis<br />

Prismatolaimus intermedius<br />

Paratrichodorus anemones<br />

Paratrichodorus pachydermus<br />

Trichodorus primitivus<br />

Mermis nigrescens<br />

Mylonchulus arenicolus<br />

Xiphinema rivesi<br />

Longidorus elongatus<br />

Trichuris muris<br />

Trichinella spiralis<br />

Gordius aquaticus<br />

Gordius albopunctatus<br />

Chordodes morgani<br />

Rhopalura ophiocomae<br />

Echinorhynchus gadi<br />

Polymorphus altmani<br />

Corynosoma enhydri<br />

Centrorhynchus conspectus<br />

Plagiorhynchus cylindraceus<br />

Pomphorhynchus bulbocoli<br />

Leptorhynchoides thecatus<br />

Neoechinorhynchus crassus<br />

Neoechinorhynchus pseudemydis<br />

Macracanthorhynchus ingens<br />

Moliniformis moliniformis<br />

Mediorhynchus grandis<br />

Philodina acuticornis<br />

Brachionus plicatilis<br />

Lepidodermella squammata<br />

Gnathostomula paradoxa<br />

Trichoplax adhaerens<br />

Haliplanella lucia<br />

Flosmaris mutsuensis<br />

Anthopleura kurogane<br />

Anthopleura midori<br />

Anemonia sulcata<br />

Rhizopsammia minuta<br />

Epiactis japonica<br />

Tubastraea aurea<br />

Antipathes galapagensis<br />

Antipathes lata<br />

Parazoanthus axinellae<br />

Calicogorgia granulosa<br />

Bellonella rigida<br />

Euplexaura crassa<br />

Alcyonium gracillimum<br />

Leioptilus fimbriatus<br />

Virgularia gustaviana<br />

Coryne pusilla<br />

Hydra littoralis<br />

Gymnangium hians<br />

Selaginopsis cornigera<br />

Polypodium hydriforme<br />

Tripedalia cystophora<br />

Atolla vanhoeffeni<br />

Craterolophus convolvulus<br />

Mycale fibrexilis<br />

Microciona prolifera<br />

Suberites ficus<br />

Axinella polypoides<br />

Tetilla japonica<br />

Eunapius fragilis<br />

Spongilla lacustris<br />

Ephydatia muelleri<br />

Rhabdocalyptus dawsoni<br />

Scypha ciliata<br />

Sycon calcaravis<br />

Clathrina cerebrum<br />

Beroe cucumis<br />

Mnemiopsis leidyi<br />

Teleaulax amphioxeia<br />

Hemiselmis brunnescens<br />

Hemiselmis virescens<br />

Hemiselmis rufescens<br />

Plagiomonas amylosa<br />

Proteomonas sulcata<br />

Guillardia theta<br />

Goniomonas truncata<br />

Acanthamoeba lenticulata<br />

Acanthamoeba pustulosa<br />

Acanthamoeba palestinensis<br />

Acanthamoeba griffini<br />

Acanthamoeba pearcei<br />

Acanthamoeba hatchetti<br />

Acanthamoeba stevensoni<br />

Acanthamoeba castellanii<br />

Acanthamoeba lugdunensis<br />

Acanthamoeba rhysodes<br />

Acanthamoeba royreba<br />

Acanthamoeba polyphaga<br />

Acanthamoeba culbertsoni<br />

Acanthamoeba healyi<br />

Acanthamoeba comandoni<br />

Acanthamoeba tubiashi<br />

Acanthamoeba astronyxis<br />

Cyanophora paradoxa<br />

Cyanoptyche gloeocystis<br />

Glaucocystis nostochinearum<br />

Arthrocardia filicula<br />

Serraticardia macmillanii<br />

Bossiella orbigniana<br />

Calliarthron cheilosporioides<br />

Calliarthron tuberculosum<br />

Bossiella californica<br />

Corallina officinalis<br />

Corallina elongata<br />

Jania rubens<br />

Cheilosporum sagittatum<br />

Jania crassa<br />

Haliptilon roseum<br />

Metagoniolithon chara<br />

Metagoniolithon stelliferum<br />

Metagoniolithon radiatum<br />

Spongites yendoi<br />

Lithophyllum kotschyanum<br />

Lithothrix aspergillum<br />

Amphiroa fragilissima<br />

Synarthrophyton patena<br />

Mesophyllum engelhartii<br />

Mesophyllum erubescens<br />

Lithothamnion tophiforme<br />

Lithothamnion glaciale<br />

Phymatolithon laevigatum<br />

Phymatolithon lenormandii<br />

Leptophytum acervatum<br />

Leptophytum ferox<br />

Mastophoropsis caniculata<br />

Clathromorphum compactum<br />

Clathromorphum parcum<br />

Heydrichia woelkerlingii<br />

Sporolithon durum<br />

Rhodogorgon carriebowensis<br />

Audouinella pectinata<br />

Audouinella proskaueri<br />

Audouinella asparagopsis<br />

Audouinella tetraspora<br />

Audouinella dasyae<br />

Audouinella endophytica<br />

Audouinella caespitosa<br />

Audouinella rhizoidea<br />

Audouinella daviesii<br />

Audouinella amphiroae<br />

Audouinella arcuata<br />

Audouinella secundata<br />

Audouinella hermannii<br />

Audouinella tenue<br />

Rhodophysema elegans<br />

Devaleraea ramentacea<br />

Meiodiscus spetsbergensis<br />

Palmaria palmata<br />

Halosaccion glandiforme<br />

Rhodothamniella floridula<br />

Camontagnea oxyclada<br />

Nemalion helminthoides<br />

Galaxaura marginata<br />

Rhodochorton purpureum<br />

Rhododraparnaldia oregonica<br />

Batrachospermum boryanum<br />

Tuomeya americana<br />

Sirodotia suecica<br />

Sirodotia huillensis<br />

Lemanea fluviatilis<br />

Paralemanea catenata<br />

Batrachospermum gelatinosum<br />

Batrachospermum helminthosum<br />

Batrachospermum turfosum<br />

Psilosiphon scoparium<br />

Batrachospermum macrosporum<br />

Batrachospermum virgato decaisn<br />

Batrachospermum louisianae<br />

Nothocladus nodosus<br />

Thorea violacea<br />

Gelidium pusillum<br />

Gelidium latifolium<br />

Gelidium floridanum<br />

Gelidium sesquipedale<br />

Gelidium serrulatum<br />

Gelidium americanum<br />

Gelidium vagum<br />

Griffithsia globulifera<br />

Onikusa pristoides<br />

Capreolia implexa<br />

Gelidium caulacantheum<br />

Pterocladia lucida<br />

Pterocladia capillacea<br />

Pterocladiella capillacea<br />

Pterocladiella melanoidea<br />

Ptilophora pinnatifida<br />

Ptilophora subcostata<br />

Gelidiella acerosa<br />

Grateloupia filicina<br />

Cryptonemia undulata<br />

Carpopeltis phyllophora<br />

Halymenia plana<br />

Sebdenia flabellata<br />

Lomentaria australis<br />

Lomentaria baileyana<br />

Gloioderma fruticulosa<br />

Champia affinis<br />

Cephalocystis furcellata<br />

Cephalocystis leucobotrys<br />

Erythrocolon podagricum<br />

Epymenia wilsonis<br />

Rhodymenia linearis<br />

Cordylecladia erecta<br />

Plocamiocolax pulvinata<br />

Plocamium cartilagineum<br />

Plocamium angustum<br />

Gracilaria verrucosa<br />

Gracilaria pacifica<br />

Gracilaria tikvahiae<br />

Gracilaria cornea<br />

Gracilaria chilensis<br />

Melanthalia obtusata<br />

Curdiea flabellata<br />

Gracilaria lemaneiformis<br />

Gracilariophila oryzoides<br />

Schizymenia dubyi<br />

Mastocarpus stellatus<br />

Gigartina crassicaulis<br />

Schottera nicaeensis<br />

Gardneriella tuberifera<br />

Sarcodiotheca gaudichaudii<br />

Sarcodiotheca furcata<br />

Eucheuma denticulata<br />

Eucheuma isiforme<br />

Kappaphycus alvarezii<br />

Mychodea carnosa<br />

Areschougia congesta<br />

Endocladia muricata<br />

Gleiopeltis furcata<br />

Phacelocarpus peperocarpos<br />

Nizymenia australis<br />

Sphaerococcus coronopifolius<br />

Farlowia mollis<br />

Dilsea carnosa<br />

Dasyphloea insignis<br />

Callophyllis rangiferina<br />

Bonnemaisonia hamifera<br />

Ceramium macilentum<br />

Ceramium rubrum<br />

Dasya baillouviana<br />

Phycodrys rubens<br />

Rhodomela confervoides<br />

Anotrichium furcellatum<br />

Griffithsia monilis<br />

Crouania attenuata<br />

Hildenbrandia rubra<br />

Apophlaea lyallii<br />

Dixoniella grisea<br />

Rhodella maculata<br />

Boldia erythrosiphon<br />

Erythrotrichia carnea<br />

Porphyra pseudolinearis<br />

Porphyra katadae<br />

Porphyra yezoensis<br />

Porphyra tenera<br />

Porphyra leucosticta<br />

Porphyra haitanensis<br />

Porphyra dentata<br />

Bangia atropurpurea<br />

Porphyra acanthophora<br />

Porphyra suborbiculata<br />

Porphyra miniata<br />

Porphyra umbilicalis<br />

Porphyra purpurea<br />

Stylonema alsidii<br />

Cosmarium botrytis<br />

Sphaerozosma granulatum<br />

Cosmocladium saxonicum<br />

Gonatozygon aculeatum<br />

Genicularia spirotaenia<br />

Mesotaenium caldariorum<br />

Mougeotia scalaris<br />

Spirogyra grevilleana<br />

Zygnemopsis circumcarinata<br />

Dioscorea bulbifera<br />

Tacca plantaginea<br />

Calectasia intermedia<br />

Zea mays<br />

Oryza sativa<br />

Joinvillea ascendens<br />

Sparganium eurycarpum<br />

Cyperus albostriatus<br />

Glomeropitcairnia penduliflora<br />

Anigozanthos flavidus<br />

Eichhornia crassipes<br />

Elasis hirsuta<br />

Tradescantia ohiensis<br />

Costus barbatus<br />

Maranta bicolor<br />

Calathea loeseneri<br />

Zingiber gramineum<br />

Canna indica<br />

Heliconia indica<br />

Ravenala madagascariensis<br />

Orchidantha fimbriata<br />

Phenakospermum guyannense<br />

Strelitzia nicolai<br />

Musa acuminata<br />

Calochortus albus<br />

Colchicum autumnale<br />

Veitchia sessilifolia<br />

Drymophloeus subdisticha<br />

Chamaedorea seifrizii<br />

Trachycarpus wagnerianus<br />

Cyanella capensis<br />

Gladiolus buckerveldii<br />

Isophysis tasmanica<br />

Bowiea volubilis<br />

Xanthorrhoea quadrangulata<br />

Asparagus falcatus<br />

Ledebouria socialis<br />

Chlorophytum nepalense<br />

Allium thunbergii<br />

Eucharis grandiflora<br />

Burmannia disticha<br />

Apostasia stylidioides<br />

Gymnosiphon suaveolens<br />

Calla palustris<br />

Vallisneria americana<br />

Sagittaria trifolia<br />

Ananas comosus<br />

Scheuchzeria palustris<br />

Gymnostachys anceps<br />

Corallorhiza maculata<br />

Aplectrum hyemale<br />

Neottia nidus avis<br />

Eburophyton austinae<br />

Oncidium sphacelatum<br />

Oncidium excavatum<br />

Cypripedium calceolus<br />

Acorus calamus<br />

Lilium formosanum<br />

Illicium parviflorum<br />

Schisandra chinensis<br />

Austrobaileya scandens<br />

Nuphar japonica<br />

Nuphar shimadai<br />

Nymphaea tuberosa<br />

Amborella trichopoda<br />

Arabidopsis thaliana<br />

Sinapis alba<br />

Cleome hasleriana<br />

Pentadiplandra brazzeana<br />

Reseda alba<br />

Gyrostemon tepperi<br />

Tropaeolum majus<br />

Moringa oleifera<br />

Carica papaya papaya<br />

Floerkea proserpinacoides<br />

Batis maritima<br />

Pilea cadierei<br />

Euonymus alatus<br />

Brexia madagascarensis<br />

Parnassia fimbriata<br />

