The research team, working in the Susa Valley in Piedmont at elevations of 800 to 900 meters, collected 88 adult dung beetles from cow dung in May, spanning nine species, four tribes, and all three major nesting strategies known from mid-altitude Alpine pastures. The species included dwellers such as Aphodius pedellus and Colobopterus erraticus, which lay their eggs within the dung mass; tunnellers such as Anoplotrupes stercorosus, Geotrupes mutator, Trypocopris pyrenaeus, and three Onthophagus species, which bury brood balls in tunnels beneath the dung; and a single roller, Sisyphus schaefferi, which shapes dung into a ball and rolls it away for burial. By sourcing every individual from the same dung, deposited by a herd of Piedmontese cattle, the researchers minimised dietary variation, ensuring that any differences in gut microbiota could be attributed to the host rather than the meal.

To characterise the microbial communities, the team employed an amplicon sequence variant (ASV)-based metabarcoding approach, a technique that offers higher taxonomic resolution and reproducibility than traditional operational taxonomic units. For prokaryotes, the 16S ribosomal RNA gene was amplified using the primer set 515fB and 806rB, while for fungi, the internal transcribed spacer 2 (ITS2) region was targeted through a semi-nested PCR protocol. Sequencing was performed on an Illumina NovaSeq platform, generating paired-end reads of 250 base pairs. Bioinformatic processing in QIIME2, with denoising and chimera removal handled by the DADA2 plugin, yielded 12,501 prokaryotic ASVs and 3,301 fungal ASVs. Taxonomic assignment drew on the Greengenes2 database for prokaryotes and the UNITE database for fungi. Environmental ASVs shared between beetles and dung or soil samples were removed before diversity analyses to isolate the gut-associated fraction of the microbiota.

The results revealed a fundamental asymmetry between the prokaryotic and fungal components of the gut microbiota. Prokaryotic communities exhibited strong host-dependent structuring: distance-based redundancy analysis (dbRDA) of Bray-Curtis dissimilarities showed that the nine beetle species separated into four non-overlapping clusters corresponding precisely to their four tribes. Species identity explained 88.1 percent of the variation in prokaryotic community composition, followed by tribe at 79.7 percent and nesting strategy at 44.7 percent, all highly significant. Sex, by contrast, accounted for a negligible and non-significant 2.74 percent. This pattern is consistent with phylosymbiosis, the phenomenon whereby host phylogeny structures associated microbial communities through evolutionary filtering and partially conserved symbiotic associations.

Fungal communities told a very different story. The dbRDA ordination showed extensive overlap among seven of the nine species, with only Aphodius pedellus and Anoplotrupes stercorosus forming distinct clusters. Species explained 80.6 percent of the variation, but tribe accounted for just 26.4 percent and nesting strategy 23.2 percent, suggesting that fungal assemblages are weakly constrained by host evolutionary history. The researchers attribute this to greater environmental acquisition: dung beetles continuously ingest microbially rich dung and soil, and fungal propagules from these substrates likely colonise the gut more transiently than bacteria, which appear to form more stable mutualistic associations.

The analysis of exclusive and core ASVs reinforced this asymmetry. Exclusive prokaryotic ASVs, unique to individual beetle species, numbered 10,677 of the 12,501 detected, representing 85.4 percent of all ASVs but only 21.3 percent of total reads. Exclusive fungal ASVs comprised 83.6 percent of detected taxa but only 34.1 percent of reads. Most species-exclusive ASVs were detected in a single individual, casting doubt on their biological exclusivity and highlighting the importance of sampling at least eight to ten individuals per species. In contrast, the core microbiota shared across all nine species was numerically scarce, with only 47 prokaryotic and nine fungal ASVs, yet these accounted for a disproportionate 19.5 percent of prokaryotic and 5.7 percent of fungal read abundance. The most abundant prokaryotic core genera included Vagococcus_B, Apibacter, and Acinetobacter, while over half of the fungal core ASVs belonged to the genus Candida.

