Animal microbiome最新文献

{"title":"Convergent enrichment of Gammaproteobacteria along Aedes aegypti development across different breeding sites.","authors":"Aboubakar Sanon, Lander De Coninck, Lanjiao Wang, Athanase Badolo, Jelle Matthijnssens, Katrien Trappeniers, Leen Delang","doi":"10.1186/s42523-026-00578-1","DOIUrl":"10.1186/s42523-026-00578-1","url":null,"abstract":"<p><strong>Background: </strong>Aedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti, we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing.</p><p><strong>Results: </strong>We observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria. Our data suggest that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as \"diagonal transmission\". Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adults.</p><p><strong>Conclusion: </strong>This study provided new data on the microbiome composition of field-collected Ae. aegypti, contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13352839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147935928","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":"Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.","authors":"Kayla C Evens, Ingrid Bakke, Brendan J M Bohannan","doi":"10.1186/s42523-026-00573-6","DOIUrl":"10.1186/s42523-026-00573-6","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We compared water and zebrafish gut microbiomes across five aquaculture facilities two in the United States and three in Norway- using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity analyses revealed significant clustering by sample type, facility, and geographic location, with facility identity explaining the largest proportion of compositional variance. Multivariate dispersion also differed significantly across facilities, indicating that observed compositional differences reflect both shifts in community composition and differences in within-facility variability. Each facility harbored a distinct microbial community in both water and fish gut samples, with geographic location further structuring community composition between Oregon and Norwegian facilities. Similarity Percentage analysis identified key taxa driving facility differences, including Cetobacterium, Vibrio, and Aeromonas in fish gut microbiomes and Pseudomonas and Rheinheimera in tank water. Microbial source tracking using FEAST revealed that facility-level tank water contributed measurably to fish gut microbiome composition in most facilities, though unknown sources dominated estimates across all facilities (71-99%) and the strength of fish-water microbiome association varied substantially across facilities.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This study demonstrates that zebrafish aquaculture facilities harbor unique microbial communities shaped by both environmental and geographic factors. While tank water microbiomes show associations with zebrafish gut microbiome composition, the dominant contribution of unknown sources to gut microbiome composition suggests that factors beyond the immediate tank water environment- including diet, host physiology, and other facility-specific conditions- are primary drivers of gut microbiome variation. The strength of this association varied considerably across facilities and appeared related to fish domestication history, a pattern that warrants direct experimental investigation. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration,","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13321582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846792","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":"Bacillus amyloliquefaciens regulates oxidative damage through ssc-miR-10390 by targeting WT1 in the intestine of piglets.","authors":"Junmeng Yuan, Yu Liu, Yaowei Sun, Huawei Liu, Kai Zhang, Jinshan Zhao, Weifen Li, Yang Wang","doi":"10.1186/s42523-025-00505-w","DOIUrl":"10.1186/s42523-025-00505-w","url":null,"abstract":"<p><p>Early weaning or enteric pathogen exposure frequently induces intestinal epithelial oxidative stress in piglets, which disrupts redox homeostasis, impairs tight junction integrity, and ultimately compromises intestinal barrier function. Bacillus amyloliquefaciens SC06 (SC06) was reported to regulate oxidative stress and intestinal barrier function in piglets, but the role of miRNA remains unclear in these processes. In this study, we aimed to investigate the effects of SC06 on miRNA profiles and its potential mechanisms of action. A total of 32 weaned piglets or IPEC-J2 cells were divided into four groups using a 2 × 2 factorial design (with or without SC06 treatment, and with or without diquat (DQ) treatment). Results showed that DQ increased the MDA content, reduced the activity of antioxidant enzymes and impaired the barrier function in intestine and IPEC-J2 cells. SC06 enhanced the antioxidant capacity and barrier function and also regulated the miRNA profiles, such as ssc-miR-10390 in piglets and IPEC-J2 cells. Further, the function of ssc-miR-10390 in ameliorating jejunal oxidative damage was confirmed. By using ssc-miR-10390 mimic, ssc-miR-10390 inhibitor and siRNA, we found that ssc-miR-10390 can enhance the antioxidant function and tight junction, and alleviate cellular inflammation in IPEC-J2 cells by targeting WT1. In conclusion, ssc-miR-10390-WT1 pathway plays an important role in SC06-mediated alleviation of oxidative damage in jejunal mucosa of piglets.