Animal microbiome最新文献

{"title":"Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.","authors":"Xiaoxing Ye, Goutam Sahana, Mogens Sandø Lund, Bingjie Li, Zexi Cai","doi":"10.1186/s42523-025-00386-z","DOIUrl":"10.1186/s42523-025-00386-z","url":null,"abstract":"<p><strong>Background: </strong>Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.</p><p><strong>Results: </strong>This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.</p><p><strong>Conclusions: </strong>The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"24"},"PeriodicalIF":4.9,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606754","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":"Interactions between gilthead seabream intestinal transcriptome and microbiota upon Enteromyxum leei infection: a multi-omic approach.","authors":"Socorro Toxqui-Rodríguez, Itziar Estensoro, Ricardo Domingo-Bretón, Raquel Del Pozo, Jaume Pérez-Sánchez, Detmer Sipkema, Ariadna Sitjà-Bobadilla, M Carla Piazzon","doi":"10.1186/s42523-025-00388-x","DOIUrl":"10.1186/s42523-025-00388-x","url":null,"abstract":"<p><strong>Background: </strong>The enteric myxozoan parasite Enteromyxum leei is an important problem in gilthead seabream aquaculture invading the intestinal epithelium and leading to chronic intestinal inflammation, poor food conversion rates, cachexia, and mortalities, with no treatments available, resulting in significant economic losses. It is known that myxozoan infections are affected by factors such as temperature, duration of exposure, stocking densities, and seasonality. Gut microbiota has key effects on host health, including disease resistance and immune system training and development, tightly interacting with the host, affecting systemic and local physiological functions. This study aimed to gain insights into the host-microbiota-parasite interactions integrating metataxonomics, host transcriptomics, and metatranscriptomics within this disease model.</p><p><strong>Results: </strong>Exposure to E. leei together with temperature and age differences led to alterations in gilthead seabream intestinal microbiota. Samples from 240 g fish kept at 18ºC during a winter trial at 10 weeks post-parasite exposure showed the highest significant changes in their microbial composition with Proteobacteria increasing in abundance from 32.3% in the control group up to 89.8% in the infected group, while Firmicutes and Actinobacteria significantly decreased in relative abundance from 23% and 37.8-2.4% and 1.1%, respectively. After LEfSe analysis, Acinetobacter was identified as the best biomarker for the parasite-exposed group. Parasite exposure also altered the expression of 935 host genes, highlighting genes involved in immune responses such as pathways related to Interleukins, MHCI and Interferons. Microbial transcripts, also showed significant changes upon parasite infection. Integration of the results revealed differential effects on the host induced directly by the parasite or indirectly by parasite-induced microbial shift.</p><p><strong>Conclusions: </strong>Intestinal microbiota and local host gene expression showed significant changes upon en enteromyxosis. The detected activation of the host immune response was not exclusively linked to the parasite infection but also to changes in microbiota, demonstrating the key role of the different components of the mucosal system during disease. These results provided different datasets of bacterial taxa and microbial and host transcripts that will allow a better understanding of host-microbiota-parasite interactions and can serve as starting points for studying and evaluating mucosal health in aquaculture during parasitosis or other diseases.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"22"},"PeriodicalIF":4.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11884135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574856","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":"Composition of the fecal, vaginal and colostrum microbiotas of dams at parturition and their relationship with neonatal outcomes in dogs.","authors":"Quentin Garrigues, Emmanuelle Apper, Fanny Mercier, Ana Rodiles, Nicoletta Rovere, Sylvie Chastant, Hanna Mila","doi":"10.1186/s42523-025-00384-1","DOIUrl":"10.1186/s42523-025-00384-1","url":null,"abstract":"<p><strong>Background: </strong>Microbial seeding in early life is critical for the host's short- and long-term health, and the mother is the first source of bacteria for the newborn. The objective of this study was to characterize the maternal fecal, vaginal, and colostral microbiotas in the canine species one day after parturition and to evaluate the relationship between the microbial profiles of 36 dams and the neonatal outcomes of 284 newborns.</p><p><strong>Results: </strong>The first part of the study revealed the presence of 2 fecal, 3 vaginal, and 2 colostral microbial clusters on the basis of the core microbiota of the dams. Among these three maternal microbiotas, only the vaginal microbiome was found to be associated with neonatal outcomes. Compared with those in the other clusters, females in Cluster 1, with the lowest stillbirth and neonatal mortality ratios, presented a greater abundance of Moraxellaceae in their vaginal microbiota; Cluster 2, with a greater abundance of Pasteurellaceae, mostly from the Haemophilus genus; and Cluster 3 (with the highest stillbirth and neonatal mortality ratios), a greater abundance of Enterobacteriaceae, mostly E. coli. Moreover, Cluster 3 dams presented significantly lower species richness according to the Shannon index than did dams from the other clusters.</p><p><strong>Conclusions: </strong>This study underscores the strong association between maternal microbiota, particularly the vaginal microbiota, and newborn health. The results of this study call for further research to gain a deeper understanding of the optimal vaginal microbiota composition in canine species and the ways to modulate it to improve neonatal outcomes.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"23"},"PeriodicalIF":4.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574855","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":"Gut microbiome community profiling of Bornean bats with different feeding guilds.","authors":"Muhd Amsyari Morni, Julius William-Dee, Emy Ritta Jinggong, Nor Al-Shuhada Sabaruddin, Nur Afiqah Aqilah Azhar, Muhammad Amin Iman, Peter A Larsen, Jaya Seelan Sathiya Seelan, Lesley Maurice Bilung, Faisal Ali Anwarali Khan","doi":"10.1186/s42523-025-00389-w","DOIUrl":"10.1186/s42523-025-00389-w","url":null,"abstract":"<p><p>Bats are extraordinary mammals. They have evolved to consume various dietary sources, such as insects, fruits, nectar, blood, and meat. This diversity has generated considerable interest in the scientific community, resulting in efforts to leverage bats as model organisms to study the correlation between diet and gut microbiome community. Although such studies now commonly use Next Generation Sequencing (NGS), similar studies are early in their development in Southeast Asia, especially in Malaysia, which harbours an incredibly diverse bat fauna. This study provides pioneering NGS metabarcoding information on Bornean bats. By using a high-throughput Nanopore-based 16S rRNA gene sequencing method, Bacillota, Pseudomonadota, and Campylobacterota were found in insectivorous bats and phytophagous bats. Both insectivorous and phytophagous groups harboured no dominant taxon (D = 0.076; D = 0.085). A comparative analysis of gut bacteria functional groups identified eight major groups in both phytophagous and insectivorous bats, with fermentation being the predominant group. The correlation network analysis revealed a negative correlation between the 'good bacteria' Lactobacillus and various pathogenic bacteria genera, such as Salmonella (-0.4124) and Yersinia (-0.4654), demonstrating its prebiotic characteristics. This study broadens our understanding of the bat gut microbiome from various diets, with emphasis on new data from Borneo.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"21"},"PeriodicalIF":4.9,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569017","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":"Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans.","authors":"Beatriz do Carmo Dias, Alessandra Pavan Lamarca, Douglas Terra Machado, Vinicius Prata Kloh, Fabíola Marques de Carvalho, Ana Tereza Ribeiro Vasconcelos","doi":"10.1186/s42523-025-00379-y","DOIUrl":"10.1186/s42523-025-00379-y","url":null,"abstract":"<p><p>Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"20"},"PeriodicalIF":4.9,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11874851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544697","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":"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}