Archaea of the order Methanomassiliicoccales use methylated amines such as trimethylamine as the substrates for methanogenesis. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and “Candidatus Methanomethylophilus,” which has none. Questions remain regarding their distribution across biomes and human populations, their association with other taxa in the gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales clade, particularly its human-associated members, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n = 4,472, representing 22 populations), nonhuman animal gut (n = 145), and nonhost environments (n = 160). Our analyses showed that all taxa are generalists; they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut and the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales spp. correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group and may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease.

中文翻译：

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三甲胺利用产甲烷菌适应包括人类肠道在内的不同栖息地的基因组学见解

古细菌的顺序Methanomassiliicoccales使用甲基化的胺，如三甲胺作为产甲烷的底物。它们形成两个大的系统发育进化枝，并存在于从土壤到人类肠道的不同环境中。人类肠道中有两个属，每个进化枝一个属：Methanomassiliicoccus，有一个培养的代表，而“ Candidatus Methanomethylophilus”，没有。关于它们在生物群落和人群中的分布、它们与肠道中其他分类群的关联以及宿主遗传学是否与它们的丰度相关等问题仍然存在。深入了解甲烷球菌进化枝，特别是与人类相关的成员，我们对 72 个甲烷球菌基因组进行了基因组比较，并评估了它们在源自人类肠道（n = 4,472，代表 22 个种群）、非人类动物肠道（n = 145）和非宿主的宏基因组中的存在环境 ( n= 160）。我们的分析表明，所有分类群都是通才；它们在动物肠道和环境样本中被检测到。我们确认了两个大型进化枝，一个富含肠道，另一个富含环境，但有明显的例外。对肠道的基因组适应包括基因组减少和涉及莽草酸途径和胆汁抗性的基因。基因组适应因进化枝而异，而不是栖息地偏好，表明进化枝之间的趋同进化。在人类肠道中，甲烷球菌属的相对丰度。与产三甲胺细菌相关，与宿主基因型无关。我们的结果阐明了该组的微生物生态学，并可能有助于指导甲烷球菌属-基于三甲胺缓解心血管疾病的策略。