Animal microbiome最新文献

{"title":"Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.","authors":"Alexandru S Barcan, Joseph L Humble, Sandeep Kasaragod, Mohammad Saiful Islam Sajib, Rares A Barcan, Philip McGinnity, Timothy J Welch, Brendan Robertson, Emanuel Vamanu, Antonella Bacigalupo, Martin S Llewellyn, Francisca Samsing","doi":"10.1186/s42523-025-00377-0","DOIUrl":"10.1186/s42523-025-00377-0","url":null,"abstract":"<p><strong>Background: </strong>The development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.</p><p><strong>Results: </strong>Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.</p><p><strong>Conclusions: </strong>Our findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"18"},"PeriodicalIF":4.9,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduction of enteric methane emission using methanotroph-based probiotics in Hanwoo steers.","authors":"Tenzin Tseten, Rey Anthony Sanjorjo, Jong-Wook Son, Keun Sik Baik, Janine I Berdos, Seon-Ho Kim, Sang-Hwal Yoon, Min-Kyoung Kang, Moonhyuk Kwon, Sang-Suk Lee, Seon-Won Kim","doi":"10.1186/s42523-025-00385-0","DOIUrl":"10.1186/s42523-025-00385-0","url":null,"abstract":"<p><strong>Background: </strong>Methane emission from enteric rumen fermentation is a main source of greenhouse gas (GHG) emission and a major concern for global warming.</p><p><strong>Results: </strong>In this study, we isolated methanotroph-methylotroph consortium NC52PC from the rumen after a series of sub-culture and repetitive streaking on an agar plate and polycarbonate membrane filter. The NC52PC comprises methanotroph species (Methylocystis sp.) and methylotroph species (Methylobacterium sp.), forming a consortium capable of growing solely on methane as a carbon source. Their morphology, growth, and genome sequence were characterized. We assessed its effectiveness in mitigating methane emissions through both in vitro and in vivo experiments. During the in vitro trial, the introduction of NC52PC (at a concentration of 5.1 × 10⁷ CFUs/ml) demonstrated a reduction in methane production exceeding 40% and 50% after 12 and 24 h, respectively. Also, NC52PC did not significantly alter other aspects of the in vitro rumen fermentation parameters such as pH, total gas production, and digestibility. Further investigation involved testing NC52PC as a dietary supplement in 12 young Hanwoo steers over three 30-day test periods. The steers received a diet comprising 70.8% concentrate and 29.2% bluegrass on a dry matter basis, with variations including 3 × 10⁷ CFUs/ml of NC52PC (LOW) and 3 × 10⁸ CFUs/ml (HIGH) of NC52PC, and without NC52PC as a control (CON). Steers administered with HIGH and LOW concentrations of NC52PC exhibited reduced enteric methane emission (g/day) by 14.4% and 12.0%, respectively.</p><p><strong>Conclusion: </strong>Feeding methanotroph-methylotroph consortium NC52PC significantly reduced methane emissions in Korean beef cattle without any adverse effects on animal health. These findings suggest that this probiotic could serve as a promising feed additive to effectively mitigate methane emissions from ruminants. However, further research is needed to evaluate the long-term effects of NC52PC on animal health, and on meat and milk quality.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"19"},"PeriodicalIF":4.9,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intrauterine growth restriction, defined by an elevated brain-to-liver weight ratio, affects faecal microbiota composition and, to a lesser extent, plasma metabolome profile at different ages in pigs.","authors":"Roberta Ruggeri, Giuseppe Bee, Federico Correa, Paolo Trevisi, Catherine Ollagnier","doi":"10.1186/s42523-024-00358-9","DOIUrl":"10.1186/s42523-024-00358-9","url":null,"abstract":"<p><strong>Background: </strong>Intrauterine growth restriction (IUGR) affects up to 30% of piglets in a litter. Piglets exposed to IUGR prioritize brain development during gestation, resulting in a higher brain-to-liver weight ratio (BrW/LW) at birth. IUGR is associated with increased mortality, compromised metabolism, and gut health. However, the dynamic metabolic and microbial shifts in IUGR-affected pigs remain poorly understood. This study aimed to investigate the longitudinal effects of IUGR, defined by a high BrW/LW, on the composition of faecal microbiota and plasma metabolome in pigs from birth to slaughter. One day (± 1) after birth, computed tomography was performed on each piglet to assess their brain and liver weights. The pigs with the highest (IUGR = 12) and the lowest (NORM = 12) BrW/LW were selected to collect faeces and blood during lactation (day 16 ± 0.6, T1) and at the end of the starter period (day 63 ± 8.6, T2) and faeces at the beginning (day 119 ± 11.4, T3) and end of the finisher period (day 162 ± 14.3, T4).