Wild Birds Research Articles

Isolation and molecular characterization of velogenic Newcastle disease virus genotype VII.1.1 from commercial broilers and wild birds in Matrouh governorate, Egypt

Isolation and molecular characterization of velogenic Newcastle disease virus genotype VII.1.1 from commercial broilers and wild birds in Matrouh governorate, Egypt

A case study of the 2023 highly pathogenic avian influenza (HPAI) outbreak in tern (Sternidae) colonies on the east coast of the Republic of Ireland

ABSTRACT Capsule:HPAI H5N1 had a significant impact on breeding Common Terns Sterna hirundo, Arctic Terns Sterna paradisaea and Roseate Terns Sterna dougallii on the east coast of the Republic of Ireland (ROI) in 2023, with a lesser impact on Sandwich Terns Thalasseus sandvicensis and only two cases among Little Terns Sternula albifrons. Aims: To document the outbreak of HPAI H5N1 in the tern colonies on the east coast of ROI during the 2023 breeding season. Methods:Precautions were taken from the start of the breeding season, including personal protective equipment (PPE) and safe operating procedures. Regular meetings were held between BirdWatch Ireland and the National Parks and Wildlife Service (NPWS) to respond to the emerging situation. Once HPAI was confirmed in a colony, all ringing and nest visits were stopped. Carcass removal was carried out at all affected colonies and most carcasses were incinerated. Results: Common Terns suffered the highest mortality across all colonies in 2023, with smaller but notable numbers of dead Roseate Terns and Arctic Terns, but very few Sandwich Terns and only two Little Tern deaths were attributed to HPAI. Conclusion: Regular meetings between relevant organizations were invaluable in preparing for outbreaks and ensuring an adaptive approach as the situation changed over time and between colonies. There was no way of knowing if the actions taken were effective, as the pattern of virus spread between species and sites remains poorly understood. Future clarity over the role of various state agencies and other relevant bodies in responding to HPAI in wild birds, greater sharing of real-time information, and pre-arranged agreements to ensure rapid testing and disposal of carcasses, would be useful to ensure an effective response to future outbreaks.

Backyard flock sampling and artificial intelligence: A dual strategy for early detection of Avian Influenza and Newcastle Disease

Avian Influenza (AI) and Newcastle Disease (ND) are significant avian diseases that pose substantial threats to the commercial poultry industry due to their high contagion rates and potential for severe outcomes. Recent shifts in the epidemiology and ecology of both viruses have led to devastating impacts on wild bird and poultry populations, as well as farms and communities worldwide. These challenges underscore the necessity for One Health approaches to pandemic prevention and preparedness, emphasizing the need for multisectoral collaboration among animal, environmental, and public health sectors. To mitigate future pandemic risks, it is essential to control the transmission of AI and ND viruses among domestic and wild animals as well as humans. This involves addressing the upstream drivers of outbreaks, ensuring rapid response mechanisms, and conducting thorough risk assessments for zoonotic diseases. Effective implementation and maintenance of prevention programs, surveillance, and outbreak responses require strong political commitment and sustainable funding. A robust combination of active and passive surveillance strategies should be applied to monitor and control them. In addition, the integration of modern technologies, such as artificial intelligence and big data analytics, can enhance both active and passive surveillance efforts by improving the accuracy and speed of data collection, analysis, and reporting. The use of backyard flocks as an early warning system for avian diseases represents a proactive approach to understanding and managing the risks associated with AI and ND through targeted surveillance and timely interventions. In response to these challenges, the EpirORNIS Project aimed to leverage these sentinel backyard flocks for early detection of AI and ND, thereby enhancing surveillance and control strategies.

Transmission of a human isolate of clade 2.3.4.4b A(H5N1) virus in ferrets.

