Data from: Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

Correlation between gut microbiota and host phylogeny could reflect codiversification over shared evolutionary history or a selective environment that is more similar in related hosts. These alternatives imply substantial differences in the relationship between host and symbiont, but can they be distinguished based on patterns in the community data themselves? We explored patterns of phylogenetic correlation in the distribution of gut bacteria among species of turtle ants (genus Cephalotes), which host a dense gut microbial community. We used 16S rRNA pyrosequencing from 25 Cephalotes species to show that their gut community is remarkably stable, from the colony to the genus level. Despite this overall similarity, the existing differences among species' microbiota significantly correlated with host phylogeny. We introduced a novel analytical technique to test whether these phylogenetic correlations are derived from recent bacterial evolution, as would be expected in the case of codiversification, or from broader shifts more likely to reflect environmental filters imposed by factors such as diet or habitat. We also tested this technique on a published data set of ape microbiota, confirming earlier results while revealing previously undescribed patterns of phylogenetic correlation. Our results indicated a high degree of partner fidelity in the Cephalotes microbiota, suggesting that vertical transmission of the entire community could play an important role in the evolution and maintenance of the association. As additional comparative microbiota data become available, the techniques presented here can be used to explore trends in the evolution of host-associated microbial communities.肠道微生物组（gut microbiota）与宿主系统发育（host phylogeny）之间的相关性，既可能反映二者在共同演化历史中产生的共多样化（codiversification），也可能源于近缘宿主所共享的更为相似的选择环境。这两种潜在情形意味着宿主与共生体（symbiont）之间的关系存在本质差异，但能否仅凭群落数据自身的分布模式对二者加以区分？本研究以拥有致密肠道微生物群落的龟蚁属（Cephalotes）物种为研究对象，探讨了其肠道细菌分布与宿主系统发育的相关性模式。我们通过对25种龟蚁开展16S rRNA焦磷酸测序（16S rRNA pyrosequencing），发现其肠道微生物群落在蚁群乃至属级水平上均表现出显著的稳定性。尽管整体群落结构相似，但不同龟蚁物种间的微生物组差异仍与宿主系统发育呈现显著相关性。为此，我们开发了一种新型分析技术，用于检验这类系统发育相关性究竟源于细菌近期的演化（若为共多样化情形则符合此预期），还是来自更广泛的群落转变——后者更可能反映饮食、栖息地等因素施加的环境过滤作用。我们还将该技术应用于已发表的类人猿微生物组数据集，在验证既往研究结论的同时，揭示了此前未被报道的系统发育相关性模式。本研究结果表明，龟蚁肠道微生物组与宿主间存在高度的伙伴保真度，这意味着整个微生物群落的垂直传播可能在该共生关联的演化与维持中发挥重要作用。随着更多比较微生物组数据的公开，本研究提出的分析技术可用于探索宿主相关微生物群落的演化趋势。