The work, published in the journal Individual-based Ecology, set out to answer a deceptively simple question: do pigeons that move differently also carry different microbes? The feedback between host behavior and disease transmission is widely acknowledged in theory, but empirical studies demonstrating the strength and direction of the association between an individual’s pathogens, its microbiota composition and its movement remain rare. Pigeons, known reservoirs for agents such as Salmonella, Chlamydia, Cryptococcus and Escherichia, offered an ideal test case because they overlap constantly with people at urban roosts and with livestock at agricultural sites.

The team captured 308 pigeons between July 2019 and November 2021 at three dairy farms arranged along an urbanization gradient: Mevo Horon, an isolated rural settlement 13 kilometers northwest of Jerusalem; Ma’ale Hahamisha, a semi-rural kibbutz on an elevated ridge surrounded by several small settlements; and Mikve Israel, on the outskirts of the Tel Aviv metropolitan area, where 42 percent of the surrounding land is urban. Adults in good body condition above a 250-gram threshold were fitted with OrniTrack GPS transmitters in a backpack configuration, which sampled locations every ten minutes during daylight when batteries allowed. In total, 44 pigeons were tagged, and 32 accumulated 8,473 days of tracking data — an average of 265 days per individual, with some birds followed for more than two years.

Microbiome sampling relied on a combined swabbing of the choanal cleft and cloaca of every captured bird, preserving samples on paper cards for RNA extraction. From the tagged subset, 29 samples went through untargeted total RNA sequencing on a MiSeq machine — an approach the authors chose because it outperforms 16S amplicon sequencing and shotgun metagenomics by detecting viral and bacterial sequences outside the 16S locus, giving higher discriminatory power. Taxonomic profiling filtered results with strict cutoffs to limit false positives, and bacteria were analyzed primarily at the genus level, where classification accuracy is greatest. The researchers validated the sequencing results against classical colony-growth tests for Campylobacter and Salmonella, finding strong agreement between methods.

The movement data revealed a clear urban effect. Pigeons at the rural and semi-rural sites traveled roughly 2,100 to 2,500 meters per day on average, with maximum daily displacements exceeding 3,000 meters, while pigeons at the urban Mikve site covered only about 1,000 meters daily and displaced barely 1,300 meters from their roosts. The differences were statistically significant for both travel distance and displacement. The likely explanation is resource distribution: rural pigeons spent summer months foraging for grains at harvested fields far from their roosts, while urban birds foraged year-round on human waste and rarely visited distant fields. This pattern agrees with broader findings that urban animals move less thanks to stable, rich food sources.

All pigeons, regardless of site, roosted almost exclusively in buildings within human settlements and routinely visited their respective dairy farms and other anthropogenic food sources such as parks, poultry farms and commercial areas. Crucially, crossing among the three study sites was very rare, meaning each farm’s pigeon population operated largely as a closed local system — yet one that alternated constantly between urban roosts and livestock facilities, sometimes located within hundreds of meters of each other.

The microbiome results were equally striking. The top 20 most abundant bacterial genera across all sites included Escherichia, Campylobacter, Clostridium and Streptococcus — genera containing many species of disease-causing pathogens. At the species level, the researchers identified bacteria with documented illnesses in humans, cattle and poultry, confirming that the pigeons carry not just pathogen-relevant genera but pathogenic species themselves. Local studies have previously reported Salmonella and E. coli in Israeli pigeons, and the new sequencing data are consistent with that picture of substantial zoonotic potential.

Site-level differences in microbial diversity followed the urbanization gradient in an unexpected direction. Pigeons at the urban Mikve site carried significantly higher bacterial richness than those at the two rural sites, with around 160 genera per bird compared to roughly 70 at Mevo and Ma’ale Hahamisha. Fisher’s alpha diversity, a measure that accounts for evenness, showed the same trend, though it was not statistically significant across all indices. The authors caution that with only three sites, factors such as elevation, resource composition and local density cannot be ruled out, but the urbanization gradient is the obvious candidate explanation, and prior work has attributed increased microbial diversity in urban wildlife to parasite acquisition, natural infections and physiological stressors at urban habitats.

The study’s most novel finding concerns individual behavior. Among 19 pigeons with both high-quality GPS data and microbiome profiles, exploratory individuals — measured by the number of spatially unique stops they made per day — carried significantly richer and more diverse microbiota, independent of capture site. This positive association held similarly at all three sites, implying that birds visiting more diverse locations sample their region more thoroughly and encounter more bacteria along the way. An alternative mechanism cannot be excluded: the microbiome itself might shape behavior, either through sickness or through deliberate host manipulation by microbial agents. Prior work in barn owls found that individuals moving greater distances from the nest had higher microbiome alpha diversity, and gull colonies using a wider variety of foraging sites showed maximal bacterial diversity, lending independent support to the exposure hypothesis.

The combined picture — high mobility, high densities, constant proximity to humans at roosts and cattle at foraging sites, and opportunistic visits to open habitats — points to a strong potential for feral pigeons to transfer pathogens among livestock, humans and wildlife. The authors emphasize that these patterns matter in both directions: pigeons are similarly likely to transmit pathogens from poultry farms into wildlife populations, a scenario underscored by the massive 2022 avian influenza outbreak. Practically, the findings suggest disease management should be tailored to local conditions and individual variation — culling protocols in rural areas would need to operate across much larger areas than urban ones, and more exploratory pigeons should be prioritized when targeting is possible. The study offers a rare mechanistic example of the One Health premise, demonstrating how movement ecology tools can illuminate the individual-level pathways through which synanthropic species connect human, animal and environmental health.

Subject of Research: Association between movement patterns, microbiome diversity, and potential pathogens of feral pigeons in dairy farms

Article Title: Association between movement patterns, microbiome diversity, and potential pathogens of feral pigeons in dairy farms

Article References: Crafton, M. M., Lublin, A., Cahani, S., Rauer, L., & Spiegel, O. (2025). Association between movement patterns, microbiome diversity, and potential pathogens of feral pigeons in dairy farms. Individual-based Ecology, 1, Article e146376. https://doi.org/10.3897/ibe.1.146376

Image Credits: AI Generated

DOI: 10.3897/ibe.1.146376

Keywords: Association, between, movement, patterns, microbiome, diversity, potential, pathogens, feral, pigeons, dairy, farms