Abstract
The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.
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References
FAO (2020) The State of World Fisheries and Aquaculture (2020). Sustainability in action, Rome. https://doi.org/10.4060/ca9229en
Irianto A, Austin B (2002) Probiotics in aquaculture. J Fish Dis 25(11):633–642. https://doi.org/10.1046/j.1365-2761.2002.00422.x
Dawood MA, Koshio S, Esteban MÁ (2017) Beneficial roles of feed additives as immunostimulants in aquaculture: a review. Rev Aquac 10(4):950–974. https://doi.org/10.1111/raq.12209
Liu X, Steele JC, Meng XZ (2017) Usage, residue, and human health risk of antibiotics in Chinese aquaculture: a review. Environ Pollut 223:161–169. https://doi.org/10.1016/j.envpol.2017.01.003
Ng WK, Koh CB (2016) The utilization and mode of action of organic acids in the feeds of cultured aquatic animals. Rev Aquac 9(4):342–368. https://doi.org/10.1111/raq.12141
Burridge Burridge L, Weis JS, Cabello F, Pizarro J, Bostick K (2010) Chemical use in salmon aquaculture: a review of current practices and possible environmental effects. Aquaculture 306(1–4):7–23. https://doi.org/10.1016/j.aquaculture.2010.05.020
Assefa A, Abunna F (2018) Maintenance of fish health in aquaculture: review of epidemiological approaches for prevention and control of infectious disease of fish. Vet Med Int. https://doi.org/10.1155/2018/5432497
Martínez Cruz P, Ibáñez AL, Monroy Hermosillo OA, Ramírez Saad HC (2012) Use of probiotics in aquaculture. ISRN Microbiol. https://doi.org/10.5402/2012/916845
Merrifield DL, Dimitroglou A, Foey A, Davies SJ, Baker RT, Bøgwald J, Castex M, Ringø E (2010) The current status and future focus of probiotic and prebiotic applications for salmonids. Aquaculture 302(1–2):1–18. https://doi.org/10.1016/j.aquaculture.2010.02.007
Balcázar JL, De Blas I, Ruiz-Zarzuela I, Cunningham D, Vendrell D, Muzquiz JL (2006) The role of probiotics in aquaculture. Vet Microbiol 114(3–4):173–186. https://doi.org/10.1016/j.vetmic.2006.01.009
Gueimonde M, Sanchez B (2012) Enhancing probiotic stability in industrial processes. Microb Ecol Health Dis 23(1):18562. https://doi.org/10.3402/mehd.v23i0.18562
Terpou A, Papadaki A, Lappa IK, Kachrimanidou V, Bosnea LA, Kopsahelis N (2019) Probiotics in food systems: significance and emerging strategies towards improved viability and delivery of enhanced beneficial value. Nutrients 11(7):1591. https://doi.org/10.3390/nu11071591
Tripathi MK, Giri SK (2014) Probiotic functional foods: survival of probiotics during processing and storage. J Funct Foods 9:225–241. https://doi.org/10.1016/j.jff.2014.04.030
Kozasa M (1986) Toyocerin (Bacillus toyoi) as growth promoter for animal feeding. Microbiology. Aliment Nutr 4:121–135
Ringø E, Gatesoupe FJ (1998) Lactic acid bacteria in fish: a review. Aquaculture 160(3–4):177–203. https://doi.org/10.1016/S0044-8486(97)00299-8
Mohapatra S, Chakraborty T, Kumar V, DeBoeck G, Mohanta KN (2013) Aquaculture and stress management: a review of probiotic intervention. Journal of J Anim Physiol Anim Nutr 97(3):405–430. https://doi.org/10.1111/j.1439-0396.2012.01301.x
Kumar P, Jain KK, Sardar P (2018) Effects of dietary synbiotic on innate immunity, antioxidant activity and diseaseresistance of Cirrhinus mrigala juveniles. Fish Shellfish Immunol 80:124–132. https://doi.org/10.1016/j.fsi.2018.05.045
Tinh NTN, Linh ND, Wood TK, Dierckens K, Sorgeloos P, Bossier P (2007) Interference with the quorum sensing systems in a Vibrio harveyi strain alters the growth rate of gnotobiotically cultured rotifer Brachionus plicatilis. J Appl Microbiol. 103(1):194–203. https://doi.org/10.1111/j.1365-2672.2006.03217.x
Andrews SR, Sahu NP, Pal AK, Mukherjee SC, Kumar S (2011) Yeast extract, brewer’s yeast and spirulina indiets for Labeo rohita fingerlings affect haemato-immunological responses and survival following Aeromonas hydrophila challenge. Vet Sci Res J 91(1):103–109. https://doi.org/10.1016/j.rvsc.2010.08.009
Ringø E, Myklebust R, Mayhew TM, Olsen RE (2007) Bacterial translocation and pathogenesis in the digestive tract of larvae and fry. Aquaculture 268(1–4):251–264. https://doi.org/10.1016/j.aquaculture.2007.04.047
Yang G, Cao H, Jiang W, Hu B, Jian S, Wen C, Kajbaf K, Kumar V, Tao Z, Peng M (2019) Dietary supplementation of Bacillus cereus as probiotics in Pengze crucian carp (Carassius auratus var. Pengze): effects on growth performance, fillet quality, serum biochemical parameters and intestinal histology. Aquac Res 50(8):2207-2217. https://doi.org/10.1111/are.14102
Xue J, Shen K, Hu Y, Hu Y, Kumar V, Yang G, Wen C (2020) Effects of dietary Bacillus cereus, B. subtilis, Paracoccus marcusii, and Lactobacillus plantarum supplementation on the growth, immune response, antioxidant capacity, and intestinal health of juvenile grass carp (Ctenopharyngodon idellus). Aquac Rep 17:100387. https://doi.org/10.1016/j.aqrep.2020.100387
Suralikar V, Sahu NP (2001) Efffect of feeding probiotic (Lactobacillus cremoris) on growth and survival of Macrobrachium rosenbergii post larvae. J Appl Anim Res 20(1):117–124. https://doi.org/10.1080/09712119.2001.9706744
Gatesoupe FJ (1999) The use of probiotics in aquaculture. Aquaculture 180(1–2):147–165. https://doi.org/10.1016/S0044-8486(99)00187-8
Vine NG, Leukes WD, Kaiser H, Daya S, Baxter J, Hecht T (2004) Competition for attachment of aquaculture candidate probiotic and pathogenic bacteria on fish intestinal mucus. J Fish Dis 27(6):319–326. https://doi.org/10.1111/j.1365-2761.2004.00542.x
Cao H, Yu R, Zhang Y, Hu B, Jian S, Wen C, Kajbaf K, Kumar V, Yang G (2019) Effects of dietarysupplementation with β-glucan and Bacillus subtilis on growth, fillet quality, immune capacity, and antioxidant status of Pengze crucian carp (Carassius auratus var. Pengze). Aquaculture 508:106–112. https://doi.org/10.1016/j.aquaculture.2019.04.064
Yang G, Shen K, Yu R, Wu Q, Yan Q, Chen W, Ding L, Kumar V, Wen C, Peng M (2020) Probiotic (Bacillus cereus) enhanced growth of Pengze crucian carp by modulating the antioxidant defense response and exerting beneficial impacts on inflammatory response via Nrf2 activation. Aquaculture 529:735691. https://doi.org/10.1016/j.aquaculture.2020.735691
Hoseinifar SH, Ringø E, Shenavar MA, Esteban MÁ (2016) Probiotic, prebiotic and synbiotic supplements in sturgeon aquaculture: a review. Rev Aquac 8(1):89–102. https://doi.org/10.1111/raq.12082
Venkat HK, Sahu NP, Jain KK (2004) Effect of feeding Lactobacillus-based probiotics on the gut microflora, growth and survival of postlarvae of Macrobrachium rosenbergii (de Man). Aquac Res 35(5):501–507. https://doi.org/10.1111/j.1365-2109.2004.01045.x
Yang G, Tao Z, Xiao J, Tu G, Kumar V, Wen C (2020) Characterization of the gastrointestinal microbiota inpaddlefish (Polyodon spathula). Aquac Rep 17:100402
Zorriehzahra MJ, Delshad ST, Adel M, Tiwari R, Karthik K, Dhama K, Lazado CC (2016) Probiotics as beneficial microbes in aquaculture: an update on their multiple modes of action: a review. Vet Q 36(4):228–241. https://doi.org/10.1080/01652176.2016.1172132
Kumar P, Jain K, Sardar P, Jayant M, Tok NC (2018b) Effect of dietary synbiotic on growth performance, bodycomposition, digestive enzyme activity and gut microbiota in Cirrhinus mrigala (Ham.) fingerlings. Aquac Nutr 24(3):921-929. https://doi.org/10.1111/anu.12628
Ray AK, Ghosh K, Ringø E (2012) Enzyme-producing bacteria isolated from fish gut: a review. Aquac Nutr 18(5):465–492. https://doi.org/10.1111/j.1365-2095.2012.00943.x
Wang YB, Li JR, Lin J (2008) Probiotics in aquaculture: challenges and outlook. Aquaculture 281(1–4):1–4. https://doi.org/10.1016/j.aquaculture.2008.06.002
Sutherland D, Ghidossi T (2019) Archaea extract: a new heat stable micro-ingredient to improve disease resistance in aquaculture. Aquafeed: Advances in Processing and Formulation 11(3):43-45. https://issuu.com/aquafeed.com/docs/aquafeed_vol_11_issue_3_2019/43. Accessed on February 14, 2020.
