Animal microbiome最新文献

{"title":"Nasal microbial diversity is associated with survival in piglets infected by a highly virulent PRRSV-1 strain.","authors":"Pau Obregon-Gutierrez, Martí Cortey, Gerard E Martín-Valls, Hepzibar Clilverd, Florencia Correa-Fiz, Virginia Aragón, Enric Mateu","doi":"10.1186/s42523-024-00371-y","DOIUrl":"10.1186/s42523-024-00371-y","url":null,"abstract":"<p><strong>Background: </strong>Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to swine industry worldwide, especially virulent variants arising during the last years, such as Spanish PRRSV-1 Rosalia strain. The role of the nasal microbiota in respiratory viral infections is still to be unveiled but may be promisingly related with the health status of the animals and thus, their susceptibility. The goal of this project was to study the nasal microbiota composition of piglets during a highly virulent PRRSV-1 outbreak comparing animals that died due to the infection with animals that survived it. The microbiota composition was inferred by V3-V4 regions of the 16S rRNA gene sequencing and bioinformatics analysis. To deepen the analysis, we added samples taken from piglets before the outbreak as well as from the sows giving birth to piglets under study.</p><p><strong>Results: </strong>Piglets that survived the PRRSV-1 outbreak reported a more diverse and different nasal microbiota at three weeks of age compared to piglets dying, which was highly related with the litter of origin and the sow of the piglets. In addition, a high abundance of classical swine nasal colonizers belonging to genera such as Bergeyella, Glaesserella, Neisseria and Moraxella (among others), was related with good outcome. On the other hand, a dysbiotic community dominated by Escherichia and a different clade of Moraxella was found in piglets with bad outcome. Moreover, samples taken before the outbreak showed similar dynamics prior to virulent PRRSV-1 arrival, suggesting that microbiota-related susceptibility was already occurring in the animals and that the increase in mortality seen was related to the new highly virulent strain.</p><p><strong>Conclusion: </strong>Our study suggests that the susceptibility to an infection such as PRRSV could be related to the nasal microbiota composition at the moment of infection and may serve as starting point to explore animal resilience. Since the dysbiosis detected as an initial response to infection may be not specific for this virus, further investigations should explore this phenomenon in the context of other viral infections.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"9"},"PeriodicalIF":4.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11742779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017313","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":"Probiotic administration aggravates dextran sulfate sodium salt-induced inflammation and intestinal epithelium disruption in weaned pig.","authors":"Kunhong Xie, Weidong Cai, Lingjie Li, Bing Yu, Yuheng Luo, Zhiqing Huang, Xiangbing Mao, Jie Yu, Ping Zheng, Hui Yan, Hua Li, Jun He","doi":"10.1186/s42523-024-00375-8","DOIUrl":"10.1186/s42523-024-00375-8","url":null,"abstract":"<p><strong>Background: </strong>A. muciniphila (AKK) has attracted extensive research interest as a potential next-generation probiotics, but its role in intestinal pathology is remains unclear. Herein, this study was conducted to investigate the effects of A. muciniphila DSM 22,959 on growth performance, intestinal barrier function, microecology and inflammatory response of weaned piglets stimulated by dextran sulfate sodium salt (DSS).</p><p><strong>Method: </strong>Twenty-four Duroc × Landrace × Yorkshire (DLY) weaned piglets used for a 2 × 2 factorial arrangement of treatments were divided into four groups with six piglets in each group. From 1 to 15 d, the CA and DA groups were orally fed with 1.0 × 10¹¹ colony-forming units A. muciniphila per day, while the CON and DCON groups were received gastric infusion of anaerobic sterile saline per day. The pigs were orally challenged (DCON, DA) or not (CON, CA) with DSS from day 9 to the end of the experiment and slaughtered on day 16.</p><p><strong>Results: </strong>Presence of A. muciniphila in DSS-challenged weaned pigs resulted in numerically increased diarrhea rate, blood neutrophilic granulocyte, serum C-reactive protein and immunoglobulin M levels, and numerically reduced final weight, average daily feed intake and average daily gain. The decrease in intestinal villus height, villous height: crypt depth ratio and digestibility was accompanied by lower expression of ZO1, ZO2, Claudin1, DMT1, CAT1, SGLT1 and PBD114 genes, as well as decreased enzyme activities of intestinal alkaline phosphatase, lactase, sucrase and maltase of piglets in DA group compared to piglets in DCON group. The abundance of Bifdobacterium, Lactobacillus, A. muciniphila, Ruminococcus gnavus was numerically higher in digesta of pigs in DA group than those in DCON group. The inflammatory responses of piglets were dramatically changed by the simultaneous presence of A. muciniphila and DSS: expression level of IL17A, IL17F, IL23, RORγt, Stat3 was elevated in DA pigs compared to the other pig groups.