Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli
Wang,Yong1; Huang,Jiao-Mei1,2; Zhou,Ying-Li1,2; Almeida,Alexandre3,4; Finn,Robert D.3; Danchin,Antoine5,6; He,Li-Sheng1
2020-06-17
Source PublicationBMC Genomics
ISSN1471-2164
Volume21Issue:1Pages:12
AbstractAbstractBackgroundThe metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes.ResultsSeveral environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment.ConclusionsThis study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
KeywordBacilli Autotrophy Pathogen Gut microbiome Environmental Tenericutes
DOI10.1186/s12864-020-06807-4
Indexed BySCI ; SCI
Funding OrganizationNational Key Research and Development Program of China ; European Molecular Biology Laboratory core funds
Language英语
Funding ProjectNational Key Research and Development Program of China[2016YFC0302504] ; National Key Research and Development Program of China[2018YFC0310005] ; European Molecular Biology Laboratory core funds
WOS KeywordBACTERIAL ; METABOLISM ; SEQUENCES ; ALIGNMENT ; MODEL ; DEEP ; GENE ; MYCOPLASMAS ; CONTRACTILE ; COMMUNITIES
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDBMC:10.1186/s12864-020-06807-4
PublisherBioMed Central
Citation statistics
Document Type期刊论文
Identifierhttp://ir.idsse.ac.cn/handle/183446/7687
Collection深海科学研究部_深海生物学研究室_深海微生物基因组学研究组
研究生部
Corresponding AuthorWang,Yong
Affiliation1.Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences
2.University of Chinese Academy of Sciences
3.European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus; European Molecular Biology Laboratory
4.Wellcome Sanger Institute, Wellcome Genome Campus
5.Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes; Kodikos, Department of Infection, Immunity and Inflammation
6.School of Biomedical Sciences, University of Hong Kong; Li Kashing Faculty of Medicine
Recommended Citation
GB/T 7714
Wang,Yong,Huang,Jiao-Mei,Zhou,Ying-Li,et al. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli[J]. BMC Genomics,2020,21(1):12.
APA Wang,Yong.,Huang,Jiao-Mei.,Zhou,Ying-Li.,Almeida,Alexandre.,Finn,Robert D..,...&He,Li-Sheng.(2020).Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli.BMC Genomics,21(1),12.
MLA Wang,Yong,et al."Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli".BMC Genomics 21.1(2020):12.
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