Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life

Biology Direct

Philippe Lopez¹  Sébastien Halary²  Eric Bapteste¹ 

[1] Team ‘Adaptation, Integration, Reticulation, Evolution’ – UMR CNRS 7138 Evolution Paris Seine – Institut de Biologie Paris Seine – Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France

[2] Département de Sciences Biologiques, Institut de recherche en biologie végétale, Université de Montréal, Montréal H1X 2B2, QC, Canada

关键词: Environmental diversity;    Networks;    Comparative analysis;    Metagenomics;    Microbiology;   

Others  :  1230608
DOI  :  10.1186/s13062-015-0092-3

 received in 2015-07-30, accepted in 2015-10-13,  发布年份 2015

【 摘 要 】

Background

Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks.

Results

Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain.

Conclusions

Many genes families included environmental homologs that were highly divergent from cultured homologs in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.

Reviewers

This article was reviewed by Eugene Koonin, William Martin and James McInerney.

【 授权许可】

   
2015 Lopez et al.

【 图 表 】

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