Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.

中文翻译：

---

肠道微生物组组成和功能的生物地理分布通过粪便移植到无菌小鼠中部分概括


粪便微生物群移植对于确定是否可以通过微生物组赋予宿主表型至关重要。然而，是否可以在粪便定植的无菌小鼠中概括沿小鼠胃肠道的现有微生物生态学仍然未知。我们首先在跨越两个设施的三组特定无病原体小鼠中确定了六个肠道区域特异性的微生物及其预测功能。在这些区域特异性微生物中，与结肠相比，与健康相关的 Akkermansia 属在小肠腔中持续富集。鸟枪法测序数据中概括的 16S rRNA 基因扩增子测序数据的预测功能模型显示，小肠中微生物中枢代谢、脂解发酵和交叉喂养增加，而丁酸盐合成是结肠富集的。神经活性化合物代谢也表现出区域特异性，包括小肠富集的 γ-氨基丁酸降解和结肠富集色氨酸降解。具体来说，空肠和回肠作为具有高预测代谢和神经调控活性的部位脱颖而出。胃肠道每个部位的管腔和粘膜微生物组之间的差异在很大程度上是设施特异性的，尽管在特定的无病原体小鼠中，微生物代谢有一些一致的模式。这些包括小肠和结肠内中枢代谢的管腔富集和交叉喂养，以及结肠内丁酸盐合成的粘膜富集。在用小鼠或人类粪便定植的三组无菌小鼠中，组成和功能区域特异性的再现不一致。 这些结果强调了研究肠道微生物组的空间变化以更好地了解其对宿主生理学影响的重要性。