Sanders ME (2011) Impact of probiotics on colonizing microbiota of the gut. J Clin Gastroenterol 45:S115–S119. https://doi.org/10.1097/MCG.0b013e318227414a
Hemarajata P, Versalovic J (2013) Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol 6(1):39–51. https://doi.org/10.1177/1756283X12459294
Azad M, Kalam A, Sarker M, Li T, Yin J (2018) Probiotic species in the modulation of gut microbiota: an overview. Biomed Res Int. https://doi.org/10.1155/2018/9478630
El Hage R, Hernandez-Sanabria E, Van de Wiele TJF (2017) Emerging trends in “smart probiotics”: functional consideration for the development of novel health and industrial applications. Front Microbial 8:1889. https://doi.org/10.3389/fmicb.2017.01889
Bang C, Schmitz RA (2018) Archaea: forgotten players in the microbiome. Emerg Top Life Sci 2(4):459–468. https://doi.org/10.1042/ETLS20180035
Hania WB, Ballet N, Vandeckerkove P, Ollivier B, O’Toole PW, Brugère JF (2017) Archaebiotics: Archaea as pharmabiotics for treating chronic disease in humans?. In: Sghaier H, Najjari A, Ghedira K (eds) Archaea—new biocatalysts, novel pharmaceuticals and various biotechnological applications. IntechOpen: Rijeka, Croatia: 41-62. https://doi.org/10.5772/intechopen.69945
Chang CJ, Lin TL, Tsai YL, Wu TR, Lai WF, Lu CC, Lai HC (2019) Next generation probiotics in disease amelioration. J Food Drug Anal 27(3):615–622. https://doi.org/10.1016/j.jfda.2018.12.011
Sun Y, Liu Y, Pan J, Wang F, Li M (2019) Perspectives on cultivation strategies of Archaea. Microb Ecol 79(3):770–784. https://doi.org/10.1007/s00248-019-01422-7
Woese CR (1993) The Archaea: their history and significance. In: Kates M, Kushner DJ, Matheson AT (eds) The biochemistry of Archaea (Archaebacteria). Elsevier Science Publishers BV, New York. pp. vii–xxix
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci 74(11):5088–5090. https://doi.org/10.1073/pnas.74.11.5088
Canganella F, Wiegel J (2014) Anaerobic thermophiles. Life 4(1):77–104. https://doi.org/10.3390/life4010077
Spang A, Martijn J, Saw JH, Lind AE, Guy L, Ettema TJ (2013) Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. Archaea. https://doi.org/10.1155/2013/202358
Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C (2020) The host-associated archaeome. Nat Rev Microbiol. https://doi.org/10.1038/s41579-020-0407-y
Levy J (2010) The world of microbes: bacteria, viruses, and other microorganisms. The Rosen Publishing Group, Inc
Oren A (2014) Taxonomy of halophilic Archaea: current status and future challenges. Extremophiles 18(5):825–834. https://doi.org/10.1007/s00792-014-0654-9
Jain S, Caforio Driessen AJ (2014) Biosynthesis of archaeal membrane ether lipids. Front Microbiol 5:641. https://doi.org/10.3389/fmicb.2014.00641
Koga Y, Morii H (2007) Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev 71:97–120. https://doi.org/10.1128/MMBR.00033-06
Koga Y (2012) Thermal adaptation of the archaeal and bacterial lipid membranes. Archaea. https://doi.org/10.1155/2012/789652
Matsumi R, Atomi H, Driessen AJ, van der Oost J (2011) Isoprenoid biosynthesis in archaea–biochemical and evolutionary implications. Res J Microbiol 162(1):39–52. https://doi.org/10.1016/j.resmic.2010.10.003
Balleza D, Garcia-Arribas AB, Sot J, Ruiz-Mirazo K, Goñi FM (2014) Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains. Biophys J 107(6):1364–1374. https://doi.org/10.1016/j.bpj.2014.07.036
Chong PLG (2010) Archaebacterial bipolar tetraether lipids: physico-chemical and membrane properties. Chem Phys Lipids 163(3):253–265. https://doi.org/10.1016/j.chemphyslip.2009.12.006
Peretó J, López-García P, Moreira D (2004) Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem Sci 29(9):469–477. https://doi.org/10.1016/j.tibs.2004.07.002
Siliakus MF, van der Oost J, Kengen SW (2017) Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 21(4):651–670. https://doi.org/10.1007/s00792-017-0939-x
Gambacorta A, Trincone A, Nicolaus B, Lama L, De Rosa M (1993) Unique features of lipids of archaea. Syst Appl Microbiol 16(4):518–527. https://doi.org/10.1016/S0723-2020(11)80321-8
Kates M (1993) Membrane lipids of Archaea. In: Kates M, Kushner DJ, Matheson AT (eds) The biochemistry of Archaea (Archaebacteria). Elsevier Biomedical Press, Amsterdam. The Netherlands. pp.261–295. https://www.sciencedirect.com/bookseries/new-comprehensive-biochemistry/vol/26
McLain JET (2005) Archaea. Encyclopedia of soils in the environment. https://doi.org/10.1016/b0-12-348530-4/00525-7
Gill EE, Brinkman FS (2011) The proportional lack of archaeal pathogens: do viruses/phages hold the key? Bioessays 33(4):248–254. https://doi.org/10.1002/bies.201000091
Reed CJ, Lewis H, Trejo E, Winston V, Evilia C (2013) Protein adaptations in archaeal extremophiles. Archaea. https://doi.org/10.1155/2013/373275
Straub CT, Counts JA, Nguyen DM, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MW (2018) Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 42(5):543–578. https://doi.org/10.1093/femsre/fuy012
Cavicchioli R (2006) Cold-adapted archaea. Nat Rev Microbiol 4(5):331–343
Purwantini Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B (2014) Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 5:634. https://doi.org/10.3389/fmicb.2014.00634
Bräsen C, Esser D, Rauch B, Siebers B (2014) Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 78(1):89–175. https://doi.org/10.1128/MMBR.00041-13
Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF (2014) Archaea and the human gut: new beginning of an old story. World J Gastroenterol 20(43):16062. https://doi.org/10.3748/wjg.v20.i43.16062
Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K (2018) Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr 57(1):1–24. https://doi.org/10.1007/s00394-017-1445-8
Ishaq SL, Moses PL, Wright ADG (2016) The pathology of methanogenic archaea in human gastrointestinal tract disease. In: Mozsik G (ed.) The Gut Microbiome. IntechOpen: Rijeka, Croatia. https://doi.org/10.5772/64637
Brugère JF, Borrel G, Gaci N, Tottey W, O’Toole PW, Malpuech-Brugère C (2014) Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5(1):5–10. https://doi.org/10.4161/gmic.26749
Ramezani A, Nolin TD, Barrows IR, Serrano MG, Buck GA, Regunathan-Shenk R, West RE, Latham PS, Amdur R, Raj DS (2018) Gut colonization with methanogenic archaea lowers plasma trimethylamine N-oxide concentrations in apolipoprotein e−/− mice. Sci Rep 8(1):1–11. https://doi.org/10.1038/s41598-018-33018-5
Fennema D, Phillips IR, Shephard EA (2016) Trimethylamine and trimethylamine N-oxide, a flavin-containing monooxygenase 3 (FMO3)-mediated host-microbiome metabolic axis implicated in health and disease. Drug Metab Dispo 44(11):1839–1850. https://doi.org/10.1124/dmd.116.070615
Janeiro MH, Ramírez MJ, Milagro FI, Martínez JA, Solas M (2018) Implication of trimethylamine N-Oxide (TMAO) in disease: potential biomarker or new therapeutic target. Nutrients 10(10):1398. https://doi.org/10.3390/nu10101398
Seibel BA, Walsh PJ (2002) Trimethylamine oxide accumulation in marine animals: relationship to acylglycerol storage. J Exp Biol 205:297–306
Brugère JF, Hania WB, Arnal ME, Ribière C, Ballet N, Vandeckerkove P, Ribière C, Ballet N, Vandeckerkove P, OllivierO’toole PW, B (2018) Archaea: microbial candidates in next-generation probiotics development. J Clin Gastroenterol 52:S71–S73. https://doi.org/10.1097/MCG.0000000000001043
Bang C, Schmitz RA (2015) Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol Rev 39(5):631–648. https://doi.org/10.1093/femsre/fuv010
Bang C, Weidenbach K, Gutsmann T, Heine H, Schmitz RA (2014) The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells. PLoS ONE 9(6):e99411. https://doi.org/10.1371/journal.pone.0099411
Lazar V, Ditu LM, Pircalabioru GG, Gheorghe I, Curutiu C, Holban AM (2018) Aspects of gut microbiota and immune system interactions in infectious diseases, immunopathology, and cancer. Front Immunol 9:1830. https://doi.org/10.3389/fimmu.2018.01830
Lurie-Weinberger MN, Gophna U (2015) Archaea in and on the human body: health implications and future directions. PLoS Pathog 11(6):e1004833. https://doi.org/10.1371/journal.ppat.1004833
Eckburg PB, Lepp PW, Relman DA (2003) Archaea and their potential role in human disease. Infect Immun 71(2):591–596. https://doi.org/10.1128/IAI.71.2.591-596.2003
Wu S, Ren Y, Peng C, Hao Y, Xiong F, Wang G, Li W, Zou H, Angert ER (2015) Metatranscriptomic discovery of plant biomass-degrading capacity from grass carp intestinal microbiomes. FEMS Microbiol Ecol 91(10):fiv107. https://doi.org/10.1093/femsec/fiv107
Egerton S, Culloty S, Whooley J, Stanton C, Ross RP (2018) The gut microbiota of marine fish. Front Microbiol 9:873. https://doi.org/10.3389/fmicb.2018.00873
Ni J, Yan Q, Yu Y, Zhang T (2014) Factors influencing the grass carp gut microbiome and its effect on metabolism. FEMS Microbiol Ecol 87(3):704–714. https://doi.org/10.1111/1574-6941.12256
Talwar C, Nagar S, Lal R, Negi RK (2018) Fish gut microbiome: current approaches and future perspectives. Indian J Microbiol 58(4):397–414. https://doi.org/10.1007/s12088-018-0760-y
Tarnecki AM, Burgos FA, Ray CL, Arias CR (2017) Fish intestinal microbiome diversity and symbiosis unravelled by metagenomics. J Appl Microbiol 123(1):2–17. https://doi.org/10.1111/jam.13415
Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH (2014) The intestinal microbiome of fish under starvation. BMC Genom 15(1):266. https://doi.org/10.1186/1471-2164-15-266
Califano G, Castanho S, Soares F, Ribeiro L, Cox CJ, Mata L, Costa R (2017) Molecular taxonomic profiling of bacterial communities in a gilthead seabream (Sparus aurata) hatchery. Front Microbiol 8:204. https://doi.org/10.3389/fmicb.2017.00204
van der Maarel MJ, Artz RR, Haanstra R, Forney LJ (1998) Association of marine archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol 64(8):2894–2898. https://doi.org/10.1128/AEM.64.8.2894-2898.1998
Kormas KA, Meziti A, Mente E, Frentzos A (2014) Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata). Microbiologyopen 3(5):718–728. https://doi.org/10.1002/mbo3.202
Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE (2020) Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota. Appl Environ Microbiol 86(12). https://doi.org/10.1128/AEM.00411-20
Deb S, Das L, Das SK (2020) Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia). Arch Microbiol. https://doi.org/10.1007/s00203-020-01997-7
Romero J, Ringø E, Merrifield DL (2014) The gut microbiota of fish. In: Merrifield DL, Ringo E (eds) Aquaculture nutrition: gut health, probiotics and prebiotics. John Wiley & Sons:75–100. https://doi.org/10.1002/9781118897263.ch4
Davis C (2014) Enumeration of probiotic strains: review of culture-dependent and alternative techniques to quantify viable bacteria. J Microbiol Methods 103:9–17. https://doi.org/10.1016/j.mimet.2014.04.012
Ringø E (2004) Lactic acid bacteria in fish and fish farming. In: Salminen S, von Wright A, Ouwehand A (eds) Lactic acid bacteria- Microbiological and functional aspects, 3rd edn. Marcel Dekker Inc., New York, pp 581–610
Nagpal R, Kumar A, Kumar M, Behare PV, Jain S, Yadav H (2012) Probiotics, their health benefits and applications for developing healthier foods: a review. FEMS Microbiol Lett 334(1):1–15. https://doi.org/10.1111/j.1574-6968.2012.02593.x
Bonnet M, Lagier JC, Raoult D, Khelaifia S (2019) Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microbes New Infect 34:100622. https://doi.org/10.1016/j.nmni.2019.100622
Sandle T (2011) History and development of microbiological culture media. J Inst Sci Technol 10–14
Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M (2015) Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 6:475. https://doi.org/10.3389/fmicb.2015.00475
Jarrell KF, Bayley DP, Correia JD, Thomas NA (1999) Recent excitement about the Archaea: the Archaea are valuable for studying basic biological questions and have novel biotechnology applications. BioScience 49(7):530–541. https://doi.org/10.2307/1313474
Balch WE, Wolfe RS (1976) New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressureized atmosphere. Appl Environ Microbiol 32(6):781-791. https://aem.asm.org/content/32/6/781.short
Cheng L, Qiu TL, Li X, Wang WD, Deng Y, Yin XB, Zhang H (2008) Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett 285(1):65-71. https://doi.org/10.1111/j.1574-6968.2008.01212.x
Ferrari A, Brusa T, Rutili A, Canzi E, Biavati B (1994) Isolation and characterization Methanobrevibacter oralis sp. nov. Curr Microbiol 29:7–12. https://doi.org/10.1007/BF01570184
Khelaifia S, Raoult D, Drancourt M (2013) A versatile medium for cultivating methanogenic archaea. PLoS ONE 8(4):e61563. https://doi.org/10.1371/journal.pone.0061563
Lackner N, Hintersonnleitner A, Wagner AO, Illmer P (2018) Hydrogenotrophic methanogenesis and autotrophic growth of Methanosarcina thermophila. Archaea. https://doi.org/10.1155/2018/4712608
Rothe O, Thomm M (2000) A simplified method for the cultivation of extreme anaerobic archaea based on the use of sodium sulfite as reducing agent. Extremophiles 4(4):247–252. https://doi.org/10.1007/PL00010716
Scherer P, Sahm H (1981) Effect of trace elements and vitamins on the growth of Methanosarcina barkeri. Acta Biotechnologica 1(1):57–65. https://doi.org/10.1002/abio.370010108
Wolfe RS (2011) Techniques for cultivating methanogens. Methods Enzymol 494:1–22. https://doi.org/10.1016/B978-0-12-385112-3.00001-9
Varnava KG, Ronimus RS, Sarojini V (2017) A review on comparative mechanistic studies of antimicrobial peptides against archaea. Biotechnol Bioeng 114(11):2457–2473. https://doi.org/10.1002/bit.26387
Huber K, Lafferty RM (1988) Cultivation and preservation of methanogenic bacteria. Zentralblatt für Mikrobiologie 143(2):149–155. https://doi.org/10.1016/S0232-4393(88)80100-8
Maestrojuan GM, Boone DR (1991) Characterization of Methanosarcina barkeri MST and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-761T. Int J Syst Evol Microbiol 41(2):267–274. https://doi.org/10.1099/00207713-41-2-267
Kurr M, Huber R, König H, Jannasch HW, Fricke H, Trincone A, Kristjansson JK, Stetter KO (1991) Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110 °C. Arch Microbiol 156(4):239-247. https://doi.org/10.1007/BF00262992
Nakagawa S, Takai K (2006) The isolation of thermophiles from deep-sea hydrothermal environments. In: Rainey FA, Oren A (ed.) Methods in Microbiology: Extremophiles. Elsevier: New York:55-91. https://doi.org/10.1016/S0580-9517(08)70006-0
Shih CJ, Chen SC, Weng CY, Lai MC, Yang YL (2015) Rapid identification of haloarchaea and methanoarchaea using the matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Rep 5(1):1–11. https://doi.org/10.1038/srep16326
Khelaifia S, Lagier JC, Nkamga VD, Guilhot E, Drancourt M, Raoult D (2016) Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis 35(6):985–991. https://doi.org/10.1007/s10096-016-2627-7
Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF (2016) Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents. Front Microbiol 7:1240. https://doi.org/10.3389/fmicb.2016.01240
Long F, Wang L, Lupa B, Whitman WB (2017) A flexible system for cultivation of Methanococcus and other formate-utilizing methanogens. Archaea. https://doi.org/10.1155/2017/7046026
Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PloSone 4(9):p.e7063. https://doi.org/10.1371/journal.pone.0007063
Aklujkar M, Risso C, Smith J, Beaulieu D, Dubay R, Giloteaux L, DiBurro K, Holmes D (2014) Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus. Microbiology 160(12):2694–2709. https://doi.org/10.1099/mic.0.083261-0
Ferry JG (2015) Acetate metabolism in anaerobes from the domain Archaea. Life. 5(2):1454–1471. https://doi.org/10.3390/life5021454
Tanner RS, Wolfe RS (1988) Nutritional requirements of Methanomicrobium mobile. Appl Environ Microbiol 54:625–8. https://aem.asm.org/content/54/3/625.short
Sprott DG, Patel GB, Choquet CG, Ekiel I (1993) Formation of stable liposomes from lipid extracts of archaeobacteria (archaea). WIPO (PCT) Patent WO1993008202A1, 29 April 1993
Lai MJ, Shiu SH (2004) Novel polyhydroxyalkanoate by extreme halophilic archaea. Taiwan Patent TW579390B, 11 March 2004
Bult CJ, White OR, Smith HO, Woese CR, Venter JC (2004) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. United States Patent US6797466B1, 28 September 2004
Rodelet JF (2005) Fraction extracted from archaebacteria for cosmetic purposes. United States Patent US6849279B2, 1 February 2005
Gordon JI, Samuel SB (2006) The use of archaea to modulate the nutrient harvesting functions of the gastrointestinal microbiota. WIPO (PCT) Patent WO(2006)102350A1, 28 September 2006.
Slesarev A, Malykh A, Pavlov A, Pavlova N, Kozyavkin S (2006) Complete genome and protein sequence of the hyperthermophile Methanopyrus kandleri av19 and monophyly of archael methanogens and methods of use thereof. United States Patent US (2006) 0068386A1, 30 March 2006.
Kowalczykowski SC, Chédin F, Seitz EM (2010) Single stranded DNA binding proteins from Archaea and uses therefor. United States Patent US7666591B2, 23 February 2010
Zimmermann D, Patzelt H, Majewski E, Sachse J, Stoll C (2011) Archaea and lipid compositions obtained therefrom. WIPO (PCT) Patent WO2011100955A1, 25 August 2011
Dierickx W, Cuyper DD, Ulrih NP, Gunde-Cimerman N (2012) Method for producing a polymer product from polar lipids from archaea as carriers of living microbial cells and biological barriers in plastic and textile. European Patent EP2518138A1, 31 October 2012
Hua X, Jing H, Qiuhe L (2012) Extremely halophilic archaea polyhydroxy fatty acid ester synthases and encoding gene and application. China Patent CN101139575A, 4 January 2012
Fardeau ML, Ollivier B, Hirschler-Rea A, Khelifi N (2013) Use of thermophilic sulphate-reducing archaea for the implementation of a process for the degradation of hydrocarbons. United States Patent US8455240B2, 4 June 2013
Drancourt M, Dridi B, Fardeau ML, Ollivier B, Raoult D (2013) Culturing and detection of a methanogenic archaeon. WIPO (PCT) Patent WO2013004933A1, 10 January (2013)
Zitomer D (2013) Preservation of methanogenic, hydrogen-utilizing microbial cultures. US8557563B2, 15 October 2013
Rongqing Z, Cuirong H, Jia Z (2013) Rapid and effective cellar mud archaea community analysis method. China Patent CN102912025A, 6 February 2013
Drancourt M, Khelaifia S, Raoult D (2013) New archaea Methanomassiliicoccus luminyensis isolated and established in culture, comprising 16S ribosomal DNA gene-specific sequence or a complementary sequence, useful for diagnostic purposes. France Patent FR2990954A1, 29 November 2013
