Gut Of Birds Research Articles

Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data

Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).

Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes

Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C.jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C.jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C.jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.

Isolation and identification of uric acid-dependent Aciduricibacillus chroicocephali gen. nov., sp. nov. from seagull feces and implications for hyperuricemia treatment.

The increasing disease burden of hyperuricemia highlights the need for new therapeutic drugs and treatment strategies. Our study describes the developmental and application values of natural uric acid-degrading bacteria found in the gut of birds and broadened the source of bacteria with potential therapeutic value. Furthermore, the special physiology characteristics and genomic features of strain 44XBT are valuable for further study.

Validating the use of a newly developed cinnamaldehyde product in commercial broiler production

Essential oils (EOs) have been considered as an alternative to antibiotics for animal production. In the current study, 4 trials were conducted on a commercial broiler farm to investigate the effects of dietary supplementation of an encapsulated cinnamon EO product (NE-OFF) on the bird growth performance, gut health, and gene expression in the ileum, spleen, and liver relating to the host response to heat and other stresses, including potential NE challenge. In each trial, approximately 30,000 Cobb or Ross broilers were randomly allocated to 4 treatments: a raised without antibiotics (RWA) commercial diet as positive control, an adjusted RWA commercial diet as negative control, and the negative control diet supplemented with 2 different dosages of NE-OFF, which was added during feed pelleting. Although the final average body weight did not differ significantly among treatment groups, birds fed NE-OFF had an increased ratio of villus height and crypt depth in the jejunum, and reduced fecal oocyst counts. Trial 2 was conducted in the summer and had a necrotic enteritis (NE) outbreak. The supplementation of NE-OFF reduced the NE incidence and bird mortality. The samples from Trial 2 were hence selected for the analyses of Clostridium perfringens and NetB toxin gene abundance in the ileum, and host responses. The C. perfringens population appeared to be positively correlated with the NetB gene abundance. The gene expression analysis suggested that NE-OFF supplementation improved nutrient absorption and transportation as well as antioxidant activities to help the birds against stress. These on-farm trial results support the hypothesis that the use of NE-OFF as a feed additive can improve bird gut health and performance in commercial broiler production, especially for preventing NE outbreaks when birds are under stress.

Impact of Plasmodium relictum Infection on the Colonization Resistance of Bird Gut Microbiota: A Preliminary Study.

Avian malaria infection has been known to affect host microbiota, but the impact of Plasmodium infection on the colonization resistance in bird gut microbiota remains unexplored. This study investigated the dynamics of Plasmodium relictum infection in canaries, aiming to explore the hypothesis that microbiota modulation by P. relictum would reduce colonization resistance. Canaries were infected with P. relictum, while a control group was maintained. The results revealed the presence of P. relictum in the blood of all infected canaries. Analysis of the host microbiota showed no significant differences in alpha diversity metrics between infected and control groups. However, significant differences in beta diversity indicated alterations in the microbial taxa composition of infected birds. Differential abundance analysis identified specific taxa with varying prevalence between infected and control groups at different time points. Network analysis demonstrated a decrease in correlations and revealed that P. relictum infection compromised the bird microbiota's ability to resist the removal of taxa but did not affect network robustness with the addition of new nodes. These findings suggest that P. relictum infection reduces gut microbiota stability and has an impact on colonization resistance. Understanding these interactions is crucial for developing strategies to enhance colonization resistance and maintain host health in the face of parasitic infections.

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

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

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Bacterial detoxification of plant defence secondary metabolites mediates the interaction between a shrub and frugivorous birds

Many plants produce fleshy fruits, attracting fruit-eating animals that disperse the seeds in their droppings. Such seed dispersal results in a conflict between the plant and the animal, as digestion of seeds can be highly beneficial to the animal but reduces plant fitness. The plant Ochradenus baccatus uses the myrosinase-glucosinolates system to protect its seeds. We show that hydrolysis of the O. baccatus fruit glucosinolates by the myrosinase enzyme inhibited digestive enzymes and hampered digestion in naïve individuals of the bird Pycnonotus xanthopygos. However, digestion in birds regularly feeding on O. baccatus fruits was unaffected. We find that Pantoea bacteria, dominating the gut of these experienced birds as well as the fruits, thrive on glucosinolates hydrolysis products in culture. Augmentation of Pantoea protects both naïve birds and plant seedlings from the effects of glucosinolates hydrolysis products. Our findings demonstrate a tripartite interaction, where the plant-bird mutually beneficial interactions are mediated by a communal bacterial tenant.

