Animal microbiome最新文献

{"title":"Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.","authors":"Xingwei Shi, Fei Chen, Min Dai, Yongjing Tang, Jishan Wang, Yuheng Lin, Minhui Shi, Tianming Lan, Huan Liu, Xin Jin, Liang Xiao, Karsten Kristiansen, Xiaoping Li","doi":"10.1186/s42523-026-00533-0","DOIUrl":"10.1186/s42523-026-00533-0","url":null,"abstract":"<p><p>BACKGROUND: The gut microbiota plays a crucial role in metabolism, immune regulation, and ecological adaptation of mammals. Although significant advancements have been made in shotgun metagenomic sequencing and the emergence of algorithms for generation of metagenome-assembled genomes (MAGs), a comprehensive investigation of the gut microbiota at the species level of wild mammals, among these the Asian elephant (Elephas maximus), is still lacking. RESULTS: Here, based on a total of 82 fresh fecal samples collected from Asian elephants residing in distinct regions of the Yunnan Province, we established a comprehensive genome catalog containing 1421 species-level genome bins (SGBs) and a gene catalog comprising 44,596,628 non-redundant genes covering the gut microbiota composition of representative Asian elephant populations. At the species level, 1368 bacteria and 53 archaea were identified, and more than 93% of the SGBs remained unclassified, indicating that there are a large number of potential new species in the Asian elephant gut microbiota. At the functional level, carbohydrate hydrolases, biosynthetic gene clusters, and metabolic pathways dominated the gut microbiome of Asian elephants. Lifestyle and migration affected the composition and functional potential of the gut microbiota of Asian elephants. A northward migration was accompanied by an increase in gut microbiota diversity, an increase in the abundance of the phylum Bacteroidota, and a decrease in the presence of potentially pathogenic genera. In contrast, a southward migration of elephant herds was accompanied by exposure to unfavorable environments, with changes in gut microbiota including increased xenobiotic degradation and metabolic capacity. CONCLUSIONS: We constructed comprehensive catalogs of gut microbial genes and genomes representative for Asian elephant populations, providing a valuable data resource for future research. Our study elucidates migration and lifestyle may modulate the composition and functionality of the gut microbiota in Asian elephants, offering critical insights for monitoring their health and enhancing conservation strategies for wild populations. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13064403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147349825","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":"Host-microbiome interplay supports heat stress resilience in zebu calves.","authors":"Brijesh Yadav, Goutam Banerjee, Anandita Srivastava, Arun Kumar Madan, Ravindra Kumar, Pratik Banerjee","doi":"10.1186/s42523-026-00539-8","DOIUrl":"10.1186/s42523-026-00539-8","url":null,"abstract":"<p><p>This study delineates the impact of heat stress (HS) on rumen microbial diversity and its association with host physiological responses in zebu calves, aiming to elucidate the microbiome-mediated mechanisms underlying thermal resilience. Six zebu calves (8–11 months; 120–150 kg) were sequentially subjected to thermoneutral (TN) [temperature-humidity index (THI) of 72.32] and HS (THI of 94.82) conditions for 21 days each, with a 10-day acclimatization and a 45-day washout interval. Physiological assessment under HS revealed significant (p < 0.05) elevations in rectal temperature, respiratory rate, cortisol, and IL-6 levels, along with significant (p < 0.05) declines in plasma aspartate aminotransferase (AST) activity and triglyceride levels. The volatile fatty acid (VFA) concentration remained unaltered, suggesting functional stability of the fermentative activity during HS. HS significantly altered the microbial diversity in the rumen of zebu calves, especially among bacteria, fungi, and protozoa, with archaeal changes limited to alpha diversity. HS led to a shift toward Pseudomonadota (notably Pseudomonas and Stenotrophomonas), whereas the TN condition favored Bacillota (e.g., Aerococcus and Soilbacillus). The genus-level fungal profile exhibited a high abundance of Thermothielavioides in the HS group and Schizosaccharomyces in the TN group. Species-level profiling indicated the enrichment of S. pombe in both groups. Similarly, the species-level protozoal profiles indicated a high abundance of Entodinium caudatum in both groups. Although the archaeal composition remained largely stable, the relative abundance of Methanobrevibacter (particularly M. ruminantium) was more prevalent in both groups. This study also indicated that HS enriched folate and amino acid biosynthesis pathways, while TN favored glycolytic metabolism. Microbial taxa like Stenotrophomonas and Aerococcus correlated strongly with stress and metabolic markers like IL-6, cortisol, HSP-90, AST, and triglycerides. Despite the increased abundance of opportunistic taxa under HS, the maintenance of VFA homeostasis and strong taxa–phenotype associations underscore the integral role of the rumen microbiome in mediating host adaptation to HS, thereby contributing to the thermal resilience of zebu calves.