Animal microbiome最新文献

{"title":"Oregano essential oil enhanced body weight and well-being by modulating the HPA axis and 23-nordeoxycholic acid of cecal microbiota in Holstein steers under cold stress.","authors":"Yongliang Huang, Siyu Cheng, Jinping Shi, Pengjia He, Yue Ma, Xu Zhang, Yongzhi Cao, Zhaomin Lei","doi":"10.1186/s42523-025-00401-3","DOIUrl":"10.1186/s42523-025-00401-3","url":null,"abstract":"<p><strong>Background: </strong>Prolonged exposure to cold stress in cattle increases basal energy consumption and impedes optimal production. Consequently, herds require adequate attention during cold, extended winters to alleviate cold stress and maintain profitability. This study investigated the effects of oregano essential oil (EO) on body weight (BW), well-being, blood parameters, and cecal microbiota. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CK) or the same diet supplemented with 20 g/(d·head) EO for 270 days.</p><p><strong>Results: </strong>EO increased BW by increasing cecal microbial abundance and carbohydrate metabolism CAZymes, leading to elevated the total volatile fatty acids (VFA) levels. Cold stress activated the HPA axis, and mitigated stress by reducing serum levels of cortisol (COR), corticosterone (CORT), adrenocorticotropic hormone (ACTH), and dopamine (DA). EO increased well-being by decreasing viral species without apparent contribution to drug or antibiotic resistance development, and cecal metabolites were primarily enriched in growth, carbohydrate metabolism, and amino acid metabolism pathways. Specifically, tryptophan metabolism (2-picolinic acid, quinolinic acid, and oxindole) enhanced steer well-being by increasing antioxidants (superoxide dismutase (SOD), peroxidases (POD), and glutathione (GSH)) and reducing inflammatory factors (interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α)) following EO treatment. Notably, low-abundance microorganisms (s_Streptomyces_gardneri, s_Paenibacillus_sp._S09, and s_Nocardia_sp._Root136) may play a significant role in growth and immunity.</p><p><strong>Conclusion: </strong>These findings provide fundamental insights into how EO alleviates cold stress by modulating the HPA axis, promotes growth and well-being of steers under cold stress by influencing mediates tryptophan metabolism of cecal microbiota in Holstein steers.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"34"},"PeriodicalIF":4.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765910","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":"Deep culturing the fecal microbiota of healthy laying hens.","authors":"Zhixuan Feng, Natalia Lorenc, Bridget O'Brien, Guangwen Sun, Zhiwei Li, Dongyun Jung, Jennifer Ronholm","doi":"10.1186/s42523-025-00395-y","DOIUrl":"10.1186/s42523-025-00395-y","url":null,"abstract":"<p><strong>Background: </strong>The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.</p><p><strong>Results: </strong>In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.</p><p><strong>Conclusions: </strong>Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733412","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":"Causal estimation of the relationship between reproductive performance and the fecal bacteriome in cattle.","authors":"Yutaka Taguchi, Haruki Yamano, Yudai Inabu, Hirokuni Miyamoto, Koki Hayasaki, Noriyuki Maeda, Yoshiro Kanmera, Seiji Yamasaki, Noboru Ota, Kenji Mukawa, Atsushi Kurotani, Shigeharu Moriya, Teruno Nakaguma, Chitose Ishii, Makiko Matsuura, Tetsuji Etoh, Yuji Shiotsuka, Ryoichi Fujino, Motoaki Udagawa, Satoshi Wada, Jun Kikuchi, Hiroshi Ohno, Hideyuki Takahashi","doi":"10.1186/s42523-025-00396-x","DOIUrl":"https://doi.org/10.1186/s42523-025-00396-x","url":null,"abstract":"<p><strong>Background: </strong>The gut bacteriome influences host metabolic and physiological functions. However, its relationship with reproductive performance remains unclear. In this study, we evaluated the relationship between the gut bacteriome and reproductive performance in beef cattle, such as Japanese black heifers. Artificial insemination (AI) was performed after 300 days of age, and the number of AI required for pregnancy (AI number) was evaluated. The relationship of the fecal bacteriome at 150 and 300 days of age and reproductive performance was visualized using statistical structural equation modelling between traits based on four types of machine-learning algorithms (linear discriminant analysis, association analysis, random forest, and XGBoost).</p><p><strong>Results: </strong>The heifers were classified into superior (1.04 ± 0.04 cycles, n = 26) and inferior groups (3.87 ± 0.27 cycles, n = 23) according to the median frequency of AI. The fecal bacteria of the two groups were examined and compared using differential analysis, which demonstrated that the genera Rikenellaceae RC9 gut group and Christensenellaceae R-7 group were increased in the superior group. Subsequently, correlation analysis evaluated the interrelationships between bacteriomes, which demonstrated that the patterns exhibited distinct characteristics. Therefore, four machine-learning algorithms were employed to identify the distinctive factors between the two groups. The directed acyclic graphs carried out by DirectLiNGAM based on these extracted factors inferred that the family Erysipelotrichaceae and the genera Clostridium sensu stricto 1 and Family XIII AD3011 group at 150 days of age were strongly associated with an increase in AI number. Furthermore, a pathway involved in creatinine degradation (PWY-4722) at 150 days of age was related to an increase in AI number. However, bacteriomes and/or pathways at 300 days of age were not necessarily related to AI number.