The research, led by Julie Teresa Shapiro of the University of Florida and the French Agency for Food, Environmental and Occupational Health and Safety, together with colleagues from the University of Copenhagen, Aarhus University, the University of Pretoria, and the University of Eswatini, analyzed fecal samples from 109 individual little free-tailed bats captured between November 2015 and July 2016 at 28 sites across the Lowveld region of eastern Eswatini. This area, part of the Maputaland-Pondoland-Albany biodiversity hotspot, is dominated by commercial sugarcane plantations, subsistence maize fields, grazing lands, rural villages, and protected parks, making it an ideal natural laboratory for asking how anthropogenic disturbance shapes the invisible ecosystems inside wildlife.

The team used a molecular technique called amplicon sequencing, targeting the V3–V4 region of the 16S ribosomal RNA gene, a genetic marker widely used to identify bacteria. After extracting DNA from fecal samples preserved with silica gel, the researchers amplified the bacterial marker, sequenced the products on an Illumina MiSeq platform, and processed the reads through the DADA2 pipeline, which identifies distinct amplicon sequence variants, or ASVs, the finest practical resolution of bacterial identity. Rigorous contamination controls, including extraction blanks, PCR blanks, and the requirement that a bacterial variant appear in at least two of three PCR replicates before being counted, ensured the results reflected genuine biology rather than laboratory artifacts.

The scale of bacterial diversity they uncovered was impressive. Across the 109 bats, the team identified 2,249 unique bacterial ASVs, and a statistical technique called rarefaction, which plots species accumulation against sampling effort, showed the curves reaching a clear asymptote. The Chao1 estimator, a method for extrapolating total richness from observed data, suggested the true diversity was between 2,250 and 2,253 species, meaning the researchers had captured essentially the complete bacterial inventory of this species’ gut in the region. Individual bats carried anywhere from 3 to 185 ASVs, with a mean of 47, and phylogenetic diversity, measured with Faith’s index, ranged from 0.6 to 24.1.

Perhaps the most striking pattern was the extraordinary individuality of each bat’s microbiome. Fully 72 percent of the identified bacterial variants, some 1,622 of them, were found in only a single bat, and fewer than 1 percent appeared in more than a quarter of the animals sampled. The most common single variant, an unknown species of Mycoplasma, was still detected in only 66 percent of bats. The dominant phyla across the population were Proteobacteria and Firmicutes, present in every individual, followed by Actinobacteria in 84 percent and Bacteroidota in just over half. The researchers suggest this high individual variability likely reflects the bat’s generalist insectivorous diet: previous molecular diet studies have shown that Mops pumilus feeds on a wide and individually variable array of insect prey, and since diet is a major driver of gut microbial composition, no two bats end up with quite the same internal community.

Then came the pathogen findings. Screening the ASV table against a list of bacterial genera known to be potentially zoonotic and frequently found in bats, the team detected five: Mycoplasma, Rickettsia, Salmonella, Bartonella, and Campylobacter. Four of these occurred at remarkably high prevalence. Mycoplasma topped the list at 88 percent of individuals, present at all but two of the 17 roosts surveyed in the landscape analysis. Rickettsia was found in 36 percent of bats, Salmonella in 34 percent, and Bartonella in 23 percent, while Campylobacter appeared in just 4 percent. Co-occurrence was common: 27 bats carried two of these genera simultaneously, 23 carried three, seven carried four, and one individual harbored all five.

Crucially, none of the bats showed signs of illness. The researchers found no correlation between bacterial richness or phylogenetic diversity and body condition, calculated as mass divided by forearm length, a standard health proxy in bats. This absence of disease, combined with the sheer prevalence of the bacteria, suggests the animals are likely asymptomatic carriers, or that the detected DNA originated in their insect prey rather than establishing infection in the bats themselves. Rickettsia in particular is a common insect endosymbiont, and its presence in feces could simply reflect a recent meal of infected insects or ticks groomed off the fur. Salmonella, by contrast, is usually reported in bats at prevalences below 12 percent, making the 34 percent figure here notably high, and raising questions about environmental reservoirs such as contaminated water, which has been implicated in other studies.

