🧬 biology

Gut microbiota of insectivorous bats in Japan harbor Chlamydophila psittaci and Shiga toxin-producing Escherichia coli: host species and location shape community structure

This study characterizes the gut microbiota of three insectivorous bat species in Japan, revealing that both host species and sampling location significantly shape community composition while identifying the first detection of *Chlamydophila psittaci* alongside other pathogens like *Bacillus cereus* and Shiga toxin-producing *Escherichia coli*, thereby highlighting the importance of wildlife microbiome surveillance for One Health.

Original authors: Rosalia Mwongeli Makau, Bett Evalyne Chepkirui, Ishara Uhanie Perera, Takashi Shimizu, Masanori Hashino, Hiroshi Shimoda, Miyuka Nishizato, Ai Takano, Tetsuya Yanagida, Fumito Maruyama, Jianjian Hou

Published 2026-07-02

📖 5 min read🧠 Deep dive

CC BY 4.0

Original authors: Rosalia Mwongeli Makau, Bett Evalyne Chepkirui, Ishara Uhanie Perera, Takashi Shimizu, Masanori Hashino, Hiroshi Shimoda, Miyuka Nishizato, Ai Takano, Tetsuya Yanagida, Fumito Maruyama, Jianjian Hou, Kenta Watanabe, Masahisa Watarai

Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). ⚕️ This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer

Imagine bats as tiny, flying cities. Inside each city (the bat's gut), there is a bustling population of microscopic residents called bacteria. These residents aren't just living there; they are the city's sanitation crew, energy workers, and security guards, all working together to keep the bat healthy.

This research paper is like a detailed census and security check of three different bat "neighborhoods" in Yamaguchi, Japan. The scientists wanted to know: Who lives in these cities? Does the type of bat or the cave they live in change the population? And, most importantly, are there any dangerous "criminals" hiding in the crowd?

Here is the breakdown of their findings:

1. The Neighborhoods and the Residents

The researchers studied three different species of insect-eating bats:

The Eastern Bent-wing Bat (Miniopterus fuliginosus)
The Eastern Long-fingered Bat (Myotis macrodactylus)
The Greater Horseshoe Bat (Rhinolophus ferrumequinum)

They collected samples from three different locations: two tunnels and one cave.

The Big Picture:
The bacterial "citizens" in these guts are mostly made up of two major groups (phyla): Pseudomonadota (about 64%) and Bacillota (about 22%). Think of these as the two main political parties running the city.

The "Global Core" Ten:
Even though there are hundreds of different bacterial species, the researchers found a "core group" of just 10 genera (a family-level group of bacteria) that showed up in almost every bat, no matter the species or location. These ten are the VIPs of the bat gut world, making up nearly 75% of the total population. They are the reliable, everyday workers keeping the system running.

2. What Shapes the City? (Host vs. Location)

The scientists asked: Does the bat's species matter more, or does the cave they live in matter more?

The Answer: Both matter, but they work together like a recipe and the kitchen.
The Bat Species: Different bat species have slightly different "city layouts." The bacteria in a Miniopterus bat look different from those in a Rhinolophus bat.
The Location: Where the bat lives (the specific tunnel or cave) also changes the bacterial mix.
The Interaction: The study found that the effect of the bat's species actually changes depending on where they are. It's like how a specific recipe might taste different depending on the local water quality in the kitchen.

However, despite these differences in who is living there (the names and types of bacteria), the jobs they do remain surprisingly the same. Whether it's a bat in a tunnel or a cave, the bacteria are all busy doing the same metabolic work: breaking down food and generating energy. This suggests that while the "staff" might change, the "factory output" stays consistent.

3. The Security Check: Finding the "Criminals"

This is the most critical part of the study. The researchers didn't just count the bacteria; they looked for specific "wanted posters" for dangerous pathogens.

Using a highly sensitive molecular search (like a metal detector for DNA), they found evidence of three specific troublemakers in the bat guts:

Chlamydophila psittaci: This is a first-time discovery in bats. This bacteria is known to cause "psittacosis" (parrot fever) in humans and birds, usually causing flu-like symptoms. Finding its DNA in bats suggests these flying mammals might be a new, previously unknown host for this germ.
Bacillus cereus: A bacteria known to cause food poisoning.
Shiga toxin-producing Escherichia coli (STEC): A dangerous strain of E. coli that can cause severe illness in humans.

Important Note: The study found the DNA (the genetic blueprint) of these bacteria, proving they were present. However, they did not grow live cultures of them in a lab, so they confirmed the bacteria's presence but didn't test if they were currently "active" or infectious.

4. The Social Network

The researchers also mapped out how these bacteria interact with each other, like drawing a map of who talks to whom in the city.

Some bat species had very complex social networks where bacteria were tightly connected (like a busy city with lots of traffic).
Others had simpler networks.
Interestingly, the "criminals" (the pathogenic bacteria) were only connected to the network in certain bat species, suggesting they might be temporary visitors in some and more established residents in others.

The Bottom Line

This study is like a new chapter in the "Bat City Guide." It tells us that:

Bats have unique bacterial cities shaped by both who they are and where they live.
Despite the differences, the bacteria all do the same essential jobs to keep the bat flying.
There are hidden dangers: For the first time, scientists found genetic evidence of Chlamydophila psittaci in bats, along with other known pathogens.