</p><p><strong>Conclusions: </strong>In this study, a causal inference methodology was applied to investigate AI-dependent gut bacterial communities in pregnant cattle. These findings suggest that AI numbers, which are crucial for beef cattle production management, could be inferred from the fecal bacterial patterns nearly six months before the AI, rather than immediately before. This study provides a novel perspective of the gut environment and its role in reproductive performance.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"33"},"PeriodicalIF":4.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744584","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":"Idiopathic epilepsy in dogs is associated with dysbiotic faecal microbiota.","authors":"Marco Silvestrino, Mattia Pirolo, Angelica Bianco, Stefano Castellana, Laura Del Sambro, Viviana Domenica Tarallo, Luca Guardabassi, Andrea Zatelli, Floriana Gernone","doi":"10.1186/s42523-025-00397-w","DOIUrl":"10.1186/s42523-025-00397-w","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays a crucial role in modulating various physiological and pathological processes through its metabolites, including short-chain fatty acids (SCFA), which impact immune system development, gastrointestinal health, and brain functions via the gut-brain axis. Dysbiosis, an imbalance in gut microbiota composition, has been linked to neuroinflammatory and neurodegenerative conditions, including epilepsy. In dogs, idiopathic epilepsy has been hypothesized to be influenced by gut microbiota composition, although studies on this association are limited and show inconsistent results. Here, we compared the faecal microbiota of idiopathic epileptic drug-naïve dogs and healthy controls. To this aim, we recruited 19 idiopathic epileptic dogs and 17 healthy controls which met stringent inclusion criteria and characterized their faecal microbiome by 16 S rRNA sequencing.</p><p><strong>Results: </strong>No significant differences were observed between the two groups regarding age, breed, body condition score, diet, or reproductive status, though males were significantly overrepresented in the idiopathic epileptic group. Epileptic dogs showed a marked reduction in bacterial richness and a trend towards lower evenness (α-diversity) compared to healthy controls, while no differences in community composition (β-diversity) were observed between the two groups. Moreover, a decrease in SCFA-producing bacteria, namely Faecalibacterium, Prevotella, and Blautia, was observed alongside an increase in Escherichia coli, Clostridium perfringens, and Bacteroides in epileptic dogs.</p><p><strong>Conclusions: </strong>Idiopathic epileptic dogs exhibit dysbiosis, with reduced bacterial diversity, loss of beneficial genera, and overgrowth of opportunistic pathogens. These alterations in microbiota diversity and composition may contribute to epilepsy via the gut-brain axis, highlighting the need for further research to explore dietary or probiotic interventions targeting gut microbiota modulation as adjunctive therapies for managing epilepsy in dogs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"31"},"PeriodicalIF":4.9,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733413","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":"Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake.","authors":"Rongbing Guo, Yuguang Chang, Dandan Wang, Hanxue Sun, Tiantian Gu, Yibo Zong, Shiheng Zhou, Zhizhou Huang, Li Chen, Yong Tian, Wenwu Xu, Lizhi Lu, Tao Zeng","doi":"10.1186/s42523-025-00394-z","DOIUrl":"10.1186/s42523-025-00394-z","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota exerts a critical influence on energy metabolism homeostasis and productive performance in avian species. Given the diminishing availability of arable land and intensifying competition for finite resources between livestock production and human populations, the agricultural sector faces dual imperatives to enhance productive efficiency while mitigating ecological footprints. Within this paradigm, optimizing nutrient assimilation efficiency in commercial waterfowl operations emerges as a strategic priority. This investigation employs an integrated multi-omics approach framework (metagenomic, metabolomic, and transcriptomic analyses) to elucidate the mechanistic relationships between cecal microbial consortia and feed conversion ratios in Shan Partridge ducks.