Lepuropetalon spathulatum<br />

Albizzia julibrissin<br />

Trifolium repens<br />

Pisum sativum<br />

Glycine max<br />

Abobra tenuifolia<br />

Corallocarpus bainesii<br />

Luffa quinquefida<br />

Marah macrocarpa<br />

Coriaria arborea<br />

Datisca cannabina<br />

Datisca glomerata<br />

Begonia glabra<br />

Hillebrandia sandwichensis<br />

Begonia metallica x Begonia sangu<br />

Begonia boisiana<br />

Begonia oxyloba<br />

Octomeles sumatrana<br />

Tetrameles nudiflora<br />

Crossosoma californicum<br />

Morus alba<br />

Celtis yunnanensis<br />

Ceanothus sanguineus<br />

Elaeagnus umbellata<br />

Francoa sonchifolia<br />

Greyia radlkoferi<br />

Zelkova serrata<br />

Fragaria ananassa<br />

Spiraea x vanhouttei<br />

Photinia fraseri<br />

Prunus persica<br />

Ricinus communis<br />

Adriana glabrata<br />

Chrysobalanus icaco<br />

Licania tomentosa<br />

Linum perenne<br />

Gossypium hirsutum<br />

Luehea seemannii<br />

Bombax ceiba<br />

Koeberlinia spinosa<br />

Muntingia calabura<br />

Turnera ulmifolia<br />

Drypetes roxburghii<br />

Malpighia coccigera<br />

Mirabilis jalapa<br />

Tetragonia expansa<br />

Mollugo verticillata<br />

Phytolacca americana<br />

Spinacia oleracea<br />

Plumbago auriculata<br />

Polygonum chinense<br />

Coccoloba uvifera<br />

Drosera capensis<br />

Euphorbia pulcherrima<br />

Citrus aurantium<br />

Koelreuteria paniculata<br />

Acer rubrum<br />

Dillenia alata<br />

Gunnera manicata<br />

Mkilua fragrans<br />

Guaiacum sanctum<br />

Cephalotus follicularis<br />

Eucryphia lucida<br />

Ceratopetalum gummiferum<br />

Sloanea latifolia<br />

Bauera rubioides<br />

Casuarina equisetifolia<br />

Betula papyrifera<br />

Alnus glutinosa<br />

Dendrophthora clavata<br />

Phoradendron californicum<br />

Phoradendron serotinum<br />

Dendrophthora domingensis<br />

Arceuthobium verticilliflorum<br />

Arceuthobium pendens<br />

Arceuthobium oxycedri<br />

Viscum album<br />

Viscum articulatum<br />

Korthalsella complanata<br />

Korthalsella lindsayi<br />

Ginalloa arnottiana<br />

Notothixos leiophyllus<br />

Notothixos subaureus<br />

Buckleya distichophylla<br />

Pyrularia pubera<br />

Thesium impeditum<br />

Comandra umbellata<br />

Geocaulon lividum<br />

Eubrachion ambiguum<br />

Exocarpos bidwillii<br />

Nestronia umbellula<br />

Dendrotrophe varians<br />

Dufrenoya sphaerocarpa<br />

Antidaphne viscoidea<br />

Santalum album<br />

Osyris lanceolata<br />

Opilia amentacea<br />

Cansjera leptostachya<br />

Agonandra macrocarpa<br />

Champereia manillana<br />

Alepis flavida<br />

Lysiana exocarpi<br />

Dendropemon bicolor<br />

Oryctanthus occidentalis<br />

Tripodanthus acutifolius<br />

Psittacanthus angustifolius<br />

Struthanthus oerstedii<br />

Gaiadendron punctatum<br />

Tupeia antarctica<br />

Amyema glabrum<br />

Diplatia furcata<br />

Globimetula dinklagei<br />

Erianthemum dregei<br />

Helixanthera kirkii<br />

Moquiniella rubra<br />

Tapinanthus quinquangulus<br />

Englerina woodfordioides<br />

Agelanthus sansibaricus<br />

Decaisnina hollrungii<br />

Loranthus europaeus<br />

Ligaria cuneifolia<br />

Phthirusa pyrifolia<br />

Schoepfia arenaria<br />

Schoepfia schreberi<br />

Misodendrum brachystachyum<br />

Scorodocarpus borneensis<br />

Strombosia philippinensis<br />

Heisteria concinna<br />

Ximenia americana<br />

Olax aphylla<br />

Minquartia guianensis<br />

Polygala pauciflora<br />

Punica granatum<br />

Cercidiphyllum japonicum<br />

Tetracarpaea tasmanica<br />

Haloragis erecta<br />

Myriophyllum exalbescens<br />

Penthorum sedoides<br />

Dudleya viscida<br />

Kalanchoe daigremontiana<br />

Sedum rubrotintum<br />

Crassula marnierana<br />

Sullivantia oregana<br />

Saxifraga mertensiana<br />

Saxifraga integrifolia<br />

Chrysosplenium iowense<br />

Peltoboykinia tellimoides<br />

Heuchera micrantha<br />

Boykinia intermedia<br />

Itea virginica<br />

Pterostemon rotundifolius<br />

Paeonia suffruticosa<br />

Paeonia lactiflora<br />

Liquidambar styraciflua<br />

Ribes aureum<br />

Pedicularis lanceolata<br />

Pedicularis racemosa<br />

Orthocarpus erianthus<br />

Orthocarpus luteus<br />

Castilleja miniata<br />

Orobanche multiflora<br />

Orobanche ludoviciana<br />

Orobanche fasciculata<br />

Lathraea clandestina<br />

Harveya speciosa<br />

Hyobanche atropurpurea<br />

Conopholis alpina<br />

Conopholis americana<br />

Epifagus virginiana<br />

Boschniakia rossica<br />

Bourreria succulenta<br />

Ehretia cymosa<br />

Pholisma arenarium<br />

Cuscuta gronovii<br />

Byblis liniflora<br />

Byblis gigantea<br />

Aeschynanthus radicans<br />

Chionophila jamesii<br />

Linaria vulgaris<br />

Ipomoea hederacea<br />

Solanum tuberosum<br />

Lycopersicon esculentum<br />

Montinia caryophyllacea<br />

Mitchella repens<br />

Vahlia capensis<br />

Helwingia japonica<br />

Phyllonoma laticuspis<br />

Panax japonicus<br />

Panax quinquefolius<br />

Panax ginseng<br />

Hedera helix<br />

Hydrocotyle sibthorpioides<br />

Pittosporum japonicum<br />

Ligusticum chuanxiong<br />

Cnidium officinale<br />

Lomatium triternatium<br />

Angelica acutiloba<br />

Lonicera maackii<br />

Symphoricarpos albus<br />

Corokia cotoneaster<br />

Escallonia coquimbensis<br />

Eremosyne pectinata<br />

Campanula ramulosa<br />

Lobelia erinus<br />

Tragopogon dubius<br />

Roussea simplex<br />

Berzelia lanuginosa<br />

Eucommia ulmoides<br />

Aucuba japonica<br />

Garrya elliptica<br />

Manilkara zapota<br />

Impatiens palida<br />

Clethra alnifolia<br />

Pyrola picta<br />

Styrax americana<br />

Pterospora andromedea<br />

Sarcodes sanguinea<br />

Monotropa uniflora<br />

Sarracenia purpurea<br />

Cyrilla racemiflora<br />

Symplocos paniculata<br />

Diospyros virginiana<br />

Camellia japonica<br />

Fouquieria columnaris<br />

Nyssa sylvatica<br />

Philadelphus lewisii<br />

Hydrangea macrophylla<br />

Nyssa ogeche<br />

Camptotheca acuminata<br />

Cornus florida<br />

Cornus racemosa<br />

Cornus officinalis<br />

Tetracentron sinense<br />

Trochodendron aralioides<br />

Buxus sempervirens<br />

Sabia swinhoei<br />

Nelumbo lutea<br />

Platanus occidentalis<br />

Dicentra eximia<br />

Hypecoum imberba<br />

Argemone mexicana<br />

Stauntonia hexaphylla<br />

Holboellia latifolia<br />

Akebia quinata<br />

Lardizabala biternata<br />

Boquila trifoliata<br />

Decaisnea fargesii<br />

Sinofranchetia chinensis<br />

Sargentodoxa cuneata<br />

Euptelea polyandra<br />

Tinospora caffra<br />

Menispermum canadensis<br />

Ranunculus taisanensis<br />

Ranunculus sardous<br />

Xanthorhiza simplicissima<br />

Coptis trifolia<br />

Glaucidium palmatum<br />

Hydrastis canadensis<br />

Caulophyllum thalictroides<br />

Podophyllum peltatum<br />

Nandina domestica<br />

Knightia excelsa<br />

Placospermum coriaceum<br />

Ceratophyllum demersum<br />

Sassafras albidum<br />

Calycanthus floridus<br />

Hedyosmum arborescens<br />

Drimys winteri<br />

Drimys aromatica<br />

Magnolia acuminata<br />

Saruma henryi<br />

Asarum hayatanum<br />

Asarum canadense<br />

Aristolochia tomentosa<br />

Lactoris fernandeziana<br />

Saururus cernuus<br />

Saururus chinensis<br />

Chloranthus spicatus<br />

Houttuynia cordata<br />

Peperomia serpens<br />

Piper kadsura<br />

Prosopanche americana<br />

Hydnora africana<br />

Cytinus ruber<br />

Ombrophytum subterraneum<br />

Scybalium jamaicense<br />

Helosis cayennensis<br />

Corynaea crassa<br />

Rafflesia keithii<br />

Rhizanthes zipellii<br />

Balanophora fungosa<br />

Langsdorffia hypogaea<br />

Cynomorium coccineum<br />

Pinus wallichiana<br />

Pinus luchuensis<br />

Pinus elliottii<br />

Picea mariana<br />

Abies lasiocarpa<br />

Larix leptolepis<br />

Lagarostrobos franklinii<br />

Parasitaxis ustus<br />

Prumnopitys taxifolia<br />

Phyllocladus hypophyllus<br />

Phyllocladus trichomonoides<br />

Podocarpus costalis<br />

Podocarpus elatus<br />

Nageia nagi<br />

Nageia falcatus<br />

Saxegothaea conspicua<br />

Microcachrys tetragona<br />

Microstrobos fitzgeraldii<br />

Podocarpus totara<br />

Dacrycarpus dacrydioides<br />

Dacrycarpus imbricatus<br />

Dacrydium cupressinum<br />

Agathis robusta<br />

Araucaria columnaris<br />

Araucaria heterophylla<br />

Araucaria cunninghamii<br />

Araucaria excelsa<br />

Agathis borneensis<br />

Taiwania cryptomerioides<br />

Juniperus chinensis<br />

Cupressus macrocarpa<br />

Calocedrus formosana<br />

Calocedrus decurrens<br />

Metasequoia glyptostroboides<br />

Cryptomeria japonica<br />

Cephalotaxus wilsoniana<br />

Torreya nucifera<br />

Amentotaxus formosana<br />

Taxus mairei<br />

Sciadopitys verticillata<br />

Ephedra sinica<br />

Ephedra californica<br />

Ephedra saxatilis<br />

Ephedra antisyphilitica<br />

Gnetum urens<br />

Gnetum leyboldii<br />

Gnetum nodiflorum<br />

Gnetum africanum<br />

Welwitschia mirabilis<br />

Zamia pumila<br />

Cycas taitungensis<br />

Ginkgo biloba<br />

Botrychium lunaria<br />

Blechnum occidentale<br />

Hypolepis muelleri<br />

Paesia scaberula<br />

Histiopteris incisa<br />

Pteridium aquilinum<br />

Dicksonia antarctica<br />

Lonchitis hirsuta<br />

Odontosoria chinensis<br />

Dicranopteris linearis<br />

Vandenboschia davallioides<br />

Adiantum raddianum<br />

Lygodium japonicum<br />

Asplenium nidus<br />

Osmunda cinnamomea<br />

Angiopteris lygodiifolia<br />

Ophioglossum petiolatum<br />

Psilotum nudum<br />

Tmesipteris tannensis<br />

Equisetum robustum<br />

Equisetum hyemale<br />

Salvinia natans<br />

Lycopodiella inundata<br />

Lycopodium tristachyum<br />

Huperzia lucidula<br />

Huperzia taxifolia<br />

Lycopodium phlegmaria<br />

Selaginella vogelii<br />

Selaginella umbrosa<br />

Isoetes engelmannii<br />

Isoetes durieui<br />

Sphagnum cuspidatum<br />