The central hypothesis of the study, however, was largely not borne out. Drawing on prior work showing that habitat degradation can reduce gut microbial diversity in primates, rodents, and other bats, the researchers expected that anthropogenic land covers and fragmentation would diminish bacterial richness and shift community composition. They classified the landscape from Landsat 8 satellite imagery into savanna, sugarcane, rural settlement, and water, then calculated composition metrics and configuration metrics such as savanna edge density and a fragmentation index at both a fine scale around roosts and a landscape scale matching the bats’ nightly foraging ranges, which can exceed four kilometers. Using generalized linear mixed models and distance-based redundancy analysis, they found no association between any land cover variable and bacterial richness, phylogenetic diversity, or the prevalence of potentially pathogenic genera. Land cover explained only a small fraction, about 6.7 percent, of the variation in community composition, with fine-scale rural and savanna cover and landscape-scale sugarcane cover and savanna splitting emerging as statistically significant but weak predictors.

The authors interpret this muted response as a reflection of the species’ ecological flexibility. Unlike bats that avoid disturbed habitats, Mops pumilus actively uses and even prefers agricultural landscapes, roosting in buildings and feeding over irrigated monocultures where water and insect prey remain available year-round. Because its activity and foraging are not negatively affected by human land use, its gut microbiome may be similarly buffered. The researchers also point to factors their sampling design could not fully disentangle, including social transmission of microbes within roosts, local environmental microbial communities, and roost characteristics, any of which might outweigh landscape composition in shaping these internal ecosystems. Seasonal effects, too, remain untested, although the species neither migrates nor hibernates, which may dampen the seasonal microbiome shifts documented in other bat species.

The findings carry real weight for the One Health framework, the principle that human, animal, and environmental health are interconnected. Bats are already recognized as reservoirs of numerous viruses, and bacterial genera such as Bartonella and Mycoplasma have documented links to human disease, including Bartonella mayotimonensis carried by Myotis bats in northern Europe and Mycoplasma haemohominis carried by flying foxes in New Caledonia. While there is currently no evidence that the bacteria detected in Eswatini cause illness in the bats or can infect people, Mycoplasma species are considered emerging pathogens that have caused mortality in other wildlife, and the authors argue that continued surveillance of this abundant, human-associated bat species is warranted. As savannas across southern Africa continue to convert to agriculture, understanding which species tolerate, and which are quietly transformed by, the changing landscape will be essential for conserving both the bats and the health of the systems they inhabit.

Subject of Research: Gut microbiome diversity and potentially pathogenic bacteria in the little free-tailed bat (Mops pumilus) in relation to land cover change in Eswatini

Article Title: Gut microbiomes of the little free-tailed bat (Mops pumilus) show high prevalence of potential bacterial pathogens but limited responses to land cover

Article References: Shapiro, J. T., Barnes, C., Nielsen, I. B., Rasmussen, L., Monadjem, A., McCleery, R. A., & Hansen, A. J. (2026). Gut microbiomes of the little free-tailed bat ( Mops pumilus ) show high prevalence of potential bacterial pathogens but limited responses to land cover. Web Ecology, 26(2), 223-242. https://doi.org/10.5194/we-26-223-2026

Image Credits: AI Generated

DOI: 10.5194/we-26-223-2026

Keywords: gut microbiome, bats, Mops pumilus, 16S rRNA sequencing, bacterial pathogens, Mycoplasma, Salmonella, land cover change, Eswatini, One Health, wildlife disease, savanna

A team of researchers led by Maciej Kamiński and Piotr Minias of the University of Lodz in Poland set out to answer a deceptively simple question: does living at high density in heavily urbanized habitats change the diversity and composition of a bird’s gut bacteria? The feral pigeon, Columba livia domestica, was an ideal candidate. These birds form some of the densest aggregations of any urban wildlife species, sometimes numbering hundreds of individuals at a single site. According to classic ecological theory, such crowding should promote horizontal transmission of microbes between individuals, which in turn should boost the diversity of the gut microbiome. If density matters anywhere, it should matter in pigeons.

To test this idea, the researchers collected faecal samples from 200 individual pigeons across study plots situated within five large Polish cities. Crucially, the plots varied along two independent axes: the degree of habitat urbanization, measured by the character of the surrounding built environment, and the local density of the pigeon population itself. This two-dimensional design allowed the team to disentangle the effects of the physical environment from the effects of social crowding, a distinction that many previous urban microbiome studies had failed to make.

The laboratory work relied on high-throughput sequencing of the 16S rRNA gene, the standard molecular tool for cataloguing bacterial communities without needing to culture them. The results were striking in their sheer scale. Across all samples, the team detected nearly 35,000 Amplicon Sequence Variants, or ASVs, which are the finest-resolution units in modern microbiome science, roughly equivalent to individual bacterial strains. These variants belonged to 561 bacterial families and could be grouped into 75 distinct functional categories, reflecting the metabolic roles the bacteria perform. For a bird often dismissed as a city pest, the feral pigeon carries a remarkably rich internal ecosystem.