</p><p><strong>Conclusions: </strong>Our result showed that the oral A. muciniphila aggravates DSS-induced health damage of weaned piglet, which may attribute to the deteriorating intestinal morphology, dysbiosis of microbiota and inflammatory response disorders.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"8"},"PeriodicalIF":4.9,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017329","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 subtilis HGCC-1 improves growth performance and liver health via regulating gut microbiota in golden pompano.","authors":"Ming Li, Hui Liang, Jian Zhang, Jie Chen, Shichang Xu, Wenhao Zhou, Qianwen Ding, Yalin Yang, Zhen Zhang, Yuanyuan Yao, Chao Ran, Zhigang Zhou","doi":"10.1186/s42523-024-00372-x","DOIUrl":"10.1186/s42523-024-00372-x","url":null,"abstract":"<p><p>Probiotics as green inputs have been reported to regulate metabolism and immunity of fish. However, the mechanisms by which probiotics improve growth and health of fish are unclear. Therefore, the aim of this study was to investigate the effect of Bacillus subtilis HGCC-1, an indigenous probiotic isolated from fish, on growth performance, host lipid metabolism, liver inflammation and gut microbiota of golden pompano. 160,000 golden pompanos with the initial body weight of 93.6 ± 5.0 g was randomly assigned to two dietary groups: Control and HGCC-1 (control diet supplemented with 0.3 g/kg Bacillus subtilis HGCC-1 fermentation product), and after three weeks of feeding, 26 golden pompanos were randomly collected from each group for gut microbiome and host phenotype analysis. Dietary supplementation with Bacillus subtilis HGCC-1 significantly promoted growth performance (P < 0.05) and enhanced feed utilization. Besides, HGCC-1 improved liver health and alleviated hepatic steatosis and inflammation. Furthermore, Bacillus subtilis HGCC-1 enhanced intestinal lipid absorption, promoted hepatic utilization of dietary fat by improving hepatic lipid uptake/transport and fatty acid β-oxidation to provide energy, and reduced hepatic TG level (P < 0.05), which may be the potential mechanism of Bacillus subtilis HGCC-1-mediated growth promotion. Finally, Bacillus subtilis HGCC-1 significantly altered the structure and function of gut microbiota (P < 0.05), leading to enrichment of beneficial taxa such as Bacillus (P < 0.0001) and increased of the ratio of \"Functional Group 2/Functional Group 1\" (P = 0.00092). Interestingly, the ratio of \"Functional Group 2/Functional Group 1\" was linked to the growth traits (Spearman, P < 0.05), while the intestinal abundance of Bacillus was correlated with serum TG in fish (Spearman, R = 0.47, P = 0.00091), suggesting a role of the intestinal microbiota in HGCC-1 mediated effect on growth and lipid metabolism. In summary, Bacillus subtilis HGCC-1 promotes growth performance, alleviate hepatic steatosis and enhances liver health via regulating gut microbiota in golden pompano, which ultimately showed as beneficial effect of fish growth and health.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"7"},"PeriodicalIF":4.9,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980938","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 Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya.","authors":"Richard Nyamota, Earl A Middlebrook, Hussein M Abkallo, James Akoko, Francis Gakuya, Lillian Wambua, Bernard Ronoh, Isaac Lekolool, Athman Mwatondo, Mathew Muturi, Bernard Bett, Jeanne M Fair, Andrew W Bartlow","doi":"10.1186/s42523-024-00374-9","DOIUrl":"10.1186/s42523-024-00374-9","url":null,"abstract":"<p><strong>Background: </strong>African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance. This study investigated the blood microbiome of clinically healthy wild buffaloes in Kenya to determine its applicability in agnostic testing for bacteria in apparently healthy wild animals.</p><p><strong>Methods: </strong>Whole blood and serum samples were collected from 46 wild African buffalos from Meru National Park (30), Buffalo Springs (6) and Shaba (10) National Reserves in upper eastern Kenya. Total deoxyribonucleic acid (DNA) was extracted from these samples and subjected to amplicon-based sequencing targeting the 16 S rRNA gene. The bacteria operational taxonomic units (OTU) were identified to species levels by mapping the generated V12 and V45 regions of 16 S rRNA gene to the SILVA database. These OTU tables were used to infer the microbial abundance in each sample type and at the individual animal level. The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest.