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Blow flies (Lucilia sericataandPhormia regina) are necrophagous insects that interact with dense microbial reservoirs and are opportunistic vectors of human and animal pathogens. Despite constant exposure to diverse environmental microbes, it is unclear whether their bacterial communities are primarily acquired stochastically or shaped by host factors that could influence pathogen carriage. We conducted a systematic comparison of wildL. sericataandP. reginacollected from seven cities across an urban-rural gradient to determine whether microbiome composition is structured by host species identity or environmental variables. Using 16S rRNA gene sequencing of individual flies, we profiled bacterial communities and applied alpha- and beta-diversity analyses, PERMANOVA, and Random Forest classification to quantify species-level microbiome differentiation. Species identity was the strongest predictor of microbiome composition (PERMANOVA,p = 0.001), while location, land cover type, sampling month, and sex had no significant effects. Random Forest modeling identified multiple bacterial taxa that consistently distinguished the two species, includingIgnatzschineriaandDysgonomonas, which were enriched inP. regina, andVagococcusandEscherichia-Shigella, which were enriched inL. sericata. These taxa are of clinical relevance, withIgnatzschineriain particular increasingly reported from human myiasis and soft-tissue infections, sometimes exhibiting antimicrobial resistance. Our findings demonstrate that wild blow flies maintain species-specific microbiomes despite shared environments, suggesting that host identity strongly filters microbial communities. The presence of opportunistic pathogens within these structured microbiomes underscores the need to understand how blow fly–microbe associations contribute to pathogen persistence and dissemination. By revealing predictable, species-dependent microbiome patterns, this study highlights potential targets for microbiome-based strategies aimed at mitigating blow fly–associated disease risks. 

Despite the clinical relevance of major tuberculous pathogens to domestic animals and humans, the understanding of mycobacterial transmission modes, pathways, and interactions in their natural habitats remains very limited. The reason for this is primarily because ecological and evolutionary concepts have not yet been widely applied to the understanding of these bacteria. Most existing research on mycobacterial transmission is not founded on hypothesis testing but rather tends to accept the most recent explanation and turn it into a canonical fact. In this comparative review, we discuss plausible alternative hypotheses against a null hypothesis of environmental origin to intensify research on mycobacterial pathogens and their capacity to spread in the context of global change. We highlight a major bias in perceptions of mycobacterial infection transmission, with most work concentrating only on the contagious stage of tuberculous clones. We suggest broadening the field to include research on environmental non-tuberculous mycobacteria and their life histories. A deeper understanding of mycobacterial ecology and evolution is more important now than ever, considering the vast diversity of known and unknown mycobacterial species in natural ecosystems. Infectious disease medicine, veterinary science, and public health surveillance should take a more integrative disease ecology approach to enhance the development of new approaches for control of these animal and human pathogens.