Hill JE, Chaban BL (2014) Methods and compositions for the detection and identification of archaea based on the type II chaperonin (thermosome) gene. United States Patent US8758999B2, 24 June 2014
Yannone SM, Barnebey A(2014) Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic archaea. Canada Patent CA2930688A1, 30 May 2014
Grunden AM, Sederoff HIA, Yalamanchili RD (2014) Transgenic expression of archaea superoxide reductase. United States Patent US(2014)0026255A1, 23 January 2014
Larter SR, Head MI, Jones DM, Erdmann M, Wilhelms A (2015) Process for stimulating production of methane from petroleum in subterranean formations. United States Patent US9068107B2, 30 June 2015
Hua X, Dahe Z (2015) Extreme halophilic archaea engineering bacteria for producing bioplastics PHBV by effectively utilizing carbon source. China Patent CN103451201A, 10 June 2015
Krajete A, Herwig C, Rittmann S, Seifert A, Bernacchi S (2015) Method and system for producing methane using methanogenic microorganisms and applying specific nitrogen concentrations in the liquid phase. European Patent EP2959003A1, 30 December 2015
Zimmermann D, Patzelt H, Majewski E, Sachse JH, Wehr C (2016) Archaea and lipid compositions obtained therefrom. United States Patent US20160265016A1, 15 September 2016
Zhixin JW, Yangyang Y, Zhaoyun L (2016) Enrichment culture method of ammonia-oxidizing archaea in sewage treatment system. China Patent CN103451120A, 20 January 2016
Sutherland DB, Zaiss MM (2016) Archaebacteria in bioactive animal feed, method of making the composition and methods employing the composition. WIPO (PCT) Patent WO2016147121A1, 22 September 2016
Shinsuke F, Fujiwara A (2016) DNA amplification method using dead-box RNA helicase derived from thermophilic archaea or variant thereof, and dead-box RNA helicase derived from thermophilic archaea and variant thereof to be used for DNA amplification method. WIPO (PCT) Patent WO2016013620A1, 28 January 2016
Patel GB, Chen W (2017) Archaeal polar lipid aggregates for administration to animals. Canada Patent CA2672338C, 6 June 2017
Parks JM, Josh A (2018) Mercury methylation genes in bacteria and archaea. United States Patent US20140179553A1, 31 July 2018
Barrangou R, Selle KM (2018) Methods for screening bacteria, archaea, algae, and yeast using CRISPR nucleic acids. United States Patent US(2016)0345578A1, 27 November 2018
Murphy NRB, Weber KA, Aldridge JT, Carr SR (2020) Production of isoprene by methane-producing archaea. United States Patent US10533192B2, 14 January 2020
Millen DD, De Beni Arrigoni M, Lauritano Pacheco RD (2016) Rumenology. Springer International Publishing, Cham, Switzerland
Lin C, Raskin L, Stahl DA (1997) Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiol Ecol 22(4):281–294. https://doi.org/10.1111/j.1574-6941.1997.tb00380.x
Janssen PH, Kirs M (2008) Structure of the archaeal community of the rumen. Appl Environ Microbiol 74(12):619–3625. https://doi.org/10.1128/AEM.02812-07
Henderson G, Cox F, Ganesh S, Jonker A, Young W, Abecia L (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5:14567. https://doi.org/10.1038/srep14567
Vaidya JD, van Gastelen S, Smidt H, Plugge CM, Edwards JE (2020) Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets. PLoS ONE 15(3):e0229887. https://doi.org/10.1371/journal.pone.0229887
Zhu Z, Kristensen L, Difford GF, Poulsen M, Noel SJ, Al-Soud WA, Sørensen SJ, Lassen J, Løvendahl P, Højberg O (2018) Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows. J Dairy Sci 101(11):9847–9862. https://doi.org/10.3168/jds.2017-14366
Müller M (1993) The hydrogenosome. Microbiology 139(12):2879–2889
Wedlock DN, Pedersen G, Denis M, Dey D, Janssen PH, Buddle BM (2010) Development of a vaccine to mitigate greenhouse gas emissions in agriculture: vaccination of sheep with methanogen fractions induces antibodies that block methane production in vitro. N Z Vet J 58(1):29–36. https://doi.org/10.1080/00480169.2010.65058
Wright ADG, Kennedy P, O’Neill CJ, Toovey AF, Popovski S, Rea SM, Pimm CL, Klein L (2004) Reducing methane emissions in sheep by immunization against rumen methanogens. Vaccine 22(29–30):3976–3985. https://doi.org/10.1016/j.vaccine.2004.03.053
Wright ADG, Klieve AV (2011) Does the complexity of the rumen microbial ecology preclude methane mitigation? Anim Feed Sci Technol 166:248–253. https://doi.org/10.1016/j.anifeedsci.2011.04.015
Islam M, Lee SS (2019) Advanced estimation and mitigation strategies: a cumulative approach to enteric methane abatement from ruminants. J Anim Sci Technol 61(3):122. https://doi.org/10.5187/jast.2019.61.3.122
Kataria RP (2015) Use of feed additives for reducing greenhouse gas emissions from dairy farms. Microbiol Res. https://doi.org/10.4081/mr.2015.6120
Ankri S, Mirelman D (1999) Antimicrobial properties of allicin from garlic. Microbes Infect 1(2):125–129. https://doi.org/10.1016/S1286-4579(99)80003-3
Florin TH, Jabbar IA (1994) A possible role for bile acid in the control of methanogenesis and the accumulation of hydrogen gas in the human colon. J Gastroenterol Hepatol 9(2):112–117. https://doi.org/10.1111/j.1440-1746.1994.tb01228.x
Cholewińska P, Czyż K, Nowakowski P, Wyrostek A (2020) The microbiome of the digestive system of ruminants—a review. Anim Health Res Rev. https://doi.org/10.1017/S1466252319000069
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 5:207. https://doi.org/10.3389/fmicb.2014.00207
Wang AR, Ran C, Ringø E, Zhou ZG (2018) Progress in fish gastrointestinal microbiota research. Rev Aquac 10(3):626–640. https://doi.org/10.1111/raq.12191
Foysal MJ, Momtaz F, Kawsar AR, Rahman MM, Gupta SK, Tay ACY (2020) Next-generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis). Lett Appl Microbiol 70(3):173–180. https://doi.org/10.1111/lam.13256
Dridi B, Khelaifia S, Fardeau ML, Ollivier B, Drancourt M (2012) Tungsten-enhanced growth of Methanosphaera stadtmanae. BMC Res Notes 5(1):238. https://doi.org/10.1186/1756-0500-5-238
Fadhlaoui K, Arnal ME, Martineau M, Camponova P, Ollivier B, O’Toole PW Brugère JF (2020) Archaea, specific genetic traits and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics. Appl Microbiol Biotechnol:1-12. https://doi.org/10.1007/s00253-020-10599-8
Stenman LK, Burcelin R, Lahtinen S (2016) Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans–towards treatment with probiotics. Benef Microbes 7(1):11–22. https://doi.org/10.3920/BM2015.0069
Vierbuchen T, Bang C, Rosigkeit H, HeineH, Schmitz RA (2017) The human-associated archaeon Methanosphaera stadtmanae is recognized through its RNA and induces TLR8-dependent NLRP3 inflammasome activation. Front Immunol 8:1535. https://doi.org/10.3389/fimmu.2017.01535
Hsiao WW, Metz C, Singh DP, Roth J (2008) The microbes of the intestine: an introduction to their metabolic and signaling capabilities. Endocrinol Metab Clin North Am 37(4):857–871. https://doi.org/10.1016/j.ecl.2008.08.006
Salazarde N, los Reyes-Gavilán CG (2016) Insights into microbe-microbe interactions in human microbial ecosystems: strategies to be competitive. Front Microbiol 7:1508. https://doi.org/10.3389/fmicb.2016.01508
Schulze S, Adams Z, Cerletti M, De Castro R, Ferreira-Cerca S, Fufezan C, Giménez MI, Hippler M, Jevtic Z, Knüppel R, Legerme G (2020) The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 11(1):1–14. https://doi.org/10.1038/s41467-020-16784-7
Gildberg A, Mikkelsen H, Sandaker E, Ringø E (1997) Probiotic effect of lactic acid bacteria in the feed on growth and survival of fry of Atlantic cod (Gadus morhua). Hydrobiologia 352:279–285. http://hdl.handle.net/10524/19065
Jöborn A, Olsson JC, Westerdahl A, Conway PL, Kjelleberg S (1997) Colonization in the fish intestinal tract and production of inhibitory substances in intestinal mucus and faecal extracts by Carnobacterium sp. strain K1. J Fish Dis 20:383–392. https://doi.org/10.1046/j.1365-2761.1997.00316.x
Gildberg A, Mikkelsen H (1998) Effects of supplementing the feed to Atlantic cod (Gadus morhua) fry with lactic acid bacteria and immuno-stimulating peptides during a challenge trial with Vibrio anguillarum. Aquaculture 167:103–113. https://doi.org/10.1016/S0044-8486(98)00296-8
Robertson PAW, O'Dowd C, Burrells C, Williams P, Austin B (2000) Use of Carnobacterium sp. as a probiotic for Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss, Walbaum). Aquaculture 185(3-4):235-243. https://doi.org/10.1016/S0044-8486(99)00349-X
Nikoskelainen S, Ouwehand A, Salminen S, Bylund G (2001) Protection of rainbow trout (Oncorhynchus mykiss) from furunculosis by Lactobacillus rhamnosus. Aquaculture 198(3–4):229–236. https://doi.org/10.1016/S0044-8486(01)00593-2
Chang CI, Liu WY (2002) An evaluation of two probiotic bacterial strains, Enterococcus faecium SF68 and Bacillus toyoi, for reducing edwardsiellosis in cultured European eel. Anguilla anguilla L. J Fish Dis 25(5):311–315. https://doi.org/10.1046/j.1365-2761.2002.00365.x
Gatesoupe FJ (2002) Probiotic and formaldehyde treatments of Artemia nauplii as food for larval pollack, Pollachius pollachius. Aquaculture 212:347–360. https://doi.org/10.1016/S0044-8486(02)00138-2
Ortuño J, Cuesta A, Rodrı́guez A, Esteban MA, Meseguer J (2002) Oral administration of yeast, Saccharomyces cerevisiae, enhances the cellular innate immune response of gilthead seabream (Sparus aurata L.). Vet Immunol Immunopathol 85(1-2):41-50. https://doi.org/10.1016/S0165-2427(01)00406-8
