Gut Microbiome of Two Rodent Species (Niviventer confucianus and Apodemus agrarius) from Two Regions Exhibit Different Structures and Assembly Mechanisms
by
,
Haotian Li
1,2
,
Qian Gao
1,
Jiawen Han
1,
Qiuyue Song
1,
Fangheng Yan
1,
Yunzhao Xu
1,
Chuansheng Zhang
1,
Xin Wang
1 and
Yuchun Li
2,* 1
College of Agriculture and Biology, Liaocheng University, Liaocheng 252059, China
2
Marine College, Shandong University (Weihai), Weihai 264209, China
*
Author to whom correspondence should be addressed.
Animals 2025, 15(21), 3187; https://doi.org/10.3390/ani15213187
Submission received: 22 August 2025
/
Revised: 16 October 2025
/
Accepted: 30 October 2025
/
Published: 1 November 2025
(This article belongs to the Section Mammals)
Simple Summary
The influence of different regions on the structure and assembly mechanisms of the animal gut microbiome has long been of interest to scientists. This study investigated the gut microbiome of Niviventer confucianus and Apodemus agrarius collected from Anhui and Hubei provinces. We aimed to characterize the bacterial co-occurrence networks and elucidate the assembly mechanisms of the gut microbiota in conspecific hosts across different geographical regions. We found that the geographic region shaped the gut microbiome of conspecific rodents by altering the alpha diversity, co-occurrence networks, and assembly processes. However, further analysis is needed to determine which factor of the two geographical regions is the main factor affecting the gut microbiota of the two rodent species.
Abstract
The structure and assembly mechanism of wild animal gut microbiota represent persistent research hotspots. Among, the impact of geographic factors on the bacterial co-occurrence network characteristics and assembly mechanism of the gut microbiome remains unclear. Therefore, this study analyzed the gut microbiome of Niviventer confucianus and Apodemus agrarius from Anhui and Hubei provinces. The same alpha diversity pattern was found in the gut microbiome of species from the same region. The gut microbiome of the two rodent species in Anhui region exhibited “small world” characteristics, such as nodes with more local connections to allow interaction information (such as metabolites) to rapidly spread throughout the entire microbial community. In addition, dispersal limitations and heterogeneous selection accounted for higher proportions of the gut microbiome in the rodents from the Anhui and Hubei regions, respectively. The higher proportion of heterogeneous selection may exacerbate selection pressure in the Hubei region. Multiple regression on distance matrices analysis revealed that geographic region exerted a limited but significant influence (0 < R2 < 0.2, * p < 0.05) on the gut microbiome, surpassing the effects of host phylogeny, gender, and weight. Nevertheless, the roles of regional factors—such as environmental microbes, pollutants, and diet—remain unexamined, and their potential as key drivers of microbiota variation in these rodents warrants further investigation.
