How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies

Barbora Bendová,Jakub Kreisinger,Jaroslav Piálek,Dagmar Čížková,Ľudovít Ďureje,Jean-Francois Martin,Lucie Schmiedová

doi:10.1186/s12866-020-01859-8

Barbora Bendová, Jakub Kreisinger + Show 5 more

Open Access

https://doi.org/10.1186/s12866-020-01859-8

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Abstract

BackgroundThe vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus).ResultsUsing Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant.ConclusionsThough differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.

Highlights

The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype
At both the phylum and class level, Gut bacteriome (GB) content was comparable between Mus musculus (MM) and Mus spicilegus (MS); the dominant bacterial phyla and classes tended to vary between gut sections (Fig. 1, Table S1)
Massive changes in gut bacteriome composition, explaining ~ 20% of total GB variation, have been documented in several previous studies following introduction of MM from commensal populations to breeding facilities [34]. These changes had a dramatic effect on host physiology, immune function and fitness [43, 61], with important implications on the usage of captive MM colonised by breeding facility-specific gastrointestinal microbiota as models for biomedical research

Summary

Introduction

The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Little is known about the effect of a commensal lifestyle on the composition and function of microbial communities harboured within commensal bodies [11] and putative phenotype changes that may be induced by variation in microbial populations. Animal-associated microbiota exhibit considerable plasticity due to changing physiological states and environmental conditions, including diet variation, stress or parasite infection [16, 21,22,23]. There is a high expectation that remodulation of a host’s microbiota due to a commensal lifestyle may parallel widely observed changes in microbial populations after translocation of free-living individuals into captivity [24,25,26,27]

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