Avian gut passage reduces the germination light response of pokeweed (Phytolaca americana)

It has been shown that passage through a bird's gut has the potential to alter seed germinability (overall percent germination) and the timing of germination. However, little is known about the potential of avian gut passage to alter the germination response of seeds to abiotic gradients, such as light availability. Specifically, it is unclear whether gut passage makes seeds more or less sensitive to variability in light. We addressed this issue using a growth chamber experiment where the germination rate of both gut-passed and control (de-pulped) seeds of the understory herb Phytolaca americana (pokeweed) was compared across three light levels. Both avian gut passage and light increased germination rate. Additionally, it was found that gut passage and light interacted to influence the germination rate, such that gut-passed seeds showed no response to light and control seeds had a strong, positive light response. Results from this experiment suggest that avian gut passage has the potential to reduce seed's sensitivity to light, which could play a role in the recruitment of avian-dispersed plant populations across variable light environments.

Bacterial chondronecrosis with osteomyelitis related Enterococcus cecorum isolates are genetically distinct from the commensal population and are more virulent in an embryo mortality model

Bacterial chondronecrosis with osteomyelitis (BCO) is a common cause of broiler lameness. Bacteria that are found in BCO lesions are intestinal bacteria that are proposed to have translocated through the intestinal epithelium and have spread systemically. One of the specific bacterial species frequently isolated in BCO cases is Enterococcus cecorum. In the current study, caecal isolates were obtained from birds derived from healthy flocks (12 isolates from 6 flocks), while isolates derived from caeca, colon, pericardium, caudal thoracic vertebrae, coxo-femoral joint, knee joint and intertarsal joint (hock) were obtained from broilers derived from BCO outbreaks (111 isolates from 10 flocks). Pulsed field gel electrophoresis was performed to determine similarity. Clonal E. cecorum populations were isolated from different bones/joints and pericardium from animals within the same flock, with intestinal strains carrying the same pulsotype, pointing to the intestinal origin of the systemically present bacteria. Isolates from the intestinal tract of birds from healthy flocks clustered away from the BCO strains. Isolates from the gut, bones/joints and pericardium of affected animals contained a set of genes that were absent in isolates from the gut of healthy animals, such as genes encoding for enterococcal polysaccharide antigens (epa genes), cell wall structural components and nutrient transporters. Isolates derived from the affected birds induced a significant higher mortality in the embryo mortality model as compared to the isolates from the gut of healthy birds, pointing to an increased virulence.

A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Birds maintain complex and intimate associations with a diverse community of microbes in their intestine. Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses. However, the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings. Through performing a network meta-analysis for 13 published bird gut microbiome studies, here we attempt to investigate the comparability of these invasive and non-invasive sampling methods. The two most used non-invasive sampling methods (cloacal swabs and fecal samples) showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples. Overall, non-invasive samples showed decreased alpha diversity compared to intestinal samples, but the alpha diversities of fecal samples were more comparable to the intestinal samples. On the contrary, the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples, but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples. Phylogenetic status, diet, and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples. Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa, while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions. The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.

Immunogenic Modification of Ligilactobacillus agilis by Specific Amino Acid Substitution of Flagellin.

Ligilactobacillus agilis is a flagellated motile commensal microbe that resides in the gastrointestinal tract of mammals and birds. Flagellin, the major subunit protein of flagellar filament, from pathogenic bacteria is generally a proinflammatory molecule that stimulates immune cells via Toll-like receptor 5 (TLR5). Interestingly, the flagellins of L. agilis are known to be immunologically attenuated despite the fact that the structure of the proteins, including the TLR5 recognition site, is highly conserved among bacteria. The results of our previous study suggested that this is attributed to the differences in three specific amino acids within the conserved TLR5 recognition site; however, this hypothesis remains to be confirmed. In this study, a series of recombinant L. agilis flagellins, with amino acid substitutions at the TLR5 recognition site, were constructed, and their immunogenic activity was evaluated in vitro. Then, an L. agilis strain with an active immunogenic TLR5 recognition site was generated. In vitro and in vivo immunological studies revealed that the mutant L. agilis strain with the modified flagellin was more immunogenic than the wild-type strain. In conclusion, the specific amino acid residues in L. agilis flagellins likely contribute to the discrimination between pathogens and commensals by the host defense system. Additionally, the immunogenically potent L. agilis mutants may serve as a useful platform for oral vaccine delivery. IMPORTANCE The interactions between gut microbes and immune cells play an important role in the health and disease of hosts. Ligilactobacillus agilis is a flagellated commensal bacterium found in the gut of mammals and birds. However, the flagellin proteins of L. agilis are immunologically attenuated and barely induce TLR5-dependent inflammation, unlike the flagellins of several pathogenic bacteria. This study demonstrated that three specific amino acids in the flagellin protein are responsible for this low immunogenicity in L. agilis. The results obtained herein improve our understanding of the symbiosis between gut microbes and their hosts.

