Dataset Information

Marked seasonal variation in the wild mouse gut microbiota.

ABSTRACT: Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16?S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.

SUBMITTER: Maurice CF

PROVIDER: S-EPMC4611506 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Marked seasonal variation in the wild mouse gut microbiota.

Maurice Corinne F CF Knowles Sarah C L SC Ladau Joshua J Pollard Katherine S KS Fenton Andy A Pedersen Amy B AB Turnbaugh Peter J PJ

The ISME journal 20150529 11

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroid ...[more]

PMID: 26023870

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Project description:Musk deer (Moschus spp.) is a globally endangered species due to excessive hunting and habitat fragmentation. Captive breeding of musk deer can efficiently relieve the hunting pressure and contribute to the conservation of the wild population and musk supply. However, its effect on the gut microbiota of musk deer is unclear. Recent studies have indicated that gut microbiota is associated with host health and its environmental adaption, influenced by many factors. Herein, high-throughput sequencing of the 16S rRNA gene was used based on 262 fecal samples from forest musk deer (M. berezovskii) (FMD) and 90 samples from alpine musk deer (M. chrysogaster) (AMD). We sought to determine whether seasonal variation can affect the structure and function of gut microbiota in musk deer. The results demonstrated that FMD and AMD had higher α-diversity of gut microbiota in the cold season than in the warm season, suggesting that season change can affect gut microbiota diversity in musk deer. Principal coordinate analysis (PCoA) also revealed significant seasonal differences in the structure and function of gut microbiota in AMD and FMD. Particularly, phyla Firmicutes and Bacteroidetes significantly dominated the 352 fecal samples from captive FMD and AMD. The relative abundance of Firmicutes and the ratio of Firmicutes to Bacteroidetes were significantly decreased in summer than in spring and substantially increased in winter than in summer. In contrast, the relative abundance of Bacteroidetes showed opposite results. Furthermore, dominant bacterial genera and main metabolic functions of gut microbiota in musk deer showed significant seasonal differences. Overall, the abundance of main gut microbiota metabolic functions in FMD was significantly higher in the cold season. WGCNA analysis indicated that OTU6606, OTU5027, OTU7522, and OTU3787 were at the core of the network and significantly related with the seasonal variation. These results indicated that the structure and function in the gut microbiota of captive musk deer vary with seasons, which is beneficial to the environmental adaptation and the digestion and metabolism of food. This study provides valuable insights into the healthy captive breeding of musk deer and future reintroduction programs to recover wild populations.

Project description:The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent "core" gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.

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Dataset Information

Marked seasonal variation in the wild mouse gut microbiota.

Publications

Marked seasonal variation in the wild mouse gut microbiota.

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