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147823826","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":"Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.","authors":"Ziyu Liu, Chengming Meng, Junhua Shen, Huisong Wang, Jiaqing Guo, Jiangchao Zhao, Chunlong Mu, Weiyun Zhu","doi":"10.1186/s42523-026-00542-z","DOIUrl":"10.1186/s42523-026-00542-z","url":null,"abstract":"<p><p>Dietary protein plays a crucial role in shaping the gut microbiome and modulating intestinal amino acid metabolism. Gut microbiome is recognized as a reservoir for carrying antimicrobial resistance genes. However, the relationship between amino acids metabolism and antibiotic resistome remains poorly understood. Here, a pig model was used to study this relationship by comparing the impact of dietary casein hydrolysate diet with those of an intact casein diet. Metabolomics analysis revealed that casein hydrolysate supplementation primarily altered amino acid metabolism, characterized by significantly reduced levels of several amino acids, including tyrosine and glutamine, accompanied by increased levels of amino acid–derived metabolites. Metagenomics analyses indicated that these metabolic shifts were closely associated with microbial changes in the gut, particularly the genera Escherichia and Bifidobacterium. Consistently, microbial genes related to amino acid transport and metabolism exhibited higher abundances. Notably, the abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were significantly enriched in response to casein hydrolysate supplementation. Integrated metabolome–resistome correlation analyses revealed significant associations between multiple amino acids, including tyrosine and glutamine, and distinct ARG subtypes, indicating a tight coupling between amino acid metabolism and antibiotic resistance potential. Metagenomics binning and assembly further resolved the taxonomic origins of these functional traits. Specifically, in Escherichia fergusonii and Bifidobacterium thermophilum, genes related to amino acid metabolism, ARGs, and MGEs were co-localized on the same contigs with close genomic proximity. Together, these findings highlight a strong link between microbial amino acid metabolism and the resistome, suggesting that dietary casein hydrolysate reshapes both microbial metabolic functions and antibiotic resistance potential within the intestinal ecosystem.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824064","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":"The uropygial gland of the European hoopoe as a symbiotic organ.","authors":"Manuel Martín-Vivaldi, Ángela Martínez-García, Juan M Peralta-Sánchez, Michael Schaub, Raphaël Arlettaz, Antonio M Martín-Platero, Ester Martínez-Renau, María Dolores Barón, Magdalena Ruiz-Rodríguez, Estefanía López-Hernández, Manuel Martínez-Bueno, Eva Valdivia, Juan J Soler","doi":"10.1186/s42523-026-00543-y","DOIUrl":"10.1186/s42523-026-00543-y","url":null,"abstract":"<p><p>BACKGROUND: Animals rely on symbiotic bacteria living within/on their tissues for multiple functions, while simultaneously needing to protect themselves via immune functions or other defenses from potentially pathogenic microorganisms that could invade those tissues. As a result, interactions with complex assemblages of bacteria have driven the evolution of host strategies to control established symbioses. One such strategy involves the development of organs specialized in maintaining associations with beneficial members of the microbial community — so-called symbiotic organs. These organs are characterized by compartmentalizing spaces where favorable conditions for the beneficial bacteria are promoted, while preventing colonization of other tissues. Although several model systems of symbiotic organs have been studied in animals, none have been recognized in non-aquatic vertebrates except for the intestinal crypts of mammals. Here, we propose that bird´s uropygial glands may be specialized symbiotic organs. RESULTS: We tested this hypothesis using the uropygial gland of the hoopoe (Upupa epops) as a model, which hosts a complex bacterial community that includes antimicrobial-producing symbionts. First, we examined whether the uropygial gland supports a specific symbiotic community, by comparing the microbiome composition of the uropygial secretions and eggshell surfaces in two European hoopoe populations. Additionally, using histological staining and fluorescence in situ hybridization, we looked for structural specializations for compartmentalization and bacterial targeting in the glands of nesting hoopoes in comparison to non-breeding individuals lacking the symbiosis. Results show that, in comparison with bacterial communities of the eggshells, those of the uropygial gland were more conserved between both populations. Moreover, uropygial glands of nesting hoopoes were strictly compartmentalized by a special tissue, properties that are absent in the non-breeding individuals lacking the symbiosis. Finally, bacteria were organized within the organ, suggesting the existence of special physical niches to promote specialized mutualistic symbionts. CONCLUSIONS: All evidence supports that the hoopoe uropygial gland is a specialized symbiotic organ for bacterial cultivation, paving the way for new insights into vertebrates’ exocrine glands’ role in microbial symbiosis. CLINICAL TRIAL NUMBER: Not applicable. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13130528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824030","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":"Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.","authors":"Mirena Ivanova, Birgitta Svensmark, Emilie Egholm Bruun Jensen, Frank M Aarestrup, Håkan Vigre, Saria Otani","doi":"10.1186/s42523-026-00577-2","DOIUrl":"10.1186/s42523-026-00577-2","url":null,"abstract":"<p><p>BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13277185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790516","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":"Temporal dynamics shifts in multi-kingdom rumen microbiota and fermentation profiles of water buffalo under heat stress.","authors":"Yanzhi Wu, Jian Li, Jinchi Yu, Chengjian Yang, Shengyong Mao","doi":"10.1186/s42523-026-00570-9","DOIUrl":"10.1186/s42523-026-00570-9","url":null,"abstract":"<p><p>BACKGROUND: Buffaloes (Bubalus bubalis), widely distributed in tropical and subtropical regions, possess physiological and behavioral adaptations that support heat tolerance and make them vital for food security and rural livelihoods in developing countries. However, climate change–driven increases in heat stress compromise their productivity, reproduction, and health, thereby threatening agricultural sustainability. To address this gap, ten ruminally cannulated buffaloes (Nili-Ravi × Murrah, average body weight 571.2 ± 31.1 kg) were randomly assigned to either a heat stress group or a non-heat stress group, with cooling management applied in the latter. This study specifically investigated the temporal dynamics of rumen microbial community composition in dairy buffaloes during mid-term heat stress exposure lasting approximately 28 days, while exploring interactions among microbial taxa and between microbes and rumen fermentation characteristics. RESULTS: Heat stress significantly reduced the concentrations of propionate, butyrate, and ammonia nitrogen (NH3-N), and altered the profile of volatile fatty acids. These changes were accompanied by notable disruption of microbial diversity and reorganization of microbial interaction networks. Specifically, heat stress weakened the modularity and hub diversity of microbial co-occurrence networks while enhancing their robustness. Key taxa responsive to heat stress included Anaeroplasma, Lentimicrobium, Segatella, Christensenellaceae R-7 group and Pseudobutyrivibrio, which were identified as topologically central nodes in the co-occurrence network. By day 28 of heat stress, the number of differential genera declined and network modularity showed partial convergence, indicating progressive temporal changes in community structure. CONCLUSIONS: Heat stress markedly alters rumen fermentation patterns and reshapes microbial community structure in buffaloes, characterized by pronounced initial shifts followed by progressive temporal changes with partial convergence over time. The identification of microbial taxa that were topologically central in the co-occurrence network highlights their potential relevance as targets for nutritional interventions. These findings provide new insights into the dynamic associations between rumen microbes and rumen fermentation parameter profiles under thermal stress, offering a theoretical basis for precision regulation strategies in buffalo production. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13277167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790526","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":"Effects of dietary chitin supplementation on body weight, haematology and serum biochemistry, fecal scores and gut microbiota of captive pangolins.","authors":"Xinmei Wang, Chungang Xie, Rongquan Zheng, Shanjian Zheng, Yanni Wang, Jia Xu","doi":"10.1186/s42523-026-00576-3","DOIUrl":"10.1186/s42523-026-00576-3","url":null,"abstract":"<p><p>Termites are a natural component of the diet of Malayan pangolins, whereas artificial diets used under captive conditions may differ substantially from wild prey in structure and composition, particularly in chitin content. This study evaluated the effects of dietary supplementation with termites or chitin in seven captive male Malayan pangolins exposed sequentially to three dietary conditions: artificial diet alone, artificial diet supplemented with termites, and artificial diet supplemented with chitin. Body weight, hematological and serum biochemical parameters, fecal scores, and gut microbiota composition were assessed. The results showed that the effects of termite and chitin supplementation were not consistent. Compared with the other dietary phases, chitin supplementation was associated with body weight reduction in some individuals and changes in several physiological parameters, including white blood cells, lymphocytes, mean corpuscular volume, eosinophils, and even significantly reduced in phosphorus, calcium, albumin, and cholesterol (p < 0.05). In the gut microbiota analysis, termite supplementation significantly increased Chao1 richness and observed OTUs (p < 0.05), while the overall microbiota composition differed between the termite- and chitin-supplemented phases. In addition, the chitin-supplemented phase showed a higher relative abundance of some taxa previously reported to be associated with potential pathogenicity. In conclusion, supplementation with termites and chitin produced different physiological and microbiota responses in captive Malayan pangolins. Under the conditions of this study, supplementation with 3% chitin was associated with less favorable outcomes than termite supplementation. Future studies should further evaluate dietary composition, including chitin and other nutrient components, to support the development of optimized diets for captive pangolins.