Since 2020, there has been unprecedented global spread of highly pathogenic avian influenza A(H5N1) in wild bird populations with spillover into a variety of mammalian species and sporadically humans1. In March 2024, clade 2.3.4.4b A(H5N1) virus was first detected in dairy cattle in the U.S., with subsequent detection in numerous states2, leading to over a dozen confirmed human cases3,4. In this study, we employed the ferret model, a well-characterized species that permits concurrent investigation of viral pathogenicity and transmissibility5 in the evaluation of A/Texas/37/2024 (TX/37) A(H5N1) virus isolated from a dairy farm worker in Texas6. Here, we show that the virus has a remarkable ability for robust systemic infection in ferrets, leading to high levels of virus shedding and spread to naïve contacts. Ferrets inoculated with TX/37 rapidly exhibited a severe and fatal infection, characterized by viremia and extrapulmonary spread. The virus efficiently transmitted in a direct contact setting and was capable of indirect transmission via fomites. Airborne transmission was corroborated by the detection of infectious virus shed into the air by infected animals, albeit at lower levels compared to the highly transmissible human seasonal and swine-origin H1 subtype strains. Our results show that despite maintaining anavian-like receptor binding specificity, TX/37 displays heightened virulence, transmissibility, and airborne shedding relative to other clade 2.3.4.4b virus isolated prior to the 2024 cattle outbreaks7, underscoring the need for continued public health vigilance.

Influenza A as a True Zoonotic Pathogen: Transmission through Reservoir Hosts

Influenza A virus (IAV) represents a considerable global health threat due to its rapid mutation rates and broad host range, facilitating cross-species transmission and enabling the virus to evade immune defenses. This review explores the molecular mechanisms underlying IAV's pathogenicity, focusing on its zoonotic potential through reservoir hosts, such as wild birds and swine. The virus's ability to undergo antigenic shift and drift allows it to continually adapt to new hosts and environments, posing challenges for control and treatment. Current antiviral therapies are limited by the emergence of resistant strains, underscoring the necessity for innovative vaccine development and treatment strategies. By examining IAV's molecular evolution, immune evasion tactics, and transmission dynamics, this review highlights the critical need for enhanced surveillance, improved therapeutic options, and international cooperation to mitigate future outbreaks. A deeper understanding of these processes is essential to inform public health efforts and combat the persistent threat of IAV.

Surveillance for Avian Influenza in Wild Birds in the Lombardy Region (Italy) in the Period 2022–2024

Influenza A virus (AIV) circulation was investigated in the Lombardy region, during 2022–2024, in wild ducks (through hunting and sampling of faecal samples within natural parks) and wild birds found dead. Samples were analysed through real-time RT-PCRs for Influenza A virus, H5 and H7. Whole genome sequencing was performed on AIV-positive samples. Screening of 3497 hunted Anatidae revealed a total of 184 positive samples. Complete sequencing of 136 samples highlighted the presence of 21 different subtypes ranging from H1N1 to H12N5. The H5N1 HPAIV (high pathogenic AIV) subtype, clade 2.3.4.4b, was the most common during the 2022–2023 winter season (31.8%), while H5 LPAI (low pathogenic AIV) strains were the most prevalent (28.6%) in the 2023–2024 season. The molecular survey on wild birds found dead (n = 481) showed two positive buzzards (14%, 2/14), one grey heron (5.5%, 1/18) and one kestrel (7.6%, 1/13). Regarding the order of Charadriiformes, the dead gulls sampled in 2022 (17 birds) were all negative, whereas 85 out of 167 (51%) individuals were positive in 2023. All positives were caused by an H5N1 HPAIV clade 2.3.4.4b virus belonging to genotype BB. All the faecal samples (1699) received from passive surveillance in nature parks were analysed for AIV with negative results.

Phylogenetic Characterization of Novel Reassortant 2.3.4.4b H5N8 Highly Pathogenic Avian Influenza Viruses Isolated from Domestic Ducks in Egypt During the Winter Season 2021–2022

Avian influenza (AI) is an extremely contagious viral disease of domestic and wild birds that can spread rapidly among bird populations, inducing serious economic losses in the poultry industry. During the winter season 2021–2022, we isolated seventeen highly pathogenic avian influenza (HPAI) H5N8 viruses from outbreaks involving ducks in Egypt, occurring in both backyard and farm settings. The aim of this study was to pinpoint genetic key substitutions (KSs) that could heighten the risk of a human pandemic by influencing the virus’s virulence, replication ability, host specificity, susceptibility to drugs, or transmissibility. To understand their evolution, origin, and potential risks for a human pandemic, whole-genome sequencing and phylogenetic analysis were conducted. Our analysis identified numerous distinctive mutations in the Egyptian H5N8 viruses, suggesting potential enhancements in virulence, resistance to antiviral drugs, and facilitation of transmission in mammals. In this study, at least five genotypes within one genome constellation of H5N8 viruses were identified, raising concerns about the potential emergence of novel viruses with altered characteristics through reassortment between different genotypes and distinct groups. These findings underscore the role of ducks in the virus’s evolutionary process and emphasize the urgent need for enhanced biosecurity measures in domestic duck farms to mitigate pandemic risk.