</p><p><strong>Results: </strong>Faecal microbial Alpha diversity remained unaffected by IUGR across all time points. However, the Beta diversity was influenced by IUGR at T1 (P = 0.002), T2 (P = 0.08), and T3 (P = 0.03). Specifically, IUGR pigs displayed higher abundances of Clostridium sensu stricto 1 (P_adj = 0.03) and Romboutsia (P_adj = 0.05) at T1, Prevotellaceae NK3B31 group (P_adj = 0.02), Rikenellaceae RC9 gut group (P_adj = 0.03), and Alloprevotella (P_adj = 0.03) at T2, and p-2534-18B5 gut group (P_adj = 0.03) at T3. Conversely, the NORM group exhibited higher abundances of Ruminococcus (P_adj = 0.01) at T1, HT002 (P_adj = 0.05) at T2, and Prevotella_9 (P_adj < 0.001) at T3. None of the plasma metabolites showed significant differences at T1 between the IUGR and NORM pigs. However, at T2, asparagine was lower in the IUGR compared to the NORM group (P < 0.05).</p><p><strong>Conclusions: </strong>These findings show that growth restriction in the uterus has a significant impact on the faecal microbiota composition in pigs, from birth to the beginning of the finisher period, but minimally affects the plasma metabolome profile.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"17"},"PeriodicalIF":4.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nasal pathobiont abundance does not differ between dairy cattle with or without clinical symptoms of bovine respiratory disease.","authors":"Ruth Eunice Centeno-Delphia, Erica A Long, Audrey C Ellis, Sarah Hofmann, Kara Mosier, Noelmi Ulloa, Johnnie Junior Cheng, Andrew Richards, Jacquelyn P Boerman, Jennifer Koziol, Mohit S Verma, Timothy A Johnson","doi":"10.1186/s42523-025-00382-3","DOIUrl":"10.1186/s42523-025-00382-3","url":null,"abstract":"<p><strong>Background: </strong>Bovine respiratory disease (BRD) remains a significant health and economic problem to the dairy cattle industry. Multiple risk factors contribute to BRD susceptibility including the bacterial pathobionts Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Studies have characterized and quantified the abundance of these bacteria in the nasal cavity of cattle to infer and help disease diagnosis; nonetheless, there is still discrepancy in the results observed of when these microbes are commensal or pathogenic. Additionally, some of these studies are limited to a specific farm. The goal of this study is to compare the nasal microbiome community (diversity and composition) and the abundance of the four bacterial pathogens (by qPCR) in the nasal cavity to identify differences between dairy calves that are apparently healthy and those identified to have BRD. Nasal swabs were collected from approximately 50 apparently healthy and 50 BRD-affected calves sampled from five different dairy farms in the US (CA, IN, NY (two farms), and TX).</p><p><strong>Results: </strong>Calves diagnosed with BRD in NY, and TX had lower nasal microbiome diversity compared to the apparently healthy calves. Differences in the nasal microbiome composition were observed between the different farms predicted by Bray-Curtis and weighted UniFrac dissimilarities. Commensal and pathobiont genera Acinetobacter, Moraxella, Psychrobacter, Histophilus, Mannheimia, Mycoplasma, and Pasteurella were prevalent in the bovine nasal microbiome regardless of farm or disease status. The BRD-pathobiont H. somni was the most prevalent pathobiont among all the samples and M. bovis the least prevalent. Only in CA was the abundance of a pathobiont different according to disease status, where M. haemolytica was significantly more abundant in the BRD-affected animals than apparently healthy animals.</p><p><strong>Conclusions: </strong>This study offers insight into the nasal microbiome community composition in both animals diagnosed with BRD and healthy animals, and shows that the farm effect plays a more significant role in determining the microbiome community than disease status in young dairy calves.