Avian gut microbiomes taking flight

Metagenomic comparison of gut communities between wild and captive Himalayan griffons

Introduction

Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited.

Methods

In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions.

Results

Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs).

Discussion

In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

Similarities and differences: species and diet impact gut microbiota of captive pheasants

The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.

Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes

Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.

Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?

The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.

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.

Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes

Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.

Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

IMPORTANCE

This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.

Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains

Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.

Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine

In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.

The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird

Gut-associated microbial communities are known to play a vital role in the health and fitness of their hosts. Though studies investigating the factors associated with among-individual variation in microbiome structure in wild animal species are increasing, knowledge of this variation at the individual level is scarce, despite the clear link between microbiome and nutritional status uncovered in humans and model organisms. Here, we combine detailed observational data on life history and foraging preference with 16S rRNA profiling of the faecal microbiome to investigate the relationship between diet, microbiome stability and rates of body mass gain in a migratory capital-breeding bird, the light-bellied Brent goose (Branta bernicla hrota). Our findings suggest that generalist feeders have microbiomes that are intermediate in diversity and composition between two foraging specialisms, and also show higher within-individual plasticity. We also suggest a link between foraging phenotype and the rates of mass gain during the spring staging of a capital breeder. This study offers rare insight into individual-level temporal dynamics of the gut microbiome of a wild host. Further work is needed to uncover the functional link between individual dietary choices, gut microbiome structure and stability, and the implications this has for the reproductive success of this capital breeder.

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds

Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai'i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai'i 'amakihi (Chlorodrepanis virens), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 'amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai'i Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.

Convergence of gut microbiota in myrmecophagous amphibians

The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.

Convergent remodelling of the gut microbiome is associated with host energetic condition over long-distance migration

The gut microbiome can be thought of as a virtual organ given its immense metabolic capacity and profound effects on host physiology. Migratory birds are capable of adaptively modulating many aspects of their physiology to facilitate long-distance movements, raising the hypothesis that their microbiome may undergo a parallel remodeling process that helps to meet the energetic demands of migration.To test this hypothesis, we investigated changes in gut microbiome composition and function over the fall migration of the Blackpoll Warbler (Setophaga striata), which exhibits one of the longest known autumnal migratory routes of any songbird and rapidly undergoes extensive physiological remodeling during migration.Overall, our results showed that the Blackpoll Warbler microbiome differed significantly across phases of fall migration. This pattern was driven by a dramatic increase in the relative abundance of Proteobacteria, and more specifically a single 16S rRNA gene amplicon sequence variant belonging to the family Enterobacteriaceae. Further, Blackpoll Warblers exhibited a progressive reduction in microbiome diversity and within-group variance over migration, indicating convergence of microbiome composition among individuals during long-distance migration. Metagenomic analysis revealed that the gut microbiome of staging individuals was enriched in bacterial pathways involved in vitamin, amino acid, and fatty acid biosynthesis, as well as carbohydrate metabolism, and that these pathways were in turn positively associated with host body mass and subcutaneous fat deposits.Together, these results provide evidence that the gut microbiome of migratory birds may undergo adaptive remodeling to meet the physiological and energetic demands of long-distance migration.

Responses of the gut microbiota to environmental heavy metal pollution in tree sparrow (Passer montanus) nestlings

Gut microbiota plays a critical role in regulating the health and adaptation of wildlife. However, our understanding of how exposure to environmental heavy metals influences the gut microbiota of wild birds, particularly during the vulnerable and sensitive nestling stage, remains limited. In order to investigate the relationship between heavy metals and the gut microbiota, we analyzed the characteristics of gut microbiota and heavy metals levels in tree sparrow nestlings at different ages (6, 9 and 12-day-old). The study was conducted in two distinct areas: Baiyin (BY), which is heavily contaminated with heavy metals, and Liujiaxia (LJX), a relatively unpolluted area. Our result reveled a decrease in gut microbiota diversity and increased inter-individual variation among nestlings in BY. However, we also observed an increase in the abundance of bacterial groups and an up-regulation of bacterial metabolic functions associated with resistance to heavy metals toxicity in BY. Furthermore, we identified a metal-associated shift in the relative abundance of microbial taxa in 12-day-old tree sparrow nestlings in BY, particularly involving Aeromonadaceae, Ruminococcaceae and Pseudomonadaceae. Moreover, a significant positive correlation was found between the body condition of tree sparrow nestlings and the abundance of Bifidobacteriaceae in BY. Collectively, our findings indicate that the gut microbiota of tree sparrow nestlings is susceptible to heavy metals during early development. However, the results also highlight the presence of adaptive responses that enable them to effectively cope with environmental heavy metal pollution.

Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China

The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.

16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method

The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.

Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures

Introduction

Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown.

Methods

In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures.