Tovar D, Zambonino J, Cahu C, Gatesoupe FJ, Vázquez-Juárez R, Lésel R (2002) Effect of live yeast incorporation in compound diet on digestive enzyme activity in sea bass (Dicentrarchus labrax) larvae. Aquaculture 204(1–2):113–123. https://doi.org/10.1016/S0044-8486(01)00650-0
Ghosh K, Sen SK, Ray AK (2003) Supplementation of an isolated fish gutbacterium, Bacillus circulans, in formulated diets for rohu, Labeo rohita, fingerlings. Isr J Aquac 55:13–21. http://hdl.handle.net/10524/19065
Irianto A, Austin B (2003) Use of dead probiotic cells to control furunculosis in rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 26(1):59–62
Irianto A, Robertson PAW, Austin B (2003) Oral administration of formalin-inactivated cells of Aeromonas hydrophila A3–51 controls infection by atypical A. salmonicida in goldfish, Carassius auratus (L.). J Fish Dis 26:117–120. https://doi.org/10.1046/j.1365-2761.2003.00439.x
Lara-Flores M, Olvera-Novoa MA, Guzmán-Méndez BE, López-Madrid W (2003) Use of the bacteria Streptococcus faecium and Lactobacillus acidophilus, and the yeast Saccharomyces cerevisiae as growth promoters in Nile tilapia (Oreochromis niloticus). Aquaculture 216:193–201. https://doi.org/10.1016/S0044-8486(02)00277-6
Nikoskelainen S, Ouwehand AC, Bylund G, Salminen S, Lilius EM (2003) Immune enhancement in rainbow trout (Oncorhynchus mykiss) by potential probiotic bacteria (Lactobacillus rhamnosus). Fish Shellfish Immunol 15:443–452. https://doi.org/10.1016/S1050-4648(03)00023-8
Raida MK, Larsen JL, Nielsen ME, Buchmann K (2003) Enhanced resistance of rainbow trout, Oncorhynchus mykiss (Walbaum), against Yersinia ruckeri challenge following oral administration of Bacillus subtilis and B. licheniformis (BioPlus2B). J Fish Dis 26:495–498. https://doi.org/10.1046/j.1365-2761.2003.00480.x
Carnevali O, Zamponi MC, Sulpizio R, Rollo A, Nardi M, Orpianesi C, Silvi S, Caggiano M, Polzonetti AM, Cresci A (2004) Administration of probiotic strain to improve sea bream wellness during development. Aquac Int 12(4–5):377–386. https://doi.org/10.1023/B:AQUI.0000042141.85977.bb
Panigrahi A, Kiron V, Puangkaew J, Kobayashi T, Satoh S, Sugita H (2005) The viability of probiotic bacteria as a factor influencing the immune response in rainbow trout Oncorhynchus mykiss. Aquaculture 243:241–254. https://doi.org/10.1016/j.aquaculture.2004.09.032
Tovar-Ramırez D, Infante JZ, Cahu C, Gatesoupe FJ, Vázquez-Juárez R (2004) Influence of dietary live yeast on European sea bass (Dicentrarchus labrax) larval development. Aquaculture. 234(1–4):415–427. https://doi.org/10.1016/j.aquaculture.2004.01.028
Aubin J, Gatesoupe FJ, Labbé L, Lebrun L (2005) Trial of probiotics to prevent the vertebral column compression syndrome in rainbow trout (Oncorhynchus mykiss Walbaum). Aquac Res 36(8):758–767. https://doi.org/10.1111/j.1365-2109.2005.01280.x
Brunt J, Austin B (2005) Use of a probiotic to control lactococcosis and streptococcosis in rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 28(12):693–701. https://doi.org/10.1111/j.1365-2761.2005.00672.x
Chabrillón M, Rico RM, Arijo S, Díaz-Rosales P, Balebonz MC, Moriñigo MA (2005) Interactions of microorganisms isolated from gilthead sea bream, Sparus aurata L., on Vibrio harveyi, a pathogen of farmed Senegalese sole, Solea senegalensis (Kaup). J Fish Dis 28:531–537. https://doi.org/10.1111/j.1365-2761.2005.00657.x
Panigrahi A, Kiron V, Satoh S, Hirono I, Kobayashi T, Sugita H, Puangkaew J, Aoki T (2007) Immune modulation and expression of cytokine genes in rainbow trout Oncorhynchus mykiss upon probiotic feeding. Dev Comp Immunol 31(4):372–382. https://doi.org/10.1016/j.dci.2006.07.004
Refstie S, Sahlström S, Bråthen E, Baeverfjord G, Krogedal P (2005) Lactic acid fermentation eliminates indigestible carbohydrates and antinutritional factors in soybean meal for Atlantic salmon (Salmo salar). Aquaculture 246(1–4):331–345. https://doi.org/10.1016/j.aquaculture.2005.01.001
Salinas I, Cuesta A, Esteban MÁ, Meseguer J (2005) Dietary administration of Lactobacillus delbrüeckii and Bacillus subtilis, single or combined, on gilthead seabream cellular innate immune responses. Fish Shellfish Immunol 19(1):67–77. https://doi.org/10.1016/j.fsi.2004.11.007
Díaz-Rosales P, Salinas I, Rodríguez A, Cuesta A, Chabrillon M, Balebona MC, Morinigo MA, Esteban MA, Meseguer J (2006) Gilthead seabream (Sparus aurata L.) innate immune response after dietary administration of heat-inactivated potential probiotics. Fish Shellfish Immunol 20(4):482-492. https://doi.org/10.1016/j.fsi.2005.06.007
Kim DH, Austin B (2006) Innate immune responses in rainbow trout (Oncorhynchus mykiss, Walbaum) induced by probiotics. Fish Shellfish Immunol 21:513–524. https://doi.org/10.1016/j.fsi.2006.02.007
Kumar R, Mukherjee SC, Prasad KP, Pal AK (2006) Evaluation of Bacillus subtilis as a probiotic to Indian major carp Labeo rohita (Ham.) Aquac Res 37(12):1215-1221. https://doi.org/10.1111/j.1365-2109.(2006).01551.x
Pirarat N, Kobayashi T, Katagiri T, Maita M, Endo M (2006) Protective effects and mechanisms of a probiotic bacterium Lactobacillus rhamnosus against experimental Edwardsiella tarda infection in tilapia (Oreochromis niloticus). Vet Immunol Immunopathol 113(3–4):339–347. https://doi.org/10.1016/j.vetimm.2006.06.003
Rollo A, Sulpizio R, Nardi M, Silvi S, Orpianesi C, Caggiano M, Cresci A, Carnevali O (2006) Live microbial feed supplement in aquaculture for improvement of stress tolerance. Fish Physiol Biochem 32(2):167–177. https://doi.org/10.1007/s10695-006-0009-2
Song ZF, Wu TX, Cai LS, Zhang LJ, Zheng XD (2006) Effects of dietary supplementation with Clostridium butyricum on the growth performance and humoral immune response in Miichthys miiuy. J Zhejiang Univ Sci B 7(7):596–602. https://doi.org/10.1631/jzus.2006.B0596
Taoka Y, Maeda H, Jo JY, Jeon MJ, Bai SC, Lee WJ, Yuge K, Koshio S (2006) Growth, stress tolerance and non-specific immune response of Japanese flounder Paralichthys olivaceus to probiotics in a closed recirculating system. Fish Sci 72(2):310–321. https://doi.org/10.1111/j.1444-2906.2006.01152.x
Taoka Y, Maeda H, Jo JY, Kim SM, Park SI, Yoshikawa T, Sakata T (2006) Use of live and dead probiotic cells in tilapia Oreochromis niloticus. Fish Sci 72:755–766. https://doi.org/10.1111/j.1444-2906.2006.01215.x
Waché Y, Auffray F, Gatesoupe FJ, Zambonino J, Gayet V, Labbé L, Quentel C (2006) Cross effects of the strain of dietary Saccharomyces cerevisiae and rearing conditions on the onset of intestinal microbiota and digestive enzymes in rainbow trout, Onchorhynchus mykiss, fry. Aquaculture 258(1–4):470–478. https://doi.org/10.1016/j.aquaculture.2006.04.002
Yanbo W, Zirong X (2006) Effect of probiotics for common carp (Cyprinus carpio) based on growth performance and digestive enzyme activities. Anim Feed Sci Technol 127(3–4):283–292. https://doi.org/10.1016/j.anifeedsci.2005.09.003
Balcázar JL, De Blas I, Ruiz-Zarzuela I, Vendrell D, Gironés O, Muzquiz JL (2007) Enhancement of the immune response and protection induced by probiotic lactic acid bacteria against furunculosis in rainbow trout (Oncorhynchus mykiss). FEMS Immunol Med Microbiol 51(1):185–193. https://doi.org/10.1111/j.1574-695X.2007.00294.x
Balcázar JL, De Blas I, Ruiz-Zarzuela I, Vendrell D, Calvo AC, Márquez I, Gironés O, Muzquiz JL (2007) Changes in intestinal microbiota and humoral immune response following probiotic administration in brown trout (Salmo trutta). Br J Nutr 97(3):522–527. https://doi.org/10.1017/S0007114507432986
Brunt J, Newaj-Fyzul A, Austin B (2007) The development of probiotics for the control of multiple bacterial diseases of rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 30(10):573–579. https://doi.org/10.1111/j.1365-2761.2007.00836.x
Newaj-Fyzul A, Adesiyun AA, Mutani A, Ramsubhag A, Brunt J, Austin B (2007) Bacillus subtilis AB1 controls Aeromonas infection in rainbow trout (Oncorhynchus mykiss, Walbaum). J Appl Microbiol 103(5):1699–1706. https://doi.org/10.1111/j.1365-2672.2007.03402.x
Aly SM, Ahmed YAG, Ghareeb AAA, Mohamed MF (2008) Studies on Bacillus subtilis and Lactobacillus acidophilus, as potential probiotics, on the immune response and resistance of Tilapia nilotica (Oreochromis niloticus) to challenge infections. Fish Shellfish Immunol 25(1–2):128–136. https://doi.org/10.1016/j.fsi.2008.03.013
Bagheri T, Hedayati SA, Yavari V, Alizade M, Farzanfar A (2008) Growth, survival and gut microbial load of rainbow trout (Onchorhynchus mykiss) fry given diet supplemented with probiotic during the two months of first feeding. Turkish J Fish Aquat Sci 8(1):43-48. http://www.trjfas.org/abstract.php?lang=en&id=587
Kumar R, Mukherjee SC, Ranjan R, Nayak SK (2008) Enhanced innate immune parameters in Labeo rohita (Ham.) following oral administration of Bacillus subtilis. Fish Shellfish Immunol 24(2):168-172. https://doi.org/10.1016/j.fsi.2007.10.008
Pan X, Wu T, Song Z, Tang H, Zhao Z (2008) Immune responses and enhanced disease resistance in Chinese drum, Miichthys miiuy (Basilewsky), after oral administration of live or dead cells of Clostridium butyrium CB2. J Fish Dis 31(9):679–686. https://doi.org/10.1111/j.1365-2761.2008.00955.x
Pieters N, Brunt J, Austin B, Lyndon AR (2008) Efficacy of in-feed probiotics against Aeromonas bestiarum and Ichthyophthirius multifiliis skin infections in rainbow trout (Oncorhynchus mykiss, Walbaum). J Appl Microbiol 105(3):723–732. https://doi.org/10.1111/j.1365-2672.2008.03817.x