Sphagnum palustre<br />

Ricciocarpos natans<br />

Riccia fluitans<br />

Plagiochasma rupestre<br />

Conocephalum conicum<br />

Reboulia hemisphaerica<br />

Preissia quadrata<br />

Bucegia romanica<br />

Marchantia polymorpha<br />

Riella helicophylla<br />

Sphaerocarpos donnelli<br />

Sphaerocarpus texanus<br />

Aulacomnium androgynum<br />

Aulacomnium turgidum<br />

Eurhynchium hians<br />

Blindia acuta<br />

Wardia hygrometrica<br />

Ulota phyllantha<br />

Orthotrichum stramineum<br />

Tortula ruralis<br />

Pottia truncata<br />

Fissidens taxifolius<br />

Dicranum scoparium<br />

Ptychomitrium gardneri<br />

Plagiomnium affine<br />

Cyrtomnium hymenophyllum<br />

Mnium hornum<br />

Cinclidium stygium<br />

Pohlia cruda<br />

Mielichhoferia bryoides<br />

Mielichhoferia elongata<br />

Pohlia bolanderi<br />

Leptostomum macrocarpum<br />

Meesia uliginosa<br />

Leptobryum pyriforme<br />

Tetraplodon mnioides<br />

Splachnum luteum<br />

Tayloria lingulata<br />

Brachymenium pulchrum<br />

Rhodobryum giganteum<br />

Bryum donianum<br />

Bryum alpinum<br />

Bryum caespiticium<br />

Anomobryum julaceum<br />

Bryum argenteum<br />

Encalypta rhapdocarpa<br />

Bryobrittonia longipes<br />

Scouleria aquatica<br />

Fontinalis antipyretica<br />

Orthodontium lineare<br />

Bartramia stricta<br />

Hedwigia ciliata<br />

Rhacocarpus purpurascens<br />

Philonotis fontana<br />

Bartramia pomiformis<br />

Pyrrhobryum vallis gratiae<br />

Plagiothecium undulatum<br />

Brachythecium rutabulum<br />

Calliergonella cuspidata<br />

Hypnum cupressiforme<br />

Hylocomium splendens<br />

Rhytidiadelphus squarrosus<br />

Physcomitrium pyriforme<br />

Funaria hygrometrica<br />

Physcomitrella patens<br />

Timmia sibirica<br />

Jamesoniella autumnalis<br />

Jungermannia leiantha<br />

Calypogeia arguta<br />

Polytrichum commune<br />

Atrichum angustatum<br />

Polytrichum formosum<br />

Atrichum undulatum<br />

Tetraphis pellucida<br />

Andreaea rupestris<br />

Takakia lepidozioides<br />

Andreaea rothii<br />

Anthoceros agrestis<br />

Anthoceros laevis<br />

Pellia epiphylla<br />

Scapania nemorea<br />

Symphyogyna brongartii<br />

Plagiochila adiantoides<br />

Trichocolea tomentella<br />

Lophocolea heterophylla<br />

Fossombronia pusilla<br />

Fossombronia brasiliensis<br />

Metzgeria furcata<br />

Haplomitrium hookeri<br />

Riccardia pinguis<br />

Chara hornemannii<br />

Chara curtissii<br />

Chara hispida<br />

Chara foetida<br />

Chara vulgaris<br />

Chara connivens<br />

Chara muelleri<br />

Chara australis<br />

Lamprothamnium macropogon<br />

Lamprothamnium papulosum<br />

Lychnothamnus barbatus<br />

Nitellopsis obtusa<br />

Chara preissii<br />

Nitella axillaris<br />

Tolypella porteri<br />

Nitella flexilis<br />

Coleochaete scutata<br />

Coleochaete orbicularis<br />

Klebsormidium flaccidum<br />

Chlorokybus atmophyticus<br />

Raphidonema longiseta<br />

Bracteacoccus aerius<br />

Bracteacoccus grandis<br />

Bracteacoccus medionucleatus<br />

Bracteacoccus minor<br />

Bracteacoccus giganteus<br />

Chlorella zofingiensis<br />

Ankistrodesmus stipitatus<br />

Scenedesmus ovalternus<br />

Scenedesmus producto capitatus<br />

Scenedesmus obliquus<br />

Scenedesmus rubescens<br />

Scenedesmus vacuolatus<br />

Scotiellopsis oocystiformis<br />

Scotiellopsis terrestris<br />

Coelastrella multistriata<br />

Scenedesmus pupukensis<br />

Scenedesmus costato granulatus<br />

Scenedesmus abundans<br />

Scenedesmus communis<br />

Neochloris aquatica<br />

Neochloris vigenis<br />

Characium hindakii<br />

Hydrodictyon reticulatum<br />

Pediastrum duplex<br />

Tetracystis aeria<br />

Chlorococcum echinozygotum<br />

Chlorococcum hypnosporum<br />

Chlamydomonas moewusii<br />

Chlamydomonas pitschmannii<br />

Chlamydomonas noctigama<br />

Carteria radiosa<br />

Carteria crucifera<br />

Polytoma oviforme<br />

Chlamydomonas monadina<br />

Chlamydomonas fimbriata<br />

Chlamydomonas rapa<br />

Chlamydomonas asymmetrica<br />

Hormotila blennista<br />

Gloeococcus maximus<br />

Chlamydomonas baca<br />

Chlamydomonas zebra<br />

Chloromonas oogama<br />

Chlamydomonas debaryana<br />

Chlamydomonas reinhardtii<br />

Volvox carteri<br />

Paulschulzia pseudovolvox<br />

Polytomella parva<br />

Hafniomonas reticulata<br />

Chloromonas serbinowi<br />

Chlamydomonas nivalis<br />

Chloromonas rosae<br />

Chloromonas clathrata<br />

Chlamydomonas macrostellata<br />

Chlamydomonas mutabilis<br />

Chlamydomonas bipapillata<br />

Chlamydomonas radiata<br />

Chlorococcopsis minuta<br />

Botryococcus braunii<br />

Ascochloris multinucleata<br />

Protosiphon botryoides<br />

Spongiochloris spongiosa<br />

Gongrosira papuasica<br />

Characium saccatum<br />

Characium vacuolatum<br />

Chloromonas perforata<br />

Chlorococcum oleofaciens<br />

Pleurastrum insigne<br />

Haematococcus zimbabwiensis<br />

Polytoma ellipticum<br />

Polytoma anomale<br />

Polytoma mirum<br />

Polytoma obtusum<br />

Polytoma uvella<br />

Polytoma difficile<br />

Chlamydomonas pulsatilla<br />

Chlamydomonas humicola<br />

Chlamydomonas dysosmos<br />

Dunaliella parva<br />

Dunaliella salina<br />

Asteromonas gracilis<br />

Spermatozopsis similis<br />

Muriella aurantica<br />

Chaetophora incrassata<br />

Stigeoclonium helveticum<br />

Fritschiella tuberosa<br />

Hormotilopsis tetravacuolaris<br />

Planophila terrestris<br />

Hormotilopsis gelatinosa<br />

Chaetopeltis orbicularis<br />

Oedogonium cardiacum<br />

Oedocladium carolinianum<br />

Oedogonium angustistomum<br />

Bulbochaete hiloensis<br />

Pleurastrum paucicellulare<br />

Parietochloris pseudoalveolaris<br />

Characium perforatum<br />

Pleurastrum erumpens<br />

Pleurastrum terrestre<br />

Chlorella sorokiniana<br />

Chlorella lobophora<br />

Chlorella vulgaris<br />

Muriella terrestris<br />

Chlorella kessleri<br />

Chlorella minutissima<br />

Nanochlorum eucaryotum<br />

Prototheca wickerhamii<br />

Chlorella protothecoides<br />

Prototheca zopfii<br />

Chlorella ellipsoidea<br />

Chlorella mirabilis<br />

Stichococcus bacillaris<br />

Choricystis minor<br />

Chlorella saccharophila<br />

Chlorella luteoviridis<br />

Dictyochloropsis reticulata<br />

Trebouxia jamesii<br />

Trebouxia arboricola<br />

Trebouxia asymmetrica<br />

Trebouxia usneae<br />

Trebouxia impressa<br />

Myrmecia biatorellae<br />

Friedmannia israeliensis<br />

Myrmecia astigmatica<br />

Trebouxia magna<br />

Chlorella homosphaera<br />

Microthamnion kuetzingianum<br />

Leptosira obovata<br />

Siphonocladus tropicus<br />

Ernodesmis verticillata<br />

Cladophora prolifera<br />

Cladophora coelothrix<br />

Microdictyon boergesenii<br />

Cladophora liebetruthii<br />

Cladophora catenata<br />

Cladophora socialis<br />

Valonia utricularis<br />

Chamaedoris peniculum<br />

Cladophoropsis membranacea<br />

Cladophora pellucida<br />

Cladophoropsis zollingerii<br />

Cladophora pellucidoidea<br />

Cladophora vagabunda<br />

Cladophora sericea<br />

Cladophora albida<br />

Cladophora rupestris<br />

Acetabularia dentata<br />

Acetabularia major<br />

Acetabularia acetabulum<br />

Acicularia schenkii<br />

Polyphysa peniculus<br />

Polyphysa parvula<br />

Neomeris dumentosa<br />

Cymopolia van bosseae<br />

Chlorocladus australasicus<br />

Batophora occidentalis<br />

Batophora oerstedii<br />

Bornetella nitida<br />

Pseudoneochloris marina<br />

Gloeotilopsis planctonica<br />

Protoderma sarcinoidea<br />

Pseudendoclonium basiliense<br />

Ulothrix zonata<br />

Myrmecia bisecta<br />

Tetraselmis convolutae<br />

Tetraselmis striata<br />

Scherffelia dubia<br />

Oltmannsiellopsis viridis<br />

Pseudoscourfieldia marina<br />

Nephroselmis olivacea Stein<br />

Mantoniella squamata<br />

Coccoid green alga<br />

Achlya bisexualis<br />

Lagenidium giganteum<br />

Phytophthora megasperma<br />

Developayella elegans<br />

Hyphochytrium catenoides<br />

Cymatosira belgica<br />

Papiliocellulus elegans<br />

Thalassiosira eccentrica<br />

Thalassiosira rotula<br />

Skeletonema costatum<br />

Skeletonema pseudocostatum<br />

Lauderia borealis<br />

Porosira glacialis<br />

Chaetoceros didymus<br />

Chaetoceros rostratus<br />

Eucampia antarctica<br />

Odontella sinensis<br />

Ditylum brightwelli<br />

Streptotheca thamesis<br />

Lithodesmium undulatum<br />

Pseudo nitzschia pungens<br />

Pseudo nitzschia multiseries<br />

Bacillaria paxillifer<br />

Nitzschia apiculata<br />

Cylindrotheca closterium<br />

Asterionellopsis glacilia<br />

Rhaphoneis belgicae<br />

Thalassionema nitzschioides<br />

Fragilaria striatula<br />

Actinocyclus curvatulus<br />

Coscinodiscus radiatus<br />

Corethron criophilum<br />

Rhizosolenia setigera<br />

Melosira varians<br />

Aulacoseira ambigua<br />

Aulacoseira distans<br />

Stephanopyxis broschii<br />

Giraudyopsis stellifera<br />

Saccorhiza polyschides<br />

Desmarestia ligulata<br />

Chorda tomentosa<br />

Sporochnus comosus<br />

Costaria costata<br />

Hizikia fusiformis<br />

Myagropsis myagroides<br />

Sargassum macrocarpum<br />

Sargassum confusum<br />

Sargassum horneri<br />

Coccophora langsdorfii<br />

Cystoseira hakodatensis<br />

Fucus distichus<br />

Fucus gardneri<br />

Pelvetia babingtonii<br />

Ectocarpus siliculosus<br />

Scytosiphon lomentaria<br />

Botrydium stoloniferum<br />

Tribonema aequale<br />

Heterothrix debilis<br />

Botrydiopsis intercedens<br />

Vaucheria bursata<br />

Vacuolaria virescens<br />

Heterosigma akashiwo<br />

Chattonella subsalsa<br />

Sarcinochrysis marina<br />

Aureomonas lagunensis<br />

Coccoid pelagophyte<br />

Pelagomonas calceolata<br />

Pelagococcus subviridis<br />

Aureococcus anophagefferens<br />

Coccoid stramenopile<br />

Tessellaria volvocina<br />

Mallomonas rasilis<br />