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13064310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147349794","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-dependent gut microbiota associated with intramuscular fat deposition in Longdong cashmere goats.","authors":"Heyu Chai, Haowen Cheng, Jiayang Sun, Yuzhu Luo, Bingang Shi, Jiqing Wang, Shaobin Li, Jing Luo, Fangfang Zhao","doi":"10.1186/s42523-026-00530-3","DOIUrl":"10.1186/s42523-026-00530-3","url":null,"abstract":"<p><p>Intramuscular fat (IMF) is a key determinant of meat quality, influencing tenderness, juiciness, and flavor. Previous studies have reported that the deposition of IMF is controlled by various factors. However, there is a shortage of research exploring the variations in IMF deposition across age groups from a microbial perspective. This study evaluated the differences in IMF deposition between yearling (1-year-old) and mature (4-year-old) Longdong Cashmere goats and analyzed its association with gut microbiota. The results revealed that the IMF content in shoulder meat and blood lipid levels increased with age (p < 0.05). Conversely, the contents of lipoprotein lipase (LPL) in the liver and duodenum significantly decreased with age. Microbial diversity differed between the two age groups, with specific microbiota identified from the gut of goats involved in the lipid metabolism pathway. The concentrations of valeric and isovaleric acids in the rumen, as well as acetic, propionic and isovaleric acids in the colon, were higher in yearling goats than in mature goats (p < 0.05). Spearman correlation analysis of IMF deposition indicators with gut microbiota revealed that, within the rumen, the abundances of CAG-791 and Sodaliphilus were positively correlated with IMF content in shoulder meat and TG levels, while exhibiting a negative correlation with the contents of valeric acids. Furthermore, the abundance of Clostridium_R showed a positive association with IMF content in shoulder meat and with the abundances of CAG-791and Sodaliphilus. In contrast, the abundance of Bact_11 was negatively correlated with IMF content in shoulder meat, TG levels, and the abundances of CAG-791, Sodaliphilus and Clostridium_R. Within the abomasum, the abundances of UMGS and Hylemonella_582308 were correlated with IMF content in the shoulder meat, as well as serum LDL and VLDL levels. This study provides significant insights into the age-dependent gut microbiota associated with intramuscular fat deposition in goats and identifies several potential gut microbiota for further research on their impacts on IMF deposition.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13049821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147319161","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 velezensis alleviates PM_2.5-induced intestinal injury and dysbiosis in broilers via the \"lung-gut axis\".","authors":"Xuan Liu, Xunbozan Zhang, Christopher Peterson Daniel, Dadan Liu, Liang Chen, Hongfu Zhang","doi":"10.1186/s42523-026-00529-w","DOIUrl":"10.1186/s42523-026-00529-w","url":null,"abstract":"<p><strong>Background: </strong>This study investigated how tracheal instillation of Bacillus velezensis mitigates PM_2.5-induced lung injury and counteracts its adverse effects on distal intestinal health in broilers via the \"lung-gut axis\".</p><p><strong>Results: </strong>Five groups were randomly selected from among seventy-five 14-day-old AA broilers: Control, Saline, PM2.5, B. velezensis, and B. velezensis + PM2.5. Results showed that compared with the Saline group, PM_2.5 exposure disrupted lung structure and significantly upregulated TLR4, MyD88, NF-κB, IL-18, and IFN-γ related inflammatory factors via the TLR4/MyD88/NF-κB signaling axis (P < 0.05). In addition, it significantly reduced jejunal villus height through the action of the \"lung-gut axis\" (P < 0.05), decreased the levels of IL-10, Claudin-1, and Occludin while increasing that of IL-22 (P < 0.05). Analysis of the cecal microbiota found that PM_2.5 reduced the Shannon index of bacterial communities and raised the relative abundance of Bacteroidota, Pseudomonadota, and Flavonifractor. Co-treatment with B. velezensis + PM_2.5 reversed the above changes, significantly improved lung and intestinal morphology, enhanced jejunal barrier function, reduced lung and jejunal inflammatory responses, and increased the relative abundance of Faecalibacterium. Based on KEGG functional prediction, the PM_2.5 group was enriched in microbial metabolic pathways, such as two-component systems and ABC transporters.</p><p><strong>Conclusions: </strong>Tracheal instillation of B. velezensis can improve the expression of genes associated with lung injury via the TLR4/MyD88/NF-κB signaling axis and effectively alleviate PM_2.5-induced distal jejunal damage, barrier dysfunction, inflammatory response, and dysbiosis by mediating the \"lung-gut axis\". This could provide a theoretical support and scientific basis for seeking probiotics to improve PM_2.5 harm.