Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.
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人类口腔微生物组神秘成员之间生态位划分的功能和遗传标记。
DOI：
10.1186/s13059-020-02195-w
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发表时间：
2020-12-16
期刊：
影响因子：
12.3
通讯作者：
Eren AM
中科院分区：
文献类型：
--
作者：
Shaiber A;Willis AD;Delmont TO;Roux S;Chen LX;Schmid AC;Yousef M;Watson AR;Lolans K;Esen ÖC;Lee STM;Downey N;Morrison HG;Dewhirst FE;Mark Welch JL;Eren AM
人类口腔中的微生物居民长期以来一直是微生物学的主要焦点，因为它们对宿主健康的影响以及在缺乏扩散限制的情况下的有趣的位点特异性模式。然而，在这个栖息地的生态位划分的决定因素还没有得到充分的理解，特别是在类群属于最近发现的微生物生命的分支。在这里，我们从来自多个个体的舌和牙菌斑样本中组装宏基因组，并重建790个非冗余基因组，其中43个解析为TM 7，候选门辐射的成员，形成6个单系分支，与牙菌斑或舌明显相关。泛基因组学和RT-PCR基因组学分析都将舌特异性进化枝与其他宿主相关的TM 7基因组分组。与此相反，噬菌斑特异性TM 7组与环境TM 7基因组。除了提供更深入的生态学，进化和口腔微生物组的神秘成员的mobilome的见解，我们的研究揭示了牙菌斑和TM 7进化所指示的非宿主环境之间有趣的相似性，这表明牙菌斑可能是环境微生物适应某些微生物分支的宿主环境的垫脚石。此外，我们报告说，原噬菌体广泛存在于口腔相关的TM 7，而没有从环境TM 7，这表明原噬菌体可能发挥了作用，在适应TM 7的宿主环境。我们的数据阐明了口腔中神秘成员的生态位划分，包括TM 7，SR 1和GN 02，并提供了这种生物群系中特征不明显但普遍存在的成员的基因组，如未栽培的黄杆菌科。在线版本包含补充材料，可通过10.1186/s13059-020-02195-w获得。
Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae. The online version contains supplementary material available at 10.1186/s13059-020-02195-w.
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DOI：
10.1073/pnas.1810625115
发表时间：
2018-11-27
影响因子：
11.1
作者：
Bor B;McLean JS;Foster KR;Cen L;To TT;Serrato-Guillen A;Dewhirst FE;Shi W;He X
通讯作者：
He X
影响因子：
2.7
作者：
Delmont TO;Eren AM
通讯作者：
Eren AM
影响因子：
14.9
作者：
Chen IA;Chu K;Palaniappan K;Pillay M;Ratner A;Huang J;Huntemann M;Varghese N;White JR;Seshadri R;Smirnova T;Kirton E;Jungbluth SP;Woyke T;Eloe-Fadrosh EA;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC
影响因子：
0.8
作者：
Collins, Andrew J.;Murugkar, Pallavi P.;Dewhirst, Floyd E.
通讯作者：
Dewhirst, Floyd E.
影响因子：
14.9
作者：
Couvin D;Bernheim A;Toffano-Nioche C;Touchon M;Michalik J;Néron B;Rocha EPC;Vergnaud G;Gautheret D;Pourcel C
通讯作者：
Pourcel C