</p><p><strong>Results: </strong>Based on the analysis of metagenome data, a total of 34 phyla, 1033 genera and 3262 species of bacteria were identified by metagenomic sequencing analysis. At the phylum level, 31 phylums had higher mean abundance in the low residual feed intake ( LRFI) group than in the high residual feed intake (HRFI) group. Among them, the expression of microbiome Elusimicrobiota was significantly higher in the LRFI group than in the HRFI group (P < 0.05). And we also found a significant differences in secondary metabolites biosynthesis, transport, and catabolism pathways between the two groups in microbial function (P < 0.05). Based on metabolomic analysis, 17 different metabolites were found. Among them, Lipids and lipid molecules accounted for the highest proportion. Whereas the liver is very closely related to lipid metabolism, we are close to understanding whether an individual's energy utilization efficiency is related to gene expression in the liver. We selected six ducks from each group of six ducks each for liver transcriptome analysis. A total of 322 differential genes were identified in the transcriptome analysis results, and 319 genes were significantly down-regulated. Among them, we found that prostaglandin endoperoxide synthase 2 (PTGS2) might be a key hub gene regulating RFI by co-occurrence network analysis. Interestingly, the differential gene PTGS2 was enriched in the arachidonic acid pathway at the same time as the differential metabolite 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2). In addition, the results of the association analysis of differential metabolites with microorganisms also revealed a significant negative correlation between 15d-PGJ2 and Elusimicrobiota.</p><p><strong>Conclusion: </strong>Based on comprehensive analysis of the research results, we speculate that the Elusimicrobiota may affect the feed utilization efficiency in ducks by regulating the expression of the PTGS2 gene.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"30"},"PeriodicalIF":4.9,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677442","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":"Social organization and physical environment shape the microbiome of harvester ants.","authors":"Denisse Alejandra Gamboa, Peter J Flynn, Eva Sofia Horna-Lowell, Noa Pinter-Wollman","doi":"10.1186/s42523-025-00390-3","DOIUrl":"10.1186/s42523-025-00390-3","url":null,"abstract":"<p><p>All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"29"},"PeriodicalIF":4.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665461","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":"Age matters: exploring differential effects of antimicrobial treatment on gut microbiota of adult and juvenile brown trout (Salmo trutta).","authors":"Lisa-Marie Streb, Paulina Cholewińska, Silvia Gschwendtner, Juergen Geist, Susanne Rath, Michael Schloter","doi":"10.1186/s42523-025-00391-2","DOIUrl":"10.1186/s42523-025-00391-2","url":null,"abstract":"<p><strong>Background: </strong>Antibiotics and antiparasitics are essential tools in controlling infectious disease outbreaks in commercial aquaculture. While the negative effects of antimicrobials on the gut microbiome of various farmed fish species are well documented, the influence of underlying host factors, such as age, on microbiome responses remains poorly understood. This is especially evident for peracetic acid, whose impact on the gut microbiome has not yet been studied. Understanding how microbiome dynamics vary by host age is critical to improving antibiotic stewardship in aquaculture. In this study, juvenile and sexually mature brown trout (Salmo trutta) were used as a model to investigate the age-dependent effects of florfenicol and peracetic acid on the gut microbiome using a 16S rRNA metabarcoding approach.</p><p><strong>Results: </strong>Fish age significantly shaped taxonomic composition and microbial co-occurrence network structure of the gut microbiome, regardless of treatment. Juvenile trout exhibited greater microbiome volatility and a stronger response to both florfenicol and peracetic acid compared to adult fish, with disruptions persisting up to 11 days post-treatment. Temporal dynamics were also evident, with microbial shifts characterized by a decline in beneficial commensals like Cetobacterium and Lactococcus. Although overall abundance recovered by 18 days post-treatment, network positions of key microbial community members remained altered, particularly in juvenile fish. Opportunistic pathogens, including Aeromonas and Streptococcus, were enriched and assumed more central roles within the microbial networks in treated fish.</p><p><strong>Conclusion: </strong>The initial composition of the gut microbiome in brown trout is strongly influenced by fish age, which in turn affects the microbiome's response to antibiotic disruption. Juveniles displayed higher susceptibility to microbiome perturbation, and although recovery was observed at the community level, network properties remained altered. This study also provides the first evidence that external peracetic acid application can disrupt gut microbial communities. Since compositional shifts are often linked to functional alterations, even short-term disruptions may have important consequences for host health in developing fish. These findings emphasize the importance of considering gut microbial community structure in relation to fish age in aquaculture management practices.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"28"},"PeriodicalIF":4.9,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652355","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 is a moderate feedlot-dependent indicator of bovine respiratory disease in beef cattle.","authors":"Ruth Eunice Centeno-Delphia, Natalie Glidden, Erica Long, Audrey Ellis, Sarah Hoffman, Kara Mosier, Noelmi Ulloa, Johnnie Junior Cheng, Josiah Levi Davidson, Suraj Mohan, Mohamed Kamel, Josh I Szasz, Jon Schoonmaker, Jennifer Koziol, Jacquelyn P Boerman, Aaron Ault, Mohit S Verma, Timothy A Johnson","doi":"10.1186/s42523-025-00387-y","DOIUrl":"10.1186/s42523-025-00387-y","url":null,"abstract":"<p><strong>Background: </strong>Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.