Mallomonas papillosa<br />

Synura petersenii<br />

Synura glabra<br />

Synura sphagnicola<br />

Synura spinosa<br />

Synura mammillosa<br />

Mallomonas caudata<br />

Mallomonas matvienkoae<br />

Mallomonas akrokomos<br />

Synura uvella<br />

Mallomonas annulata<br />

Mallomonas striata<br />

Mallomonas adamas<br />

Mallomonas splendens<br />

Chrysonephele palustris<br />

Ochromonas danica<br />

Paraphysomonas vestita<br />

Oikomonas mutabilis<br />

Hibberdia magna<br />

Chromulina chromophila<br />

Paraphysomonas foraminifera<br />

Nannochloropsis granulata<br />

Nannochloropsis oculata<br />

Nannochloropsis salina<br />

Apedinella radians<br />

Pteridomonas danica<br />

Pseudopedinella elastica<br />

Rhizochromulina cf marina<br />

Ciliophrys infusionum<br />

Dictyocha speculum<br />

Thraustochytrium kinnei<br />

Labyrinthuloides haliotidis<br />

Ulkenia profunda<br />

Labyrinthuloides minuta<br />

Syluania monomastiga<br />

Cafeteria roenbergensis<br />

Blastocystis hominis<br />

Proteromonas lacertae<br />

Loxodes magnus<br />

Loxodes striatus<br />

Blepharisma americanum<br />

Eufolliculina uhligi<br />

Climacostomum virens<br />

Spirostomum ambiguum<br />

Tetrahymena nanneyi<br />

Tetrahymena hyperangularis<br />

Tetrahymena pigmentosa<br />

Tetrahymena patula<br />

Tetrahymena capricornis<br />

Tetrahymena hegewischi<br />

Tetrahymena australis<br />

Tetrahymena thermophila<br />

Tetrahymena malaccensis<br />

Tetrahymena borealis<br />

Tetrahymena canadensis<br />

Tetrahymena pyriformis<br />

Tetrahymena tropicalis<br />

Tetrahymena corlissi<br />

Tetrahymena empidokyrea<br />

Glaucoma chattoni<br />

Colpidium campylum<br />

Ophryoglena catenula<br />

Ichthyophthirius multifiliis<br />

Opisthonecta henneguyi<br />

Vorticella microstoma<br />

Vorticella convallaria<br />

Paramecium tetraurelia<br />

Uronema marinum<br />

Cohnilembus verminus<br />

Pseudocohnilembus marinus<br />

Anophyroides haemophila<br />

Cyclidium plouneouri<br />

Cyclidium glaucoma<br />

Cyclidium porcatum<br />

Plagiopyla nasuta<br />

Plagiopyla frontata<br />

Trimyema compressum<br />

Prorodon teres<br />

Oxytricha granulifera<br />

Onychodromus quadricornutus<br />

Oxytricha nova<br />

Stylonychia pustulata<br />

Metopus palaeformis<br />

Nyctotherus cordiformis<br />

Nyctotherus ovalis<br />

Nyctotherus velox<br />

Metopus contortus<br />

Euplotes aediculatus<br />

Diplodinium dentatum<br />

Polyplastron multivesiculatum<br />

Eudiplodinium maggii<br />

Epidinium caudatum<br />

Ophryoscolex purkynjei<br />

Entodinium caudatum<br />

Dasytricha ruminantium<br />

Isotricha intestinalis<br />

Didinium nasutum<br />

Homalozoon vermiculare<br />

Loxophyllum utriculariae<br />

Bursaria truncatella<br />

Colpoda inflata<br />

Obertrumia georgiana<br />

Furgasonia blochmanni<br />

Pseudomicrothorax dubius<br />

Trithigmostoma steini<br />

Discophrya collini<br />

Uronema acuminata<br />

Minchinia teredinis<br />

Haplosporidium costale<br />

Haplosporidium nelsoni<br />

Haplosporidium louisiana<br />

Urosporidium crescens<br />

Babesia bovis<br />

Babesia bigemina<br />

Babesia caballi<br />

Babesia divergens<br />

Babesia odocoilei<br />

Babesia canis<br />

Theileria parva<br />

Theileria annulata<br />

Theileria taurotragi<br />

Theileria velifera<br />

Theileria buffeli<br />

Theileria sergenti<br />

Theileria cervi<br />

Theileria mutans<br />

Cytauxzoon felis<br />

Babesia equi<br />

Babesia rodhaini<br />

Babesia microti<br />

Sarcocystis tenella<br />

Sarcocystis arieticanis<br />

Sarcocystis cruzi<br />

Sarcocystis gigantea<br />

Sarcocystis hirsuta<br />

Sarcocystis buffalonis<br />

Sarcocystis fusiformis<br />

Sarcocystis hominis<br />

Sarcocystis aucheniae<br />

Toxoplasma gondii<br />

Neospora caninum<br />

Isospora ohioensis<br />

Isospora suis<br />

Isospora belli<br />

Sarcocystis muris<br />

Frenkelia glareoli<br />

Frenkelia microti<br />

Sarcocystis neurona<br />

Eimeria tenella<br />

Eimeria necatrix<br />

Eimeria acervulina<br />

Eimeria praecox<br />

Eimeria mitis<br />

Eimeria brunetti<br />

Eimeria nieschulzi<br />

Eimeria bovis<br />

Plasmodium berghei<br />

Plasmodium vivax<br />

Plasmodium fragile<br />

Plasmodium inui<br />

Plasmodium knowlesi<br />

Plasmodium cynomolgi<br />

Plasmodium simium<br />

Plasmodium malariae<br />

Plasmodium falciparum<br />

Plasmodium reichenowi<br />

Plasmodium floridense<br />

Plasmodium mexicanum<br />

Plasmodium gallinaceum<br />

Plasmodium lophurae<br />

Plasmodium ovale<br />

Cryptosporidium parvum<br />

Cryptosporidium wrairi<br />

Cryptosporidium baileyi<br />

Cryptosporidium muris<br />

Cryptosporidium serpentis<br />

Prorocentrum emarginatum<br />

Prorocentrum arenarium<br />

Prorocentrum lima<br />

Prorocentrum maculosum<br />

Prorocentrum concavum<br />

Alexandrium tamarense<br />

Alexandrium fundyense<br />

Alexandrium minutum<br />

Alexandrium ostenfeldii<br />

Alexandrium margalefeii<br />

Pyrocystis noctiluca<br />

Fragilidium subglobosum<br />

Ceratocorys horrida<br />

Ceratium tenue<br />

Ceratium fusus<br />

Amphidinium belauense<br />

Gonyaulax spinifera<br />

Crypthecodinium cohnii<br />

Gymnodinium beii<br />

Gymnodinium simplex<br />

Symbiodinium corculorum<br />

Symbiodinium meandrinae<br />

Symbiodinium pilosum<br />

Symbiodinium microadriaticum<br />

Gloeodinium viscum<br />

Prorocentrum panamensis<br />

Gymnodinium fuscum<br />

Lepidodinium viride<br />

Gymnodinium catenatum<br />

Gyrodinium impudicum<br />

Cachonina hallii<br />

Heterocapsa triquetra<br />

Gymnodinium sanguineum<br />

Scrippsiella nutricula<br />

Prorocentrum micans<br />

Prorocentrum mexicanum<br />

Prorocentrum minimum<br />

Pentapharsodinium tyrrhenicum<br />

Gymnodinium mikimotoi<br />

Cryptoperidonopis brodyi<br />

Pfiesteria piscicida<br />

Amyloodinium ocellatum<br />

Noctiluca scintillans<br />

Perkinsus marinus<br />

Gymnochlora stellata<br />

Lotharella vacuolata<br />

Chlorarachnion CCMP242<br />

Rhinomonas pauca<br />

Storeatula major<br />

Rhodomonas abbreviata<br />

Rhodomonas salina<br />

Rhodomonas mariana<br />

Cryptomonas CCMP325<br />

Geminigera cryophila<br />

Komma caudata<br />

Chilomonas paramecium<br />

Ammonia beccarii<br />

Sorites orbiculus<br />

Entamoeba dispar<br />

Entamoeba histolytica<br />

Entamoeba gingivalis<br />

Lotharella globosa<br />

Chlorarachnion reptans<br />

Pedinomonas minutissima<br />

Unnamed chlorarachniophyte CCMP<br />

Unnamed chlorarachniophyte<br />

Dictyostelium discoideum<br />

Physarum polycephalum<br />

Trypanosoma boissoni<br />

Trypanosoma triglae<br />

Trypanosoma rotatorium<br />

Trypanosoma therezieni<br />

Trypanosoma mega<br />

Trypanosoma scelopori<br />

Trypanosoma varani<br />

Trypanosoma avium<br />

Trypanosoma bennetti<br />

Trypanosoma theileri<br />

Trypanosoma grayi<br />

Trypanosoma musculi<br />

Trypanosoma lewisi<br />

Trypanosoma microti<br />

Trypanosoma cruzi<br />

Trypanosoma rangeli<br />

Trypanosoma vespertilionis<br />

Trypanosoma pestanai<br />

Trypanosoma congolense<br />

Trypanosoma simiae<br />

Trypanosoma evansi<br />

Trypanosoma equiperdum<br />

Trypanosoma brucei<br />

Blastocrithidia culicis<br />

Crithidia oncopelti<br />

Herpetomonas roitmani<br />

Phytomonas serpens<br />

Herpetomonas mariadeanei<br />

Leishmania guyanensis<br />

Leishmania tarentolae<br />

Endotrypanum monterogeii<br />

Leishmania major<br />

Leishmania amazonensis<br />

Leishmania donovani<br />

Crithidia fasciculata<br />

Herpetomonas muscarum<br />

Herpetomonas megaseliae<br />

Herpetomonas samuelpessoai<br />

Bodo caudatus<br />

Trypanoplasma borreli<br />

Rhynchobodo U67183<br />

Dimastigella trypaniformis<br />

Petalomonas cantuscygni<br />

Peranema trichophorum<br />

Khawkinea quartana<br />

Lepocinclis ovum<br />

Lepocinclis ovata<br />

Euglena gracilis<br />

Hexamita inflata<br />

Trepomonas agilis<br />

Spironucleus muris<br />

Giardia ardeae<br />

Giardia microti<br />

Giardia intestinalis<br />

Giardia duodenalis<br />

Giardia lamblia<br />

Giardia muris<br />

Nosema necatrix<br />

Vairimorpha necatrix<br />

Nosema oulemae<br />

Nosema vespula<br />

Nosema ceranae<br />

Nosema apis<br />

Nosema trichoplusiae<br />

Nosema bombycis<br />

Nosema furnacalis<br />

Encephalitozoon hellem<br />

Encephalitozoon cuniculi<br />

Septata intestinalis<br />

Enterocytozoon bieneusi<br />

Enterocytozoon salmonis<br />

Vittaforma corneae<br />

Endoreticulatus schubergi<br />

Ameson michaelis<br />

Glugea anomala<br />

Glugea stephani<br />

Glugea atherinae<br />

Pleistophora anguillarum<br />

Vavraia oncoperae<br />

Spraguea lophii<br />

Glugea americanus<br />

Visvesvaria acridophagus<br />

Visvesvaria algerae<br />

Culicosporella lunata<br />

Amblyospora stimuli<br />

Edhazardia aedis<br />

Amblyospora californica<br />

Parathelohania anophelis<br />

Antonospora scoticae<br />

Protists<br />

Archaea<br />

Bacteria<br />

You are here<br />

Animals<br />

Fungi<br />

Plants<br />

Bacillus coagulans<br />

Staphylococcus aureus<br />

Enterococcus sulfureus<br />

Streptococcus bovis<br />

Lactobacillus acidophilus<br />

Spiroplasma tiawanense<br />

Clostridium butyricum<br />

Heliobacterium gestii<br />

Thermoanaerobacter lacticus<br />

Deinococcus radiodurans<br />

Flavobacterium odoratum<br />

Chlamydia pneumoniae<br />

Fusobacterium perfoetens<br />

Escherichia coli<br />

Salmonella agona<br />

Vibrio aestuarianus<br />

Pseudomonas mendocina<br />

Legionella pneumophila<br />

Neisseria gonorrhoeae<br />

Burkholderia solanacearum<br />

Agrobacterium vitis<br />

Rhizobium leguminosarum<br />

Rickettsia montana<br />

Campylobacter hyointestinalis<br />

Helicobacter cholecystus<br />

Desulfoacinum infernum<br />

