From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

从昆虫到哺乳动物，种​​类繁多的动物在它们的肠道中拥有复杂的细菌群落，这些细菌群落在健康和疾病中起着重要作用。为了进一步了解肠道细菌群落如何组装和发挥作用，我们采用自下而上的方法研究秀丽隐杆线虫微生物群，方法是用细菌单一培养物以及两到八种细菌的混合物喂养这种线虫。我们发现，由于种间细菌相互作用，在单一培养中定植良好的细菌在共培养中并不总是表现良好。此外，随着群落多样性的增加，在单一培养中定植蠕虫肠道的能力变得不如种间相互作用在决定群落组装方面重要。为了探索宿主-微生物适应的作用，我们比较了从C. elegans肠道和非本地分离物，我们发现定殖的成功更多地取决于物种的分类而不是分离源。最后，通过比较两个秀丽隐杆线虫突变体中组装的微生物群，我们发现通过 p38 MAPK 途径的先天免疫降低了细菌丰度，但对微生物群组成几乎没有影响。这些结果强调，细菌种间相互作用，比宿主-微生物适应或肠道环境过滤，在秀丽隐杆线虫微生物群的组装中起主导作用。