Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.
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DOI：
10.1186/s13059-021-02427-7
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发表时间：
2021-07-14
期刊：
影响因子：
12.3
通讯作者：
Segata N
中科院分区：
文献类型：
--
作者：
Karcher N;Nigro E;Punčochář M;Blanco-Míguez A;Ciciani M;Manghi P;Zolfo M;Cumbo F;Manara S;Golzato D;Cereseto A;Arumugam M;Bui TPN;Tytgat HLP;Valles-Colomer M;de Vos WM;Segata N
嗜粘蛋白阿克曼氏菌是一种人类肠道微生物，在肠道粘液层的生理学中起关键作用，并报告了与体重下降和肠道屏障功能和健康增加的相关性。尽管其生物医学意义，A。muciniphila的研究尚不充分，而与之密切相关的物种中，除了A. glycaniphila，unexplored.我们提出了一个大规模的人口基因组学分析阿克曼属使用188个分离的基因组和2226个基因组组装从18,600宏基因组从人类和其他动物。虽然我们没有检测到A。根据嗜聚糖阿克曼氏菌的分类，人类肠道中的阿克曼氏菌菌株可以分为五个不同的候选物种，包括A.粘蛋白体，尽管惊人地相似的16 S rRNA基因序列，显示出显着的全基因组分歧。这些候选物种可能是人类特有的，因为它们几乎只在圈养的小鼠和非人类灵长类动物中被检测到。在人类中，阿克曼氏菌候选物种显示出生态共排斥，多样化的功能能力，以及与宿主体重的不同关联模式。CRISPR-Cas基因座的分析揭示了靶向新发现的推定噬菌体的新变体和间隔区。值得注意的是，我们观察到增加的阿克曼氏菌的相对丰度时，同源预测的噬菌体存在，这表明生态相互作用。A.嗜粘蛋白菌还表现出亚种水平的遗传分层，其具有相关的功能差异，例如推定的外切/脂多糖操纵子。我们发现了一个大的系统发育和功能的阿克曼属在人类的多样性。在正在进行的实验和宏基因组研究中，应该考虑这种变异性，以表征A.嗜粘蛋白菌和相关细菌。在线版本包含补充材料，可通过10.1186/s13059-021-02427-7获得。
Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria. The online version contains supplementary material available at 10.1186/s13059-021-02427-7.
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影响因子：
2.8
作者：
de Vos, Willem M.
通讯作者：
de Vos, Willem M.
影响因子：
9.2
作者：
De Filippis, Francesca;Pasolli, Edoardo;Ercolini, Danilo
通讯作者：
Ercolini, Danilo
影响因子：
82.9
作者：
Depommier, Clara;Everard, Amandine;Cani, Patrice D.
通讯作者：
Cani, Patrice D.
DOI：
10.1073/pnas.1219451110
发表时间：
2013-05-28
影响因子：
11.1
作者：
Everard, Amandine;Belzer, Clara;Cani, Patrice D.
通讯作者：
Cani, Patrice D.
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T