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13049975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147319133","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":"Disordered colonic microbiota as a potential contributor to inflammation in diarrheal Jinhua weaned piglets.","authors":"Jiaheng Li, Chengzeng Luo, Fangfang Lou, Xiaojun Zhang, Jiujun Duan, Zeou Wei, Xujin Hu, Pingguang Tu, Xizhong Du, Ruqing Zhong, Liang Chen, Hongfu Zhang","doi":"10.1186/s42523-026-00525-0","DOIUrl":"10.1186/s42523-026-00525-0","url":null,"abstract":"<p><p>Diarrhea is a major cause of mortality in Jinhua piglets, accounting for up to 80% of total piglet deaths and severely restricting the sustainability of pig production systems. In this study, colonic morphology, organ indices, gut microbiota composition, and transcriptomic profiles were compared between diarrheal piglets (DG) and healthy piglets (HG) to identify diarrhea associated bacteria in Jinhua piglets and to explore potential microbial intervention strategies. The results revealed that diarrheal piglets had lower organ indices (p < 0.01) and worse intestinal conditions such as inflammatory factor infiltration, reduced number of goblet cells (p < 0.05), and increased colonic crypt depth (p < 0.05). Transcriptomics analysis of colonic mucosa revealed that differentially expressed genes (DEGs) between two groups (FC > 1.5, p < 0.05) were enriched mainly in Th1 and Th2 cell differentiation and Th17 cell differentiation. Microbiota analysis showed that bacteria such as Clostridium_sensu_stricto_1, which were enriched in the colon of piglets in HG, may contribute to host metabolic and immune modulation via metabolic products such as short chain fatty acids and crosstalk with other microbial taxa. In contrast, potential harmful bacteria, particularly Fusobacterium, were significantly enriched in the colon of piglets in DG. Correlation analysis further identified IL-2Rβ, TBX21, and LCK as key immune related genes associated with differentially abundant microbes. Enriched Fusobacterium showed associations with inflammatory gene expression, whereas Clostridium_sensu_stricto_1 exhibited opposite correlations. In conclusion, harmful bacterial colonization may promote intestinal inflammation and diarrhea in Jinhua piglets, while beneficial bacteria exert protective effects that support piglets’ growth and intestinal health. These beneficial microbes may serve as potential probiotic candidates for improving the health of Jinhua piglets.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13049971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147319135","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 fermented grape pomace on growth performance and intestinal health of weaned piglets.","authors":"Mingyu Wang, Qi Li, Ao Guo, Jiaqi Yue, Lin Zhang, Guangquan Lv, Taiyong Yu","doi":"10.1186/s42523-025-00507-8","DOIUrl":"10.1186/s42523-025-00507-8","url":null,"abstract":"<p><p>The improvement of forage quality through proper fermentation is well documented. Grape pomace (GP), an economically valuable by-product, remains underutilized despite its potential benefits. This study explores the effects of fermented GP (FGP) supplementation on weaned piglets, focusing on immune and antioxidant capacity, intestinal flora homeostasis, growth performance, and diarrhea reduction. We first analyzed and compared the nutritional composition of GP before and after fermentation. Subsequently, a diet supplemented with 5% FGP was formulated. From an initial pool of 480 weaned piglets, 120 healthy animals (28 days old, average weight 8.42 ± 0.19 kg) were randomly assigned to two groups: a control group (CON) fed a basal diet and an experimental group receiving the 5% FGP-supplemented diet. The results demonstrated that fermentation significantly enhanced the levels of key nutrients and amino acids (e.g., Ca, P, Glu) in GP (P < 0.05). Dietary supplementation with FGP significantly improved feed efficiency, as indicated by a reduced feed-to-gain ratio (F/G), and decreased the incidence of diarrhea (P < 0.05). Additionally, FGP exhibited notable antioxidant activity, reflected by reduced serum malondialdehyde (MDA) levels and mitigation of oxidative stress (P < 0.05). Immunomodulatory benefits were also observed, including elevated serum immunoglobulin G (IgG) and interleukin-10 (IL-10), along with decreased tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) levels (P < 0.05). Morphological improvements in intestinal architecture were evident, with increased villus height (VH) in the duodenum, jejunum, and ileum, as well as an enhanced villus height-to-crypt depth ratio (V/C) (P < 0.05). In conclusion, dietary inclusion of FGP enhances disease resistance in piglets by improving antioxidant capacity, modulating immune responses, enhancing intestinal morphology, and enriching microbial diversity. These findings support FGP as a viable nutritional strategy for boosting health and optimizing the utilization of grape processing by-products.