</p><p><strong>Results: </strong>Here, we demonstrate that buffaloes harbor many bacteria in their blood. We also report a diversity of 16 S rRNA gene sequences for Anaplasma and Mycoplasma from individual animals. By sequencing both whole blood and serum in triplicate for each animal, we provide evidence of the differences in detecting bacteria in both sample types.</p><p><strong>Conclusions: </strong>Diverse bacteria, including some potential pathogens, can be found in the blood of clinically healthy wild African buffalo. Agnostic surveillance for such pathogens can be achieved through blood microbiome sequencing. However, considerations for the question being asked for the blood microbiome in wildlife will impact the choice for using whole blood or serum for sequencing.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"6"},"PeriodicalIF":4.9,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973602","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":"Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris.","authors":"Valérie Perez, Viviane Boulo, Julien De Lorgeril, Dominique Pham, Dominique Ansquer, Gwenola Plougoulen, Valentine Ballan, Jean-Sébastien Lam, Océane Romatif, Jeremy Le Luyer, Corinne Falchetto, Caline Basset, Stanley Flohr, Moana Maamaatuaiahutapu, Marc André Lafille, Christophe Lau, Denis Saulnier, Nelly Wabete, Nolwenn Callac","doi":"10.1186/s42523-025-00376-1","DOIUrl":"10.1186/s42523-025-00376-1","url":null,"abstract":"<p><strong>Background: </strong>In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).</p><p><strong>Results: </strong>We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.</p><p><strong>Conclusions: </strong>Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"5"},"PeriodicalIF":4.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973578","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":"Multi-omics integration and immune profiling identify possible causal networks leading to uterine microbiome dysbiosis in dairy cows that develop metritis.","authors":"S Casaro, J G Prim, T D Gonzalez, F Cunha, A C M Silva, H Yu, R S Bisinotto, R C Chebel, J E P Santos, C D Nelson, S J Jeon, R C Bicalho, J P Driver, Klibs N Galvão","doi":"10.1186/s42523-024-00366-9","DOIUrl":"10.1186/s42523-024-00366-9","url":null,"abstract":"<p><strong>Background: </strong>Cows that develop metritis experience dysbiosis of their uterine microbiome, where opportunistic pathogens overtake uterine commensals. An effective immune response is critical for maintaining uterine health. Nonetheless, periparturient cows experience immune dysregulation, which seems to be intensified by prepartum over-condition. Herein, Bayesian networks were applied to investigate the directional correlations between prepartum body weight (BW), BW loss, pre- and postpartum systemic immune profiling and plasma metabolome, and postpartum uterine metabolome and microbiome.</p><p><strong>Results: </strong>The Bayesian network analysis showed a positive directional correlation between prepartum BW, prepartum BW loss, and plasma fatty acids at parturition, suggesting that heavier cows were in lower energy balance than lighter cows. There was a positive directional correlation between prepartum BW, prepartum systemic leukocyte death, immune activation, systemic inflammation, and metabolomic changes associated with oxidative stress prepartum and at parturition. Immune activation and systemic inflammation were characterized by increased proportion of circulating polymorphonuclear cells (PMN) prepartum, B-cell activation at parturition, interleukin-8 prepartum and at parturition, and interleukin-1β at parturition. These immune changes together with plasma fatty acids at parturition had a positive directional correlation with PMN extravasation postpartum, which had a positive directional correlation with uterine metabolites associated with tissue damage. These results suggest that excessive PMN migration to the uterus leads to excessive endometrial damage. The aforementioned changes had a positive directional correlation with Fusobacterium, Porphyromonas, and Bacteroides in cows that developed metritis, suggesting that excessive tissue damage may disrupt physical barriers or increase substrate availability for bacterial growth.