Gut Microbes of Japanese Insectivorous Bats Shift with Species, Site and Season

The gut microbiota of three insectivorous bat species in Japan has been mapped in detail by researchers working in Yamaguchi Prefecture, revealing that host species, geographical location and season each leave a measurable imprint on the bacterial communities living in these animals’ intestines. The study, published in the journal Animal Microbiome, used high-throughput 16S rRNA gene sequencing of the V3–V4 region to characterise the gut microbial communities of Miniopterus fuliginosus, Myotis macrodactylus and Rhinolophus ferrumequinum, and paired this community profiling with an exploratory nested PCR screen for bacterial pathogens in selected samples.

The sequencing results showed gut communities dominated by two bacterial phyla: Pseudomonadota, which accounted for 63.6 percent of relative abundance, and Bacillota, which made up 22.3 percent. Ten genera belonging to the proposed global core gut microbiota together represented 74.5 percent of total relative abundance, indicating that a relatively small number of bacterial lineages underpin the gut ecosystem of these insectivorous bats.

To disentangle the factors shaping these communities, the researchers applied a multivariable marginal PERMANOVA model to Bray-Curtis distances, simultaneously considering host species, location, season, sex and body weight. Bacterial community composition was significantly associated with host species, which explained 10 percent of the variation (R² = 0.10, p = 0.005), with geographical location (R² = 0.06, p = 0.005) and with season (R² = 0.05, p = 0.015). The authors note, however, that these factors were partly confounded in the sampling design, so the individual contributions should be interpreted with caution.

Alpha diversity, measured with the Shannon index, differed significantly across seasons (p = 0.023), but not among host species or sampling locations.

When the team used PICRUSt2 to infer functional profiles from the 16S data, no significant differences emerged among host species (p = 0.114) or locations (p = 0.412). The researchers are careful to frame these functional predictions and their co-occurrence network analysis as hypothesis-generating rather than direct evidence of microbial function or ecological interaction. The network analysis did, however, suggest species- and location-specific patterns in the connectivity of core taxa, hinting that the same core bacteria may interact differently depending on the host and its environment.

The exploratory pathogen screening added a public health dimension to the work. The authors emphasise that these are screening-level findings, and that further studies are needed to characterise the identified taxa and assess their potential One Health relevance.

Bat gut microbiota is increasingly studied for its ecological and public health significance, yet the factors shaping gut microbial communities in insectivorous bats in Japan, including host species, environmental location and seasonal and ecological variation, had remained poorly understood.

The authors conclude that their work identifies host-, location- and season-associated differences in gut community composition while highlighting the value of integrating gut microbiome profiling with exploratory bacterial surveillance in wildlife. Because the PICRUSt2 predictions and co-occurrence networks are indirect, and because species, site and season were partly confounded, the study’s inferences are deliberately conservative.

Subject of Research: Gut microbiota community structure of insectivorous bats in Japan and exploratory screening for bacterial pathogen targets

Article Title: Gut microbiota of insectivorous bats in Japan: host-, location- and season-associated community structure and exploratory screening for bacterial pathogen targets

Article References: Makau, R. M., Chepkirui, B. E., Perera, I. U., Shimizu, T., Hashino, M., Shimoda, H., Nishizato, M., Takano, A., Yanagida, T., Maruyama, F., Hou, J., Watanabe, K., & Watarai, M. (2026). Gut microbiota of insectivorous bats in Japan: host-, location- and season-associated community structure and exploratory screening for bacterial pathogen targets. Animal Microbiome. https://doi.org/10.1186/s42523-026-00650-w

Image Credits: AI Generated

DOI: 10.1186/s42523-026-00650-w

Keywords: bat microbiome, 16S rRNA sequencing, insectivorous bats, Japan, Yamaguchi Prefecture, Pseudomonadota, Bacillota, PERMANOVA, seasonal variation, zoonotic bacteria, Bacillus cereus group, One Health