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13041460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313091","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":"Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows.","authors":"Viktoria Neubauer, Siska Aditya, Narciso M Quijada, Stefanie Urimare Wetzels, Monika Dzieciol, Poulad Pourazad, Qendrim Zebeli, Evelyne Selberherr","doi":"10.1186/s42523-025-00499-5","DOIUrl":"10.1186/s42523-025-00499-5","url":null,"abstract":"<p><p>BACKGROUND: Lipopolysaccharides (LPS) from pathogenic Gram-negative bacteria play a key role in the pathophysiology of mastitis. Subacute ruminal acidosis (SARA) induces rumen dysbiosis, leading to LPS translocation and systemic immune activation. This study investigated the effects of a high-grain diet and intramammary LPS challenge on the milk microbiome of dairy cows. Cows were first fed a baseline control diet (day-7 to d-1; CON; 40% grain; n = 18). On d1, 12 cows were switched to a SARA diet (60% grain). On d30, six SARA (SARA_LPS) and the six CON cows (CON_LPS) were challenged intramammarily with LPS, while the other six SARA cows received a placebo (SARA_PLA). No CON_PLA group was enrolled. Milk samples were collected on d-2 (before feeding challenge), d30 (after feeding challenge; before LPS), and d32 (after LPS), and analysed using 16S rRNA gene amplicon sequencing and qPCR. RESULTS: During the feeding phases, more genera (70.1%) increased in CON than SARA cows, whereas more (65.3%) genera decreased their relative abundance in SARA compared to CON (p < 0.001). This decline persisted in SARA_PLA cows, with more genera (62.4%) decreasing their abundance (p < 0.001). However, LPS injection reversed the trend of the feeding effect, with more genera (79.3%) increasing in SARA_LPS cows in comparison to the other two groups, while more genera (85.5%) decreased in CON_LPS (p < 0.001) in comparison to the other two groups. Alpha diversity correlated positively with bacterial cell equivalents. Of all genera, 22.1% correlated negatively with milk amyloid A (MAA), which increased post-LPS injection, 21.7% positively with lactose, and 13.4% positively with milk urea. SCC showed significant differences in beta-diversity, but no distinct visual clustering nor many correlations. CONCLUSION: The microbial dynamics suggest that high-grain diet and the LPS injection influence the milk bacterial community. More taxa correlated with MAA than with SCC, suggesting that MAA may better reflect immune-microbial interactions in milk. A roughage-rich diet promoted higher microbial abundance, whereas high-grain feeding reduced abundance over the timespan of 30 days. Intramammary LPS challenge decreased absolute abundance in CON but increased it in SARA cows, suggesting a diet-dependent immune modulation of the mammary environment. These findings indicate that mammary gland epithelial integrity and immune mediators jointly shape the milk microbiome under metabolic and inflammatory stress. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12937525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Composition of microbiota from chicken caecal mucosa considerably differs from microbiota in the caecal lumen.","authors":"Jiri Volf, Daniela Karasova, Magdalena Crhanova, Marcela Faldynova, Hana Prikrylova, Michal Zeman, Vladimir Babak, Jana Rajova, Pavel Kulich, Ivan Rychlik","doi":"10.1186/s42523-026-00536-x","DOIUrl":"10.1186/s42523-026-00536-x","url":null,"abstract":"<p><strong>Background: </strong>Despite the importance of microbiota at mucosal surfaces of the gut and their different composition in comparison to those colonising the gut lumen, only a few papers specifically addressed this topic. In this study, we therefore defined mucosa-associated and lumen-associated microbiota from the chicken caecum.</p><p><strong>Results: </strong>To identify mucosa-adapted microbiota members, caeca from adult hens instead of chicks should be analysed. Mucosa-adapted microbiota included Treponema-like species, Brachyspira innocens, Mucispirillum sp., Helicobacter pullorum, Desulfovibrio sp. and Anaerobiospirillum sp. On the other hand, representatives of Bacteroidota were enriched in the caecal lumen. Reduced colonization of the mucosal surface in one-week-old chicks was a consequence of the lack of appropriate microbiota source in chicks obtained from hatcheries since when the chicks were raised in the presence of adult hens, they were efficiently colonised by mucosa-adapted microbiota within the first week of life. The identified mucosa-associated bacteria were of helical shape, chemotactic and motile, and expressed type VI secretion system in vivo. Brachyspira innocens and Anaerobiospirillum fermented carbohydrates while Mucispirillum sp. and Helicobacter pullorum preferred amino-acid fermentation.</p><p><strong>Conclusions: </strong>Here, we defined mucosal microbiota of chicken caecum, microbiota which are in closer contact with chicken host than the luminal microbiota and may therefore considerably affect the behaviour of chickens.