Results

In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome.

Discussion

Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.

Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds

The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.

Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration

Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks

Gut microbial communities are complex and heterogeneous and play critical roles for animal hosts. Early-life disruptions to microbiome establishment can negatively impact host fitness and development. However, the consequences of such early-life disruptions remain unknown in wild birds. To help fill this gap, we investigated the effect of continuous early-life gut microbiome disruptions on the establishment and development of gut communities in wild Great tit (Parus major) and Blue tit (Cyanistes caeruleus) nestlings by applying antibiotics and probiotics. Treatment neither affected nestling growth nor their gut microbiome composition. Independent of treatment, nestling gut microbiomes of both species grouped by brood, which shared the highest numbers of bacterial taxa with both nest environment and their mother. Although fathers showed different gut communities than their nestlings and nests, they still contributed to structuring chick microbiomes. Lastly, we observed that the distance between nests increased inter-brood microbiome dissimilarity, but only in Great tits, indicating that species-specific foraging behaviour and/or microhabitat influence gut microbiomes. Overall, the strong maternal effect, driven by continuous recolonization from the nest environment and vertical transfer of microbes during feeding, appears to provide resilience towards early-life disruptions in nestling gut microbiomes.

No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings

BACKGROUND

The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured.

RESULTS

Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival.

CONCLUSIONS

We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae)

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick

Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 posthatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 posthatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis and gas chromatography-mass spectrometry on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of enterococci in STm-infected chicks. Unique metabolites, including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, were present only in the cecal content of STm-infected chicks. The metagenomic data suggested that the microbiota in STm-infected chicks contained a higher abundance of genes, from STm itself, involved in branched-chain amino acid synthesis. We generated an ilvC deletion mutant (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of l-isoleucine and l-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored the growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development. IMPORTANCE Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses, we captured the development of chick microbiota to 19 days posthatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched-chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make l-isoleucine and l-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.

Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird

Background

The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela.

Methods

Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO.

Results

The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences.

Conclusion

Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.

Advances in the study of microbiota in reproductive biology: A short review of recent research, following Leclaire et al. (2022)

Research on microbiota dynamics in humans (Gilbert et al., 2018), model organisms (Douglas, 2019), and free-ranging, wild animals (Grond et al., 2018) has taken off in the past decades, and even in nonmodel organisms, research has already shifted from initial characterization studies to those examining associations with behaviour and fitness (Bodawatta et al., 2022; Corl et al., 2020; Risely et al., 2018; Turjeman et al., 2020). The microbiota is known to change through pregnancy and parturition (Koren et al., 2012), and there is also evidence in humans that infertility may be associated with microbiota composition (Silva & Giacobini, 2019), but how the microbiota is related to reproductive fitness in free-ranging species is largely understudied or primarily focused on pathogen transmission (sexually transmitted infection) (Lombardo, 1998; Sheldon, 1993). In a From the Cover article in this issue of Molecular Ecology, Leclaire et al. (2022) begin to tease apart the relationship between the microbiota and reproductive fitness using the black-legged kittiwake (Rissa tridactyla) as their study species. Following characterization of the microbiota in multiple body sites of breeders and nonbreeders, they discovered that breeding and nonbreeding females had distinct microbiota, that higher performing female breeders had lower abundances of potentially pathogenic taxa, and that feathers of these birds were characterized by reduced microbiota diversity compared to low-performance breeders. Leclaire and her colleagues provide some of the first evidence of body-wide differences in microbiota composition in relation to breeding status. Their research further supports the relationship between the microbiota and host fitness, and additional studies focusing on this topic can continue to unravel intricacies in host-microbiota-reproductive strategy evolution (Comizzoli et al., 2021; Rowe et al., 2020). Here, I review the results of Leclaire et al. (2022) and provide a wider context for their research by reviewing other studies in the field, focusing on avian species.

Past and future: Urbanization and the avian endocrine system

Urban environments are evolutionarily novel and differ from natural environments in many respects including food and/or water availability, predation, noise, light, air quality, pathogens, biodiversity, and temperature. The success of organisms in urban environments requires physiological plasticity and adjustments that have been described extensively, including in birds residing in geographically and climatically diverse regions. These studies have revealed a few relatively consistent differences between urban and non-urban conspecifics. For example, seasonally breeding urban birds often develop their reproductive system earlier than non-urban birds, perhaps in response to more abundant trophic resources. In most instances, however, analyses of existing data indicate no general pattern distinguishing urban and non-urban birds. It is, for instance, often hypothesized that urban environments are stressful, yet the activity of the hypothalamus-pituitary-adrenal axis does not differ consistently between urban and non-urban birds. A similar conclusion is reached by comparing blood indices of metabolism. The origin of these disparities remains poorly understood, partly because many studies are correlative rather than aiming at establishing causality, which effectively limits our ability to formulate specific hypotheses regarding the impacts of urbanization on wildlife. We suggest that future research will benefit from prioritizing mechanistic approaches to identify environmental factors that shape the phenotypic responses of organisms to urbanization and the neuroendocrine and metabolic bases of these responses. Further, it will be critical to elucidate whether factors affect these responses (a) cumulatively or synergistically; and (b) differentially as a function of age, sex, reproductive status, season, and mobility within the urban environment. Research to date has used various taxa that differ greatly not only phylogenetically, but also with regard to ecological requirements, social systems, propensity to consume anthropogenic food, and behavioral responses to human presence. Researchers may instead benefit from standardizing approaches to examine a small number of representative models with wide geographic distribution and that occupy diverse urban ecosystems.

Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia (Leiothrix argentauris) living in mining area

The complex gut bacterial communities have a major impact on organismal health. However, knowledge of the effects of habitat change on the gut microbiota of wild birds is limited. In this study, we characterized the gut microbiota of two different subspecies of the Silver-eared Mesia (Leiothrix argentauris), the native subspecies (L. a. rubrogularis) and immigrant subspecies (L. a. vernayi), using 16S rRNA gene high-throughput sequencing. These two subspecies live in a trace metal-contaminated area, and L. a. vernayi was trafficked. They are an excellent system for studying how the gut microbiome of wild animal changes when they move to new habitats. We hypothesized that the immigrant subspecies would develop the same adaptations as the native subspecies in response to habitat changes. The results showed that there were no significant differences in the composition, diversity, or functional metabolism of gut microbiota between native and immigrant subspecies under the combined action of similar influencing factors (the p values of all analyses of variance >0.05). In addition, the composition and functional metabolism of gut microbiota in two subspecies showed adaptation against trace metal damage. Linear discriminant analysis effect size (LEfSe) analysis revealed that Massilia in the intestinal microbiota of immigrant subspecies was significantly higher than that of native subspecies, suggesting that immigrant subspecies suffered habitat change. Finally, we found that these two subspecies living in the mining area had an extremely high proportion of pathogenic bacteria in their gut microbiota (about 90%), much higher than in other species (about 50%) living in wild environment. Our results revealed the adaptation of intestinal microbiota of immigrant Silver-eared Mesias under heavy metals stress, which would provide guidance for biodiversity conservation and pollution management in mining area.

Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

BACKGROUND

Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.

RESULTS

The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae.

CONCLUSIONS

While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers

Understanding the factors that shape microbiomes can provide insight into the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary and evolutionary influences on gut microbiome structure. We performed faecal metabarcoding to characterize both the gut microbiome and diet of 15 wood-warbler species across a 4-year period and from two geographical localities. We find host taxonomy generally explained ~10% of the variation between individuals, which is ~6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (bla_TEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.

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.

An urban diet differentially alters the gut microbiome and metabolomic profiles compared with a seed diet in mourning doves

Urbanization influences food quality and availability for many avian species, with increased access to human refuse and food subsidies in built environments. In relation to such nutritional intakes and their presumed impact on microbes harbored in the intestinal tract and metabolic profiles of host physiological systems, our overall knowledge of the role of gut microbiome (GM) and metabolomic expression in the avian host lags far behind our understanding of mammals. Therefore, the objective of this investigation was to examine the potential differential effect of an urban modeled versus control (i.e., bird seed) diet on the GM, the metabolic profiles of plasma, liver, adipose, kidney, and muscle tissues, and circulating endotoxin and inflammatory factors in urban-caught mourning doves (Zenaida macroura). We hypothesized that the urban diet would differently impact the profiles of the GM and tissue metabolomes and increase plasma lipopolysaccharide (LPS) and proinflammatory factors compared with animals fed a seed diet. After a 4-wk-diet period, contents of the large intestine were sequenced to profile the microbiome, metabolomic analyses were performed on plasma and tissue homogenates, and circulating LPS and inflammatory markers were assessed. The composition of the GM was significantly dissimilar between diets, with greater abundance of Erysipelatoclostridiaceae, Sanguibacteraceae, Oribacterium, and Sanguibacter and decreased circulating LPS in the urban-fed birds. These differences were largely not reflected in the surveyed metabolomes and plasma inflammatory markers. This research supports the notion that the microbial composition in urban doves is impacted by diet, though may only weakly associate with host physiology.

Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter

BACKGROUND

The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material.

RESULTS

Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria.

CONCLUSIONS

Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.

