Microbial Ecology of Reptilian Gut Microbiomes

The gut microbiomes of reptiles are increasingly recognised as dynamic ecosystems that underpin host nutrition, immunity and environmental adaptation. Dominated by bacterial phyla such as Firmicutes, Bacteroidetes and Proteobacteria, these communities vary with diet, developmental stage, thermal regime and habitat. Ectothermic physiology imposes wide fluctuations in gut temperature, shaping microbial composition and metabolic function, while seasonal cycles of feeding and fasting can prompt shifts in taxa that degrade host-derived mucins or ferment polysaccharides. Comparative studies reveal that wild and captive populations often differ in diversity and stability, with potential consequences for disease susceptibility and reintroduction success. Investigations across diverse reptiles—from desert‐dwelling geckos to herbivorous turtles—highlight core microbial taxa that persist across individuals alongside site-specific or host-specific lineages. This integrative perspective underscores the global relevance of reptilian gut ecology for conservation, captive management and understanding host–microbe co-evolution in changing environments.

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Microbial Ecology of Reptilian Gut Microbiomes publication trend

The graph below shows the total number of articles in microbial ecology of reptilian gut microbiomes across all publications each year (not limited to Nature Index journals).

Technical terms

16S rRNA gene amplicon sequencing: high-throughput method to profile bacterial community composition by targeting a conserved ribosomal gene region.

Alpha diversity: measure of species richness and evenness within a single microbial community.

Beta diversity: comparison of microbial community composition between samples or environments.

Operational taxonomic unit (OTU): proxy for microbial species defined by sequence similarity thresholds in amplicon studies.

Parabasalid protist: flagellated single-celled eukaryotes that reside in animal guts and influence host immunity and nutrition.

Core microbiome: set of microbial taxa consistently present across individuals of a host species.

References

1. Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts. mBio (2023).
2. Comparison of the intestinal flora of wild and artificial breeding green turtles (Chelonia mydas). Frontiers in Microbiology (2024).
3. Insights into the Gut Microbiome of the South American Leaf-Toed Gecko (Phylodactylus gerropygus) Inhabiting the Core of the Atacama Desert. Microorganisms (2024).
4. Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator. Frontiers in Microbiology (2019).