Exploring the Ecological Implications of Microbiota Diversity in Birds: Natural Barriers Against Avian Malaria.

Natural antibodies (Abs), produced in response to bacterial gut microbiota, drive resistance to infection in vertebrates. In natural systems, gut microbiota diversity is expected to shape the spectrum of natural Abs and resistance to parasites. This hypothesis has not been empirically tested. In this ‘Hypothesis and Theory’ paper, we propose that enteric microbiota diversity shapes the immune response to the carbohydrate α-Gal and resistance to avian malaria. We further propose that anti-α-Gal Abs are transmitted from mother to eggs for early malaria protection in chicks. Microbiota modulation by anti-α-Gal Abs is also proposed as a mechanism favoring the early colonization of bacterial taxa with α1,3-galactosyltransferase (α1,3GT) activity in the bird gut. Our preliminary data shows that bacterial α1,3GT genes are widely distributed in the gut microbiome of wild and domestic birds. We also showed that experimental infection with the avian malaria parasite P. relictum induces anti-α-Gal Abs in bird sera. The bird-malaria-microbiota system allows combining field studies with infection and transmission experiments in laboratory animals to test the association between microbiota composition, anti-α-Gal Abs, and malaria infection in natural populations of wild birds. Understanding how the gut microbiome influences resistance to malaria can bring insights on how these mechanisms influence the prevalence of malaria parasites in juvenile birds and shape the host population dynamics.

Got the travel bug?

Like many of us in 2021, I miss the glee of traveling to new and exciting locations on vacation (and can't wait to get back these adventures post-pandemic). Yet, what I don't miss are the inevitable bugs I pick up along the way. Whether it be a cold or a stomach flu, many of us come down with some sort of infection when we are away from home. Many things could contribute to these illnesses, including travel-induced sleep deprivation, novel foods or the concentration of viruses on mass transit. But, could it be that our bodies are just not primed to defend us against the diseases in foreign locales? Agnes Piecyk from the Max Planck Institute for Evolutionary Biology, Germany, and colleagues from the USA and Germany wanted to investigate this theory to figure out whether hosts and parasites develop specialized relationships depending on their geographic origin.So, they took advantage of a host–parasite system that is found throughout the northern hemisphere: the three-spined stickleback Gasterosteus aculeatus and its tapeworm Schistocephalus solidus. The stickleback picks up this nasty worm in a way commonly found on our own human travels – in its food. One of its favourite foods, the copepod, is commonly infected by this parasite. Once consumed, the parasite burrows through the fish's gut, invading its body and quickly growing to fill every nook and cranny of the fish's insides. The parasite steals much of its host's food, forcing the stickleback to feed constantly to keep up with its own energy needs and the demand of its unwanted guest. This voracious feeding makes it less likely to take shelter to avoid predators because of an overwhelming need for food, attracting the attention of its primary predators – and the next host in the parasite's life cycle – fish-eating birds. The parasite then gladly makes its way to the bird's gut, where it sexually reproduces, starting the process again when the bird deposits the parasite's eggs back into waterways containing the copepod (its first host) through its feces. This incredible chain of events has evolved through an evolutionary arms race among the parasite and its three host species.Using sticklebacks and tapeworms from Europe and Alaska, the researchers set about testing the feasibility of inter-continental infections, exposing Alaskan sticklebacks to European tapeworms and vice versa. Surprisingly, while the Alaskan parasite readily infected the European fish host, the Alaskan stickleback put up a stronger fight against the European tapeworm, with hosts from certain Alaskan regions effectively preventing infection altogether. For those unlucky fish that succumbed to infection, their worms varied greatly in size depending on the host's origin. In addition, even when the Alaskan sticklebacks did pick up an infection, their immune systems succeeded in keeping the worm in check, with much smaller worms relative to their body size than European sticklebacks. While we would typically cheer the hosts that entirely prevented a parasite invasion, those uninfected sticklebacks were skinnier than otherwise healthy sticklebacks, indicating the hidden energetic cost of their unseen battle.While the researchers’ work sheds light on the complex interactions between hosts and parasites on a local scale, we still have much to learn about how these geographic differences develop and whether there are epidemiological implications due to geographic differences in disease susceptibility. And hopefully this knowledge might one day help us to avoid the dreaded vacation bug (once we are finally back out there, galivanting in exciting new places).

