Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents

Abstract

Host–microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.

Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents

“…Finally, high‐throughput sequencing was done on a MiSeq (Illumina, San Diego) 300 bp paired‐end platform using a Reagent kit v3 after library preparation using Nextera XT Index Kit v2 set A, B, C, or D following the manufacturer's instructions. A more detailed description of the DNA processing methods can be found in Anders et al ( 2021 ), and raw sequences have been submitted to the DNA database of Japan (DDBJ) with the accession numbers DRA011343 and DRA011772.…”

“…Based on alpha rarefaction analysis, samples were rarified to a sampling depth of 10,000 reads to calculate diversity metrics to maximize coverage of the variation in the microbiome while limiting sample omission, similar to Anders et al ( 2021 ). A total of six samples (three small intestine and one feces from M. rufocanus and two small intestine from A. speciosus ) with low sequence counts were excluded from diversity analyses.…”

Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations

“…Although we detect similar phyla and families than these previous studies, our in-depth data allow us to detect other taxa as well as differences in their relative abundance. These differences likely depend on the nature of the samples considered (faecal, colon or caecum samples), given there is strong variation of the gut bacteriome both along the rodent digestive tract (e.g., in mice Anders et al ., 2021; Gu et al ., 2013) and between digestive tract and faeces (Anders et al ., 2021) of a single host individual.…”

The role of the gut microbiota in toxicity and risk assessment of masked Fusarium mycotoxins

“…When using fecal samples to characterize intestinal microbial metabolism, it is of importance to note that there are differences in bacterial numbers and composition along the intestinal tract, which might lead to region specific differences. Unique microbial communities reside within each gut region, with those in the upper and lower digestive tract being distinctly different from each other as has been demonstrated in several groups of animals such as rodents, pigs, chickens, and lizards (Kohl et al, 2017(Kohl et al, , 2018Anders et al, 2021;Suzui et al, 2016;Gu et al, 2013;Kelly et al, 2017). However, overlap exists in the physiology and functionality of the different regions of the low gastrointestinal tract, and similar gut microbiota in different regions are likely to respond in a similar way to xenobiotic changes (Anders et al, 2021).…”

“…The GI tract is a complex ecosystem occupied by a diverse community of microbiome that impact many aspects of the host biology such as behavior, digestion, and immune system function through interactions with the host (Hooper et al, 2002;Amato et al, 2013). Each animal species or human may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits (Anders et al, 2021). Thus, for different host species, the microbiome and enzymes involved in metabolization by the gut microbiota may be different.…”