Reyes-Becerril M, Tovar-Ramírez D, Ascencio-Valle F, Civera-Cerecedo R, Gracia-López V, Barbosa-Solomieu V (2008) Effects of dietary live yeast Debaryomyces hansenii on the immune and antioxidant system in juvenile leopard grouper Mycteroperca rosacea exposed to stress. Aquaculture 280(1–4):39–44. https://doi.org/10.1016/j.aquaculture.2008.03.056
Vendrell D, Balcázar JL, de Blas I, Ruiz-Zarzuela I, Gironés O, Múzquiz JL (2008) Protection of rainbow trout (Oncorhynchus mykiss) from lactococcosis by probiotic bacteria. Comp Immunol Microbiol Infect Dis 31(4):337–345. https://doi.org/10.1016/j.cimid.2007.04.002
Al-Dohail MA, Hashim R, Aliyu-Paiko M (2009) Effects of the probiotic, Lactobacillus acidophilus, on the growth performance, haematology parameters and immunoglobulin concentration in African Catfish (Clarias gariepinus, Burchell 1822) fingerling. Aquac Res 40(14):1642–1652. https://doi.org/10.1111/j.1365-2109.2009.02265.x
Balcázar JL, Vendrell D, De Blas I, Ruiz-Zarzuela I, Múzquiz JL (2009) Effect of Lactococcus lactis CLFP 100 and Leuconostoc mesenteroides CLFP 196 on Aeromonas salmonicida infection in brown trout (Salmo trutta). J Mol Microbiol Biotechnol 17(3):153–157. https://doi.org/10.1159/000226588
Bandyopadhyay P, Mohapatra PKD (2009) Effect of a probiotic bacterium Bacillus circulans PB7 in the formulated diets: on growth, nutritional quality and immunity of Catla catla (Ham.). Fish Physiol Biochem 35(3): 467-478. https://doi.org/10.1007/s10695-008-9272-8
Capkin E, Altinok I (2009) Effects of dietary probiotic supplementations on prevention/treatment of yersiniosis disease. J Appl Microbiol 106(4):1147–1153. https://doi.org/10.1111/j.1365-2672.2008.04080.x
Díaz-Rosales P, Arijo S, Chabrillón M, Alarcón FJ, Tapia-Paniagua ST, Martínez-Manzanares E, Balebona MC, Moriñigo MA (2009) Effects of two closely related probiotics on respiratory burst activity of Senegalese sole (Solea senegalensis, Kaup) phagocytes, and protection against Photobacterium damselae subsp. piscicida. Aquaculture 293(1-2):16-21. https://doi.org/10.1016/j.aquaculture.2009.03.050
Picchietti S, Fausto AM, Randelli E, Carnevali O, Taddei AR, Buonocore F, Scapigliati G, Abelli L (2009) Early treatment with Lactobacillus delbrueckii strain induces an increase in intestinal T-cells and granulocytes and modulates immune-related genes of larval Dicentrarchus labrax (L.). Fish Shellfish Immunol 26(3):368-376. https://doi.org/10.1016/j.fsi.2008.10.008
Son VM, Chang CC, Wu MC, Guu YK, Chiu CH, Cheng W (2009) Dietary administration of the probiotic, Lactobacillus plantarum, enhanced the growth, innate immune responses and disease resistance of the grouper Epinephelus coioides. Fish Shellfish Immunol 26(5):691–698. https://doi.org/10.1016/j.fsi.2009.02.018
Abbass A, Sharifuzzaman SM, Austin B (2010) Cellular components of probiotics control Yersinia ruckeri infection in rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 33(1):31–37. https://doi.org/10.1111/j.1365-2761.2009.01086.x
Dhanaraj M, Haniffa MA, Singh SA, Arockiaraj AJ, Ramakrishanan CM, Seetharaman S, Arthimanju R (2010) Effect of probiotics on growth performance of koi carp (Cyprinus carpio). J Appl Aquac 22(3):202–209. https://doi.org/10.1080/10454438.2010.497739
Ferguson RMW, Merrifield DL, Harper GM, Rawling MD, Mustafa S, Picchietti S, Balcàzar JL, Davies SJ (2010) The effect of Pediococcus acidilactici on the gut microbiota and immune status of on-growing red tilapia (Oreochromis niloticus). J Appl Microbiol 109(3):851–862. https://doi.org/10.1111/j.1365-2672.2010.04713.x
Harikrishnan R, Balasundaram C, Heo MS (2010) Effect of probiotics enriched diet on Paralichthys olivaceus infected with lymphocystis disease virus (LCDV). Fish Shellfish Immunol 29(5):868–874. https://doi.org/10.1016/j.fsi.2010.07.031
Kim JS, Harikrishnan R, Kim MC, Balasundaram C, Heo MS (2010) Dietary administration of Zooshikella sp. enhance the innate immune response and disease resistance of Paralichthys olivaceus against Streptococcus iniae. Fish Shellfish Immunol 29(1):104-110. https://doi.org/10.1016/j.fsi.2010.02.022
Nayak SK, Mukherjee SC (2010) Screening of gastrointestinal bacteria of Indian major carps for a candidate probiotic species for aquaculture practices. Aquac Res 42(7):1034–1041. https://doi.org/10.1111/j.1365-2109.2010.02686.x
Sharifuzzaman SM, Austin B (2010) Kocuria SM1 controls vibriosis in rainbow trout (Oncorhynchus mykiss, Walbaum). J Appl Microbiol 108(6):2162–2170. https://doi.org/10.1111/j.1365-2672.(2009).04618.x
Sun YZ, Yang HL, Ma RL, Lin WY (2010) Probiotic applications of two dominant gut Bacillus strains with antagonistic activity improved the growth performance and immune responses of grouper Epinephelus coioides. Fish Shellfish Immunol 29(5):803–809. https://doi.org/10.1016/j.fsi.2010.07.018
Varela JL, Ruiz-Jarabo I, Vargas-Chacoff L, Arijo S, León-Rubio JM, García-Millán I, Del Río MM, Moriñigo MA, Mancera JM (2010) Dietary administration of probiotic Pdp11 promotes growth and improves stress tolerance to high stocking density in gilthead seabream Sparus auratus. Aquaculture 309(1–4):265–271. https://doi.org/10.1016/j.aquaculture.2010.09.029
Burbank DR, Shah DH, LaPatra SE, Fornshell G, Cain KD (2011) Enhanced resistance to coldwater disease following feeding of probiotic bacterial strains to rainbow trout (Oncorhynchus mykiss). Aquaculture 321(3–4):185–190. https://doi.org/10.1016/j.aquaculture.2011.09.004
García de la Banda I, Lobo C, Chabrillón M, León-Rubio JM, Arijo S, Pazos G, María Lucas L, Moriñigo MÁ (2011) Influence of dietary administration of a probiotic strain Shewanella putrefaciens on Senegalese sole (Solea senegalensis, Kaup 1858) growth, body composition and resistance to Photobacterium damselae subsp piscicida. Aquac Res 43(5):662–669. https://doi.org/10.1111/j.1365-2109.2011.02871.x
Gopalakannan A, Arul V (2011) Inhibitory activity of probiotic Enterococcus faecium MC13 against Aeromonas hydrophila confers protection against hemorrhagic septicemia in common carp Cyprinus carpio. Aquac Int 19(5):973–985. https://doi.org/10.1007/s10499-011-9415-2
Hoseinifar SH, Mirvaghefi A, Merrifield DL (2011) The effects of dietary inactive brewer's yeast Saccharomyces cerevisiae var. ellipsoideus on the growth, physiological responses and gut microbiota of juvenile beluga (Huso huso). Aquaculture 318(1-2):90-94. https://doi.org/10.1016/j.aquaculture.2011.04.043
Pérez-Sánchez T, Balcázar JL, Merrifield DL, Carnevali O, Gioacchini G, de Blas Ruiz-Zarzuela I (2011) Expression of immune-related genes in rainbow trout (Oncorhynchus mykiss) induced by probiotic bacteria during Lactococcus garvieae infection. Fish Shellfish Immunol 31(2):196–201. https://doi.org/10.1016/j.fsi.2011.05.005
Sharifuzzaman SM, Abbass A, Tinsley JW, Austin B (2011) Subcellular components of probiotics Kocuria SM1 and Rhodococcus SM2 induce protective immunity in rainbow trout (Oncorhynchus mykiss, Walbaum) against Vibrio anguillarum. Fish Shellfish Immunol 30(1):347–353. https://doi.org/10.1016/j.fsi.2010.11.005
Tukmechi A, Andani HRR, Manaffar R, Sheikhzadeh N (2011) Dietary administration of beta-mercapto-ethanol treated Saccharomyces cerevisiae enhanced the growth, innate immune response and disease resistance of the rainbow trout. Oncorhynchus mykiss. Fish Shellfish Immunol 30(3):923–928. https://doi.org/10.1016/j.fsi.2011.01.016
Wang Y (2011) Use of probiotics Bacillus coagulans, Rhodopseudomonas palustris and Lactobacillus acidophilus as growth promoters in grass carp (Ctenopharyngodon idella) fingerlings. Aquac Nutr 17(2):e372–e378. https://doi.org/10.1111/j.1365-2095.2010.00771.x
Giri SS, Sen SS, Sukumaran V (2012) Effects of dietary supplementation of potential probiotic Pseudomonas aeruginosa VSG-2 on the innate immunity and disease resistance of tropical freshwater fish. Labeo rohita. Fish Shellfish Immunol 32(6):1135–1140. https://doi.org/10.1016/j.fsi.2012.03.019
Liu CH, Chiu CH, Wang SW, Cheng W (2012) Dietary administration of the probiotic, Bacillus subtilis E20, enhances the growth, innate immune responses and disease resistance of the grouper. Epinephelus coioides. Fish Shellfish Immunol 33(4):699–706. https://doi.org/10.1016/j.fsi.2012.06.012
Mahdhi A, Kamoun F, Messina C, Bakhrouf A (2012) Probiotic properties of Brevibacillus brevis and its influence on sea bass (Dicentrarchus labrax) larval rearing. Afr J Microbiol Res 6(35):6487–6495. https://doi.org/10.5897/AJMR12.1201
Mohapatra S, Chakraborty T, Prusty AK, Das P, MohantaKN, Paniprasad K (2012) Use of different microbial probiotics in the diet of rohu, Labeo rohita fingerlings: effects on growth, nutrient digestibility and retention, digestive enzyme activities and intestinal microflora. Aquac Nutr 18(1):1–11. https://doi.org/10.1111/j.1365-2095.2011.00866.x
Ran C, Carrias A, Williams MA, Capps N, Dan BC, Newton JC, Kloepper JW, Ooi EL, Browdy CL, Terhune JS, Liles MR (2012) Identification of Bacillus strains for biological control of catfish pathogens. PLoS ONE 7(9):e45793. https://doi.org/10.1371/journal.pone.0045793