Myxococcus coralloides<br />

Spirochaeta alkalica<br />

Spirulina subsalsa<br />

Chlorobium phaeovibrioides<br />

Trichotomospora caesia<br />

Streptomyces lavendulae<br />

Microbacterium lacticum<br />

Nocardia calcarea<br />

Corynebacterium acetoacidophilum<br />

Kineococcus aurantiacus<br />

Geodermatophilus obscurus<br />

Bifidobacterium catenulatum<br />

Chloroflexus aurantiacus<br />

Aquifex pyrophilus<br />

Thermotoga maritima<br />

Pyrodictium occultum<br />

Thermoproteus tenax<br />

Thermococcus stetteri<br />

Thermococcus fumicolans<br />

Methanococcus jannaschii A<br />

Methanococcus maripaludis<br />

Methanobacterium bryantii<br />

Methanobacterium subterraneum<br />

Methanosarcina siciliae<br />

Thermoplasma acidophilum<br />

Halobacterium marismortui<br />

Haloferax denitrificans<br />

Coemansia reversa<br />

Spirodactylon aureum<br />

Coemansia braziliensis<br />

Dipsacomyces acuminosporus<br />

Linderina pennispora<br />

Kickxella alabastrina<br />

Martensiomyces pterosporus<br />

Smittium culisetae<br />

Capniomyces stellatus<br />

Furculomyces boomerangus<br />

Genistelloides hibernus<br />

Spiromyces aspiralis<br />

Spiromyces minutus<br />

Conidiobolus thromboides<br />

Macrobiotophthora vermicola<br />

Strongwellsea castrans<br />

Pandora neoaphidis<br />

Zoophthora culisetae<br />

Zoophthora radicans<br />

Eryniopsis ptycopterae<br />

Entomophaga aulicae<br />

Entomophthora muscae<br />

Entomophthora schizophora<br />

Conidiobolus coronatus<br />

Mucor ramannianus<br />

Mucor mucedo<br />

Mucor racemosus<br />

Syncephalastrum racemosum<br />

Basidiobolus ranarum<br />

Endogone pisiformis<br />

Mortierella polycephala<br />

Acaulospora rugosa<br />

Acaulospora spinosa<br />

Entrophospora columbiana<br />

Glomus mosseae<br />

Glomus cf geosporum<br />

Glomus mossae<br />

Glomus manihotis<br />

Glomus intraradices<br />

Glomus etunicatum<br />

Glomus claroideum<br />

Glomus versiforme<br />

Scuttellospora pellucida<br />

Scutellospora castanea<br />

Scutellospora heterogama<br />

Scuttellospora dipapillosa<br />

Gigaspora albida<br />

Gigaspora margarita<br />

Gigaspora decipiens<br />

Gigaspora gigantea<br />

Acaulospora gerdemannii<br />

Geosiphon pyriforme<br />

Aleurodiscus botryosus<br />

Stereum hirsutum<br />

Gloeocystidiellum leucoxantha<br />

Stereum annosum<br />

Heterobasidion annosum<br />

Laxitextum bicolor<br />

Hericium ramosum<br />

Hericium erinaceum<br />

Lentinellus ursinus<br />

Lentinellus omphalodes<br />

Clavicorona pyxidata<br />

Auriscalpium vulgare<br />

Bondarzewia berkeleyi<br />

Scytinostroma alutum<br />

Peniophora nuda<br />

Echinodontium tinctorium<br />

Russula compacta<br />

Inonotus hispidus<br />

Phellinus igniarius<br />

Trichaptum biforme<br />

Trichaptum abietinum<br />

Trichaptum fusco violaceum<br />

Trichaptum laricinum<br />

Basidioradulum radula<br />

Coltricia perennis<br />

Schizopora paradoxa<br />

Hyphodontia alutaria<br />

Sphaerobolus stellatus<br />

Geastrum saccatum<br />

Ramaria stricta<br />

Clavariadelphus pistillaris<br />

Gomphus floccosus<br />

Pseudocolus fusiformis<br />

Auricularia polytricha<br />

Auricularia auricula<br />

Pseudohydnum gelatinosum<br />

Boletus satanas<br />

Xerocomus chrysenteron<br />

Calostoma ravenelii<br />

Calostoma cinnabarinum<br />

Scleroderma citrina<br />

Paxillus panuoides<br />

Leucoagaricus gongylophorus<br />

Basid symb of Atta cephalotes<br />

Basid symb of Sericomyrmex bond<br />

Basid symb of Trachymyrmex bugn<br />

Basid symb of Cyphomyrmex rimos<br />

Basid symb of Apterostigma coll<br />

Athelia bombacina<br />

Panellus stipticus<br />

Typhula phacorrhiza<br />

Panellus serotinus<br />

Tricholoma matsutake<br />

Omphalina umbellifera<br />

Pleurotus ostreatus<br />

Coprinus cinereus<br />

Cortinarius iodes<br />

Lepiota procera<br />

Crucibulum laeve<br />

Stropharia rugosoannulata<br />

Calvatia gigantea<br />

Cyathus striat

---

How complex are different environments?<br />

Species complexity varies enormously across environments!<br />

Sequence 16s rRNA from<br />

agricultural soil and<br />

surroundings of deep-sea<br />

whale carcasses.<br />

Soil species diversity is<br />

immense, ≈850 species<br />

detected (but estimated to<br />

be ≥3000).

---

Reading & backpacking<br />

through Italy<br />

Visit the town libraries along the route.<br />

Read ancient texts in each library in 12word<br />

fragments.<br />

Assignment: Reconstruct libraries.<br />

Caveat: You don’t have enough time to<br />

read all 12-word fragments at any<br />

library.

---

percent similarity<br />

50 100<br />

Bible: Fragment recruitment

---

41 samples (from surface waters): Filter<br />

(0.1-3µM), E. coli is 2µm by 0.1µm.<br />

6.25 Gigabases: 2.7M pages (at 2200<br />

characters per page): 270m stack (at<br />

0.1mm per page).<br />

How much does species composition at a<br />

single site over time?<br />

To learn about the:<br />

–Diversity,<br />

–Geographic distribution, and<br />

–Protein content & metabolism<br />

Sorcerer II: The beauty of shot-gun sequencing<br />

Global Ocean Sampling (GOS) survey:<br />

‣ the species diversity,<br />

‣ geographic distribution,<br />

‣ gene content and metabolism<br />

From Nova Scotia to Hawaii:<br />

6.25 x 10^9 bp from 41 sites.<br />

Protocol:<br />

‣ Collect sea surface water samples,<br />

‣ filter (0.1-3.0µm) to recover<br />

bacteria,<br />

‣ Extract DNA, fragment and clone<br />

into a plasmid library.<br />

‣ Sequence DNA in plasmid library.

---

Yooseph et al., 2007

---

Extreme Assembly of U<br />

The analyses describe<br />

organisms with repres<br />

genomes were readily<br />

other abundant but u<br />

provide valuable physio<br />

that could eventually<br />

organisms, help elucida<br />

ity, and allow similar an<br />

such as those performe<br />

assembly efforts and the<br />

that there is consider<br />

variation among related<br />

to disrupt whole-genom<br />

assembly approach that<br />

this approach ‘‘extreme<br />

ods). This approach cu<br />

pairing data and, the<br />

scaffolded sequences. U<br />

as 900 kb could be alig<br />

marinus MIT9312 and P<br />

2J–2L). Consistent pat<br />

below) generally provi<br />

contigs belonging to<br />

Accordingly, large con<br />

were used to investigat<br />

structure, as described<br />

assemblies demonstrab<br />

assembly artifacts, inclu<br />

sequences (Figure 6).<br />

assembly was employed<br />

Yooseph et al., 2007

---

Ocean’s diversity landscape is far from uniform<br />

a<br />

deals<br />

the in the series deals<br />

ences. s encoded in the<br />

uence OS) sequences.<br />

uence rotein sequence<br />

ses and of sequence<br />

com- dundancy and<br />

s argest is a huge com-<br />

ingle, ably the largest<br />

r t, using this a single,<br />

ema. ltiple In fact, this<br />

tering cludes multiple<br />

stan- and clustering<br />

e ely of to the substan-<br />

in k and the is likely to<br />

ic GOS studies bin<br />

the<br />

ults with of the GOS<br />

nterpreted matic with<br />

icted e bioinformatic<br />

of the<br />

predicted<br />

novel are parts of the<br />

These eemingly novel<br />

proteins. con- These<br />

iously<br />

a<br />

43,244 (3%)<br />

59,086 (4%)<br />

151,123 (10%)<br />

60,650 (4%)<br />

208,999 (14%)<br />

43,244 (3%)<br />

59,086 (4%)<br />

151,123 (10%)<br />

60,650 (4%)<br />

208,999 (14%)<br />

59 (0%)<br />

811 16S ribotypes identified (≈species); half of which are novel:<br />

b 124 (1%) 59 (0%)<br />

GOS only<br />

‣ Only 60 abundant ribotypes (1<br />

124<br />

previously<br />

(1%)<br />

unknown). GOS + known GOS prokaryotic only<br />

Distribution 3,547 of identifiable (21%) bacteria is strikingly 3,995 non-uniform: (24%) Conserved<br />

5 genera account for ≈97% of<br />

GOS + viral/eukaryotic<br />

the sequences. 3,547 (21%) 3,995 (24%) Conserved<br />

Extensive diversity within ribotypes:<br />

922,677 (65%)<br />

N E W S A N D V I E W S<br />

N E W S A N D V I E<br />

Pelagibacter<br />

Prochlorococcus Pelagibacter<br />

Synechococcus Prochlorococcus<br />

BurkholderiaSynechococcus<br />

Shewanella Burkholderia<br />

Other Shewanella<br />

922,677 (65%)<br />

Other<br />

GOS + known prokaryotic<br />

Viral/eukaryotic GOS only + viral/eukaryotic<br />

Known prokaryotic Viral/eukaryotic only only<br />

Known prokaryotic Known + prokaryotic viral/eukaryotic only<br />

‣ Few identical genomic sequences found: 85% were unique using a 98% identity cutoff.<br />

Known prokaryotic + viral/euk

---

-<br />

g<br />

e<br />

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t<br />

4<br />

r<br />

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)<br />

p<br />

b<br />

M<br />

(<br />

e<br />

z<br />

i<br />

s<br />

e<br />

m<br />

o<br />

n<br />

e<br />

G<br />

10.0<br />

5.0<br />

1.0<br />

0.5<br />

0.1<br />

Free-living<br />

Host-associated<br />

Obligate symbionts/parasites<br />

Pelagibacter ubique<br />

Mycoplasma genitalium<br />

Coxiella burnetii<br />

Bartonella henselae<br />

Thermoplasma acidophilum<br />

Bartonella quintana<br />

Ehrlichia ruminantium<br />

Mesoplasma florum<br />

Wigglesworthia glossinidia<br />

Nanoarchaeum equitans<br />

Rickettsia conorii<br />

Prochlorococcus marinus SS120<br />

Prochlorococcus marinus MED4<br />

Pelagibacter ubique<br />

Streptomyces coelicolor<br />

Rhodopirellula<br />

baltica<br />

Silicibacter pomeroyi<br />

Synechococcus sp.WH8102<br />

Prochlorococcus marinus MIT9313<br />

500 5000<br />

100 1000 10000<br />

Number of protein encoding genes

---

How much sequencing does it take?<br />

# reads required<br />

γ genome size (bp)<br />

r read length (bp)<br />

f<br />

fold coverage<br />

(mean)

