Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors

The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.