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A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species

  • Environmental Microbiology
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Abstract

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.

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Funding

This study was partially supported by the National Natural Science Foundation of China (31560111) and the Hundred Oversea Talents Recruitmsent Program of Yunnan Province.

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Authors and Affiliations

  1. School of Life Sciences, Yunnan University, Kunming, 650500, China

    Hongyu Chen, Chunqing Li, Tao Liu, Shanyuan Chen & Heng Xiao

  2. National Demonstration Center for Experimental Life Sciences Education (Yunnan University), Yunnan University, Kunming, China

    Shanyuan Chen

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  1. Hongyu Chen
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  2. Chunqing Li
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Correspondence to Shanyuan Chen or Heng Xiao.

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Electronic supplementary material

Online resource 1

The rarefaction analysis of each fish gut samples (PDF 387 kb) The rarefaction curves showing the quantity of OTUs per sample on the basis of number of reads for 33 specimens. (PNG 2308 kb)

Online resource 2

Unique OTUs in three groups of Sinocyclocheilus fish. Pie chart shows the characteristics of unique OTUs form cavefish group (a), surface fish group1(b) and surface group 2 (c) with a frequency higher than 1%. (PNG 2308 kb)

High Resolution Image (TIF 2173 kb)

Online resource 3

Significant differences in the abundance among intestinal microbes the phylum and genus levels between three group. The significant differences (*: P < 0.05; **: P < 0.0; ***: P < 0.001) of abundant at gut bacterial phylum (a) and genus (b) between three groups were calculated by Kruskal-Wallis rank-test. Three groups are represented by different colors, respectively: surface group 2(green), surface group 1(red), cave group (blue). The most abundant taxa (top10 at phylum level, top 15 at genus level) of bacteria used for compare show in the ordinate. (PNG 265 kb)

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Chen, H., Li, C., Liu, T. et al. A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species. Microb Ecol 79, 299–311 (2020). https://doi.org/10.1007/s00248-019-01409-4

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  • DOI: https://doi.org/10.1007/s00248-019-01409-4

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