Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4599-606. doi: 10.1073/pnas.1000071108. Epub 2011 Feb 11.
The human gut microbiota harbors three main groups of H(2)-consuming microbes: methanogens including the dominant archaeon, Methanobrevibacter smithii, a polyphyletic group of acetogens, and sulfate-reducing bacteria. Defining their roles in the gut is important for understanding how hydrogen metabolism affects the efficiency of fermentation of dietary components. We quantified methanogens in fecal samples from 40 healthy adult female monozygotic (MZ) and 28 dizygotic (DZ) twin pairs, analyzed bacterial 16S rRNA datasets generated from their fecal samples to identify taxa that co-occur with methanogens, sequenced the genomes of 20 M. smithii strains isolated from families of MZ and DZ twins, and performed RNA-Seq of a subset of strains to identify their responses to varied formate concentrations. The concordance rate for methanogen carriage was significantly higher for MZ versus DZ twin pairs. Co-occurrence analysis revealed 22 bacterial species-level taxa positively correlated with methanogens: all but two were members of the Clostridiales, with several being, or related to, known hydrogen-producing and -consuming bacteria. The M. smithii pan-genome contains 987 genes conserved in all strains, and 1,860 variably represented genes. Strains from MZ and DZ twin pairs had a similar degree of shared genes and SNPs, and were significantly more similar than strains isolated from mothers or members of other families. The 101 adhesin-like proteins (ALPs) in the pan-genome (45 ± 6 per strain) exhibit strain-specific differences in expression and responsiveness to formate. We hypothesize that M. smithii strains use their different repertoires of ALPs to create diversity in their metabolic niches, by allowing them to establish syntrophic relationships with bacterial partners with differing metabolic capabilities and patterns of co-occurrence.
人类肠道微生物群含有三大类消耗 H(2) 的微生物：产甲烷菌，包括优势古菌 Methanobrevibacter smithii、多系的产乙酸菌和硫酸盐还原菌。了解它们在肠道中的作用对于理解氢气代谢如何影响膳食成分发酵的效率非常重要。我们定量分析了 40 对健康成年女性同卵（MZ）和 28 对异卵（DZ）双胞胎粪便样本中的产甲烷菌，分析了从其粪便样本中生成的细菌 16S rRNA 数据集，以确定与产甲烷菌共同存在的分类群，从 MZ 和 DZ 双胞胎家庭中分离出 20 株 M. smithii 株的基因组，并对亚组菌株进行 RNA-Seq 以鉴定其对不同甲酸盐浓度的反应。MZ 双胞胎对产甲烷菌携带的一致性率明显高于 DZ 双胞胎。共现分析显示，22 种细菌种水平分类群与产甲烷菌呈正相关：除两种外均为梭菌目成员，其中几种是或与已知的产氢和耗氢细菌有关。M. smithii 泛基因组包含 987 个在所有菌株中保守的基因和 1860 个可变代表的基因。来自 MZ 和 DZ 双胞胎的菌株具有相似程度的共享基因和 SNP，并且比来自母亲或其他家庭成员的菌株更相似。泛基因组中的 101 个粘附素样蛋白（ALP）（每个菌株 45±6 个）在表达和对甲酸盐的反应性方面表现出菌株特异性差异。我们假设 M. smithii 菌株利用其不同的 ALP 库在其代谢小生境中创造多样性，使它们能够与具有不同代谢能力和共现模式的细菌伙伴建立共生关系。
