**Background:** Microplastics (<5 mm) are ubiquitous environmental contaminants ingested by numerous species, with demonstrated negative health effects. The gut microbiome is essential to host health, but the effects of microplastic ingestion on gut microbial communities in wild populations remain poorly understood. This study investigated whether microplastic ingestion is associated with changes in the gut microbiomes of two wild seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters.
**Methods:** The study included 27 northern fulmar adults collected during the breeding season (July–August 2018) near Qikiqtarjuaq, Nunavut, Canada, and 58 Cory's shearwater fledglings collected during take-off season (October–November 2017 and 2018) on the Azores archipelago, Portugal. Sterile swabs were used to sample both the proventriculus (n=85) and cloaca (n=84) of each individual. Microplastic debris from the gastrointestinal tract was collected over a 1 mm sieve, examined under light microscopy, and characterized. DNA was extracted from whole swabs, and the V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq. After bioinformatic processing (QIIME 2, DADA2), the final dataset consisted of 4,602,578 reads across 2,517 ASVs and 169 samples, with an average sequencing depth of 27,234 ± 5,999 reads per sample. Alpha diversity was assessed using observed ASVs, Shannon index, Faith's phylogenetic diversity (PD), and Allen's H metric. Linear mixed models tested associations with microplastic count and mass (standardized by bird mass), with individual bird ID as a random factor. Beta diversity was analyzed using weighted and unweighted UniFrac distances and Aitchison's log-ratio approach with permutation tests (vegan::adonis, 9,999 permutations). Differential abundance analysis was performed using ANCOM (w0=0.70).
**Key Results:** Microplastic count was significantly positively correlated with all alpha diversity metrics in the proventriculus (observed ASVs: β=0.67, t81=2.96, P=0.004; Shannon index: β=0.27, t81=2.85, P=0.006; Faith's PD: β=1.68, t81=3.46, P<0.001; Allen's H metric: β=0.07, t81=2.73, P=0.007). These associations were significantly greater in the proventriculus than the cloaca (observed ASVs: P=0.011; Faith's PD: P=0.001). In contrast, microplastic mass was significantly negatively correlated with Shannon index (β=−0.20, t81=−2.38, P=0.020), Faith's PD (β=−1.12, t81=−2.47, P=0.016), and Allen's H metric (β=−0.06, t81=−2.54, P=0.013) in the proventriculus. Microplastic count was significantly correlated with beta diversity (weighted UniFrac: P<0.001; unweighted UniFrac: P<0.001; Aitchison: P<0.001), with effects depending on GIT location and host species. ANCOM identified 17 differentially abundant ASVs. As microplastic count increased, commensal microbiota decreased (e.g., Pseudoalteromonas, Psychrobacter, Enterococcus, Catellicoccus, Staphylococcus), while potential pathogens increased (e.g., Corynebacterium xerosis, Parvimonas, Cetobacterium). Clostridium perfringens showed the greatest positive association with microplastic mass. Effects on alpha diversity were similar between species, but beta diversity effects were species-specific. Body condition was not a significant predictor in alpha diversity models.
**Clinical Implications:** This study provides evidence that environmentally relevant microplastic concentrations are associated with gut dysbiosis in wild seabird populations, characterized by reduced commensal bacteria and increased potential pathogens and antibiotic-resistant microbes. The findings suggest that microplastics may act as vectors for foreign microbes and that effects may be more pronounced in the upper gastrointestinal tract. The authors note that northern fulmars are established bioindicators of microplastic pollution, and these results raise concerns about chronic exposure effects, particularly as microplastics can be retained for weeks or months in Procellariiformes. The study also highlights implications for human health, given that humans are also exposed to micro- and nanoplastics, and underscores the importance of understanding how plastic pollution may contribute to emerging zoonotic diseases.