The authors conclude that because these bats carry these bacteria, we need to keep an eye on the connection between wildlife, humans, and animals (a concept called "One Health"). Just because we found the DNA doesn't mean a pandemic is starting, but it does mean we need to keep our "security cameras" on these flying cities to understand how diseases might jump between species.

Technical Summary: Gut Microbiota of Insectivorous Bats in Japan

Problem Statement
While the gut microbiota of bats is recognized for its ecological and public health significance, the specific factors shaping these microbial communities in free-ranging insectivorous bats in Japan remain poorly understood. Previous research has heavily focused on viral pathogens (e.g., SARS-CoV-2) and human/captive animal microbiomes, leaving a gap in knowledge regarding the bacterial composition of wild Japanese bats, the influence of host species versus environmental location, and the prevalence of specific pathogenic bacteria within these populations.

Methodology
The study characterized the gut microbiota of three insectivorous bat species collected from three distinct sites in Yamaguchi Prefecture, Japan: the eastern bent-wing bat (Miniopterus fuliginosus), the eastern long-fingered bat (Myotis macrodactylus), and the greater horseshoe bat (Rhinolophus ferrumequinum).

Sampling: 75 bats were captured from Muikaichi Tunnel, Yamane Tunnel, and Beppu Cave. Distal large intestine sections were collected, and fecal content was extracted for DNA analysis.
Sequencing: High-throughput amplicon sequencing of the 16S rRNA gene (V3–V4 region) was performed. Due to low biomass, amplification required 40 cycles, resulting in successful sequencing of 31 samples. Data were processed using QIIME 2 and DADA2 to generate Amplicon Sequence Variants (ASVs).
Pathogen Screening: In addition to sequencing, a species-specific nested PCR approach was employed to screen for specific pathogenic species, including Chlamydophila psittaci, Bacillus cereus, Staphylococcus aureus, Yersinia enterocolitica, Chlamydophila pneumoniae, Streptococcus pneumoniae, and Shiga toxin-producing Escherichia coli (STEC).
Statistical Analysis: Alpha and beta diversity were assessed using Shannon, Chao1, Faith's PD, and Bray-Curtis dissimilarity metrics. PERMANOVA was used to test the effects of host species and location. Functional profiles were predicted using PICRUSt2, and co-occurrence networks were generated using SparCC.

Key Results

Microbial Composition: The gut microbiota was dominated by the phyla Pseudomonadota (63.6%) and Bacillota (22.3%). A global core of ten genera (including Hafnia, Dwaynesavagella, Serratia, and Staphylococcus) accounted for 74.5% of the total relative abundance across all species and locations.
Pathogen Detection: Nested PCR successfully detected DNA of Chlamydophila psittaci, Bacillus cereus, and Shiga toxin 1-producing Escherichia coli in the bat samples. While 16S sequencing identified genera containing potential pathogens (e.g., Staphylococcus, Streptococcus), species-specific PCR did not confirm the presence of S. aureus, Y. enterocolitica, C. pneumoniae, or S. pneumoniae.
Drivers of Diversity:
- Alpha Diversity: No significant differences were found in taxonomic richness or evenness among bat species or locations, except for a pairwise difference in Shannon index between Yamane Tunnel and Beppu Cave.
- Beta Diversity: Both host species ( $R^2 = 0.166, p = 0.001$ ) and sampling location ( $R^2 = 0.132, p = 0.001$ ) significantly influenced community composition. A significant species-location interaction was also observed.
- Functional Profiles: Predicted metabolic functions (via PICRUSt2) showed no significant differentiation among species or locations, suggesting functional redundancy despite taxonomic variation.
Network Analysis: Co-occurrence networks revealed species-specific and location-specific patterns. R. ferrumequinum exhibited the most complex network, while M. fuliginosus showed the simplest. Pathogenic taxa like Chlamydophila were integrated into the networks of M. fuliginosus and R. ferrumequinum but not M. macrodactylus.

Key Contributions

First Detection of C. psittaci in Bats: The study reports the first detection of Chlamydophila psittaci DNA in bats, expanding the known host range of this pathogen which causes psittacosis in humans and birds.
Comprehensive Characterization: It provides the first detailed characterization of the gut microbiome of insectivorous bats in Japan, identifying specific core genera and dominant phyla.
Ecological Drivers: The research demonstrates that both host identity and geographical location are significant, independent factors shaping gut community structure in these bats.
Pathogen Surveillance: The study confirms the presence of other pathogenic bacteria (B. cereus and STEC) in Japanese bat populations, highlighting the need for bacterial surveillance alongside viral monitoring.

Significance and Claims
The authors claim that this study underscores the value of integrating wildlife microbiome surveillance into "One Health" frameworks. The detection of C. psittaci, B. cereus, and STEC suggests that bats may serve as reservoirs or disseminators of these pathogens, posing potential zoonotic risks at the human-wildlife interface. The study posits that while taxonomic composition varies significantly based on host and environment, the functional potential of the microbiome remains conserved, likely due to the high metabolic demands of flight and insectivory. The authors conclude that future research incorporating culture-based methods and whole-genome sequencing is necessary to fully assess the zoonotic potential and viability of these detected pathogens.

1. The Neighborhoods and the Residents

2. What Shapes the City? (Host vs. Location)

3. The Security Check: Finding the "Criminals"

4. The Social Network

The Bottom Line

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