This study takes two wild mammals living in the same environment, but with different evolutionary relationships and different dietary habits (Apodemus, Erinaceidae and Soricidae) as the research objects, using the 16S rRNA gene amplicon sequencing technology to analyze and compare the gut microbiota of these mammals. 5378 operational taxonomic units (OTU) are identified, mainly affiliated with Firmicutes (40.55%), Proteobacteria (34.60%), and Bacteroidetes (13.67%). Firmicutes and Bacteroidetes are the dominant phyla of the Apodemus. Proteobacteria is the dominant phylum of Erinaceidae and Soricidae. The results of diversity analyses show that the gut microbiota diversity and community composition are significantly different among Apodemus, Erinaceidae and Soricidae. LEfSe analysis shows that there are more bacteria related to complex carbohydrate fermentation in the Apodemus, while the Erinaceidae and Soricidae contains higher amino acid fermentation bacteria. Probiotics, such as Lactobacillus and Lactococcus, coexist in these three wild small mammals to regulate host health. This study reveals that phylogeny and feeding habits of the host have a profound effect on the shaping gut microbes. The gut microbiota may also play a probiotic effect on the host in many aspects.

以生活在同一生境, 但具有不同进化关系和不同食性的野生哺乳类动物(鼠科、猬科和鼩鼱科)为研究对象, 通过16S rRNA基因扩增子测序, 分析和比较其肠道菌群。共识别出5378个操作分类单位(OTUs), 主要隶属Firmicutes (40.55%), Proteobacteria (34.60%)和Bacteroidetes (13.67%)。Firmicutes和Bacteroidetes是鼠科的优势菌门, Proteobacteria是猬科和鼩鼱科的优势菌门。多样性分析表明, 鼠科、猬科与鼩鼱科的肠道微生物多样性及群落结构具有显著性差异; LEfSe分析表明, 鼠科中存在更多与复杂碳水化合物发酵相关的细菌, 猬科和鼩鼱科中含较多氨基酸发酵菌; 益生菌(如Lactobacillus和Lactococcus等)共存于这3类野生小型哺乳类动物中, 起调控宿主健康的作用。研究结果揭示, 宿主食性与进化关系影响着野生小型哺乳动物肠道菌群结构, 而肠道菌群可能在多种方面对宿主起益生作用。