</p><p><strong>Results: </strong>Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.</p><p><strong>Conclusions: </strong>Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"27"},"PeriodicalIF":4.9,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635003","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":"Diurnal oscillations of amino acids dynamically associate with microbiota and resistome in the colon of pigs.","authors":"Hongyu Wang, Yue Li, Jinwei You, Ni Feng, Dongfang Wang, Yong Su, Xiaobo Feng","doi":"10.1186/s42523-025-00393-0","DOIUrl":"10.1186/s42523-025-00393-0","url":null,"abstract":"<p><strong>Background: </strong>Nutrients are one of the key determinants of gut microbiota variation. However, the intricate associations between the amino acid (AA) profile and the dynamic fluctuations in the gut microbiota and resistome remain incompletely elucidated. Herein, we investigated the temporal dynamics of AA profile and gut microbiota in the colon of pigs over a 24-hour period, and further explored the dynamic interrelationships among AA profile, microbiota, and resistome using metagenomics and metabolomics approaches.</p><p><strong>Results: </strong>JTK_circle analysis revealed that both the AA profile and the gut microbiota exhibited rhythmic fluctuations. With respect to the feed intake, all AAs except L-homoserine (P_Adj = 0.553) demonstrated significant fluctuations. Over 50% of Lactobacillaceae, Ruminococcaceae, Clostridiaceae, and Eubacteriaceae species reached their peaks during T15 ∼ T21 when 50% of Lachnospiraceae species experienced a trough. The eLSA results showed that most AAs positively correlated with Prevotellaceae species but negatively correlated with Lactobacillaceae and Lachnospiraceae species. Moreover, most of the AAs negatively correlated with the mobile genetic elements Tn916 and istA group but positively correlated with plasmids. Further partial least squares structural equation model analysis indicated that AAs affected the antibiotic resistance gene dynamics through mobile genetic elements and the gut microbiota.</p><p><strong>Conclusions: </strong>Taken together, the AA profile and the gut microbiota exhibit robust fluctuations over a day. The AA profile can affect the gut microbiota and resistome in a direct or indirect manner. These findings may provide new insights into a potential strategy for manipulating the gut microbiota and resistome.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"26"},"PeriodicalIF":4.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626961","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":"Effect of Lactiplantibacillus plantarum N-1 and isomaltose-oligosaccharide on promoting growth performance and modulating the gastrointestinal microbiota in newborn Hu sheep.","authors":"Xinyi Xu, Zhiwei Zhou, Zhiqiang Zhou, Yudong Ma, Dongmei Luo, Senlin Zhang, Pinggui Yang, Tianwu An, Qun Sun","doi":"10.1186/s42523-025-00392-1","DOIUrl":"10.1186/s42523-025-00392-1","url":null,"abstract":"<p><strong>Background: </strong>Diarrhea is usually observed in newborn Hu lambs, while severe diarrhea may lead to the stunted growth and even death in lambs, necessitating the common practice of antibiotic administration to newborns. In order to explore the application of the effective probiotics and/or prebiotic treatment in animal feed to lessen the recline on antibiotics, 27 newborn of Hu lambs were equally allocated into three groups: control group (Con), probiotics group (Pro) receiving Lactiplantibacillus plantarum N-1 (LPN-1), and synbiotics group (Syn) receiving LPN-1 combined with isomaltose-oligosaccharide (IMO), and raised till 60 days of age.</p><p><strong>Results: </strong>Compared with the Con, the incidence of severe diarrhea was lower in both two treatment groups, accompanied by a significant reduction in terramycin administration frequency (P < 0.05). The daily feed intake in newborns significantly increased after probiotics or synbiotics treatment (P < 0.05), leading to the substantial increment in average daily gain by 48.28% and heart girth (P < 0.05), as well as enhancements in height (P < 0.01) at 60 days of the age in synbiotics treatment group. Applying probiotics and synbiotics exhibited the enhanced rumen weight (P < 0.05), and synbiotics further promoted the spleen development (P < 0.05). The inclusion of probiotics and synbiotics significantly modified the gut microbial composition of Hu lambs (P < 0.01), with an increase in Butyrivibrio proteoclasticus and Pseudoruminococcus massiliensis, which were associated with starch and sucrose metabolism. Additionally, the Syn group exhibited an upsurge in the number of species associated with amino acid metabolism and cellulolysis, as well as the raised short-chain fatty acids levels in the newborn gut (P < 0.05).</p><p><strong>Conclusions: </strong>This study demonstrated that LPN-1 and IMO had an enhanced effect to improve the growth performance and decrease the reliance on antibiotics by promoting the feed intake, balancing the gut microbiota and increasing the short-chain fatty acids content in Hu lambs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"25"},"PeriodicalIF":4.9,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617229","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}