Significant differences in intestinal fungal community of hooded cranes along the wintering periods

The intestinal microbiota play vital roles for health of wild birds in many ways. Migratory birds with unique life history might increase the risk of pathogenic transmission across the regions. However, few studies have clarified the fungal community structure and inferred the potential pathogens in guts of migratory birds. The high-throughput sequencing method was applied to analyze the fungal community structure and detect the potential fungal pathogens in guts of hooded cranes among different wintering stages. Significant differences were found in gut fungal community composition of hooded cranes among three wintering stages, with the lowest fungal diversity in the late wintering stage. In the late stage, hooded cranes harbored higher relative abundance of plant saprotroph, contributing to food digestion for hosts. Hooded cranes were associated with the lowest diversity and relative abundance of animal pathogens in the late wintering stage. There was an increasing trend of deterministic process for gut fungal community assembly, suggesting that hosts interaction with their fungal communities changed by enhanced gut selection/filtering along wintering periods. Hooded crane was associated with the strongest gut selection/filtering to obtain defined gut fungal community with retaining probiotics (i.e., plant saprotroph) and exclusion of certain pathogens in the late wintering stage. Overall, these results demonstrated that hooded cranes might regulate their gut microbiota to enhance digestion and decrease gut pathogens in preparation for long-term migration.

Comparative Analysis of the Gut Microbiota of Three Sympatric Terrestrial Wild Bird Species Overwintering in Farmland Habitats

The gut microbiota of wild birds are affected by complex factors, and cross-species transmission may pose challenges for the host to maintain stable gut symbionts. Farmland habitats are environments strongly manipulated by humans, and the environmental characteristics within a large area are highly consistent. These features provide the ideal natural conditions for conducting cross-species comparative studies on gut microbiota among wild birds. This study aimed to investigate and compare the gut microbiota of three common farmland-dependent bird species, Great Bustard (Otis tarda dybowskii), Common Crane (Grus grus), and Common Coot (Fulica atra), in a homogeneous habitat during the wintering period. The results indicated that under the combined action of similar influencing factors, the gut microbiota of different host species did not undergo adaptive convergence, maintained relatively independent structures, and exhibited host-driven signals. In addition, we also detected various pathogenic genera that may cause outbreaks of periodic infections among sympatric migratory birds. We conclude that phylosymbiosis may occur between some wild birds and their gut microbiota. Usage of non-invasive methods to monitor the changes in the gut microbiota of wild bird fecal samples has important implications for the conservation of endangered species.

Incomplete Concordance Between Host Phylogeny and Gut Microbial Community in Tibetan Wetland Birds

Gut microbial communities of animals play key roles in host evolution, while the relationship between gut microbiota and host evolution in Tibetan birds remains unknown. Herein, we sequenced the gut microbiota of 67 wild birds of seven species dwelling in the Tibetan wetlands. We found an obvious species-specific structure of gut microbiota among these plateau birds whose habitats were overlapped. Different from plateau mammals, there was no strict synergy between the hierarchical tree of gut microbial community and species phylogeny. In brown-headed gulls (Larus brunnicephalus) as an example, the structure of gut microbiota differed in different habitats, and the relative abundance of bacteria, such as Lactobacillus, Streptococcus, Paracoccus, Lachnospiraceae, and Vibrio, significantly correlated with altitude. Finally, we found various pathogenic bacteria in the birds of these plateau wetlands, and the interspecific differences were related to their diet and living environments.

Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes

Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.

Bowel Movement: Integrating Host Mobility and Microbial Transmission Across Host Taxa

The gut microbiota of animals displays a high degree of plasticity with respect to environmental or dietary adaptations and is shaped by factors like social interactions, diet diversity or the local environment. But the contribution of these drivers varies across host taxa and our ability to explain microbiome variability within wild populations remains limited. Terrestrial animals have divergent mobility ranges and can either crawl, walk or fly, from a couple of centimeters toward thousands of kilometers. Animal movement has been little regarded in host microbiota frameworks, though it can directly influence major drivers of the host microbiota: (1) Aggregation movement can enhance social transmissions, (2) foraging movement can extend range of diet diversity, and (3) dispersal movement determines the local environment of a host. Here, I would like to outline how movement behaviors of different host taxa matter for microbial acquisition across mammals, birds as well as insects. Host movement can have contrasting effects and either reduce or enlarge spatial scale. Increased dispersal movement could dissolve local effects of sampling location, while aggregation could enhance inter-host transmissions and uniformity among social groups. Host movement can also extend the boundaries of microbial dispersal limitations and connect habitat patches across plant-pollinator networks, while the microbiota of wild populations could converge toward a uniform pattern when mobility is interrupted in captivity or laboratory settings. Hence, the implementation of host movement would be a valuable addition to the metacommunity concept, to comprehend microbial dispersal within and across trophic levels.

Specific gut bacterial responses to natural diets of tropical birds

The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.

Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers

Background

The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored.

Methods

We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan.

Results

A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki.

Conclusion

ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.