WNV and SLEV coinfection in avian and mosquito hosts: impact on viremia, antibody responses, and vector competence.

West Nile virus (WNV) and St. Louis encephalitis virus (SLEV) are closely related flaviviruses that can cause encephalitis in humans and related diseases in animals. In nature, both are transmitted by Culex, with wild birds, including jays, sparrows, and robins, serving as vertebrate hosts. WNV and SLEV circulate in the same environments and have recently caused concurrent disease outbreaks in humans. The extent that coinfection of mosquitoes or birds may alter transmission dynamics, however, is not well characterized. We therefore sought to determine if coinfection alters infection kinetics and virus levels in birds and infection rates in mosquitoes. Accordingly, American robins (Turdus migratorius), two species of mosquitoes, and vertebrate and invertebrate cells were infected with WNV and/or SLEV to assess how simultaneous exposure may alter infection outcomes. There was variable impact of coinfection in vertebrate cells, with some evidence that SLEV can suppress WNV replication. However, robins had comparable viremia and antibody responses regardless of coinfection. Conversely, in Culex cells and mosquitoes, we saw a minimal impact of simultaneous exposure to both viruses on replication, with comparable infection, dissemination, and transmission rates in singly infected and coinfected mosquitoes. Importantly, while WNV and SLEV levels in coinfected mosquito midguts were positively correlated, we saw no correlation between them in salivary glands and saliva. These results reveal that while coinfection can occur in both avian and mosquito hosts, the viruses minimally impact one another. The potential for coinfection to alter virus population structure or the likelihood of rare genotypes emerging remains unknown.IMPORTANCEWest Nile virus (WNV) and St. Louis encephalitis virus (SLEV) are closely related viruses that are transmitted by the same mosquitoes and infect the same birds in nature. Both viruses circulate in the same regions and have caused concurrent outbreaks in humans. It is possible that mosquitoes, birds, and/or humans could be infected with both WNV and SLEV simultaneously, as has been observed with Zika, chikungunya, and dengue viruses. To study the impact of coinfection, we experimentally infected vertebrate and invertebrate cells, American robins, and two Culex species with WNV and/or SLEV. Robins were efficiently coinfected, with no impact of coinfection on virus levels or immune response. Similarly, in mosquitoes, coinfection did not impact infection rates, and mosquitoes could transmit both WNV and SLEV together. These results reveal that WNV and SLEV coinfection in birds and mosquitoes can occur in nature, which may impact public health and human disease risk.

Antimicrobial Resistance and Pathotypes of Escherichia coli Isolates from Yellow-Legged Seagulls (Larus michahellis) in Central Italy

Seagulls are synanthropic wild birds that can contaminate, through their droppings, beaches, urban and peri-urban environments. This concern is more serious when seagulls eliminate antimicrobial-resistant pathogenic bacteria. This study analyzed the fecal samples from 137 yellow-legged seagulls (Larus michahellis) from Central Italy. A total of 218 Escherichia coli strains were isolated and analyzed for phenotypic and genotypic antimicrobial resistance and to identify the virulence genes characterizing different pathotypes. The disk diffusion method on all isolates found relevant resistance rates to ampicillin (38.99%), tetracycline (23.85%), and enrofloxacin (21.10%). On the basis of all results obtained with this test, 62 (28.44%) isolates were classified as multidrug-resistant (MDR) and 6 (2.75%) as extensive drug-resistant (XDR). Molecular analyses conducted on the strains phenotypically resistant to carbapenems, cephalosporins, and penicillins found 9/37 (24.32%) strains positive for blaOXA-48, 52/103 (50.49%) for blaTEM, 12/103 (11.65%) for blaCMY2, 3/103 (2.91%) for blaCTX, and 1/103 (0.97%,) for blaSHV. PCR to detect virulence genes characterizing different pathotypes found that 40 (18.35%) isolates had the astA gene, indicative of the enteroaggregative (EAEC) pathotype, 2 (0.92%) had cnf1, 2 (0.92%) had cnf2, and 1 (0.46%) had cdt-IV. All five (2.29%) strains were reportable as necrotoxigenic (NTEC), while 4 (1.83%) had both eaeA and escV, reportable as enteropathogenic (EPEC). Measures to limit seagulls’ access where humans and other animals reside are pivotal to reduce the risk of infection with antimicrobial-resistant and pathogenetic E. coli strains.