Interspecific competition in germination of bird-dispersed seeds in a habitat with sparse tree vegetation in South Africa

BackgroundBy transporting and scarifying the seeds during ingestion, avian frugivores reduce the competition with siblings, and may improve the germination which is critical for dispersal effectiveness and population recruitment. However, generally, there is limited knowledge on how deposited seeds interact/compete in the new microsite. We tested the hypothesis that the bird-dispersed seeds benefit from improved germination after their passage through the bird’s gut; and we investigated the potential impact of seed density on competition at the microsites by determining whether seed density and species diversity influence germination in the Free State Province, South Africa.ResultsOverall, the results partly supported the hypothesis. Germination trials with defecated seeds of five plant species compared with the manually depulped seeds showed that only Searsia lancea had significantly higher seed germination success and improved germination speed after passage through the bird gut while Ziziphus mucronata only benefited rapid germination. There was a significant correlation between seed size and the germination of bird-ingested seeds except in Olea subsp. africana possibly due to possession of extremely hard protective seed cover. Seed competition experiments pointed to Z. mucronata and O. subsp. africana having significant germination performance that was positively correlated to seed density and seed size while Ehretia rigida did not germinate at all. Seed species diversity in the germination trays did not have a significant impact since the seeds of two former plant species consistently displayed significantly higher germination across the competition levels.ConclusionsWe conclude that different plant species respond differently to seed ingestion by birds, and that further long-term tests for germination physiological responses of the seeds’ samples used in this study are required since poor germination observed in other tree/shrub species cannot be attributed to competition solely.

Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets

BackgroundGut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq.ResultsInitial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversalConclusionsThe gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations.

Identification of diverse novel genomoviruses in gut of wild birds

Genomoviridae is a virus family belonging to circular replication associated protein encoding ssDNA (CRESS-DNA) viruses, which have diverse genomic architecture and are widely distributed among different ecosystems. In this study, we characterized 39 novel genomovirus genomes including 3 from wild egrets, 9 from wild cranes, as well as 27 from wild finches in three different types of cloacal swabs of wild bird sampled in the station of Xinqing bird ringing, Maoershan Nature Reserve in Heilongjiang Province, Changbai Mountain in Jilin Province, and Hangzhou Wetland Park in Zhejiang Province, China. Here, using a Rep sequence phylogeny-based analysis, we divided the 39 genomoviruses into 8 genera within the family Genomoviridae, including Gemycircularvirus (n=20), Gemykibivirus (n=3), Gemygorvirus (n=2), Gemyvongvirus (n=2), Gemykolovirus (n=3), Gemykrogvirus (n=6), Gemytondvirus (n=1), Gemyduguivirus (n=1) and one unclassified genomovirus. The 39 genomovirus genomes belong to 36 species (27 of which are new) based on the currently accepted genomovirus pairwise nucleotide sequence identity species demarcation threshold of 78%. Overall, the research enriches our knowledge of CRESS-DNA viral diversity in China and emphasizes the prevalence of genomoviruses in nature.