The first major finding concerned urbanization. The researchers detected a clear negative relationship between habitat urbanization and taxonomic richness of the gut microbiome: the more urbanized the surroundings, the fewer bacterial types the pigeons carried. The authors suggest a likely mechanism rooted in habitat heterogeneity. Highly urbanized areas tend to be simplified environments, with uniform food sources, limited green space, and fewer ecological niches. Pigeons foraging in such settings encounter a narrower range of environmental microbes and dietary substrates, and their gut communities reflect that impoverishment. In contrast, pigeons living in less urbanized plots, with more varied habitats and food webs, harboured more diverse bacterial assemblages.

The second major finding concerned function rather than identity. When the researchers classified the bacteria by what they do rather than by what they are called, a consistent pattern emerged along the urbanization gradient. Bacteria known as commensals of the human and mammalian gut became more abundant in pigeons from highly urbanized plots, as did bacteria classified as human pathogens and nitrate-reducers, a functional group involved in processing nitrogen compounds. This shift is consistent with a phenomenon that microbiologists have dubbed the humanization of the gut microbiome in urban wildlife. In essence, pigeons living closest to people increasingly carry the microbial signature of people themselves, likely acquired through shared environments, contaminated food and water, and the general microbial fallout of dense human settlement.

The presence of human-associated pathogens in urban pigeon guts is the aspect of the study most likely to capture public attention, though the researchers frame it carefully. The findings do not establish that pigeons are significant disease vectors; they show instead that the boundary between human and animal microbial worlds becomes more permeable in cities. Urban wildlife shares our sidewalks, our refuse, and our wastewater, and the microbial consequences of that intimacy are now measurable at scale. For public health and urban planning, this makes pigeons a useful sentinel species, a living indicator of how human activity reshapes microbial circulation in the environment.

Perhaps the most surprising result, however, was what the study did not find. Despite the theoretical expectation that high population density should fuel microbial exchange and elevate microbiome diversity, the researchers detected no association between pigeon density and either taxonomic or functional microbiome diversity. Crowding, at least in this species and at the densities studied, did not translate into richer gut communities. This null result matters because it forces a rethinking of how sociality and transmission shape microbiomes. It may be that horizontal transmission saturates at relatively low densities, or that host physiological regulation, diet, and environmental filtering override the effects of contact rates. Whatever the explanation, the study suggests that density alone is a poor predictor of gut microbial diversity in urban birds.

Diversity, however, is only one dimension of the story. When the researchers examined the overall composition of the microbiome, which species and functions are present and in what proportions, they found evidence of significant turnover among study plots characterized by different urbanization levels and population densities. In other words, pigeon communities in different parts of the city carry measurably different gut ecosystems, even when their overall diversity levels are similar. This turnover implies that local environmental conditions leave a detectable fingerprint on the gut microbiome, and that composition may be a more sensitive indicator of urbanization than richness alone.

The study is among the first to address the links between population density and gut microbiome diversity in an urban context, and its implications extend well beyond pigeons. As cities expand and wildlife increasingly shares urban space with humans, understanding how the built environment modulates the microbial communities of animals becomes a question with consequences for conservation, animal welfare, and even human health. The authors point to potential fitness consequences of these microbiome modulations: gut bacteria influence digestion, immune function, and disease resistance, so shifts in community composition along urban gradients could ultimately affect the survival and reproduction of urban wildlife. For an urban exploiter like the feral pigeon, which has already solved the problem of thriving alongside humans, the gut microbiome appears to be both a record of that coexistence and, possibly, a factor in its continued success. What the pigeons carry inside them, it turns out, tells the story of the city outside.

Subject of Research: Effects of urbanization and population density on the gut microbiome diversity of feral pigeons

Article Title: Linking Taxonomic and Functional Microbiome Diversity with Population Density and Habitat Urbanization in an Urban Exploiter Bird

Article References: Kamiński, M., Jeziorski, S., Skóra, M., Strapagiel, D., & Minias, P. (2026). Linking Taxonomic and Functional Microbiome Diversity with Population Density and Habitat Urbanization in an Urban Exploiter Bird. Microbial Ecology. https://doi.org/10.1007/s00248-026-02870-8

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02870-8

Keywords: gut microbiome, feral pigeon, urbanization, 16S rRNA sequencing, microbial diversity, urban wildlife, population density, humanization, Microbial Ecology, ASVs, bacterial pathogens, urban ecology