At the genus level, the prokaryotic communities were dominated by Proteobacteria, Firmicutes_D, and Bacteroidota, which together accounted for roughly 80 percent of ASVs. The three most abundant genera across all samples were Wolbachia, Apibacter, and Vagococcus_B, but their relative contributions varied markedly among host species. Apibacter dominated the microbiota of two Onthophagus species at approximately 30 percent, Wolbachia reached 24 percent in Onthophagus verticicornis, Enterococcus_G contributed a quarter of the community in Trypocopris pyrenaeus, and Vagococcus_B peaked at 16 percent in both Geotrupes mutator and Trypocopris pyrenaeus. When species were grouped by tribe, clear tribal signatures emerged: Aphodiini showed the highest abundance of Acinetobacter, Onthophagini the highest Apibacter, and Geotrupini the highest Enterococcus_G and Vagococcus_B. Among fungi, Ascomycota and Basidiomycota accounted for 95 percent of ASVs, with Apiotrichum, Epicoccum, and an unclassified Agaricomycetes genus most abundant overall. Apiotrichum represented 38 percent of the fungal community in Geotrupes mutator, Trichosporon reached 32 percent in Sisyphus schaefferi, and Candida was found almost exclusively in Anoplotrupes stercorosus at 35 percent.

Despite this pronounced taxonomic turnover, the predicted functional profiles remained remarkably consistent across hosts. Among prokaryotes, fermentation was the predominant metabolic process, averaging 28 percent of the functional profile, while nitrogen-related pathways, including nitrate reduction, nitrate respiration, nitrite denitrification, nitrogen fixation, and ureolysis, contributed nearly one quarter and were relatively constant among species. Fungal communities were largely saprotrophic, accounting for approximately 46 percent of the trophic distribution, followed by pathotrophy at 35 percent and symbiotrophy at 19 percent. Wood saprotrophs dominated the saprotrophic guild at 15 percent, with soil, litter, and dung-associated saprotrophs present at lower abundances. These proportions were largely consistent across species, with only minor deviations in a few hosts.

This decoupling between taxonomic composition and functional potential is the study’s central finding and points to substantial functional redundancy in the dung beetle gut microbiota. The concept, well established in microbial ecology, holds that different microbial consortia assembled from different taxonomic pools can nonetheless maintain similar functional outcomes. The researchers suggest this redundancy may reflect two evolutionary pressures: the need to preserve host health and the need to sustain efficient dung degradation and nutrient cycling. Even if the composition of the gut microbiota changes dramatically, as might occur when pastoral practices shift or dung beetle communities restructure in response to land abandonment and climate change, the microbial functions underpinning dung transformation are likely to remain stable.

The implications extend beyond basic microbiome science. Pastoral ecosystems in the European Alps are undergoing rapid transformation, with grasslands giving way to woody encroachment and forest expansion driven by land abandonment and warming temperatures. The widespread reduction in extensive livestock systems further threatens dung-dependent communities. Understanding that dung beetle gut microbiota are resilient systems, capable of maintaining key metabolic roles under changing taxonomic compositions, offers a measure of reassurance about the continuity of the ecosystem services these insects provide. The authors caution, however, that the functional profiles were predicted rather than measured experimentally, and that future work integrating metagenomics or metatranscriptomics, together with experimental manipulation of diet and microbiota, will be essential to clarify the functional significance of specific microbial taxa and disentangle the relative contributions of host filtering and environmental acquisition in shaping these remarkable gut ecosystems.

Subject of Research: Gut microbiota of dung beetles shows taxonomic turnover but relative functional stability

Article Title: Gut microbiota of dung beetles shows taxonomic turnover but relative functional stability

Article References: Natta, G., Voyron, S., Lumini, E., Laini, A., Roggero, A., Palestrini, C., & Rolando, A. (2026). Gut microbiota of dung beetles shows taxonomic turnover but relative functional stability. Metabarcoding and Metagenomics, 10, Article e194720. https://doi.org/10.3897/mbmg.10.194720

Image Credits: AI Generated

DOI: 10.3897/mbmg.10.194720

Keywords: microbiota, dung, beetles, shows, taxonomic, turnover, relative, functional, stability, scientific research