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

Direct and indirect effects of pesticide exposure on the gut microbiota of a farmland raptor

Recent studies in humans have shown that certain pesticides could affect the composition and functions of the gut microbiota, an essential modulator of vertebrate physiology, leading to potential dysbiosis. However, this relationship remains largely unknown in wild birds despite the implications of pesticides in the current decline of farmland species. The present study sought to fill this gap by providing data on the association between pesticide concentrations in blood and gut microbiota characteristics in relation to individual traits in a farmland raptor, the Montagu's harrier (Circus pygargus). Results showed that females with higher body condition and higher pesticide load exhibited greater gut bacterial richness and diversity, while the relationship was opposite in males with higher body condition. In terms of taxonomic composition, Proteobacteria emerged as the dominant phylum across all nestlings. Differences in the abundance of specific phyla and genera were observed according to pesticide load, with higher levels of Bacteroidota and Leifsonia, but lower levels of Bulkholderia, in nestlings with higher pesticide concentrations in their blood. This study highlights differences in microbiota and contamination by several pesticides according to the phenotypic characteristics of a wild raptor, and shows that farmland birds can represent relevant biosentinels for assessing the health/proper functioning of ecosystems (One Health approach).

Analysis of fungal diversity in the feces of Arborophila rufipectus

Background

Intestinal fungal composition plays a crucial role in modulating host health, and thus is of great significance in the conservation of endangered bird species. However, research on gut fungal composition in birds is limited. Therefore, in this study, we aimed to examine gut fungal community and potential fecal pathogen composition in wild Arborophila rufipectus.

Methods

Fecal samples were collected from the habitats of wild A. rufipectus and Lophura nycthemera (a widely distributed species belonging to the same family as A. rufipectus) in summer and autumn. Thereafter, RNA was collected and the internal transcribed spacer rRNA gene was sequenced via high-throughput sequencing to investigate seasonal variations in intestinal core fungi, microbial fungi, and potential pathogenic fungi.

Results

The gut microbiota of A. rufipectus and L. nycthemera were highly similar and mainly consisted of three phyla, Ascomycota (58.46%), Basidiomycota (28.80%), and Zygomycota (3.56%), which accounted for 90.82% of the fungal community in all the samples. Further, the predominant genera were Ascomycota_unclassified (12.24%), Fungi_unclassified (8.37%), Davidiella (5.18%), Helotiales_unclassified (2.76%), Wickerhamomyces (1.84%), and Pleosporales_unclassified (1.14%), and the potential fecal pathogens identified included Candida, Cryptococcus, Trichosporon, and Malassezia.

Conclusion

Our results provide evidence that the diversity of intestinal fungi in the endangered species, A. rufipectus, is similar to that in the common species, L. nycthemera, and may serve as a basis for monitoring the status of A. rufipectus and for developing conservation measures.

The comparison of gut microbiota between wild and captive Asian badgers (Meles leucurus) under different seasons

The gut microbiota plays an important role in the immunology, physiology and growth and development of animals. However, currently, there is a lack of available sequencing data on the gut microbiota of Asian badgers. Studying the gut microbiota of Asian badgers could provide fundamental data for enhancing productivity and immunity of badgers' breeding, as well as for the protection of wild animals. In this study, we first characterized the composition and structure of the gut microbiota in the large intestines of wild and captive Asian badgers during summer and winter by sequencing the V3-V4 region of the 16S ribosomal RNA gene. A total of 9 dominant phyla and 12 genera among the bacterial communities of the large intestines exhibited significant differences. Our results showed that Firmicutes and Proteobacteria were the most predominant in both wild and captive badgers, regardless of the season. Romboutsia, Streptococcus and Enterococcus may represent potential sources of zoonoses, warranting further attention and study. Our findings indicated that the diversity and availability of food resources were the most important influencing factors on the gut microbiota of Asian badgers, providing fundamental data for the protection and conservation of wild animals. Variation in the gut microbiota due to season, age and sex in both wild and captive Asian badgers should be considered in future research directions. Furthermore, combined multi-omics studies could provide more information for wild animal conservation, and enhancing our understanding of the molecular mechanism between the microbiota and host.

Falcon gut microbiota is shaped by diet and enriched in Salmonella

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons-raptors of historic importance-in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.

Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center

The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.

Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks

Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.

Analysis of microbial diversity in the feces of Arborophila rufipectus

Introduction

Intestinal microbiota composition plays a crucial role in modulating the health of the host. This evaluation indicator is very sensitive and profoundly impacts the protection of endangered species. Currently, information on the gut microbiota of wild birds remains scarce. Therefore, this study aimed to describe the gut microbial community structure and potentially, the pathogen composition of wild Arborophila rufipectus.

Methods

To guarantee comprehensive data analysis, we collected fecal samples from wild A. rufipectus and Lophura nycthemera in their habitats for two quarters. The 16S rRNA gene was then sequenced using high-throughput sequencing technology to examine the intestinal core microbiota, microbial diversity, and potential pathogens with the aim of determining if the composition of the intestinal microflora varies seasonally.

Results and Discussion

The gut microbiota of A. rufipectus and L. nycthemera primarily comprised four phyla: Proteobacteria (45.98%), Firmicutes (35.65%), Bacteroidetes (11.77%), and Actinobacteria (3.48%), which accounted for 96.88% of the total microbial composition in all samples. At the genus level, core microorganisms were found, including Shigella (10.38%), Clostridium (6.16%), Pseudomonas (3.03%), and Rickettsiella (1.99%). In these genera, certain microbial species have been shown to be pathogenic. This study provides important indicators for analyzing the health status of A. rufipectus and formulating protective measures.

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)

Background

Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals.

Objectives

In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor.

Results

The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species.

Conclusions

Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity

Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.

The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years

Background

The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce.

Methods

To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually.

Results

The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years.

Conclusions

This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.