</p><p><strong>Conclusions: </strong>This work provides robust mechanistic hypotheses for how prepartum BW may impact peripartum immune and metabolic profiles, which may lead to uterine opportunistic pathogens overgrowth and metritis development.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"4"},"PeriodicalIF":4.9,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11716391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959882","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":"Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis.","authors":"M F Hares, B E Griffiths, L Barningham, E E Vamos, R Gregory, J S Duncan, G Oikonomou, C J Stewart, J L Coombes","doi":"10.1186/s42523-024-00352-1","DOIUrl":"https://doi.org/10.1186/s42523-024-00352-1","url":null,"abstract":"<p><strong>Background: </strong>Cryptosporidiosis is a diarrheal disease that commonly affects calves under 6 weeks old. The causative agent, Cryptosporidium parvum, has been associated with the abundance of specific taxa in the faecal microbiome during active infection. However, the long-term impact of these microbiome shifts, and potential effects on calf growth and health have not yet been explored in depth.</p><p><strong>Methods: </strong>Three hundred and forty-six (346) calves from three dairy farms had one faecal swab collected during the first week of life (W1). Thereafter, sampled calves were monitored for diarrhoeal disease and those that suffered a diarrhoea event were tested for C. parvum by lateral flow testing (LFT). Calves that experienced diarrhoea and tested positive for C. parvum by LFT were assigned to the Cryptosporidium-positive (Cp+) group (n = 32). Matched healthy (H) controls with no history of diarrhoea were selected from the remaining cohort (n = 33). The selected subset of calves (n = 65) was observed until weaning, collecting a faecal swab, at approximately Week 5 (W5) and Week 10 (W10) after birth, resulting in a total of 191 samples (W1; n = 65, W5; n = 64, W10; n = 62). 16S rRNA gene amplicon sequencing was performed on all extracted samples.</p><p><strong>Results: </strong>Analysis of the longitudinal microbiome showed significant changes in the microbial diversity and composition across all three time-points. Whilst Firmicutes were elevated in the Cp+ group at W5 compared to the H group, no other significant differences were detected between H and Cp+ groups. Whilst the core microbiota showed some taxa were exclusive to each group, the role of these taxa in health and disease has yet to be determined. Antibiotics were also found to have an impact on the relative abundance of some taxa. Though healthy calves received a significantly higher body condition score than Cp+ calves at W5, the difference did not reach significance at W10, suggesting that Cp+ calves may catch up to their healthy counterparts once the infection has resolved.</p><p><strong>Conclusions: </strong>The findings of this study illustrated the changes in the microbial diversity and composition during the preweaning period in dairy calves. The results also indicated that the faecal microbiome is not predictive of cryptosporidiosis and implied that cryptosporidiosis doesn't cause long-term gut dysbiosis. This study furthered our understanding of the parasite-microbiome relationship and its impact on the bovine host.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"3"},"PeriodicalIF":4.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959047","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":"Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution.","authors":"Hannah E Epstein, Tanya Brown, Ayọmikun O Akinrinade, Ryan McMinds, F Joseph Pollock, Dylan Sonett, Styles Smith, David G Bourne, Carolina S Carpenter, Rob Knight, Bette L Willis, Mónica Medina, Joleah B Lamb, Rebecca Vega Thurber, Jesse R Zaneveld","doi":"10.1186/s42523-024-00370-z","DOIUrl":"10.1186/s42523-024-00370-z","url":null,"abstract":"<p><strong>Background: </strong>Evolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea.</p><p><strong>Results: </strong>Using a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425 million years of coral evolution by conducting a cross-species coral microbiome survey (the \"Global Coral Microbiome Project\") and combining the results with long-term global disease prevalence and coral trait data. Interpreting these data in their phylogenetic context, we show that microbial dominance predicts disease susceptibility, and traced this dominance-disease association to a single putatively beneficial symbiont genus, Endozoicomonas. Endozoicomonas relative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera, while also correlating strongly with high growth rates.</p><p><strong>Conclusions: </strong>These results demonstrate that the evolution of Endozoicomonas symbiosis in corals correlates with both disease prevalence and growth rate, and suggest a mediating role. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbioses influence animal life-history tradeoffs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"1"},"PeriodicalIF":4.9,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928657","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, environmental, and developmental factors affect the microbiota of barn owls (Tyto alba) in a cross-fostering experiment.","authors":"Ammon Corl, Motti Charter, Gabe Rozman, Sondra Turjeman, Sivan Toledo, Pauline L Kamath, Wayne M Getz, Ran Nathan, Rauri C K Bowie","doi":"10.1186/s42523-024-00365-w","DOIUrl":"10.1186/s42523-024-00365-w","url":null,"abstract":"<p><strong>Background: </strong>Species host diverse microbial communities that can impact their digestion and health, which has led to much interest in understanding the factors that influence their microbiota. We studied the developmental, environmental, and social factors that influence the microbiota of nestling barn owls (Tyto alba) through a partial cross-fostering experiment that manipulated the social and nest environment of the nestlings. We then examined the nestling microbiota before and three weeks after the exchange of nestlings between nests, along with the microbiota of the adults at the nest and nestlings in unmanipulated nests.</p><p><strong>Results: </strong>We found that nestlings had higher bacterial diversity and different bacterial communities than adults. The microbiota of nestlings was more like that of their mothers than their fathers, but the similarity to the father tended to increase with the amount of time the father was in close proximity to the nest, as measured from movement data. Cross-fostered offspring had higher bacterial diversity and greater changes in bacterial community composition over time than control offspring. Cross-fostering led the microbiota of the nestlings in the experiment to converge on similar bacterial communities. The microbiota of nestling owls therefore rapidly changed along with alterations to their social and nest environments.</p><p><strong>Conclusions: </strong>These results highlight the dynamic nature of the microbiota during early development and that social interactions can shape microbial communities.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"77"},"PeriodicalIF":4.9,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11667991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886542","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":"Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles.","authors":"Nan Zhou, Weiye Chen, Luming Xia, Min Li, Huiping Ye, Chao Lv, Yiwen Chen, Zile Cheng, Tae-Jin Park, Pak-Leung Ho, Xin Gao, Xiaokui Guo, Hongjin Zhao, Huiluo Cao, Yongzhang Zhu","doi":"10.1186/s42523-024-00364-x","DOIUrl":"10.1186/s42523-024-00364-x","url":null,"abstract":"<p><strong>Background: </strong>Dogs-whether pets, rural, or stray-exhibit distinct living styles that influence their fecal microbiota and resistomes, yet these dynamics remain underexplored. This study aimed to analyze and compare the fecal microbiota and resistomes of three groups of dogs (37 pets, 20 rural, and 25 stray dogs) in Shanghai, China.</p><p><strong>Results: </strong>Metagenomic analysis revealed substantial differences in fecal microbial composition and metabolic activities among the dog groups. Pet dogs displayed the lowest microbial diversity. Using Shapley Additive Explanations (SHAP), an interpretable machine learning approach, Ligilactobacillus emerged as the most diverse genus, with significantly higher SHAP values in stray dogs, suggesting enhanced adaptability to more variable and less controlled environments. Across all samples, 587 antibiotic resistance genes (ARGs) were identified, conferring resistance to 14 antibiotic classes. A striking observation was the detection of mcr-1 in one pet dog, indicating a potential public health risk. The floR gene was identified as a key differentiator in resistance profiles, particularly in pet and rural dogs, likely due to antibiotic exposure in their environments.</p><p><strong>Conclusion: </strong>This study provides the first comprehensive assessment of fecal microbiota and resistome variations among dogs with different lifestyles, revealing a less resilient microbiome and heightened antimicrobial resistance in pet dogs, which could have public health implications.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"76"},"PeriodicalIF":4.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11663309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878735","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}