不同食性野生鸟类肠道微生物研究进展

肠道微生物是庞大而多样的微生物群落，通过促进营养摄取、宿主防御、免疫调节等，在维持机体健康方面起着至关重要的作用。宿主外部或内部环境的任何变化都会影响肠道微生物的组成，鸟类具有复杂的生活史和多样化的食性，飞翔生活使它们的生理活动面临更大的选择性压力，导致肠道微生物菌群的变化更加复杂。近年来，随着基因测序技术的发展以及对鸟类肠道微生物研究的日益重视，导致了鸟类肠道微生物研究呈指数增长。但目前的研究主要以家禽为主，野生鸟类肠道微生物报道则相对较少。野生鸟类肠道微生物结构变化及其维持机制等的研究仍处于起步阶段，有较大的研究空间。从植食性、肉食性、杂食性三种食性的鸟类肠道微生物组成及特点、影响因素等方面对前人的文献进行了全面梳理，以期为野生鸟类肠道微生物研究提供参考。总的来说，植食性鸟类肠道微生物多样性最低，以高丰度的变形菌门（Proteobacteria）、厚壁菌门（Firmicutes）为主；而杂食性鸟类肠道微生物多样性最高。遗传、生活史特征、人类活动、城市化、圈养行为等对鸟类肠道微生物的组成具有显著性的影响。;The intestinal microbes are huge and diverse microbial communities, which play key roles in maintaining organism health through promoting nutrient uptake, defense, and immune regulation. However, any change in the intrinsic and extrinsic factors can affect the composition of gut microbiota, especially the food composition. The feeding habits of birds vary wildly, from fruit, seeds, foliage to carrion and capturing live animals. Bird life-history traits are diverse, such as migratory behavior, flight capacity, diet, mating systems, longevity and physiology, all of which may affect gut microbes. With the development of gene sequencing technology, and the increasing attention to intestinal microbes, intestinal bacterial diversity of birds has received some attention. However, publications are dominated by the studies of domestic poultry. The structure changes and maintenance mechanism, and the influencing factors of gut microbes in wild birds remain less studied. Here, we review current knowledge of the intestinal microbes in wild birds, to better understand the dynamics of wild bird gut microbiota, and will contribute to the future study of avian microbiology. In general, among the wild birds with different feeding habits, herbivorous birds have the lowest intestinal bacterial diversity, with high abundance of Proteobacteria and Firmicutes; and omnivorous birds have the highest intestines bacterial diversity. Genetics, life-history, human activities, urbanization, captive behaviors, etc. have significant effects on the bacterial diversity of wilds bird gut microbes.

Dietary Phytogenic Combination with Hops and a Mixture of a Free Butyrate Acidifier and Gluconic Acid Maintaining the Health Status of the Gut and Performance in Chickens.

Simple SummaryThroughout the rearing period of broiler chickens, they are exposed to a number of stress factors that may compromise their health status. It is particularly important that the development of the gut with a balanced microbiome is not disturbed, which determines the overall health of the birds to a large extent. A number lines of evidence have indicated that substances with bioactive properties, including prebiotics, organic acids, and/or phytogenic ingredients of plants, may have beneficial actions in maintaining the good health status of the bird gut without compromising performance. In the present study, we investigated the dietary application of phytogenic ingredients from hops, licorice and arabic gum as well as a free butyrate acidifier together with a prebiotic complex in relation to the gut functional status response of the host. The present report confirmed that feeding the birds with the dietary treatments maintained bird growth and normal healthy status of the gut and improved gut morphostructure indices. Our findings indicate the potential of the investigated additives for modulating gut functional status in birds.Additives with bioactive properties can improve chickens’ gut health. This study investigated the physiological status of the gut, including its morphological structure and microbiome activities in chickens fed diets supplemented with phytogenic ingredients with hops (Anta®Phyt) or a mixture of a free butyrate acidifier and gluconic acid (PreAcid). In this study, 1155 broilers were distributed to three dietary treatments with 5 replicate pens per treatment, 77 birds each. Anta®Phyt was added at 400/300/200/200 mg/kg diet whereas PreAcid was added at 3/2/1/1 g/kg starter/grower I/grower II/finisher diet respectively. Dietary treatments did not compromise body weight in different growth periods. In the birds fed PreAcid-supplemented diet, higher gut concentration of butyric acid was observed, particularly in the early stage of growth, while the profile of the short-chain fatty acids was maintained among the treatments. Neither additive significantly affected cecal bacterial enzyme activities. Feeding the birds with Anta®Phyt and PreAcid had beneficial effects on gut morphostructure indices, including intestinal wall thickness, crypt depth and the villus height to crypt depth ratio, in 35- and 42-day old birds. In conclusion, the feeding Anta®Phyt- or PreAcid-supplemented diet exerted beneficial effects on the indices determining the physiological status of the gut and maintained good performance of birds of different ages.

Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

BackgroundComprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for 2 weeks or 2 months, respectively.ResultsWe found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens.ConclusionsOur findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. The satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.