Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from nearly 90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.

Glyphosate is the world’s most widely used agrochemical. Its use in agriculture and gardening has been proclaimed safe because humans and other animals do not have the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). However, increasing numbers of studies have demonstrated risks to humans and animals because the shikimate metabolic pathway is present in many microbes. Here, we assess the potential effect of glyphosate on healthy human microbiota. Our results demonstrate that more than one-half of human microbiome are intrinsically sensitive to glyphosate. However, further empirical studies are needed to determine the effect of glyphosate on healthy human microbiota.

Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.

Pollution-induced changes in gut microbiota may have serious effects on avian health and physiology. Particularly, early-life exposure to environmental pollutants may influence the gut microbiota development and microbiota-dependent physiological functions. We studied the associations of metal pollution with early-life microbial environment of wild passerines by exploring gut bacterial diversity and community composition in nestlings by 16S rRNA sequencing. Samples were collected from three common model species, great tits ( Parus major ), blue tits ( Cyanistes caeruleus ), and pied flycatchers ( Ficedula hypoleuca ) breeding near a copper-nickel smelter, an area with the highest rates of metal pollution in Finland. Responses of microbiota to pollution and microclimate were measured and connected to ecological measures (brood size, growth, fledging success) of nestling performance. The most abundant bacterial phyla across species were Firmicutes, Proteobacteria and Actinobacteria. Our results showed that the faecal microbial alpha diversity decreased with increasing brood size in great tits and blue tits, while in pied flycatchers the diversity increased with increasing nestling growth. However, alpha diversity did not differ between the polluted and control areas. The faecal microbial communities (beta diversity) differed between the species and study areas, and several bacterial orders were associated with metal concentrations, temperature, body mass, or fledging success. Differential abundance analyses showed species-specific differences in microbial abundances between polluted and control areas, e.g., Catellicoccus and Serratia showing elevated abundance within the polluted area. The results suggest that metal pollution may alter the early-life bacterial communities in small passerine species living in metal-polluted areas.

While the direct toxicological effects of metal exposure on animals, including birds, are well documented, indirect mechanisms remain poorly understood. This applies to effects on microbiota, despite the emerging evidence of its crucial role in host's physiological functions. We investigated the metal exposure, growth, and fledging of great tits (Parus major) in six rural vs. industrial/urban area (IUA) comparisons across Europe to identify associations with bird gut microbiota. To capture a range of pollution profiles, IUAs included both city settings and industrial sites such as a copper-nickel smelter, a metallurgical plant, a pulp mill, and a lead mine. Fecal samples from 191 broods were analyzed for bacterial 16S rRNA and concentrations of 18 elements, of which nine common contaminants were selected for further analyses. Nestlings in IUAs showed higher metal exposure than those in rural sites, except near a pulp mill, with opposing results. An index describing impervious land cover was a weak predictor for most microbiota metrics. Instead, the rural vs. IUA comparison potentially caught the environmental characteristics better, showing effects on the fledgling number, body mass, microbial composition, and abundances of several taxa, though these patterns were location dependent and may reflect secondary effects of pollution, like changes in habitat quality and diet. Taxa with links to both metal levels and nestling performance were identified. Despite reduced emissions in Europe, wild birds remain exposed to metal pollution, particularly near industrial areas. Overall, our findings suggest that anthropogenic influence associates with wildlife microbiomes and health in a context-dependent manner.