Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

Abstract

BackgroundA number of human diseases such as obesity and diabetes are associated with changes or imbalances in the gut microbiota (GM). Laboratory mice are commonly used as experimental models for such disorders. The introduction and dynamic development of next generation sequencing techniques have enabled detailed mapping of the GM of both humans and animal models. Nevertheless there is still a significant knowledge gap regarding the human and mouse common GM core and thus the applicability of the latter as an animal model. The aim of the present study was to identify inter- and intra-individual differences and similarities between the GM composition of particular mouse strains and humans.Methodology/Principal FindingsA total of 1509428 high quality tag-encoded partial 16S rRNA gene sequences determined using 454/FLX Titanium (Roche) pyro-sequencing reflecting the GM composition of 32 human samples from 16 individuals and 88 mouse samples from three laboratory mouse strains commonly used in diabetes research were analyzed using Principal Coordinate Analysis (PCoA), nonparametric multivariate analysis of similarity (ANOSIM) and alpha diversity measures. A reliable cutoff threshold for low abundant taxa estimated on the basis of the present study is recommended for similar trials.Conclusions/SignificanceDistinctive quantitative differences in the relative abundance of most taxonomic groups between the examined categories were found. All investigated mouse strains clustered separately, but with a range of shared features when compared to the human GM. However, both mouse fecal, caecal and human fecal samples shared to a large extent not only representatives of the same phyla, but also a substantial fraction of common genera, where the number of shared genera increased with sequencing depth. In conclusion, the GM of mice and humans is quantitatively different (in terms of abundance of specific phyla and species) but share a large qualitatively similar core.

Antibiotic Selection of Escherichia coli Sequence Type 131 in a Mouse Intestinal Colonization Model

“…Finally, we studied only the fecal-and not the mucosal-microflora of mice. Yet, it has been postulated that, first, the mouse fecal flora is a mixture of mucosal and luminal flora and, second, the intestinal microflora of laboratory mice is comparable to the intestinal flora in humans (30,31). We have no obvious explanation for the selective ability of dicloxacillin, since this drug had no impact on the Gram-negative anaerobic or the aerobic Gram-positive flora.…”

Gut microbial markers are associated with diabetes onset, regulatory imbalance, and IFN-γ level in NOD Mice

“…36 High quality sequences purged from chimeric reads were clustered at 97% relatedness using UCLAST. 37 The representative sequences from each cluster were aligned with pyNAST 38 and subjected to the Greengenes reference database (version 12.10).…”

Mode of Delivery Shapes Gut Colonization Pattern and Modulates Regulatory Immunity in Mice

“…Pyrosequencing data were analyzed as described by Krych et al (32) using an open source software package, Quantitative Insight Into Microbial Ecology (QIIME version 1.7.0; National Center for Biotechnology Information database accession No. SRP032495).…”

“…Also, differences in the gut microbiota between inbred mouse strains show that it is to a great extent defined by genotype (31)(32)(33). Even though the gut microbiota is influenced by its surroundings during early life, once it is established, it remains relatively stable (34).…”