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"16"},"PeriodicalIF":4.9,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.","authors":"Mauricio Hernández, Jorge Langa, Ostaizka Aizpurua, Yendi E Navarro-Noya, Antton Alberdi","doi":"10.1186/s42523-025-00381-4","DOIUrl":"10.1186/s42523-025-00381-4","url":null,"abstract":"<p><p>Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"15"},"PeriodicalIF":4.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial profiling of black soldier fly larvae reared on substrates supplemented with different mineral sources originating from phosphorus recycling technologies.","authors":"Henry Reyer, Manfred Mielenz, Gürbüz Daş, Cornelia C Metges, Klaus Wimmers","doi":"10.1186/s42523-025-00380-5","DOIUrl":"10.1186/s42523-025-00380-5","url":null,"abstract":"<p><strong>Background: </strong>Innovations to establish agricultural value chains utilising side streams and their reintegration into the feed and food supply are of great importance. Recyclates derived from biomass and waste are therefore becoming increasingly important as sources of nutrients. The larvae of the black soldier fly (BSF; Hermetia illucens) demonstrate considerable potential as livestock feed due to their ability to utilise a wide range of organic substrates. In this study, BSF larvae (BSFL) were reared on four different substrates: chicken feed diet (CD), high-fibre Gainesville fly diet (FD), or FD supplemented either with biochar (FD + BCH) or single superphosphate (FD + SSP) recyclates from sewage sludge processing. To validate the hypothesis that endogenous and substrate-associated microbiota significantly contribute to substrate conversion, the microbiota profiles of BSFL gut and frass were analysed by 16S rRNA gene amplicon sequencing. Results were associated to the different substrates as well as body composition, growth performance data, and mineral concentration of the larvae.</p><p><strong>Results: </strong>The CD substrate was superior in terms of larval growth, although it caused a lower microbial alpha diversity in the larval intestine and frass compared to FD, with a dominance of Morganellaceae and families of Lactobacillales. The addition of the two sewage sludge derived products to the FD substrate significantly increased the calcium content of BSFL, while the phosphorus content was only increased by the addition of SSP. The shifts in the microbiota profiles of BSFL gut and frass indicated that BCH contributed to the regulation of the microbial milieu with suppressing the growth of potentially pathogenic microbes. The addition of SSP resulted in an enrichment of microorganisms with attributed phosphate-solubilising properties such as Pseudomonas and fungal species, likely being responsible for improving the bioavailability of phosphorus from the substrate.</p><p><strong>Conclusions: </strong>The results demonstrate the high adaptability of the BSFL and its ability to change the substrate through specific microbiota in such a way that conditions are created for an optimal nutrient supply and thus growth of the larvae.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"14"},"PeriodicalIF":4.9,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of microbiota signatures in Iberian pig strains using machine learning algorithms.","authors":"Lamiae Azouggagh, Noelia Ibáñez-Escriche, Marina Martínez-Álvaro, Luis Varona, Joaquim Casellas, Sara Negro, Cristina Casto-Rebollo","doi":"10.1186/s42523-025-00378-z","DOIUrl":"10.1186/s42523-025-00378-z","url":null,"abstract":"<p><strong>Background: </strong>There is a growing interest in uncovering the factors that shape microbiome composition due to its association with complex phenotypic traits in livestock. Host genetic variation is increasingly recognized as a major factor influencing the microbiome. The Iberian pig breed, known for its high-quality meat products, includes various strains with recognized genetic and phenotypic variability. However, despite the microbiome's known impact on pigs' productive phenotypes such as meat quality traits, comparative analyses of gut microbial composition across Iberian pig strains are lacking. This study aims to explore the gut microbiota of two Iberian pig strains, Entrepelado (n = 74) and Retinto (n = 63), and their reciprocal crosses (n = 100), using machine learning (ML) models to identify key microbial taxa relevant for distinguishing their genetic backgrounds, which holds potential application in the pig industry. Nine ML algorithms, including tree-based, kernel-based, probabilistic, and linear algorithms, were used.