Gut Microbiota Dynamics in Murine Models

The mammalian gut harbours a complex consortium of microbial taxa whose composition and activity fluctuate in response to host genetics, diet, environment and age. Murine models have become indispensable for dissecting the mechanisms of host–microbe interactions, revealing how specific bacterial populations influence nutrient metabolism, immune maturation and disease susceptibility. Advances in high-throughput sequencing and multi-omics profiling have enabled longitudinal characterisation of colonisation dynamics, community resilience and ecological succession during perturbations such as antibiotic treatment or dietary shifts. Germ-free and gnotobiotic mice facilitate causal testing of individual strains or defined microbial assemblies, while transgenic and humanised models permit exploration of genetic and immunological determinants of colonisation. Together, these approaches continue to illuminate the principles governing microbial stability, dysbiosis and restoration, and underpin the development of therapeutic strategies targeting the gut ecosystem.

Research from Nature Portfolio

Innovative work has demonstrated that sterile-filtered virome preparations, enriched for bacteriophages and depleted of eukaryotic viruses, can modulate microbial consortia to improve glycaemic control in diet-induced obese mice, highlighting a novel route to reshape the microbiota without whole-community transfer. Separately, systematic investigation of common husbandry variables—caging design, bedding material and chow formulation—has revealed that these factors interact to drive region-specific shifts in bacterial communities, particularly in the cecum, underscoring the need for standardised environmental conditions to enhance reproducibility of microbiota studies.

Research from all publishers

A standardised complex microbiome derived from high-richness or low-richness donor communities has been shown to impart lasting effects on fetal growth trajectories, post-weaning food intake and adult body weight in outbred mice, emphasising the maternal microbiome’s role in early developmental programming. A critical appraisal of murine models for human intestinal microbiota research has synthesised comparative physiological and phylogenetic data, delineating the key similarities and differences between human and mouse gut ecosystems and offering guidelines to refine model selection and improve translational validity.

Gut Microbiota Dynamics in Murine Models publication trend

The graph below shows the total number of articles in gut microbiota dynamics in murine models across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiota: The community of bacteria, archaea, viruses and fungi inhabiting the gastrointestinal tract.

Gnotobiotic mice: Animals reared under germ-free conditions before deliberate colonisation with defined microbial consortia.

Dysbiosis: A perturbation or imbalance in microbial community structure associated with host dysfunction.

Metagenomics: Culture-independent sequencing of genetic material from entire microbial communities.

Bacteriophage: A virus that infects and replicates within bacteria, influencing bacterial population dynamics.

References

1. Transfer of modified gut viromes improves symptoms associated with metabolic syndrome in obese male mice. Nature Communications (2024).
2. The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut. Scientific Reports (2018).
3. Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice. Microorganisms (2023).
4. Mouse models for human intestinal microbiota research: a critical evaluation. Cellular and Molecular Life Sciences (2017).