---

How much sequencing does it take?<br />

fraction covered<br />

k = 0<br />

e natural base<br />

f<br />

k<br />

fold coverage<br />

(mean)<br />

exact number of<br />

times sequenced

---

# reads required<br />

fraction covered<br />

γ 7,000,000 bp<br />

r 400 bp<br />

f 5 x<br />

R 87,500 reads<br />

C 99.3%

---

Bacteriodes thetaiotaomicron 3731 7,194,490 bp

---

Sequencing of<br />

entire BAC insert<br />

Gene prediction 101 (prokaryotes)<br />

Sequencing of<br />

entire BAC insert<br />

BAC single-insert sequence<br />

Sequencing End sequencing of<br />

100N<br />

entire in BAC silico insert assemb<br />

Conse<br />

100N 100N<br />

T BAC A T single-insert C A T Figure<br />

sequence G 1 G… | Microbial community … T BAC DNA A single-insert Consensus G sequencing. C T composite sequence C G Schematic Tscaffold<br />

approaches for retrieving genomic sequence information from nat<br />

a | One approach uses large DNA inserts recovered in bacterial ar<br />

Figure 1 | Microbial community M that K are Y R each DNA R A derived sequencing. T P from S Figure Ran<br />

individual 1 Schematic | Microbial cell. diagram community Subsequent of common DNA sequenc se<br />

approaches for retrieving contiguous genomic DNA sequence sequence information approaches that is derived from for retrieving natural from microbial a single genomic cell populatio sequen in the o<br />

a | One approach uses approach large DNA is inserts based recovered on recovery a | One in approach bacterial of small inserts, artificial uses large and chromosomes DNA attempts inserts sub (Br<br />

that are Assemble each derived all reads from cloned into an unique individual DNA contigs. derived cell. from Subsequent that a genetically are each sequencing derived heterogeneous from and an assembly individual population. resu ce<br />

contiguous Perform DNA six-frame sequence of translation, DNA that sequence is derived and select that from long is contiguous a derived single ORFs (≥60 cell from DNA in aa) the many sequence<br />

with original different appropriate population. that cells. is derived b | A<br />

approach codon is frequencies. based on recovery of small inserts, approach and attempts is based subsequent on recovery assembly of small from ins<br />

cloned DNA derived from a genetically heterogeneous cloned DNA population. derived The from end a genetically result is an hete ass<br />

Translate into potential proteins.<br />

of DNA sequence that is derived from many different of DNA cells. sequence that is derived from man<br />

microbial communities. Nev<br />

ing of microbial communit<br />

if expensive, approach for h

---

Clustering Database analysis

---

Gene prediction: Clustering<br />

≥3<br />

filter

---

Gene prediction: Database analysis<br />

Pfam database<br />

Database provides models (statistical definitions) of ≈9,000 protein families.<br />

Query: Does my predicted proteins fit to a known protein family?<br />

?<br />

350 million comparisons: On a standard computer would have taken over a<br />

century to complete.

---

Sorcerer II: What Gentle lysis, did you do to my database!?<br />

Gentle lysis,<br />

extraction, DNA<br />

size separation<br />

BAC/fosmid<br />

cloning<br />

(40–100 kb)<br />

extraction, DNA<br />

size separation<br />

Million<br />

proteins<br />

Lysis, DN<br />

shearing<br />

5.7<br />

Table 2. Clustering and HMM Profiling Results Showing the Number of Predicted P<br />

Expanding the Protein<br />

ofiling Results Showing the Number of Predicted Proteins (Including Both Redundant<br />

Expanding the Protein F<br />

h Nonredundant Dataset Sequences) in Each Dataset<br />

lustering Dataset(A) HMM Original Set A Clustering \ B (A) A B HMM B A A Total \ BPredicted A B<br />

filing Table Results 2. Clustering Showing BAC/fosmid<br />

Shotgun<br />

Profiling and the (B) HMM Number Profiling of Predicted Results Proteins Showing Profiling (Including the (B) Number Proteins Both of Redundant Predicted A P<br />

h Dataset Nonredundant Sequences)<br />

cloning<br />

in Each Dataset<br />

(3<br />

[ B<br />

kb)<br />

(40–100 kb)<br />

939,056 NCBI-nr 1,645,146 2,317,995 1,566,123 1,939,056 372,9331,645,14679,023 1,566,123 2,018,079 372,93<br />

PG ORFs 3,049,695 575,729 448,159 418,503 157,22<br />

TGI-EST ORFs 5,458,820 1,097,083 606,779 576,532 520,55<br />

319,855 ENS 253,007 361,668 241,671 319,855 78,184 253,00711,336 241,671 331,191 78,18<br />

046,914 GOS ORFs<br />

39,056 NCBI-nr<br />

978,637 Total<br />

75,729 PG ORFs<br />

3,701,388 17,422,766<br />

1,645,146 2,317,995<br />

6,654,479 28,610,944<br />

448,159 3,049,695<br />

3,624,907 6,046,914<br />

1,566,123 1,939,056<br />

6,427,736 9,978,637<br />

418,503 575,729<br />

2,422,0073,701,38876,481 372,9331,645,146 79,023<br />

3,550,9016,654,479 226,743<br />

157,226 448,159 29,656<br />

3,624,907 6,123,395<br />

1,566,123 2,018,079<br />

6,427,736 10,205,380<br />

418,503 605,385<br />

2,422,00<br />

372,93<br />

3,550,90<br />

157,22<br />

97,083 TGI-EST ORFs 606,779 5,458,820 576,532 1,097,083 520,551 606,779 30,247 1,127,330 576,532 520,55<br />

ns 19,855 common ENS A \ B denotes to both the the number 253,007 clustering 361,668 of predicted and the HMM proteins 241,671 profiling; 319,855 common A toB, both the 78,184 number the clustering 253,007 of predicted 11,336 and the proteins HMM241,671 331,191 profiling; in clusters Abut B, not the 78,18 in nut<br />

ustering 575,729 Dataset (A) HMM Original 448,159 Set A Clustering 418,503 \ B (A) A 157,226 B HMMB29,656<br />

A Total A \ 605,385 BPredicted A B<br />

097,083 Profiling 606,779 (B) 576,532 520,551Profiling 30,247 (B) Proteins 1,127,330A<br />

[ B

---

The expanding universe of known proteins<br />

5.7 Million new proteins<br />

(≈1.8x previously known<br />

proteins)<br />

‣ ≈4% of viral origin<br />

Cluster previously known and<br />

GOS proteins: 17,036 clusters<br />

‣ 3,995 clusters are GOS<br />

specific!<br />

Figure 3. Venn Diagram Showing Breakdown of the 17,067 Medium and<br />

Large Clusters by Three Categories—GOS, Known Prokaryotic, and<br />

Known Nonprokaryotic<br />

doi:10.1371/journal.pbio.0050016.g003<br />

the<br />

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---

grouping shows that our current GOS sampling methodology<br />

will not cover all protein families, and perhaps misses some<br />

protein families Rate that are of exclusive protein to higher discovery eukaryotes. The<br />

large section of clusters that include all three groupings<br />

uences Are Added<br />

e y-axis denotes the number of clusters (in thousands). Seven datasets with increasing<br />

d in the text. The blue curve shows the number of core sets of size 3 for the seven<br />

own. Linear regression gives slopes 0.027 (R 2 ¼ 0.999), 0.011 (R 2 ¼ 0.999), 0.0053 (R 2 ¼<br />

nd size 20, respectively.<br />

only sequenc<br />

members of k<br />

clustering pa<br />

detected by a<br />

Figure 2. Rate of Discovery of Clusters as (Nonredundant) Sequences Are Added<br />

The x-axis denotes the number of sequences (in millions) and the y-axis denotes the number<br />

numbers of (nonredundant) sequences are chosen as described in the text. The blue curve<br />

datasets. Curves for core set sizes 5, 10, and 20 are also shown. Linear regression gives<br />

0.999), and 0.0024 (R 2 0437<br />

March 2007 | Volume 5 | Issue 3 | e16<br />

¼ 0.996) for size 3, size 5, size 10, and size Yooseph 20, et respectively. al., 2007

---

D.Man et al.<br />

Harvesting light: Proteorhodopsin<br />

Fig. 1. Structure modeling of PR (BeÂjaÁ et al., 2000a) based on the 1.55 AÊ resolution structure of bacteriorhodopsin (Luecke et al., 1999).<br />

(A) Green-absorbing eBAC31A08 variant (G-PR); (B) blue-absorbing PalE6 variant (B-PR). Hydrophilic loops and amino acids in common between<br />

the twoProteorhodopsins variants are omitted for clarity. are retinal-binding, Lys232 in helix G, Schiff fast, baselight-driven linked to retinal (marked proton green pumps. or blue), is labeled red. Structures were<br />

visualized using the ViewerLite 4.2 program (Accelrys Inc.).<br />

GOS yielded ≈2700 putative proteorhodopsins: included LEU- and GLU- variants.<br />

absorbing and green-absorbing PRs (B-PRs and G-PRs,<br />

respectively). The models (Figure 1) were constructed by<br />

threading PR sequences on the 1.55 AÊ resolution structure<br />

The difference between the two families at position 105<br />

is a non-polar leucine residue (G-PR) versus a polar<br />

glutamine residue (B-PR). Therefore two PR protein

---

Sargasso Sea<br />

North Atlantic<br />

Coast<br />

12. Distribution of Common Proteorhodopsin Variants across GOS Samples<br />

The green-tuned (LEU) variant was highly abundant in the North Atlantic samples, where as<br />

ucine (L) and methionine (M) variants absorb maximally in the green spectrum (Oded Beja, personal communication) while the glutamine (Q)<br />

t absorbs maximally blue-tuned in the(GLU) blue spectrum. variant Thedominates relative abundance in the of remaining each variant ismostly shown asopen a percentage ocean (x-axis) samples. per sample (y-axis). Total<br />

ance for all variants in read equivalents normalized by the abundance of recA protein are shown on the right side of the y-axis. The L and Q<br />

ts show a nonrandom distribution. The L variant is abundant in temperate Atlantic waters close to the U.S. and Canadian coast. The Q variant is

---

oup http://www.nature.com/natstructmolbiol<br />

Living with UV-damage: Photolyases & UVDE<br />

ARTICLES<br />

less stable than native polymerase–DNA<br />

complexes22 . Nucleotide substrates diffused<br />

out of the CPD-containing complexes during<br />

equilibration of the crystals before freezing.<br />

The resulting structures show an open<br />

conformation of the fingers, similar to that<br />

of unliganded T7 DNA polymerase (data not<br />

shown). To overcome the low affinity for<br />

nucleotide substrates in the CPD complexes,<br />

we added nucleotides to the cryopreservation<br />

buffers used for harvesting the crystals.<br />

Three different CPD-3! structures were<br />

determined using crystals equilibrated in<br />

0 mM, 1 mM or 10 mM ddATP in the<br />

harvesting solutions and they are named<br />

CPD-3!a, CPD-3!b, and CPD-3!c, respectively.<br />

Two structures of CPD-5! complexes<br />

were determined with 0 mM or 10 mM<br />

ddATP added (the CPD-5!a and CPD-5!b<br />

complexes; Table 1). All of the structures<br />

were determined by molecular replacement<br />

Photoreactivation is a repair system specific for dealing with pyrimidine dimers.<br />

Photolyase enzymes contain a FADH2 group that absorbs light between 350-500 nm,<br />

and catalyze separation of fused bases.<br />

using a model of T7 DNA polymerase 22 . The<br />

structures have been refined to resolution<br />

limits ranging from 2.2 to 2.3 Å, except for<br />

the CPD-3!c complex, which has a resolution<br />

limit of 3.2 Å (Table 2 and Figs. 1 and 2).<br />

Figure 2 A cis-syn thymine dimer and electron density maps around its binding sit<br />

structures. (a) Schematic drawing of a cis-syn thymine dimer. (b) CPD-3!a complex<br />

nucleotide in the harvesting solutions showing the electron density for the CPD out<br />

polymerase active site. (c) CPD-3!c complex with 10 mM incoming nucleotide in th

---

and phosphatases protein kinases serve andas phosphatases antagonistic serve by the as human antagonistic protein phosp by t<br />

Living with UV-damage: Photolyases & UVDE<br />

ring of Sequences Table 10. in Clustering Familiesof That Sequences Are Explored in Families in ThisThat andAre Companion ExploredPapers in This<br />

ProteinCluster FamilyID Nonredundant Cluster Sequences ID Nonredundant Total Sequences Sequences NCBI-n<br />

RecA 1146 2,897 1146 2,8977,423<br />

1,683<br />

UVDE 6239 417 6239 417 484 38<br />

Photolyase 411 1,387 411 1,3872,261<br />

19<br />

1285 5,907 1285 5,9079,796<br />

302<br />

3077 319 3077 319 482 149<br />

3454 67 3454 67 73 1<br />

Spore lyase 5283 237 5283 237 331 39<br />

PP2C phosphatase 78 2,917 78 2,9173,933<br />

762<br />

3673 62 3673 62 106<br />

GOS data provides<br />

9118<br />

a 10x increase<br />

68<br />

in diversity of<br />

9118<br />

proteins involved<br />

68<br />

in<br />

73<br />

UV-damage repair:<br />

39<br />

0<br />

‣ 7,680 photolyase 11012181 proteins 36 (four clusters). 11012181 36 69<br />

11021747 19 11021747 19 72<br />

‣ 417 UV-dimer 11066319endonucleases 19 (related 11066319 to uvrA, uvrB, uvrC; 19many<br />

38 viral).<br />

34<br />

13<br />

14<br />

(type I, II, Glutamine III) synthetase 3709 (type 4,284 I, II, III) 3709 4,28411,322<br />

1,504<br />

3072 159 3072 159 192 46<br />

4547 30 4547 30 32 1<br />

it) RuBisCO (large 3734 subunit) 1,979 3734 1,97914,149<br />

13,532

---

Sequence space vs. 3d-fold space<br />

Many proteins with different sequences fold into similar 3d-shapes: leghemoglobin<br />

(yellow lupin) and myoglobin (seal) share only 21.9% sequence identity.