</p><p><strong>Results: </strong>Beta diversity analysis on 16 S rRNA microbiome data revealed compositional divergence among genetic, age and batch groups. ML models exploring maternal, paternal and heterosis effects showed varying levels of classification performance, with the paternal effect scenario being the best, achieving a mean Area Under the ROC curve (AUROC) of 0.74 using the Catboost (CB) algorithm. However, the most genetically distant animals, the purebreds, were more easily discriminated using the ML models. The classification of the two Iberian strains reached the highest mean AUROC of 0.83 using Support Vector Machine (SVM) model. The most relevant genera in this classification performance were Acetitomaculum, Butyricicoccus and Limosilactobacillus. All of which exhibited a relevant differential abundance between purebred animals using a Bayesian linear model.</p><p><strong>Conclusions: </strong>The study confirms variations in gut microbiota among Iberian pig strains and their crosses, influenced by genetic and non-genetic factors. ML models, particularly CB and RF, as well as SVM in certain scenarios, combined with a feature selection process, effectively classified genetic groups based on microbiome data and identified key microbial taxa. These taxa were linked to short-chain fatty acids production and lipid metabolism, suggesting microbial composition differences may contribute to variations in fat-related traits among Iberian genetic groups.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"13"},"PeriodicalIF":4.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental enrichment with nylon gnaw sticks introduces variation in Sprague Dawley rat immune and lower gastrointestinal parameters with differences between sexes.","authors":"Mark Wulczynski, Stephen P J Brooks, Judy Green, Fernando Matias, Martin Kalmokoff, Julia M Green-Johnson, Sandra T Clarke","doi":"10.1186/s42523-024-00369-6","DOIUrl":"10.1186/s42523-024-00369-6","url":null,"abstract":"<p><strong>Background: </strong>Environmental enrichment (EE) is commonly included as an important component of animal housing to promote well being of laboratory animals; however, much remains to be learned about the impact of chewable forms of EE on experimental outcomes in the context of nutritional and microbiome-related studies, and whether outcomes differ between sexes. In the present study, nylon chew bones (gnaw sticks, GS) were evaluated for their effects on fermentation profiles, microbial community structure, and cytokine profiles of gastrointestinal and systemic tissues in pair-housed female and male Sprague Dawley (SD) rats.</p><p><strong>Results: </strong>Food consumption and weight gain were not significantly altered by access to GS. Cecal short-chain fatty acid and branched-chain fatty acid profiles significantly differed between sexes in rats with access to GS, and alpha diversity of the microbiome decreased in females provided GS. Sex-related tissue cytokine profiles also significantly differed between rats with and without access to GS.</p><p><strong>Conclusions: </strong>These findings indicate that including GS can influence microbiota and immune-related parameters, in a sex dependent manner. This shows that environmental enrichment strategies need to be clearly reported in publications to properly evaluate and compare experimental results, especially with respect to the use of chewable EE in the context of studies examining diet, microbiome and immune parameters.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"12"},"PeriodicalIF":4.