Using GPS and accelerometer data to remotely detect breeding events in two elusive ground-nesting steppe birds

BackgroundModern biologging technologies allow researchers to gain a better understanding of animal movements, offering opportunities to measure survival and remotely study the breeding success of wild birds, i.e., by locating nests. This is particularly useful for species whose nests are difficult to find or access, or when disturbances can impact the breeding outcome. We developed and validated, with field data, a framework to detect nesting events by two sandgrouse species, the black-bellied (Pterocles orientalis) and pin-tailed sandgrouse (Pterocles alchata), using GPS and Overall Dynamic Body Acceleration (ODBA) data. Sandgrouses are ground-nesting, cryptic, and elusive birds with biparental incubation efforts. Because both sexes take turns to incubate, a novel framework considering when tagged individuals are on incubation duty or not needs to be designed to detect nests.ResultsWe tagged 52 birds with high-resolution GPS devices to monitor their breeding during 2021–24. Using remote tracking and field data from the first 2 years (2021–22), we first determined sex-specific time windows for incubation to maximise differentiation between incubation and non-incubation behaviours. We then used a threshold-based classification to identify incubation days and inferred the minimum number of successive incubation days needed to correctly identify a nesting event. We show how ODBA and GPS data can be used to successfully detect nests incubated for only 2 or 3 days. GPS-only data or combined GPS-ODBA data had a success rate of around 95%, whereas ODBA-only data had a success rate of 100%. Cross-validation using data from 2023 to 2024 confirmed the model’s performance, showing an overall success > 90% for GPS-only and ODBA-only data and of 85% for combined GPS–ODBA data.ConclusionsBy accurately identifying nesting events, our framework offers new opportunities to study the breeding of conservation-dependent species. Besides its applicability to ground-nesting species with biparental care and sex-specific incubation schedules, the framework can be adapted to other bird species sensitive to disturbances or with inaccessible nesting sites. By doing so, it reduces the need for nest visits and associated disturbances, as well as the carbon footprint and expenses associated with fieldwork.

Data note on the Avian Contact Study: a questionnaire resource for avian influenza public health planning

The Avian Contact Study is a cross-sectional questionnaire of poultry workers and other individuals who have contact with domestic and/or wild birds in the UK. The questionnaire was launched online in May 2024 and in-person responses were gathered at the British Pig and Poultry Fair in Birmingham on 15 and 16 May 2024. This Data Note documents questionnaire development, content and delivery methods. Data collected include information on demographics, seasonal influenza vaccination, avian influenza exposure, contact with birds and people, and awareness of avian influenza. This Data Note provides insights into the first data release collected up to 31 July 2024 for 225 respondents. Data have been released as a University of Bristol held dataset available upon request. The Avian Contact Study provides a pilot resource for research into avian influenza from a zoonotic perspective.

Wild Bird Species Structure and Feeding Guilds in Agricultural Area at Zagazig District, Sharkia Governorate, Egypt

Wild Bird Species Structure and Feeding Guilds in Agricultural Area at Zagazig District, Sharkia Governorate, Egypt

Birds as reservoirs: unraveling the global spread of Gamma- and Deltacoronaviruses.

Avian migration is a global phenomenon that transcends geographical boundaries. These migratory birds serve as unwitting carriers of diverse Gammacoronaviruses (γ-CoVs) and Deltacoronaviruses (δ-CoVs). While recombination events have been documented among γ-CoVs in avian species and β-CoVs in mammals, evidence for recombination between CoVs of distinct genera remains limited. This minireview examines the prevalence of CoVs in both domestic waterfowl (ducks and geese) and wild bird populations inhabiting various regions. We investigate the dissemination patterns of γ-CoVs and δ-CoVs among these populations, highlighting their shared characteristics. Furthermore, the review explores the intricate web of cross-species transmission of δ-CoVs from wild birds to mammals, with a particular focus on pigs. Understanding the distinct features of CoVs harbored by waterfowl and wild birds and their potential for cross-species transmission is crucial for preparedness and response to future CoV epidemics.

