Microbial co-occurrence relationships in the human microbiome.
Microbial co-occurrence relationships in the human microbiome.
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DOI：
10.1371/journal.pcbi.1002606
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发表时间：
2012
影响因子：
4.3
通讯作者：
Huttenhower C
中科院分区：
文献类型：
--
作者：
Faust K;Sathirapongsasuti JF;Izard J;Segata N;Gevers D;Raes J;Huttenhower C
健康的微生物群在个体内和个体之间表现出显着的变异性。除了外部暴露，微生物居民之间的生态关系（对立和共生）是这种变化的重要贡献者。因此，评估微生物之间可能存在的关系并确定其根本原因是有意义的。最初的人类微生物组计划（HMP）队列，包括239个个体和18个不同的微生物栖息地，提供了前所未有的资源来检测，编目和分析这种关系。在这里，我们将基于多种相似性度量的集成方法与广义提升线性模型（GBLMs）相结合应用于该队列的分类标记（16S rRNA基因）谱，从而在整个人类微生物组中发生的197个分支之间产生了3，005个显著共现和共排除关系的全球网络。这个网络揭示了强大的生态位专业化，大多数微生物协会发生在身体网站和一些陪同机构间网站的关系。口咽部内的微生物群落分为三个不同的栖息地，其本身对肠道微生物群的组成没有直接影响。相反，像阴道这样的小生境几乎没有分解成特定区域的相互作用。不同的机制影响着个体的相互作用，其中一些机制如牙龈下菌斑中卟啉单胞菌家族成员和链球菌的共同排斥，这是由已知的生化依赖性支持的。这些差异在广泛的系统发生群中也各不相同，例如杆菌和梭杆菌，都富集了排除其他分支的分类群。比较细菌之间的系统发育与功能相似性，我们发现，占主导地位的细菌类群（如肠道中的普雷沃氏菌科和拟杆菌）往往竞争，而潜在的病原体（如密螺旋体和牙菌斑中的普雷沃氏菌）更有可能共同出现在互补的壁龛。因此，这种方法为人类微生物组的微生物生态学的未来靶向机制研究开辟了新的机会。人体是一个复杂的生态系统，微生物在其中竞争和合作。这些相互作用可以支持健康或促进疾病，例如在牙菌斑形成中。人类微生物组项目收集并测序了ca。来自18个不同身体部位的5，000个样本，包括气道，肠道，皮肤，口腔和阴道。这些数据允许首次评估人类相关细菌之间共存和排除的显著模式。我们将稀疏回归与相似性度量的集合相结合，以预测身体部位内和身体部位之间的微生物关系。这捕获了牙菌斑，阴道和肠道中的已知关系，并且还预测了涉及特征不足的门（如TM7）成员的新相互作用。我们检测了斑块形成所必需的关系以及肠道和阴道微生物群落中主要成员的群落组成差异。大多数关系都是强烈的生态位特异性，只有少数枢纽微生物在多个身体区域形成联系。我们还发现系统发育距离对相互作用类型有很大影响：密切相关的微生物共存于同一生态位内，而大多数排他性关系发生在关系较远的微生物之间。这建立了特定的生物体和一般原则，通过这些原则，与健康人类相关的微生物群落被组装和维持。
The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome. The human body is a complex ecosystem where microbes compete, and cooperate. These interactions can support health or promote disease, e.g. in dental plaque formation. The Human Microbiome Project collected and sequenced ca. 5,000 samples from 18 different body sites, including the airways, gut, skin, oral cavity and vagina. These data allowed the first assessment of significant patterns of co-presence and exclusion among human-associated bacteria. We combined sparse regression with an ensemble of similarity measures to predict microbial relationships within and between body sites. This captured known relationships in the dental plaque, vagina, and gut, and also predicted novel interactions involving members of under-characterized phyla such as TM7. We detected relationships necessary for plaque formation and differences in community composition among dominant members of the gut and vaginal microbiomes. Most relationships were strongly niche-specific, with only a few hub microorganisms forming links across multiple body areas. We also found that phylogenetic distance had a strong impact on the interaction type: closely related microorganisms co-occurred within the same niche, whereas most exclusive relationships occurred between more distantly related microorganisms. This establishes both the specific organisms and general principles by which microbial communities associated with healthy humans are assembled and maintained.
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影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
4.5
作者：
Buhlmann, Peter
通讯作者：
Buhlmann, Peter
DOI：
10.1007/bf01031393
发表时间：
1981-01-01
期刊：
JOURNAL OF THE INTERNATIONAL ASSOCIATION FOR MATHEMATICAL GEOLOGY
影响因子：
--
作者：
AITCHISON, J
通讯作者：
AITCHISON, J
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM
影响因子：
56.9
作者：
Barabási, AL;Albert, R
通讯作者：
Albert, R