Molteni Cristian, Forni Diego, Cagliani Rachele, Sironi Manuela
Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy.
School of Medicine and Surgery, University of Milano-Bicocca, Monza, 20900, Italy.
Biol Direct. 2025 Jul 24;20(1):90. doi: 10.1186/s13062-025-00680-5.
The mucin-degrading bacterium Akkermansia muciniphila has attracted enormous interest for its beneficial effects on human health. However, growing evidence suggests that the Akkermansia genus is populated by several species that differ in phenotypic characteristics and association with human traits.
We present the most comprehensive phylotaxonomic analysis of Akkermansia genomes in terms of sample size and host representation. By applying approaches based on average nucleotide identities and on the biological species concept, we show that the Akkermansia genus comprises at least 31 species, 13 of which can be detected in humans. The largest species diversity is contributed by non-human and non-mouse animals, and limited evidence of species-specificity is evident, with several Akkermansia species detected in phylogenetically distant animals. Analysis of accessory gene content among species also failed to reveal species-specific or diet-specific associations, but rather reflected genome size. Thus, A. muciniphila and A. ignis have, on average, small genomes and retain a part of genes that characterize either A. massiliensis or A. sp004167605/A. biwaensis. Finally, investigation of the population structure of A. muciniphila, the species that has been more intensely investigated due to its effects on human health, clearly distinguished two phylogroups corresponding to AmIa and AmIb. However, analysis of laboratory mouse-derived genomes revealed that additional populations, specific to these animals, exist. Such populations show limited evidence of admixture, suggesting bottleneck or competition effects.
Our data support the concept that the genetic diversity of Akkermansia should be taken into account in experimental settings. They also call for sequencing efforts to characterize the wider genetic diversity of Akkermansia bacteria.
黏液降解菌嗜黏蛋白阿克曼氏菌因其对人类健康的有益作用而备受关注。然而，越来越多的证据表明，阿克曼氏菌属包含几个表型特征和与人类特征关联不同的物种。
就样本量和宿主代表性而言，我们展示了对阿克曼氏菌基因组最全面的系统分类分析。通过应用基于平均核苷酸同一性和生物物种概念的方法，我们表明阿克曼氏菌属至少包含31个物种，其中13个可在人类中检测到。最大的物种多样性来自非人类和非小鼠动物，并且物种特异性的证据有限，在系统发育上遥远的动物中检测到了几种阿克曼氏菌物种。对物种间辅助基因含量的分析也未能揭示物种特异性或饮食特异性关联，而是反映了基因组大小。因此，嗜黏蛋白阿克曼氏菌和火阿克曼氏菌平均具有较小的基因组，并保留了一部分表征马西阿克曼氏菌或sp004167605/A. biwaensis的基因。最后，对嗜黏蛋白阿克曼氏菌种群结构的研究（由于其对人类健康的影响而受到更深入的研究）清楚地区分了对应于AmIa和AmIb的两个系统发育群。然而，对实验室小鼠来源基因组的分析表明，存在这些动物特有的其他种群。这些种群的混合证据有限，表明存在瓶颈或竞争效应。
我们的数据支持在实验环境中应考虑阿克曼氏菌遗传多样性的概念。它们还呼吁进行测序工作，以表征阿克曼氏菌细菌更广泛的遗传多样性。
