Microbial Ecology of the Western Gull (Larus occidentalis)

Winged resistance: Storks and gulls increase carriage of antibiotic resistance by shifting from paddy fields to landfills

Waterbirds are vectors for the dissemination of antimicrobial resistance across environments, with some species increasingly reliant on highly anthropized habitats for feeding. However, data on the impact of their feeding habits on the carriage of antibiotic resistance genes (ARGs) are still scarce. To fill this gap, we examined the microbiota (16S rRNA amplicon gene sequencing) and the prevalence of ARG (high-throughput qPCR of 47 genes) in faeces from white storks (Ciconia ciconia) and lesser black-backed gulls (Larus fuscus) feeding in highly (landfill) and less (paddy fields) polluted habitats. Faecal bacterial richness and diversity were higher in gulls feeding upon landfills and showed a greater abundance of potential pathogens, such as Staphylococcus. In contrast, faecal bacterial communities from storks were similar regardless of habitat preferences, maybe due to a less intense habitat use compared to gulls. In addition, birds feeding in the landfill carried a higher burden of ARGs compared to the surrounding soil and surface waters. Network analysis revealed strong correlations between ARGs and potential pathogens, particularly between tetM (resistance to tetracyclines), blaCMY (beta-lactam resistance), sul1 (sulfonamide resistance) and members of the genera Streptococcus, Peptostreptococcus, and Peptoclostridium. Our work demonstrates how transitioning from paddy fields to landfills fosters the carriage of ARGs and potential pathogens in the bird gut, shedding light on the ecological role of these avian vectors in antimicrobial resistance dissemination.

Comparative Analyses of the Fecal Microbiome of Five Wild Black-Billed Capercaillie (Tetrao parvirostris) Flocks

Black-billed capercaillie (Tetrao parvirostris) was listed as a first-class state-protected animal because it was endangered in China (Category I). This study is the first to examine the diversity and composition of T. parvirostris gut microbiome in the wild. We collected fecal samples from five black-billed capercaillie flock roosting sites (each 20 km apart) in one day. Thirty fecal samples were sequenced with 16S rRNA gene amplicons on the Illumina HiSeq platform. This study is the first to analyze the fecal microbiome composition and diversity of black-billed capercaillie in the wild. At the phylum level, Camplyobacterota, Bacillota, Cyanobacteria, Actinomycetota, and Bacteroidota were the most abundant in the fecal microbiome of black-billed capercaillie. At the genus level, unidentified Chloroplast, Escherichia-Shigella, Faecalitalea, Bifidobacterium, and Halomonas were the dominant genera. Based on alpha and beta diversity analyses, we found no significant differences in the fecal microbiome between five flocks of black-billed capercaillie. Protein families: genetic information processing; protein families: signaling and cellular processes, carbohydrate metabolism; protein families: metabolism and energy metabolism are the main predicted functions of the black-billed capercaillie gut microbiome through the PICRUSt2 method. This study reveals the composition and structure of the fecal microbiome of the black-billed capercaillie under wild survival conditions, and this study provides scientific data for the comprehensive conservation of the black-billed capercaillie.

Occurrence of Mycoplasma spp. in wild birds: phylogenetic analysis and potential factors affecting distribution

Different Mycoplasma species have been reported in avian hosts. However, the majority of studies focus on one particular species of Mycoplasma or one host. In our research, we screened a total of 1141 wild birds representing 55 species, 26 families, and 15 orders for the presence of mycoplasmas by conventional PCR based on the 16S rRNA gene. Selected PCR products were sequenced to perform the phylogenetic analysis. All mycoplasma-positive samples were tested for M. gallisepticum and M. synoviae, which are considered the major pathogens of commercial poultry. We also verified the influence of ecological characteristics of the tested bird species including feeding habits, habitat types, and movement patterns. The presence of Mycoplasma spp. was confirmed in 498 birds of 29 species, but none of the tested birds were positive for M. gallisepticum or M. synoviae. We found possible associations between the presence of Mycoplasma spp. and all investigated ecological factors. The phylogenetic analysis showed a high variability of Mycoplasma spp.; however, some clustering of sequences was observed regarding particular bird species. We found that wild migratory waterfowl, particularly the white-fronted goose (Anser albifrons) and mallard (Anas platyrhynchos) could be reservoirs and vectors of mycoplasmas pathogenic to commercial waterfowl.

Prevalence and Antimicrobial Resistance of Enteropathogenic Bacteria in Yellow-Legged Gulls (Larus michahellis) in Southern Italy

Wild birds may host and spread pathogens, integrating the epidemiology of infectious diseases. Particularly, Larus spp. have been described as responsible for the spread of many enteric diseases, primarily because of their large populations at landfill sites. The aim of this study was to examine the role of yellow-legged gulls as a source of enteropathogenic bacteria such as Campylobacter spp., Salmonella spp., Shiga toxin-producing Escherichia coli and Yersinia spp., with particular attention to antibiotic-resistant strains. Enteropathogenic bacteria were isolated from 93/225 yellow-legged gulls examined from April to July, during a four-year period (2016-2019). Specifically, Campylobacter spp. was isolated from 60/225 samples (26.7%), and identified as C. coli (36/60) and as C. jejuni (24/60). Salmonella spp. was isolated from 3/225 samples (1.3%), and identified as Salmonella arizonae. Shiga toxin-producing E. coli were isolated from 30/225 samples (13.3%) samples, and serotyped as E. coli O128 (12/30) O26 (9/30), O157 (6/30) and O11 (3/30); Yersinia spp. was never detected. Isolated strains exhibited multidrug resistance, including vitally important antibiotics for human medicine (i.e., fluoroquinolones, tetracyclines). Our study emphasizes the importance of yellow-legged gulls as potential reservoirs of pathogenic and resistant strains and their involvement in the dissemination of these bacteria across different environments, with resulting public health concerns.

The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center

As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue.

Interspecific comparison of the fecal microbiota structure in three Arctic migratory bird species

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink-footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink-footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink-footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink-footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink-footed geese was discussed to be related with their herbivorous diet.