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance.","authors":"Leanne A Grieves, Gregory B Gloor","doi":"10.1186/s42523-024-00367-8","DOIUrl":"10.1186/s42523-024-00367-8","url":null,"abstract":"<p><p>Symbiotic microbiota are important drivers of host behaviour, health, and fitness. While most studies focus on humans, model organisms, and domestic or economically important species, research investigating the role of host microbiota in wild populations is rapidly accumulating. Most studies focus on the gut microbiota; however, skin and other glandular microbiota also play an important role in shaping traits that may impact host fitness. The uropygial gland is an important source of chemical cues and harbours diverse microbes that could mediate chemical communication in birds, so determining the factors most important in shaping host microbiota should improve our understanding of microbially-mediated chemical communication. Hypothesizing that temporal, geographic, and taxonomic effects influence host microbiota, we evaluated the effects of season, migration distance, and taxonomy on the uropygial gland microbiota of 18 passerine species from 11 families. By sampling 473 birds at a single stopover location during spring and fall migration and using 16S rRNA sequencing, we demonstrate that season, followed by migration distance, had the strongest influence on uropygial gland microbial community composition. While statistically significant, taxonomic family and species had only weak effects on gland microbiota. Given that temporal effects on gland microbiota were nearly ubiquitous among the species we tested, determining the consequences of and mechanisms driving this seasonal variation are important next steps.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"11"},"PeriodicalIF":4.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic development of gut microbiota and metabolism during and after weaning of kittens.","authors":"Hong Zhang, Yang Ren, Siyu Wei, Hongli Jin, Yizhen Wang, Mingliang Jin","doi":"10.1186/s42523-024-00373-w","DOIUrl":"10.1186/s42523-024-00373-w","url":null,"abstract":"<p><strong>Background: </strong>As the pet population grows, there is increasing attention on the health and well-being of companion animals. Weaning, a common challenge for young mammals, often leads to issues such as diarrhea, growth retardation, and in severe cases, even mortality. However, the specific changes in gut microbiota and metabolites in kittens following weaning remain unclear. In this study, we conducted a comprehensive investigation of the dynamic changes in the gut microbiota, serum metabolism, antioxidant capacity, and immune function of kittens at various time points: days 0, 4, and 30 post-weaning.</p><p><strong>Results: </strong>Significant changes in the immune response and gut microbiota were observed in kittens following weaning. Specifically, IgM levels increased significantly (P < 0.01, n = 20), while IgA and IgG levels showed a sustained elevation. Weaning also disrupted the intestinal microbiota, leading to notable changes in serum metabolism. On day 4 post-weaning, there was a decrease in beneficial bacteria such as Bacteroides vulgatus, Fusobacterium nucleatum, Anaerostipes caccae, and Butyricico-ccaceae. However, by day 30, beneficial bacteria including Candidatus Arthro-mitus, Holdemanella, and Bifidobacterium had increased (P < 0.05, n = 20). Serum metabolites showed clear separation across time points, with day 0 and day 4 exhibiting similar patterns. A total of 45 significantly altered metabolites (P < 0.05, n = 20) were identified, primarily related to vitamins, steroids, peptides, organic acids, lipids, and carbohydrates. Pathway analysis revealed significant enrichment in eight metabolic pathways, with key changes in arginine metabolism and biosynthesis. Additionally, bacteria such as Bacteroides fragilis, Bacteroides stercoris, Leuconostoc citreum, and Bifidobacterium adolescentis were positively correlated with serum metabolic changes, emphasizing the link between gut microbiota and systemic metabolism (P < 0.05, n = 20).</p><p><strong>Conclusion: </strong>Our study demonstrated that the composition and function of intestinal microorganisms as well as serum metabolic profiles of weaned kittens presented dynamic changes. These findings not only deepen our understanding of the effects of weaning on kitten health, but also provide valuable insights into post-weaning nutritional regulation strategies for kittens.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"10"},"PeriodicalIF":4.9,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}