---

A few words on Craig Venter…

---

“Its nice to have a few trillion friends”<br />

Gut microbiome holds ≈100 trillion bacterial cells; that is 10x more bacterial cells than<br />

human cells<br />

Composite metagenome of this microbiome contains 100x more genes than our human<br />

genome:<br />

‣ Perform transformations: synthesis of essential vitamins, and metabolism of drugs &<br />

xenobiotics.<br />

‣ Affects susceptibility to pathogens and diseases.<br />

‣ Human Gut Microbiome Initiative: The next human genome project.<br />

Helicobacter pylori:<br />

Gastritis<br />

Helicobacter<br />

hepaticus:<br />

Inflammatory bowel<br />

disease<br />

What are these 2.5M<br />

genes doing in our<br />

bodies?

---

of<br />

this<br />

yloonnearrmiinoare<br />

S1.<br />

ject<br />

For<br />

nce<br />

.<br />

Bacteriodetes<br />

non-α-proteobacteria<br />

Actinobacteria<br />

Firmicutes<br />

α-proteobacteria<br />

on November 21, 20<br />

www.sciencemag.org<br />

Who’s there?<br />

Downloaded from<br />

Large-scale (13,355) prokaryotic 16S rRNA<br />

analysis identified ≈400 ribotypes (99%<br />

similarity):<br />

‣ 395 bacterial ribotypes (11,831 16s<br />

rRNA):<br />

‣ 244 novel ribotypes<br />

‣ 1 archaeal ribotype (1,524 16s rRNA):<br />

Methanobrevibacter smithii<br />

80% of the bacterial ribotypes have not<br />

been cultured.<br />

Eckburg et al., 2005

---

s<br />

-<br />

c<br />

,<br />

-<br />

s<br />

-<br />

-<br />

t<br />

r<br />

t<br />

-<br />

b<br />

Percentage of total<br />

sequences<br />

c<br />

Microbial T3 ecology alters with weight-loss<br />

T2<br />

Dieting alters the balance between Bacteriodetes and Firmicutes in humans.<br />

Bacteriodetes R enrichment is independent of diet type: carb-restricted or fatrestricted.<br />

2 = 0.8<br />

R2 30 CARB-R<br />

Figure 1 25|<br />

Correlation FAT-Rbetween<br />

body-weight loss and gut microbial ecology. a, Clustering of 16S<br />

ribosomal RNA gene sequence libraries of faecal microbiota for each person (in different colours)<br />

and time<br />

20<br />

point in diet therapy (T0, baseline; T1, 12 weeks; T2, 26 weeks; T3, 52 weeks) in the two diettreatment<br />

15 groups (fat restricted, FAT-R; carbohydrate restricted, CARB-R), based on UniFrac analysis<br />

of the 18,348-sequence phylogenetic tree. b, Relative abundance of Bacteroidetes and Firmicutes. For<br />

10<br />

each time point, values from all available = 0.5 samples were averaged (n was 11 or 12 per time point). Leansubject<br />

controls 5 include four stool samples from two people taken 1 year apart, plus three other stool<br />

samples<br />

0<br />

6 . Mean values ± s.e. are plotted. c, Change in relative abundance of Bacteroidetes in subjects<br />

with weight loss above a threshold of 2% weight loss for the CARB-R diet and 6% for the FAT-R diet.<br />

Change in Bacteroidetes<br />

abundance (%)<br />

100<br />

80<br />

60<br />

40<br />

20<br />

FAT-R<br />

T1<br />

T0<br />

T1<br />

T2<br />

T3<br />

T1<br />

T2<br />

T1<br />

T3<br />

T0<br />

T3<br />

T0<br />

T2<br />

T1<br />

T3<br />

T0<br />

T1<br />

T2<br />

T3<br />

Firmicutes Bacteroidetes<br />

CARB-R<br />

0 12 26 52 Lean<br />

Weeks on diet<br />

T1<br />

T0<br />

T1<br />

T1<br />

T2<br />

T0<br />

T2<br />

T3<br />

T1<br />

T2<br />

T3<br />

T1<br />

T1<br />

T3<br />

T3<br />

T0<br />

T0<br />

Percent<br />

seq<br />

c<br />

Change in Bacteroidetes<br />

abundance (%)<br />

40<br />

20<br />

30 CARB-R<br />

25<br />

FAT-R<br />

20<br />

15<br />

10<br />

5<br />

0<br />

0<br />

0 12 26 52 Lean<br />

Weeks on diet<br />

R 2 = 0.8<br />

R 2 = 0.5<br />

-5 -10 -15 -20<br />

Change in body weight (%)<br />

-25<br />

Ley et al., 2006

---

“The best-laid plans of mice & men go oft awry”<br />

Leptin is protein hormone that plays a key role in regulating energy intake and<br />

expenditure: It affects both appetite (decreases) and metabolism (increases).<br />

Leptin-deficient (Ob-/Ob-) mice are obese.<br />

Turnbaugh et al., 2006

---

ob2<br />

ob1<br />

metabolism (Fig. 1d; Supplementary Fig. 3 and Supplementary<br />

2 2<br />

Table 6). EGTs representing these enzymes were grouped according<br />

to their functional classifications in 0 the 0 Carbohydrate Active<br />

Enzymes (CAZy) database (http://afmb.cnrs-mrs.fr/CAZY/). The<br />

ob/ob microbiome is enriched (P , 0.05) for eight glycosideCOG hydrolase category<br />

increased adiposity is a<br />

6J mice were colonized<br />

“The best-laid plans of mice & men go oft awry”<br />

[J] [K] [J] [L] [K] [D] [L] [V] [D] [T] [M] [T] [N] [M] [U] [N] [O] [U] [R] [O] [S] [R]<br />

ob2<br />

lean1<br />

lean2<br />

lean1<br />

lean3<br />

lean2<br />

1 run<br />

lean3<br />

1 run<br />

2 runs<br />

1 run<br />

2 runs<br />

1 run<br />

2 runs<br />

3 runs<br />

2 runs<br />

3 runs<br />

All<br />

d<br />

PCA2<br />

[V] [S]<br />

COG category<br />

a 120<br />

ob1 ob1 ob1 ob2 ob2<br />

versus versus versus versus<br />

a ob2 (ob/ob) b 0.6 lean1 lean1 lean1 lean2 lean2 100<br />

ob1 ob2 ob2<br />

s versus versus<br />

KEGG KEGG category category (3730) (GS20) (3730) (GS20) (3730) (3730) KEGG KEGG pathway pathway<br />

1 lean1 lean2 lean2<br />

Carbohydrate Carbohydrate 0.14<br />

lean1<br />

2E-14 0.14 6E-04 2E-14 6E-04 Citrate cycle Citrate * cycle<br />

0.4<br />

80<br />

*<br />

Ob<br />

0) ) (GS20) (3730) COG (3730) category COG category<br />

lean2 0.066 0.066 0.011 Pentose/glucuronate 0.011 Pentose/glucuronate interconversions interconversions *<br />

58<br />

5E-05 [J] Translation [J] Translation * *<br />

0.382 0.3821 0.994 1 0.994 Galactose Galactose metabolism metabolism (ob<br />

1 1 [K] Transcription [K] Transcription * *<br />

0.2 1 1 1 Starch/sucrose 1 Starch/sucrose metabolism 60metabolism<br />

* *<br />

1 1 [L] Replication, [L] Replication, recombination, recombination, repair*<br />

ob1 repair(ob/ob)<br />

*<br />

0.532 0.5321 0.996 1 0.996 C5-branched C5-branched dibasic dibasic acid metabolism acid metabolism *<br />

76<br />

0.307 [D] Cell [D] cycle Cell control, cycle control, cell division cell division<br />

Energy Energy 0.595 PCA1 0.595 0.005 0.005 Reductive Reductive carboxylate carboxylate cycle cycle<br />

0<br />

0.084 8E-04 6E-04 Pyruvate/oxoglutarate 40<br />

1 1 [V] Defense [V] Defense mechanisms mechanisms<br />

0.084 8E-04 6E-04 Pyruvate/oxoglutarate oxidoreductases oxidoreductase<br />

[T] Signal transduction *<br />

–0.505 Lipid –0.495 0.878 –0.485 1 0.994 Glycerolipid metabolism*<br />

1 1 [T] Signal transduction *<br />

Lipid 0.878 1 0.994 Glycerolipid metabolism*<br />

[M] Cell wall/membrane/envelope biogenesis<br />

Amino acid Amino 0.022 acid 7E-07 0.022 7E-07 0.01 Phe, 0.01 Tyr Phe, and Tyr Trp and biosynthesis<br />

–0.2<br />

20 Trp biosynthesis * *<br />

65<br />

0.596 [M] Cell wall/membrane/envelope biogenesis<br />

Other amino Other acids amino 0.225 acids 0.225 0.019 0.019 β-Ala metabolism β-Ala metabolism<br />

1 1 [N] Cell [N] motility Cell * motility *<br />

lean2 (ob/+)<br />

Glycan Glycan 0.023 7E-12 0.023ob2 0.012 7E-12 0.012 Lipopolysaccharide biosynthesis biosynthesis * *<br />

48<br />

0.434 [U] Intracellular [U] Intracellular trafficking trafficking and secretion and secretion<br />

–0.4 0.826 0.8261 1 1 Glycosphingolipid 1 Glycosphingolipid metabolism 0 metabolism * *<br />

46<br />

0.894 [O] Posttranslational [O] Posttranslational modification modification<br />

Transcription Transcription 0.975 0.975 1 Unclassified 1 Unclassified transcriptional transcriptional regulators regulators * *<br />

[R] General [R] General function function prediction prediction only * only * Folding/sorting/degradation 0.835 0.835 0.957 0.957 Type III Type secretion III secretion system system<br />

[S] Function [S] Function unknown unknown<br />

Membrane Membrane –0.6 transport transport 1ob1 1 1 1 1 ABC 1 transporters ABC transporters * *<br />

Depleted Depleted Enriched Enriched<br />

Cell motility Cell motility 1 1 1 1 Flagellar Flagellar assembly assembly * *<br />

lean1 (+/+) –0.8 1 1 1 1 Bacterial Bacterial motility motility proteins proteins<br />

Cell growth Cell growth and death and death 1 1 1 1 Sporulation Sporulation * *<br />

Figure 3 | Biochemical an<br />

0.999<br />

Figure 2 | Microbiomes cluster according to host genotype. a, Clustering of experiments confirm that<br />

caecal microbiomes of obese and lean sibling lean pairs littermates. based Red on reciprocal denotes enrichment and forgreen dietary indicates energy depletion harves o<br />

Gut microbiomes TBLASTX comparisons. cluster according All possible to reciprocal host genotype: the basis TBLASTX of a cumulative ob-/ob- comparisons microbiomes binomialof test (brightness<br />

quantification are more indicates similar of<br />

the<br />

short-ch<br />

level of<br />

to each microbiomes other than (defined to that byof capillary lean mice. significance). Black indicates pathways whose representation is not<br />

sequencing) were performed from both<br />

significantly different. Asterisks indicate groups obese that (n were 5 5) consistently conventiona<br />

lean and obese sibling pairs. A distance matrix enriched was or then depleted created between using both the sibling pairs the faecal using agross more stringent energy co EG<br />

