Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

doi:10.1186/s12864-020-06807-4

CORC > 深海科学与工程研究所 > 中国科学院深海科学与工程研究所 > 深海科学研究部 > 深海生物学研究室 > 海洋微生物宏基因组与分子进化研究组

	Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli
	Wang,Yong 5; Huang,Jiao-Mei 1,5; Zhou,Ying-Li 1,5; Almeida,Alexandre 2,6; Finn,Robert D.2; Danchin,Antoine 3,4; He,Li-Sheng 5
刊名	BMC Genomics
	2020-06-17
卷号	21 期号:1 页码:12
关键词	Bacilli Autotrophy Pathogen Gut microbiome Environmental Tenericutes
ISSN号	1471-2164
DOI	10.1186/s12864-020-06807-4
英文摘要	AbstractBackgroundThe 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.
资助项目	National Key Research and Development Program of China[2016YFC0302504] ; National Key Research and Development Program of China[2018YFC0310005] ; European Molecular Biology Laboratory core funds
WOS关键词	BACTERIAL ; METABOLISM ; SEQUENCES ; ALIGNMENT ; MODEL ; DEEP ; GENE ; MYCOPLASMAS ; CONTRACTILE ; COMMUNITIES
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BioMed Central
WOS记录号	BMC:10.1186/S12864-020-06807-4
资助机构	National Key Research and Development Program of China ; European Molecular Biology Laboratory core funds
内容类型	期刊论文
源URL	[http://ir.idsse.ac.cn/handle/183446/7686]
专题	深海科学研究部_深海生物学研究室_海洋微生物宏基因组与分子进化研究组
通讯作者	Wang,Yong
作者单位	1.University of Chinese Academy of Sciences 2.European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus; European Molecular Biology Laboratory 3.Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes; Kodikos, Department of Infection, Immunity and Inflammation 4.School of Biomedical Sciences, University of Hong Kong; Li Kashing Faculty of Medicine 5.Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences 6.Wellcome Sanger Institute, Wellcome Genome Campus
推荐引用方式 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.