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13040750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313096","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":"Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.","authors":"Mattia Pirolo, Moiz Khan Sherwani, Carmen Espinosa-Gongora, Esben Østergaard Eriksen, Clara Tassinato, Antton Alberdi, Luca Guardabassi","doi":"10.1186/s42523-026-00522-3","DOIUrl":"10.1186/s42523-026-00522-3","url":null,"abstract":"<p><p>BACKGROUND: Post-weaning diarrhoea (PWD) is a major health and economic concern in intensive pig production. In this study, we hypothesized that the faecal microbiome, sampled before disease onset, could provide early prognostic markers of PWD risk and applied a machine-learning framework to identify biomarkers predictive of piglet susceptibility or resilience to PWD. At two Danish commercial farms experiencing PWD outbreaks, four pens per farm were monitored for 14 days post-weaning, with daily clinical assessments and rectal swabs collected every other day. In a nested case–control design, we profiled 140 samples from 41 piglets that developed PWD and 82 samples from 16 piglets that remained healthy by 16S rRNA sequencing. Additionally, we performed shotgun metagenomics on 56 pre-diarrhoeic samples from susceptible piglets and 47 from resilient piglets. A random-forest classifier with recursive feature elimination identified metagenome-assembled genomes (MAGs) predictive of resilience or susceptibility, trained and cross-validated independently within each farm. Negative binomial zero-inflated mixed (NBZIM) models assessed associations with known PWD risk factors (e.g. birth/weaning weights, weaning age and dam parity). RESULTS: Prior to diarrhoea onset, microbial community structures differed significantly between resilient and susceptible piglets at both farms (PERMANOVA, p < 0.05). Feature-reduced models achieved high accuracy (AUC = 0.94 and 0.82 in Farm A and Farm B, respectively) and identified 10 and 13 MAGs enriched in resilient piglets, and one and two MAGs enriched in susceptible piglets from the two farms, respectively. All MAGs were farm-specific, highlighting the multifactorial aetiology of PWD. NBZIM models indicated that most predictive MAGs were independent of established PWD risk factors. Temporally, these MAGs peaked in relative abundance early after weaning (day 4 in Farm A; day 0 in Farm B). In the farm with unclear aetiology, functional analysis showed that susceptibility-associated MAGs were depleted for arginine/ornithine and vitamin (cobalamin, thiamine) biosynthesis and lactate production traits, suggesting metabolic dysbiosis. CONCLUSIONS: Our findings indicate that pre-diarrhoeic faecal microbiome signatures predict PWD risk and provide a foundation for early prognostic tools and targeted interventions, including probiotic development, to mitigate PWD and reduce reliance on antimicrobials in pig production. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13040825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147286347","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":"Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.","authors":"Chao Wei, Zhe Chen, Yaxiang Wang, Lusheng Huang, Congying Chen","doi":"10.1186/s42523-026-00534-z","DOIUrl":"10.1186/s42523-026-00534-z","url":null,"abstract":"<p><p>BACKGROUND: Jumbo phages are phages with comparatively large genome sizes. Jumbo phages have been identified in various microbial communities. However, their diversity, genome structure, potential function, and their interactions with hosts and other phages are largely unknown due to insufficient genomic data. RESULTS: We collected 59,652,008 putative viral genomes from seven habitats by using 38 public metagenome datasets, an integrated public viral genome database (IGN), and pig gut viral genome databases. We obtained 10,754 jumbo phage genomes with sizes ranging from 200 to 831 kb. Most (94.64%) of these jumbo phage genomes were classified into Caudoviricetes, and the results have expanded the known diversity of Caudoviricetes. We found 2,389 species-like operational genome clusters that contained 3,727 (34.69%) genomes without any known viral genomes in the IGN, suggesting potential novel species-like genomes. Genome analysis suggested the potential coevolution of jumbo phages with habitat types and highlighted the utilization of alternative genetic codes and their corresponding suppressor tRNAs for recoding stop codons. CRISPR spacer analysis revealed potential bacterial or archaeal hosts of jumbo phages and uncovered competitive networks among jumbo phages. Habitat type had an important effect on the variation in phage auxiliary metabolic genes. CONCLUSIONS: This study provides an important resource and new knowledge for future studies on the interaction between jumbo phages and their bacterial or archaeal hosts. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13037316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147286395","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}