Sheikhzadeh N, Heidarieh M, Pashaki AK, Nofouzi K, Farshbafi MA, Akbari M (2012) Hilyses®, fermented Saccharomyces cerevisiae, enhances the growth performance and skin non-specific immune parameters in rainbow trout (Oncorhynchus mykiss). Fish Shellfish Immunol 32(6):1083–1087. https://doi.org/10.1016/j.fsi.2012.03.003
Sorroza L, Padilla D, Acosta F, Román L, Grasso V, Vega J, Real F (2012) Characterization of the probiotic strain Vagococcus fluvialis in the protection of European sea bass (Dicentrarchus labrax) against vibriosis by Vibrio anguillarum. Vet Microbiol 155(2–4):369–373. https://doi.org/10.1016/j.vetmic.2011.09.013
Weifen L, Xiaoping Z, Wenhui S, Bin D, Quan L, Luoqin F, Jiajia Z, Dongyou Y (2012) Effects of Bacillus preparations on immunity and antioxidant activities in grass carp (Ctenopharyngodon idellus). Fish Physiol Biochem 38(6):1585–1592. https://doi.org/10.1007/s10695-012-9652-y
Wu ZX, Feng X, Xie LL, Peng XY, Yuan J, Chen XX (2012) Effect of probiotic Bacillus subtilis Ch9 for grass carp, Ctenopharyngodon idella (Valenciennes, 1844), on growth performance, digestive enzyme activities and intestinal microflora. J Appl Ichthyol 28(5):721–727. https://doi.org/10.1111/j.1439-0426.2012.01968.x
Cerezuela R, Meseguer J (2013) Effects of dietary inulin, Bacillus subtilis and microalgae on intestinal gene expression in gilthead seabream (Sparus aurata L). Fish Shellfish Immunol 34(3):843–848. https://doi.org/10.1016/j.fsi.2012.12.026
Das A, Nakhro K, Chowdhury S, Kamilya D (2013) Effects of potential probiotic Bacillus amyloliquifaciens FPTB16 on systemic and cutaneous mucosal immune responses and disease resistance of catla (Catla catla). Fish Shellfish Immunol 35(5):1547–1553. https://doi.org/10.1016/j.fsi.2013.08.022
Del’Duca A, Cesar DE, Diniz CG, Abreu PC (2013) Evaluation of the presence and efficiency of potential probiotic bacteria in the gut of tilapia (Oreochromis niloticus) using the fluorescent in situ hybridization technique. Aquaculture 388:115–121. https://doi.org/10.1016/j.aquaculture.2013.01.019
Giri SS, Sukumaran V, Oviya M (2013) Potential probiotic Lactobacillus plantarum VSG3 improves the growth, immunity and disease resistance of tropical freshwater fish. Labeo rohita. Fish Shellfish Immunol 34(2):660–666. https://doi.org/10.1016/j.fsi.2012.12.008
Chi C, Jiang B, Yu XB, Liu TQ, Xia L, Wang GX (2014) Effects of three strains of intestinal autochthonous bacteria and their extracellular products on the immune response and disease resistance of common carp. Cyprinus carpio. Fish Shellfish Immunol 36(1):9–18. https://doi.org/10.1016/j.fsi.2013.10.003
Mohapatra S, Chakraborty T, Prusty AK, PaniPrasad K, Mohanta KN (2014) Beneficial effects of dietary probiotics mixture on hemato-immunology and cell apoptosis of Labeo rohita fingerlings reared at higher water temperatures. PloSONE 9(6):e100929. https://doi.org/10.1371/journal.pone.0100929
Huang L, Ran C, He S, Ren P, Hu J, Zhao X, Zhou Z (2015) Effects of dietary Saccharomyces cerevisiae culture or live cells with Bacillus amyloliquefaciens spores on growth performance, gut mucosal morphology, hsp70 gene expression, and disease resistance of juvenile common carp (Cyprinus carpio). Aquaculture 438:33–38. https://doi.org/10.1016/j.aquaculture.2014.12.029
Jha DK, Bhujel RC, Anal AK (2015) Dietary supplementation of probiotics improves survival and growth of Rohu (Labeo rohita Ham.) hatchlings and fry in outdoor tanks. Aquaculture 435:475–479. https://doi.org/10.1016/j.aquaculture.2014.10.026
Adeoye AA, Yomla R, Jaramillo-Torres A, Rodiles A, Merrifield DL, Davies SJ (2016) Combined effects of exogenous enzymes and probiotic on Nile tilapia (Oreochromis niloticus) growth, intestinal morphology and microbiome. Aquaculture 463:61–70. https://doi.org/10.1016/j.aquaculture.2016.05.028
Allameh SK, Yusoff FM, Ringø E, Daud HM, Saad CR, Ideris A (2016) Effects of dietary mono-and multiprobiotic strains on growth performance, gut bacteria and body composition of Javanese carp (Puntius gonionotus, Bleeker 1850). Aquac Nutr 22(2):367–373. https://doi.org/10.1111/anu.12265
Dawood MA, Koshio S, Ishikawa M, El-Sabagh M, Esteban MA, Zaineldin AI (2016) Probiotics as an environment-friendly approach to enhance red sea bream, Pagrus major growth, immune response and oxidative status. Fish Shellfish Immunol 57:170–178. https://doi.org/10.1016/j.fsi.2016.08.038
Farias THV, Levy-Pereira N, de Oliveira Alves L, de Carla Dias D, Tachibana L, Pilarski F, de Andrade Belo MA, Ranzani-Paiva MJT (2016) Probiotic feeding improves the immunity of pacus, Piaractus mesopotamicus, during Aeromonas hydrophila infection. Anim Feed Sci Technol 211:137–144. https://doi.org/10.1016/j.anifeedsci.2015.11.004
Park Y, Moniruzzaman M, Lee S, Hong J, Won S, Lee JM, Yun H, Kim KW, Ko D, Bai SC (2016) Comparison of the effects of dietary single and multi-probiotics on growth, non-specific immune responses and disease resistance in starry flounder, Platichthys stellatus. Fish Shellfish Immunol 59:351–357. https://doi.org/10.1016/j.fsi.2016.11.006
Standen BT, Peggs DL, Rawling MD, Foey A, Davies SJ, Santos GA, Merrifield DL (2016) Dietary administration of a commercial mixed-species probiotic improves growth performance and modulates the intestinal immunity of tilapia, Oreochromis niloticus. Fish Shellfish Immunol 49:427–435. https://doi.org/10.1016/j.fsi.(2015).11.037
He RP, Feng J, Tian XL, Dong SL, Wen B (2017) Effects of dietary supplementation of probiotics on the growth, activities of digestive and non-specific immune enzymes in hybrid grouper (Epinephelus lanceolatus♂× Epinephelus fuscoguttatus♀). Aquac Res 48(12):5782–5790. https://doi.org/10.1111/are.13401
Lin HL, Shiu YL, Chiu CS, Huang SL, Liu CH (2017) Screening probiotic candidates for a mixture of probiotics to enhance the growth performance, immunity, and disease resistance of Asian seabass, Lates calcarifer (Bloch), against Aeromonas hydrophila. Fish Shellfish Immunol 60:474–482. https://doi.org/10.1016/j.fsi.2016.11.026
Park Y, Lee S, Hong J, Kim D, Moniruzzaman M, Bai SC (2017) Use of probiotics to enhance growth, stimulate immunity and confer disease resistance to Aeromonas salmonicida in rainbow trout (Oncorhynchus mykiss). Aquac Res 48(6):2672–2682. https://doi.org/10.1111/are.13099
Ramesh D, Souissi S, Ahamed TS (2017) Effects of the potential probiotics Bacillus aerophilus KADR3 in inducing immunity and disease resistance in Labeo rohita. Fish Shellfish Immunol 70:408–415. https://doi.org/10.1016/j.fsi.2017.09.037
Abarike ED, Cai J, Lu Y, Yu H, Chen L, Jian J, Tang J, Jun L, Kuebutornye FK (2018) Effects of a commercial probiotic BS containing Bacillus subtilis and Bacillus licheniformis on growth, immune response and disease resistance in Nile tilapia, Oreochromis niloticus. Fish Shellfish Immunol 82:229–238. https://doi.org/10.1016/j.fsi.2018.08.037
Dias JA, Abe HA, Sousa NC, Couto MV, Cordeiro CA, Meneses JO, Cunha FS, Mouriño JLP, Martins ML, Barbas LA, Carneiro PC (2018) Dietary supplementation with autochthonous Bacillus cereus improves growth performance and survival in tambaqui Colossoma macropomum. Aquac Res 49(9):3063–3070. https://doi.org/10.1111/are.13767
Ghiasi M, Binaii M, Naghavi A, Rostami HK, Nori H, Amerizadeh A (2018) Inclusion of Pediococcus acidilactici as probiotic candidate in diets for beluga (Huso huso) modifies biochemical parameters and improves immune functions. Fish Physiol Biochem 44(4):1099–1107. https://doi.org/10.1007/s10695-018-0497-x
Gobi N, Vaseeharan B, Chen JC, Rekha R, Vijayakumar S, Anjugam M, Iswarya A (2018) Dietary supplementation of probiotic Bacillus licheniformis Dahb1 improves growth performance, mucus and serum immune parameters, antioxidant enzyme activity as well as resistance against Aeromonas hydrophila in tilapia Oreochromis mossambicus. Fish Shellfish Immunol 74:501–508. https://doi.org/10.1016/j.fsi.2017.12.066
Pereira LF, Peixoto MJ, Carvalho P, Sansuwan K, Santos GA, OzórioROA, Gonçalves JFM (2018) Cross effects of dietary probiotic supplementation and rearing temperature on growth performance, digestive enzyme activities, cumulative mortality and innate immune response in seabass (Dicentrarchus labrax). Aquac Nutr 24(1):453–460. https://doi.org/10.1111/anu.12578
Zaineldin AI, Hegazi S, Koshio S, Ishikawa M, Bakr A, El-KeredyDawood, MADossou S, Wang W, Yukun Z, AM (2018) Bacillus subtilis as probiotic candidate for red sea bream: Growth performance, oxidative status and immune response traits. Fish Shellfish Immunol 79:303–312. https://doi.org/10.1016/j.fsi.2018.05.035
Al-Hisnawi A, Rodiles A, Rawling MD, Castex M, Waines P, Gioacchini G, Carnevali O, Merrifield DL (2019) Dietary probiotic Pediococcus acidilactici MA18/5M modulates the intestinal microbiota and stimulates intestinal immunity in rainbow trout (Oncorhynchus mykiss). J World Aquac Soc 50(6):1133–1151. https://doi.org/10.1111/jwas.12642
Amir I, Zuberi A, Kamran M, Imran M (2019) Evaluation of commercial application of dietary encapsulated probiotic (Geotrichum candidum QAUGC01): effect on growth and immunological indices of rohu (Labeo rohita, Hamilton 1822) in semi-intensive culture system. Fish Shellfish Immunol 95:464–472. https://doi.org/10.1016/j.fsi.2019.11.011
Di J, Chu Z, Zhang S, Huang J, Du H, Wei Q (2019) Evaluation of the potential probiotic Bacillus subtilis isolated from two ancient sturgeons on growth performance, serum immunity and disease resistance of Acipenser dabryanus. Fish Shellfish Immunol 93:711–719. https://doi.org/10.1016/j.fsi.2019.08.020