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13244960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790462","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":"Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.","authors":"Anitha Ravi, Violetta Shestivska, Priscila Thiago Dobbler, Hana Sechovcová, Martina Maixnerová, Jaroslav Semerád, Alena Nehasilová, Mariana Vadroňová, Iñaki Odriozola, Hana Šubrtová Salmonová, Tomáš Větrovský, Šárka Musilová, Tomáš Cajthaml, Eva Pěchoučková, Alexandr Nemec, Martina Kyselková","doi":"10.1186/s42523-026-00568-3","DOIUrl":"10.1186/s42523-026-00568-3","url":null,"abstract":"<p><strong>Background: </strong>Antibiotic resistance poses a major threat to human health, with antibiotic use in livestock contributing to the selection and spread of resistance genes. The genus Acinetobacter includes human- and animal-associated species capable of acquiring resistance, yet their diversity and resistance potential in livestock remain far less explored than in humans. In this study, we investigated Acinetobacter in cattle feces from 28 Czech farms with contrasting antibiotic use, aiming to assess species composition, resistance profiles, and the potential for resistance dissemination. We applied an integrative approach combining strain isolation and characterization, enrichment cultures, metabarcoding, and shotgun metagenomics.</p><p><strong>Results: </strong>Cattle feces harbored diverse Acinetobacter species with A. indicus and A. pseudolwoffii being the core species based on both isolated strains and metabarcoding, while A. baumannii was less common. Acinetobacter species occurrence determined by metabarcoding was driven by multiple factors, including production type, herd size, and per-head antibiotic use, while their abundance was mostly influenced by sample type (higher in feces from the farm floor than in rectal samples) and production type (higher in dairy than in beef cattle). Remarkably, 37% of the 284 isolated strains could not be assigned to validly named species and represent at least 19 putative novel species. Decreased susceptibility due to acquired resistance was observed in 57 strains; notably, A. indicus and A. pseudolwoffii from antibiotic-using farms were less susceptible to streptomycin than those from antibiotic-free farms. Shotgun metagenomics revealed a greater richness of acquired resistance genes in antibiotic-using farms, including the clinically relevant carbapenemase gene bla_OXA-58. This gene was located on putative plasmid contigs alongside streptomycin resistance determinants strA-strB, suggesting horizontal dissemination under streptomycin selection pressure. Strain analysis confirmed the co-localization of bla_OXA-58 and strA-strB on a large plasmid in A. pseudolwoffii.</p><p><strong>Conclusions: </strong>Despite relatively strict regulations, Czech cattle farms constitute a reservoir of antibiotic-resistant Acinetobacter carrying mobile resistance genes of clinical concern. Commonly applied antibiotics likely co-select for such genes, posing an ongoing public health risk. Our findings reveal an unexpectedly high diversity of Acinetobacter spp. in cattle, highlighting the research bias toward human-associated species and underscoring the need for integrated One Health monitoring approaches.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790523","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":"Alleviation of heat stress-induced microbial dysbiosis in pigs through dietary supplementation with vitamins and trace elements.","authors":"Peter Fauszt, Endre Szilagyi, Maja Mikolas, Emese Szilagyi-Tolnai, Peter David, Ildiko Noemi Kovacs-Forgacs, Brigitta Csernus, Ferenc Gal, Laszlo Stundl, Sandor Biro, Csaba Szabo, Judit Remenyik, Laszlo Babinszky, Melinda Paholcsek","doi":"10.1186/s42523-026-00575-4","DOIUrl":"10.1186/s42523-026-00575-4","url":null,"abstract":"<p><strong>Background: </strong>Chronic heat stress (HS) is known to impair animal health and productivity, in part by altering gut microbiota. This study investigated how HS affects the pig gut microbiome and whether dietary supplementation with antioxidants and trace elements (vitamins E, C, selenium, and zinc) at moderate (D1) or high (D2) doses can mitigate these effects.</p><p><strong>Results: </strong>During the adaptation phase, feed efficiency was similar across groups, but as the experiment progressed, the thermoneutral control improved while the heat-stressed control deteriorated. Supplemented diets (D1/D2) partially alleviated this efficiency loss. Microbiome analysis revealed that HS progressively reduced diversity, reaching the lowest Shannon index during exposure. High-dose supplementation markedly increased richness, exceeding control levels. Total microbial abundance declined under HS, with opportunistic pathogens enriched particularly during early exposure. Guild-level indices further indicated a shift under HS. Aerotolerance indices decreased (ATi: TC > D1 > D2 > HSC), reflecting hypoxia-prone conditions favoring obligate anaerobes and SCFA producers. Among supplemented groups, D1 most closely stabilized aerotolerance toward control levels, while D2 maintained an SCFA-dominant community and enhanced butyrate capacity. Genus-level correlations with qPCR-based host gene-expression markers were assessed across all groups. HSP70 was the dominant correlate, and the most extreme associations were confined to a few taxa, indicating marked group specificity.</p><p><strong>Conclusion: </strong>Chronic HS in pigs induced microbial dysbiosis characterized by reduced diversity, loss of beneficial SCFA producers, and expansion of opportunistic pathogens. Dietary supplementation counteracted these adverse changes in a dose-dependent manner. While moderate supplementation provided partial stabilization, high-dose supplementation more effectively restored microbial diversity and enriched beneficial taxa, making it the more effective strategy for mitigating HS-induced microbiome disruption.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13245032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790459","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}