The cumulative ob-/ob- microbiome bitscore for is each enriched comparison for enzymes and the cumulative polysaccharide score for degradation: each α-<br />

assignment strategy (e-value , 10 obese (ob/ob; n 5 13) conv<br />

glucosidases, self–self comparison. α-galactosidases, Microbiomes β-galactosidases, were subsequently and clustered ABC-transporters. using of germ-free wild-type C5<br />

NEIGHBOUR (PHYLIP version 3.64). b, Principal Component Analysis from obese donors (ob/ob<br />

Increased (PCA) adiposity of KEGG pathway is a microbiota-transmissible assignments. A matrix wastrait. constructed containing percentage increase in tot<br />

the number of EGTs assigned to each KEGG pathway in each microbiome Turnbaugh from lean et donors al., 2006 (1/1; n<br />

(includes KEGG pathways with .0.6% relative abundance in at least two<br />

28 0.999<br />

lean littermates. Red denotes enrichment and green indicates depletion on<br />

the basis of a cumulative binomial test (brightness indicates the level of<br />

significance). Black indicates pathways whose representation is not<br />

significantly different. Asterisks indicate groups that were consistently<br />

enriched or depleted between both sibling pairs using a more stringent EGT<br />

assignment strategy (e-value , 10 ). For additional details see<br />

Supplementary Discussion; Supplementary Figs 5 and 6, and Supplementar<br />

Tables 6, 8 and 9.<br />

©2006 Nature Publishing Group<br />

28 ). For additional details see<br />

Supplementary Discussion; Supplementary Figs 5 and 6, and Supplementary<br />

Tables 6, 8 and 9.<br />

©2006<br />

Nature Publishing Group<br />

omparison of data sets obtained from the caecal microbiomes<br />

nd lean littermates. a, Number of observed orthologous groups<br />

cal microbiome. Black indicates the number of observed groups.<br />

ates the number of predicted missed groups. b, Relative<br />

of a subset of COG categories (BLASTX, e-value , 10 25 ison of data sets obtained from the caecal microbiomes<br />

littermates. a, Number of observed orthologous groups<br />

robiome. Black indicates the number of observed groups.<br />

number of predicted missed groups. b, Relative<br />

bset of COG categories (BLASTX, e-value , 10 ) in the<br />

and ob1 (blue) caecal microbiome, characterized by capillaryequencers<br />

(squares and triangles, respectively). c, d, A subset of<br />

ories (c) and all KEGG pathways (d) consistently enriched or<br />

the caecal microbiomes of both obese mice compared with their<br />

25 ) in the<br />

b1 (blue) caecal microbiome, characterized by capillaryers<br />

(squares and triangles, respectively). c, d, A subset of<br />

c) and all KEGG pathways (d) consistently enriched or<br />

ecal microbiomes of both obese mice compared with their<br />

All<br />

d<br />

µmol per g wet wt.<br />

caecal contents<br />

Acetate<br />

Propionate<br />

Lea<br />

(+/+<br />

Bu

---

Computational:<br />

‣ <strong>Genome</strong> assembly<br />

‣ Gene prediction<br />

Technological challenges<br />

‣ Structure and functional predictions<br />

DNA Sequencing:<br />

‣ Human <strong>Genome</strong> Project: 2.8 x 10^9 bp in 10 years.<br />

‣ How much sequencing does it take?<br />

‣ Assume ≈500 ribotypes, average genome size of 5 million bp: 2.5 x 10^9 bp<br />

‣ Representation problem<br />

Protein activities:<br />

‣ Current fastest method for assaying protein activities (protein microarrays):<br />

10^3 proteins at a time (can’t handle 20,000 proteins at a time).<br />

‣ Gut microbiome: ≈2,000,000 proteins.

---

Reads<br />

<strong>Genome</strong> coverage (%)<br />

100<br />

90<br />

80<br />

70<br />

60<br />

50<br />

10000000<br />

40<br />

9000000<br />

30<br />

20<br />

8000000<br />

10<br />

7000000<br />

6000000<br />

5000000<br />

4000000<br />

0<br />

3000000<br />

2000000<br />

1000000<br />

0<br />

1<br />

1<br />

6<br />

7<br />

<strong>Genome</strong>-centric vs. Gene-centric views<br />

11<br />

13<br />

16<br />

19<br />

21<br />

26<br />

25<br />

31<br />

31<br />

36<br />

37<br />

41<br />

43<br />

46<br />

49<br />

51<br />

55<br />

56<br />

61<br />

Species abundance (%)<br />

61<br />

66<br />

Species abundance (%)<br />

67<br />

71<br />

73<br />

76<br />

1x coverage<br />

5x coverage<br />

10x coverage<br />

79<br />

81<br />

85<br />

86<br />

91<br />

91<br />

96<br />

97<br />

For a species 10% abundant, 10x<br />

library coverage:<br />

‣ 1 million sequencing reads<br />

‣ Cover 63% of the genome<br />

Ouch.

---

Biocatalysis<br />

Bio-catalysis: Greener chemistry<br />

Cumulative number of biotransformations<br />

(enzymatic) in<br />

industries is growing rapidly:<br />

‣ Increased stereoselectivity of<br />

enzymes translates into<br />

enantiomeric purity.<br />

‣ Environmentally sustainable<br />

technologies (green chemistry)<br />

So far, have justified<br />

metagenomics from<br />

a biological/<br />

ecological and<br />

medical perspective.<br />

Now for industry.<br />

Should I include<br />

something on<br />

bioprospecting<br />

deals? Yellowstone?<br />

Costa Rica?

---

p http://www.nature.com/naturebiotechnology<br />

a b<br />

A R T I C L E S<br />

Y177GA<br />

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more likely than conservative changes to diverge from an evolutionary<br />

optimization path that leads to a specific, improved function28 .<br />

Aided by the published wild-type HHDH structure26 OH O HHDH<br />

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P175<br />

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halohydrin dehalogenase<br />

(HHDH).<br />

S132<br />

Y145<br />

ethyl-cyano-hydroxy-butyrate<br />

R149<br />

Figure 4 Positions<br />

structure. (a) A mo<br />

tetramer (pdbid: 1P<br />

((R)-SO) shown in o<br />

green. Residues th<br />

of most active varia<br />

catalytic triad S13<br />

(b) A close-up of th<br />

(R)-SO shown in or<br />

catalytic triad in ye<br />

not part of the cata<br />

HHDH can convert ethyl-chlorohydroxy-butyrate<br />

(ECHB) into<br />

(HN):<br />

mutated residues i<br />

in white, and resid<br />

active clones in pu<br />

with positions of ac<br />

Starting compound for Lipitor<br />

synthesis.<br />

in green and uncha<br />

All molecular struc<br />

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conserved betwe<br />

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positions were T7<br />

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search strategy b<br />

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present in the production put varia<br />

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(believed NC to be beneficial) that were first<br />

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sequence-activity HN data and became fixed in<br />

remaining 17 coding mutations in theseq pro

---

TTG-8 [2]<br />

TTG-9 [5]<br />

TTG-10 [39]<br />

Biofuels & Termites<br />

T. primitia termite group [1]<br />

Spirochaeta (Treponema) caldaria, M71240.1<br />

T. pallidum and amino acid fermentors<br />

T. bryantii and saccharolytic strains<br />

Spirochaeta coccoides SPN1, AJ698092.1<br />

TSG-1 [1]<br />

Spirochaeta aurantia, AY599019.1<br />

Other<br />

TSG-2 [3]<br />

TSG-3 [1]<br />

Spirochaetaceae<br />

TLG-1 [1]<br />

Leptospiraceae<br />

Leptospira<br />

Fibrobacter<br />

Candidate order TG3-1 [32]<br />

Proteobacteria [9]<br />

Deferribacteres [1]<br />

Candidate order TFG-1 [14]<br />

Candidate order TG3-2 [3]<br />

Bacteroidetes [14]<br />

Chlorobi and gut clones [1]<br />

Acidobacteria [10]<br />

Candidate phylum Endomicrobia [1]<br />

Cyanobacteria and gut clones [2]<br />

Candidate phylum ZB3 [3]<br />

Firmicutes [16]<br />

Aminanaerobia [1]<br />

Can biofuels alleviate 1,289the unambiguously energy aligned crisis? and filtered Ethanol nucleotide positions. can contribute Branching to energy and environmental<br />

goals<br />

The path forward for biofuels: cellulosic ethanol.<br />

Treponema<br />

Phylum Fibrobacteres [49]<br />

Figure 1 | Source and composition of the bacterial community analysed.<br />

a, Diagram of the gut tract extracted from the Nasutitermes host insect. The<br />

anterior of the P3 paunch was incised as indicated (dotted line) with a<br />

syringe needle. The luminal contents from about 165 specimens were<br />

collected and pooled for nucleic acid and protein analyses. b, Phylogenetic<br />

diversity of the P3 luminal microbiota. From a PCR-based inventory and<br />

from the metagenome libraries, 1,703 almost full-length and 41 full-topartial<br />

16S rRNA gene sequences were used in a maximum-likelihood<br />

analysis (RAxML). The number of distinct P3 luminal community<br />

phylotypes contained within each grouping is given in brackets (a total of<br />

216 operational taxonomical units sharing at least 99% sequence identity);<br />

black shading denotes that at least one of these phylotypes was represented<br />

within the PCR inventory or metagenome libraries (red dots). White shading<br />

denotes reference groups having no representation in this or other public<br />

inventories derived from termite gut. The phylogram was constructed from<br />

pattern confidence is visualized as follows: no circle, more than 50%;<br />

open circle, more than 70%; filled circle, more than 90%. Scale bar indicates<br />

10% estimated sequence divergence. See Supplementary Tables 1, 2 and 11<br />

and Supplementary Figs 2–9 for accession numbers and detailed<br />

phylogenetic analyses.<br />

0.10<br />

GH5 cellulases, GH94 cellobiose or cellodextrin phosphorylases<br />

GH51 endoglucanase/arabinofuranosidases, and a smaller number<br />

of GH8, GH9, GH44, GH45 and GH74 endoglucanases. In contrast<br />

gene modules corresponding to the catalytic domains of GH6 and<br />

GH48 family endoglucanases and cellobiohydrolases, key components<br />

of several well-studied microbial cellulase systems, were absent<br />

1 mm<br />

©2007 Nature Publishing Group<br />

Diverse endoglucanases<br />

(Treponema<br />

Treponema and Fi brobactere s)<br />

(see Table 1 and<br />

Supplementary Figs 10 and 11)<br />

GH94 phosphorylases<br />

(Treponema<br />

Treponema)<br />

(see Table 1)<br />

Fe-only H2ases (Treponema<br />

Treponema)<br />

(see Table 1 and<br />

Supplementary<br />

Figs 16–19)<br />

Wood-Ljungdahl pathway<br />

of CO2-reduction (Treponema<br />

Treponema)<br />

(see Supplementary<br />

Figs 20–23)<br />

Wood polysaccharides<br />

Cellulose Xylan<br />

Hydrolysis<br />

Fermentation<br />

Acetate<br />

Acetate<br />

3rd proctodeal segment (P3)<br />

Hexose oligomers Pentose oligomers<br />

Central metabolism intermediates<br />

H 2 +CO 2<br />

Diverse endoxylanases<br />

(Treponema)<br />

(seeTable 1 and<br />

Supplementary Figs 12 and 13)<br />

Diverse glycosidases<br />

(Treponema<br />

Treponema)<br />

(see Table 1)<br />

Atmospheric N 2<br />

Ammonium<br />

Microbial protein<br />

Diverse<br />

nitrogenases<br />

(Treponema and<br />

Fibrobacteres)<br />

Absorbed by termite as dominant substrate for energy and biosynthesis<br />

Figure 2 | Model of nutritional symbiosis-relevant metabolism by<br />

Nasutitermes P3 luminal bacteria. Wood is triturated by the insect’s<br />

mandibles into small particles and predigested by poorly studied upstream<br />

processes before transit into the P3 compartment. The P3 lumen is<br />

dominated by diverse species of Treponema (Spirochaetes) and<br />

Fibrobacteres. There was no evidence for methanogenesis or lignin<br />

degradation in the metagenomic data set.<br />

56

---

Supporting Material

---

Woese, 1987

---

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