Jang WJ, Lee JM, Hasan MT, Lee BJ, Lim SG, Kong IS (2019) Effects of probiotic supplementation of a plant-based protein diet on intestinal microbial diversity, digestive enzyme activity, intestinal structure, and immunity in olive flounder (Paralichthys olivaceus). Fish Shellfish Immunol 92:719–727. https://doi.org/10.1016/j.fsi.2019.06.056
Li J, Wu ZB, Zhang Z, Zha JW, Qu SY, Qi XZ, Wang GX, Ling F (2019) Effects of potential probiotic Bacillus velezensis K2 on growth, immunity and resistance to Vibrio harveyi infection of hybrid grouper (Epinephelus lanceolatus♂× E. fuscoguttatus♀). Fish Shellfish Immunol 93:1047–1055. https://doi.org/10.1016/j.fsi.2019.08.047
Midhun SJ, Arun D, Neethu S, Vysakh A, Radhakrishnan EK, Jyothis M (2019) Administration of probiotic Paenibacillus polymyxa HGA4C induces morphometric, enzymatic and gene expression changes in Oreochromis niloticus. Aquaculture 508:52–59. https://doi.org/10.1016/j.aquaculture.2019.04.061
Mohammadian T, Nasirpour M, Tabandeh MR, Heidary AA, Ghanei-Motlagh R, Hosseini SS (2019) Administrations of autochthonous probiotics altered juvenile rainbow trout Oncorhynchus mykiss health status, growth performance and resistance to Lactococcus garvieae, an experimental infection. Fish Shellfish Immunol 86:269–279. https://doi.org/10.1016/j.fsi.2018.11.052
Niu KM, Khosravi S, Kothari D, Lee WD, Lim JM, Lee BJ, Kim KW, Lim SG, Lee SM, Kim SK (2019) Effects of dietary multi-strain probiotics supplementation in a low fishmeal diet on growth performance, nutrient utilization, proximate composition, immune parameters, and gut microbiota of juvenile olive flounder (Paralichthys olivaceus). Fish Shellfish Immunol 93:258–268. https://doi.org/10.1016/j.fsi.2019.07.056
Tang Y, Han L, Chen X, Xie M, Kong W, Wu Z (2019) Dietary supplementation of probiotic Bacillus subtilis affects antioxidant defenses and immune response in grass carp under Aeromonas hydrophila challenge. Probiotics Antimicrob Proteins 11(2):545–558. https://doi.org/10.1007/s12602-018-9409-8
Vale Pereira G, Pereira SA, Soares A, Mouriño JLP, Merrifield D (2019) Autochthonous probiotic bacteria modulate intestinal microbiota of Pirarucu. Arapaima gigas. J World Aquac Soc 50(6):1152–1167. https://doi.org/10.1111/jwas.12638
Adeshina I, Abubakar MIO, Ajala BE (2020) Dietary supplementation with Lactobacillus acidophilus enhanced the growth, gut morphometry, antioxidant capacity, and the immune response in juveniles of the common carp, Cyprinus carpio. Fish Physiol Biochem 46:1375–1385. https://doi.org/10.1007/s10695-020-00796-7
Akbari NE, Falahatkar B, Sajjadi MM (2020) Dietary supplementation of probiotics and influence on feed efficiency, growth parameters and reproductive performance in female rainbow trout (Oncorhynchus mykiss) broodstock. Aquac Nutr 26(1):98–108. https://doi.org/10.1111/anu.12970
Darafsh F, Soltani M, Abdolhay HA, Shamsaei MM (2020) Improvement of growth performance, digestive enzymes and body composition of Persian sturgeon (Acipenser persicus) following feeding on probiotics: Bacillus licheniformis, Bacillus subtilis and Saccharomyces cerevisiae. Aquac Res 51(3):957–964. https://doi.org/10.1111/are.14440
Jiang Y, Zhou S, Sarkodie EK, Chu W (2020) The effects of Bacillus cereus QSI-1 on intestinal barrier function and mucosal gene transcription in Crucian carp (Carassius auratus gibelio). Aquac Rep 17:100356. https://doi.org/10.1016/j.aqrep.2020.100356
Kong Y, Li M, Li R, Shan X, Wang G (2020) Evaluation of cholesterol lowering property and antibacterial activity of two potential lactic acid bacteria isolated from the intestine of snakehead fish (Channa argus). Aquac Rep 17:100342. https://doi.org/10.1016/j.aqrep.2020.100342
Kuebutornye FK, Tang J, Cai J, Yu H, Wang Z, Abarike ED, Lu Y, Li Y, Afriyie G (2020) In vivo assessment of the probiotic potentials of three host-associated Bacillus species on growth performance, health status and disease resistance of Oreochromis niloticus against Streptococcus agalactiae. Aquaculture 527:735440. https://doi.org/10.1016/j.aquaculture.2020.735440
Li Y, Hu S, Gong L, Pan L, Li D, Cao L, Khan TA, Yang Y, Peng Y, Ding X, Yi G (2020) Isolating a new Streptomyces amritsarensis N1–32 against fish pathogens and determining its effects on disease resistance of grass carp. Fish Shellfish Immunol 98:632–640. https://doi.org/10.1016/j.fsi.2019.10.038
Liu S, Wang S, Cai Y, Li E, Ren Z, Wu Y, Guo W, Sun Y, Zhou Y (2020) Beneficial effects of a host gut-derived probiotic, Bacillus pumilus, on the growth, non-specific immune response and disease resistance of juvenile golden pompano. Trachinotus ovatus. Aquaculture 514:734446. https://doi.org/10.1016/j.aquaculture.2019.734446
Niu KM, Khosravi S, Kothari D, Lee WD, Lee BJ, Lim SG, Hur SW, Lee SM, Kim SK (2020) Potential of indigenous Bacillus spp. as probiotic feed supplements in an extruded low fish meal diet for juvenile olive flounder, Paralichthys olivaceus. J World Aquac Soc https://doi.org/10.1111/jwas.12724
Park Y, Kim H, Won S, Hamidoghli A, Hasan MT, Kong IS, Bai SC (2020) Effects of two dietary probiotics (Bacillus subtilis or licheniformis) with two prebiotics (mannan or fructo oligosaccharide) in Japanese eel. Anguilla japonica. Aquac Nutr 26(2):316–327. https://doi.org/10.1111/anu.12993
Paixãodo Couto MVS, da Costa Sousa N, Abe HA, Reis RGA, Dias JAR, Meneses JO, Cunha FS, Santos TBR, da Silva ICA, dos Santos Medeiros E, PEG (2020) Autochthonous bacterium Lactobacillus plantarum as probiotic supplementation for productive performance and sanitary improvements on clownfish Amphiprion ocellaris. Aquaculture 526:735395. https://doi.org/10.1016/j.aquaculture.2020.735395
Rhee C, Kim H, Emmanuel SA, Kim HG, Won S, Bae J, Bai SC, Koh SC (2020) Probiotic effects of mixture of Groenewaldozyma salmanticensis and Gluconacetobacter liquefaciens on growth and immune responses in Paralichthys olivaceus. Lett Appl Microbiol. https://doi.org/10.1111/lam.13282
Rostika R, Azhima MF, Ihsan YN, Andriani Y, Suryadi IBB, Dewanti LP (2020) The use of solid probiotics in feed to growth and survival rate of mantap common carp (Cyprinus carpio). Aquac Aquar Conserv Legis 13(1):199–206
Tarkhani R, Imani A, Hoseinifar SH, Moghanlou KS, Manaffar R (2020) The effects of host-associated Enterococcus faecium CGMCC1. 2136 on serum immune parameters, digestive enzymes activity and growth performance of the Caspian roach (Rutilus rutilus caspicus) fingerlings. Aquaculture 519:734741. https://doi.org/10.1016/j.aquaculture.2019.734741
Santos KO, Costa-Filho J, Spagnol KL, Nornberg BF, Lopes FM, Tesser MB, Marins LF (2020) The inclusion of a transgenic probiotic expressing recombinant phytase in a diet with a high content of vegetable matter markedly improves growth performance and the expression of growth-related genes and other selected genes in zebrafish. Aquaculture 519:734878. https://doi.org/10.1016/j.aquaculture.2019.734878
Sutthi N, Van Doan H (2020) Saccharomyces crevices and Bacillus spp. effectively enhance health tolerance of Nile tilapia under transportation stress. Aquaculture 528:735527. https://doi.org/10.1016/j.aquaculture.2020.735527
Vazirzadeh A, Roosta H, Masoumi H, Farhadi A, Jeffs A (2020) Long-term effects of three probiotics, singular or combined, on serum innate immune parameters and expressions of cytokine genes in rainbow trout during grow-out. Fish Shellfish Immunol 98:748–757. https://doi.org/10.1016/j.fsi.2019.11.023
Xia Y, Yu E, Maixin L, Xie J (2020) Effects of probiotic supplementation on gut microbiota as well as metabolite profiles within Nile tilapia. Aquaculture, Oreochromis niloticus. https://doi.org/10.1016/j.aquaculture.2020.735428
Zhang B, Li C, Wang X, Liu C, Zhou H, Mai K, He G (2020) Administration of commensal Shewanella sp. MR-7 ameliorates lipopolysaccharide-induced intestine dysfunction in turbot (Scophthalmus maximus L.). Fish Shellfish Immunol 102:460–468. https://doi.org/10.1016/j.fsi.2020.04.068
Hansen JØ, Lagos L, Lei P, Reveco-Urzua FE, Morales-Lange B, Hansen LD, Schiavone M, Mydland LT, Arntzen MØ, Mercado L, Benicio RT (2021) Down-stream processing of baker’s yeast (Saccharomyces cerevisiae)–Effect on nutrient digestibility and immune response in Atlantic salmon (Salmo salar). Aquaculture 530:735707. https://doi.org/10.1016/j.aquaculture.2020.735707
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All authors are thankful to the Director, ICAR-Central Institute of Fisheries Education (ICAR-CIFE), Mumbai, for providing all the facilities required.
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This work was conceived by all authors. Nisha Chuphal and Krishna Pada Singha drafted the first version of the manuscript and Krishna Pada Singha prepared and arranged tables and figures, while all co‐authors provided valuable feedback before approving the final version.
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Chuphal, N., Singha, K.P., Sardar, P. et al. Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?. Probiotics & Antimicro. Prot. 13, 1668–1695 (2021). https://doi.org/10.1007/s12602-021-09778-4
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DOI: https://doi.org/10.1007/s12602-021-09778-4