First evidence of age-dependent decreases in non-persistent pesticide mixtures in nestlings of a farmland raptor

Intensive use of synthetic pesticides in conventional agriculture may harm non-target organisms through sublethal effects on life-history traits. Farmland birds are exposed throughout their life cycle, but the fate of non-persistent pesticide mixtures in wild birds remains unknown. In this study, we investigated changes in pesticide contamination levels in Montagu’s harrier (Circus pygargus) nestlings during their growth. In total, 35 chicks were sampled twice during the rearing period, and blood was tested for 116 pesticides to assess pesticide load through two proxies; the number of pesticides detected and the sum of pesticide concentrations. Body mass and tarsus length were also measured to estimate body condition. Across the two sampling times, nine herbicides, five insecticides and four fungicides were detected. Contamination levels decreased significantly with nestling age irrespective of sampling date, and there was no relationship between pesticide load and body condition. Moreover, concentrations of chlorpyrifos-methyl, fenpropidin, metamitron, picloram and S-metolachlor, all detected throughout the rearing period, were unrelated to any of the explanatory variables. However, ethofumesate concentrations decreased significantly with chick age. This study provides the first evidence that non-persistent pesticide mixtures can decrease with age in wild nestlings. This has implications for understanding how chicks are contaminated and provides new insights on pesticide fate within organisms.

Effects of Urban Lighting at Night on Daytime Songbird Aggression

Many animals require sleep for daily functions. In spring, songbirds expend a great deal of energy early in the day by singing to attract mates and aggressively protecting territory. Some evidence suggests that artificial lighting at night (ALAN) in the environment of wild birds increases their nighttime activity that, in turn, contributes to sleep loss. This study investigated how ALAN affects northern cardinal (Cardinalis cardinalis) response to experimental aggressive intrusion by conspecifics. The hypothesis tested is that high ALAN near cardinal roosting spots would cause those individuals to have less energy for daytime aggressive behaviors. After selecting known dark and bright urban roosting locations, ALAN was measured at specific sites with active cardinal territories during nighttime hours. Observers returned in the morning to present cardinal territorial songs using standardized call playback protocols. Aggressive behaviors of responding cardinals were recorded and used to quantify aggression intensity. Standard aggression measures included response latency, distance from bird to speaker, number of songs, hops, and flip flops. An aggression index was obtained using factor analysis which confirmed that aggressive responses featured short latency and approach distances, few chips, and many songs, flip flops, and hops. Analysis of variance revealed that cardinals roosting in high ALAN engaged in significantly more aggressive morning responses; directly contradicting predictions and previously published findings. One possible explanation for this result is that high ALAN might improve sleep in cardinals. To test this, autonomous recording units (ARUs) were placed in study locations to record nighttime calling behaviors in high and low ALAN. Insufficient data were obtained to clarify whether nighttime activity was reduced significantly by ALAN exposure. However, results showed that nighttime activity by cardinals is strongly influenced by moonlight, and that determination of the influence of ALAN on nighttime and daytime avian behavior must include measures of lunar illumination.

Dairy cows inoculated with highly pathogenic avian influenza virus H5N1.

Highly pathogenic avian influenza (HPAI) H5N1 hemagglutinin clade 2.3.4.4b was detected in the United States in 2021. These HPAI viruses caused mortality events in poultry, wild birds, and wild mammals. On March 25, 2024, HPAI H5N1 clade 2.3.4.4b was confirmed in a dairy cow in Texas in response to a multi-state investigation into milk production losses.1 Over 200 positive herds were identified in 14 U.S. states. The case description included reduced feed intake and rumen motility in lactating cows, decreased milk production, and thick yellow milk.2,3 The diagnostic investigation revealed viral RNA in milk and mammary tissue with alveolar epithelial degeneration and necrosis and positive immunoreactivity of glandular epithelium. A single transmission event, likely from birds, was followed by limited local transmission and onward horizontal transmission of H5N1 clade 2.3.4.4b genotype B3.13.4 We sought to experimentally reproduce infection with genotype B3.13 in Holstein yearling heifers and lactating cows. Heifers were inoculated by aerosol respiratory route and cows by intramammary route. Clinical disease was mild in heifers, but infection was confirmed by virus detection, lesions, and seroconversion. Clinical disease in lactating cows included decreased rumen motility, changes to milk appearance, and production losses. Infection was confirmed by high levels of viral RNA detected in milk, virus isolation, lesions in mammary tissue, and seroconversion. This study provides the foundation to investigate additional routes of infection, pathogenesis, transmission, and intervention strategies.

Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population

Empirical studies from laboratory systems and humans show that the gut microbiota is linked to host health. Similar evidence for effects on traits linked to fitness in nature is rare, not least because experimentally manipulating the gut microbiota is challenging. We isolated, characterized, and cultured a bacterial strain, Lactobacillus kimchicus APC4233, directly from a wild bird (the great tit Parus major) and provided it as a self-administered dietary supplement. We assessed the impact of the treatment on the host microbiota community, on weight, and tested whether the treatment affected a previous result linking microbiota alpha diversity to weight in nestlings. The treatment dramatically increased L. kimchicus abundance in the gut microbiota and increased alpha diversity. This effect was strongest in the youngest birds, validating earlier findings pointing to a brief developmental window when the gut microbiota are most sensitive. In time-lagged models, nestling weight was higher in the treatment birds suggesting L. kimchicus may have probiotic potential. There was also a positive time-lagged relationship between diversity and weight in control birds but not in the treatment birds, suggesting L. kimchicus helped birds compensate for low alpha diversity. We discuss why ecological context is likely key when predicting impacts of the microbiome. The manipulation of the gut microbiota with a host native strain in this wild population provides direct evidence for the role of the microbiota in the ecology and evolution of natural populations.

Phenotypic and molecular characterization of vancomycin resistant Enterococci from wild birds: First detection of a plasmid-borne vanC1 in Enterococcus faecalis.

Vancomycin-resistant enterococci (VRE) are a public health concern as they lead to therapeutic impasses and play a pivotal role in the dissemination of vancomycin resistance genes. As recent evidence suggests that wildlife can play a role in the dissemination of bacterial resistomes, this study explored the potential role of Algerian wild birds as a reservoir of VRE. A total of 222 cloacal and fecal samples were collected from various wild bird species and screened for VRE using a selective medium. Of the 47 isolated strains, 22 were identified as Enterococcus casseliflavus with the vanC2/C3 gene, 24 as Enterococcus gallinarum (19 carrying vanC1 and five carrying vanC2/C3), and one strain as Enterococcus faecalis with the vanC1 gene. Twenty-four (24) strains were multidrug-resistant with 61.7% resistant to rifampicin while no resistance to teicoplanin, linezolid and gentamicin was found. Additionally, 53.20% of the strains exhibited at least one virulence factor. To our knowledge, this study represents the first documentation of the vanC1 gene in E. faecalis isolated from wild birds. Furthermore, this gene was found to be carried by a conjugative plasmid, highlighting its ability to spread among bacterial populations and lead to the emergence of novel resistance phenotypes.

Avian Metapneumovirus Subtype B Circulation in Poultry and Wild Birds of Colombia.

The global poultry industry, as a leading producer of animal protein, faces significant challenges related to animal health and production due to high bird density and disease risks. A major concern is the Avian Respiratory Complex (ARC), a multifactorial health issue involving pathogens such as avian metapneumovirus (aMPV), an often-underdiagnosed component of the ARC. Wild birds are seen as reservoirs and spreaders of the virus. This study aimed to detect the presence and subtypes of aMPV in samples from breeders, broilers, laying hens, and wild birds in Colombia. A total of 273 samples, including swabs from the upper respiratory and reproductive tracts, were collected from commercial poultry and wild birds. Using nested RT-PCR targeting the G gene, aMPV subtype B was identified in 23 samples (8.42%). Sequencing revealed high genetic similarity to vaccine strains, classifying all viruses as vaccine-like. In the commercial birds, aMPV-B appeared in 21 samples, regardless of symptoms, often in tests for other ARC agents, indicating diagnostic bias. In the wild birds, two samples tested positive, suggesting potential transmission between wild and domestic birds. These findings highlight the need for broader diagnostics and further research into aMPV's impact on avian health.

The Catalog of Microbial Genes and Metagenome-Assembled Genomes from the Gut Microbiomes of Five Typical Crow Species on the Qinghai-Tibetan Plateau.

While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai-Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows' digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds.