Animal microbiome最新文献

{"title":"Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.","authors":"Chi Sun Yun, Jae-Kyeom Kim, Hyojung Kwon, Moon Her, Jin San Moon","doi":"10.1186/s42523-026-00565-6","DOIUrl":"10.1186/s42523-026-00565-6","url":null,"abstract":"<p><p>BACKGROUND: Granuloma lesions in poultry are a frequent pathological finding, representing a chronic inflammatory response to persistent infectious agents, most commonly bacteria or fungi. Accurate differentiation of the underlying cause requires additional diagnostic tests, such as acid-fast staining, fungal culture, or bacterial isolation and genetic identification. However, the pathogens often remain undetermined when conventional detection methods fail. The present case aimed to investigated granulomatous disease in multiple organs of layer chickens by applying metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing. CASE PRESENTATION: A total of 35 deaths occurred in a flock of layer chickens, accompanied by a decrease in daily feed intake from 144 g to 104 g. Six carcasses from 38-weeks-old layer chickens were submitted for disease diagnosis. During necropsy, granuloma/neoplastic lesions were observed in the liver, ovary, proventriculus, pancreas and kidney. Histopathological examination revealed compartmentalized infiltration of lymphocytes and multinucleated giant cells in liver, ovary, proventriculus, pancreas and renal parenchyma. While Escherichia coli was isolated from the oviduct, no viral agents (IBV, CIAV, MDV, ALV, REV, or HEV) were detected by RT-PCR. Notably, some of the initial metagenomic shotgun results were recognized as different taxa due to the misclassification of certain reads. Following a re-analysis of these shotgun reads against the nucleotide database, both metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing identified E. coli as the dominant species in liver samples. CONCLUSION: The present case indicates that E. coli may contribute to granuloma lesions in layer chickens. While 16S rRNA amplicon sequencing provided more reliable bacterial identification for diagnostic purposes, metagenomic shotgun sequencing offers complementary insight by detecting broader microbial communities. Therefore, integrating both approaches alongside conventional diagnosis may improve the accuracy of diagnosis for granulomatous diseases in poultry. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730844","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":"Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.","authors":"Vincenzo Cuteri, Silvia Preziuso, Yubao Li, Fulvio Laus","doi":"10.1186/s42523-026-00569-2","DOIUrl":"10.1186/s42523-026-00569-2","url":null,"abstract":"<p><p>The exponential growth of the human population and associated intensifications in animal farming, pet ownership, and habitat anthropisation have dramatically increased human-animal interactions. Global livestock production now exceeds 24 billion animals annually, and pet ownership has risen to over 70% of households in many developed nations, creating unprecedented interfaces for viral exchange. This heightened contact has multiplied opportunities for zoonotic and reverse-zoonotic transmission, as tragically exemplified by the SARS-CoV-2 pandemic. The fecal virome—defined as the totality of viral nucleic acids in the gastrointestinal tract—represents a crucial, yet largely unexplored, pathway for such exchanges. While the bacterial microbiome’s role is increasingly recognized, the virome’s composition, dynamics, and transmissibility between co-habiting humans and animals remain poorly characterized. This review compiles current evidence on the fecal virome of key domestic animals (equines, livestock, pets) and their human contacts under the “One Health” framework. We critically evaluate methodological approaches—from targeted PCR to viral metagenomics—and highlight the discovery of novel viruses and identification of zoonotic agents through metagenomic approaches. Critically, we identify significant knowledge gaps, including the absence of definitive evidence for contemporary cross-species transmission versus shared ancestry or convergent evolution. We propose a strategic research agenda focused on longitudinal studies of human-animal cohorts, standardized metagenomic methodologies, and functional analyses of the virome. Elucidating the fecal virome at this interface is paramount for developing proactive surveillance strategies to predict and prevent the next emerging viral disease.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis).","authors":"Chloe Cummins, William Sutton, Taina McLeod, Jason W Dallas, Mitra Ghotbi, Lluvia Vargas-Gastélum, N Reed Alexander, Alexander J Rurik, Dale McGinnity, Sherri Doro Reinsch, Pia Sandonato, Jessica Arbour, Michael Freake, Anthony Ashley, William Ternes, Elizabeth Culp, Joseph Spatafora, Kerry McPhail, Jason E Stajich, Rebecca Hardman, Donald M Walker","doi":"10.1186/s42523-026-00537-w","DOIUrl":"10.1186/s42523-026-00537-w","url":null,"abstract":"<p><p>BACKGROUND: Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics. METHODS: 16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing a wild diet in zoo-reared hellbenders. Additionally, the bacterial composition of zoo-released individuals and wild resident hellbenders was compared to examine the response of the gut microbiome upon release into natural habitat. Selected samples were also chosen for ITS1 rDNA sequencing as a preliminary investigation of the hellbender gut mycobiome. RESULTS: Human rearing strongly affected the gut microbiome, leading to reduced bacterial richness as well as differing community structure than wild hellbenders. However, implementation of a wild diet in a zoo setting modulated the microbiome and appeared to be mainly driven by bacterial turnover. Additionally, both bacterial and fungal gut assemblages demonstrated the capacity for restructuring upon release into native habitat to become more reflective of a wild-type microbiome. CONCLUSIONS: We completed the first study elucidating the gut microbial composition patterns of hellbenders, across both zoo and wild settings. These results provide an understanding of the potential impacts of conservation populations in zoos on gut microbial communities and also inform headstart programs of the transition of the gut microbiome post-reintroduction to the wild. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13088468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700820","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 characterization of blood metabolites and cervical microbiota associated with estrus in simmental cattle.","authors":"Jiandong Wang, Xue Zhang, Youli Yu, Yanan Guo, Yuxi Zhao, Shijie Bi","doi":"10.1186/s42523-026-00571-8","DOIUrl":"10.1186/s42523-026-00571-8","url":null,"abstract":"<p><p>Accurate estrus detection is critical for optimizing reproductive efficiency in beef cattle. This study characterized blood metabolites and cervical microbiota associated with estrus in Simmental cattle using an integrated multi-omics approach. Twelve multiparous cows were assigned to estrus (n = 6) or nonestrus (n = 6) groups based on behavioral, hormonal, and ultrasonographic criteria. Serum samples were analyzed via ELISA and UPLC-MS/MS, while cervical microbiota were profiled using 16S rRNA and ITS sequencing. Serum biochemical analysis revealed elevated levels of total protein, albumin, glucose, and insulin-like growth factor-1 during estrus (p < 0.01). Untargeted metabolomics identified 258 differentially abundant metabolites enriched in amino acid and lipid metabolism pathways. Cervical microbiota analysis showed that Firmicutes and Bacteroidetes were the dominant bacterial phyla, with Bacteroidetes increasing by 13.36% during estrus. Fungal Ascomycota dominated the estrus group (78.38% vs. 67.20%), accompanied by reduced alpha diversity (p < 0.05). LEfSe analysis identified 22 bacterial and 16 fungal biomarkers associated with estrus. Correlation analysis revealed that E2 was positively correlated with Bacteroidota (r = 0.604) and fungal genera Bacteroides (r = 0.703), while progesterone showed negative correlations. This study reveals a complex microbiota-metabolite-host network specific to estrus in Simmental cattle, providing potential biomarkers for estrus detection.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13085721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694068","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 profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).","authors":"Jordyn Clough, Katarina M Mikac","doi":"10.1186/s42523-026-00564-7","DOIUrl":"10.1186/s42523-026-00564-7","url":null,"abstract":"<p><p>BACKGROUND: The microbiome is significant for conservation biology and should be considered in threatened species management programs. Commensal microbes contribute important functions for host health, while pathogenic microbes can negatively impact the host, leading to morbidity, mortality, and population declines. Shotgun metagenomics, involving the agnostic sequencing of all DNA within a sample, has utility for simultaneous microbial community profiling and pathogen detection. Herein, we used shotgun metagenomics to profile the faecal bacteriome and mycobiome of the southern greater glider (Petauroides volans), an endangered Australian marsupial, and identify putative pathogens that could represent threats to population health. RESULTS: We analysed faecal samples collected from wild southern greater gliders (n = 48) across southeastern New South Wales, Australia. Geographic location had significant effects on both bacterial and fungal community composition. The bacteriome was dominated by Firmicutes, Proteobacteria and Bacteroidetes, with 58 core bacterial species shared among all locations. The mycobiome was dominated by the Ascomycetes, with 261 core fungal species shared among all locations. Geographic location was associated with significant differences in bacterial and fungal microbiota abundance but not host sex or weight. We identified 18 bacterial pathogens and 41 fungal pathogens of veterinary interest, ranging from low prevalence to ubiquitous. Bacteroides fragilis was associated with shifts in the Firmicutes:Bacteroidetes ratio, and therefore, potential dysbiosis. CONCLUSIONS: Geographic location is a key determinant of faecal microbial community structure and abundance in southern greater gliders. Core communities of faecal bacteria and fungi are conserved within and among populations. Southern greater gliders carry genetic material from a variety of putative bacterial and fungal pathogens. These microbes may present threats to the health of greater gliders, their possum relatives, or other animals in Australian forest ecosystems. Scientists and natural resource managers should consider the holobiont, rather than just the individual, when planning for conservation management actions such as translocation. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13130779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary fiber-driven shifts in mycobiota and short-chain fatty acid landscape in porcine hindgut.","authors":"Jianwei Qin, Hua Li, Xiaofeng Deng, Shuangmei Huang, Jun He, Aimin Wu, Zhaolai Dai, Jingyi Cai, Gang Tian, Xiangbing Mao, Bing Yu, Ping Zheng, Junqiu Luo, Hui Yan, Jiayong Tang, Yuheng Luo","doi":"10.1186/s42523-026-00563-8","DOIUrl":"10.1186/s42523-026-00563-8","url":null,"abstract":"<p><p>This study employed a porcine model to investigate the dynamic effects of inulin (INU) and microcrystalline cellulose (MCC) on the profiles of intestinal short-chain fatty acids (SCFAs) and the composition of rectal fungal communities. Twenty-four healthy growing pigs were randomly allocated to three groups: a control group (CON), a 5% INU-supplemented group, and a 5% MCC-supplemented group. We hypothesized that soluble, rapidly fermentable INU and insoluble, slowly fermentable MCC would elicit distinct temporal dynamics in the fungal community, and that specific fungal taxa would correlate with SCFA profiles, reflecting a functional link between fungal succession and fiber fermentation. Gas chromatography analysis confirmed that dietary treatments induced distinct SCFA patterns in a time-dependent manner. On day 3, the concentrations of isobutyric acid (IBA) and isovaleric acid (IVA) were higher in the INU group than in the MCC group (P < 0.05). Conversely, on day 6, the concentrations of acetic acid (AA), propionic acid (PA), and total SCFA in the INU group were lower than those in both the CON and MCC groups (P < 0.05). ITS sequencing revealed that both INU and MCC markedly restructured rectal fungal communities, triggering temporal fluctuations in the relative abundances of Ascomycota and Basidiomycota, while selectively enriching functionally diverse genera. Specifically, the INU group exhibited enrichment of Vishniacozyma and Plectosphaerella at day 6, whereas the MCC group was characterized by elevated abundances of Trichosporon (day 6), Alternaria (day 10), Fusariella (day 10) and Paracremonium (day 10). Correlation analysis identified significant associations between key fungal genera and SCFA profiles. On day 3, the abundance of Aspergillus was negatively correlated with IVA and IBA concentrations. In line with this, pigs in INU group displayed reduced Aspergillus concomitant with increased IVA and IBA. On day 6, Vishniacozyma abundance was negatively associated with PA and total SCFAs, which agreed with the observation that the INU group had higher Vishniacozyma but lower PA to total SCFAs ratio relative to the CON and MCC groups (P < 0.05). Collectively, these findings highlight the functional involvement of intestinal fungi in dietary fiber degradation and offer novel insights into fungi-mediated dietary fiber digestion in the host gut.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147678841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary inulin modulates pork quality and systemic health via gut microbiome and metabolome changes in finishing pigs.","authors":"Yunpeng Wang, Kayeon Ko, Eunyoung Kim, Miroslava Kačániová, Yunkyoung Lee, Guiguo Zhang","doi":"10.1186/s42523-026-00566-5","DOIUrl":"10.1186/s42523-026-00566-5","url":null,"abstract":"<p><p>BACKGROUND: Inulin is widely recognized for its ability to improve glucolipid metabolism and modulate the gut microbiome and metabolome. However, the potential to influence pork flavor development through gut environment changes in animal husbandry remains unexplored. This study investigated the relationships among systemic health, meat flavor, gut microbiome, and metabolome in pigs fed a diet supplemented with inulin. Thirty-six male Duroc × Landrace × Yorkshire pigs (75.0 ± 1.5 kg) were divided into 2 groups, and fed either a regular diet (CON group) or a diet containing 0.5% inulin (INU group) for 60 d. RESULTS: Inulin supplementation did not adversely affect production or slaughter performance (P > 0.05) but enhanced systemic health by improving serum biochemistry indicators (P < 0.05). Descriptive analysis of pork composition revealed numerically higher levels of key fatty acids (C16:0, C18:0, C18:1) and umami-related amino acids (e.g., glutamic acid) in the INU group compared to the CON group. Inulin supplementation also modulated the gut microbiome, reducing alpha-diversity and increase specific microbes including Lactobacillus, Lachnospiraceae_NK4A136_group, Romboutsia, Family_Xlll_AD3011_group, Roseburia, and Turicibacter. Furthermore, inulin supplementation significantly altered metabolic pathways, down-regulating arginine biosynthesis, linoleic acid metabolism, riboflavin metabolism, and alanine, aspartate, and glutamate metabolism. These microbial and metabolic changes strongly correlated with the observed alterations in pork quality. CONCLUSION: Dietary inulin supplementation represents a promising strategy to modulate pork quality and systemic health without compromising productive performance. However, due to the exploratory nature of the amino acid and fatty acid analyses with limited sample size, further studies are needed to further confirm these findings. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147678782","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":"Rumenomics: evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight.","authors":"Javier Munoz Briones, Brendan K Ball, Smrutiti Jena, Timothy B Lescun, Deva D Chan, Douglas K Brubaker","doi":"10.1186/s42523-026-00558-5","DOIUrl":"10.1186/s42523-026-00558-5","url":null,"abstract":"<p><p>BACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight. RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight. CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663272","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":"Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.","authors":"Qi Wang, Chen Duan, Hongjian Dai, Donghai Lv, Zunji Shi, Najuma Joshi, Martin Gierus, Weiyun Zhu, Lizhuang Hao, Yanfen Cheng","doi":"10.1186/s42523-026-00562-9","DOIUrl":"10.1186/s42523-026-00562-9","url":null,"abstract":"<p><strong>Background: </strong>Yaks are important livestock species on the Qinghai-Tibet Plateau (QTP), but their productivity is constrained by the harsh alpine environment and the seasonal scarcity of forage resources. Improving feed efficiency has become the key to the sustainable development of Plateau Yak breeding industry. Phytosterols have shown a good application prospect in ruminant feed efficiency improvement, but the impact on yaks is not clear. This study explored the effects of dietary phytosterols supplementation on growth performance, nutrient digestibility, rumen microbial community structure and metabolic function of yaks fed in a barn.</p><p><strong>Results: </strong>Twenty-eight 1.5-year-old male yaks (137.10 ± 8.70 kg) were randomly divided into two groups after 28 days of pre feeding period: the control group (Con, n = 14) was fed with basic diet, and the experimental group (PS, n = 14) was added with 200 mg/kg phytosterols in concentrate. The formal test period was 60 days. Compared with Con group, PS group significantly increased average daily gain (P = 0.001), apparent digestibility of crude protein (P = 0.036) and neutral detergent fiber (P = 0.006), and reduced feed conversion rate (P = 0.002). The rumen fermentation mode of PS group changed, the proportion of propionate increased significantly (P = 0.001), while the proportion of acetate (P = 0.006), acetate to propionate ratio (P = 0.001) and lactate (P = 0.035) concentration decreased significantly. Phytosterols significantly changed the structure of rumen microbial community and significantly increased the copy number of rumen bacteria (P < 0.05). Metatranscriptomic analysis showed that PS group significantly increased the relative abundance of key bacteria, including Succiniclasticum, Faecalibacterium, Ruminococcus, Butyrivibrio, and Alistipes (P < 0.05). Microbial co-occurrence network analysis revealed that the number of edges, average degree and modular index of microbial community structure network in PS group increased. Rumen function analysis showed that glycolysis / gluconeogenesis and propionate metabolism were significantly enhanced in PS group (P < 0.05), and the expression of key enzymes such as hexokinase and fumarate hydratase were significantly enhanced (P < 0.05). Metabolomic analysis revealed that phosphoenolpyruvic acid, fumarate and methylmalonyl-CoA were significantly accumulated in the rumen of PS group (P < 0.05). Pathway analysis showed that the pathway impact value of propionate metabolism and glycolysis / gluconeogenesis was greater than 0.1.</p><p><strong>Conclusions: </strong>Phytosterols (200 mg/kg of concentrate) can effectively improve the feed efficiency of yaks by regulating the structure and function of rumen microorganisms and altering the fermentation patterns.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147655457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary iron and metal-based growth differentially modulate growth and gut microbiome of weaned piglets.","authors":"Shya Navazesh, Anneliek Ter Horst, Weizhang Wen, C Titus Brown, Peng Ji","doi":"10.1186/s42523-026-00561-w","DOIUrl":"10.1186/s42523-026-00561-w","url":null,"abstract":"<p><p>BACKGROUND: Weaning-associated gut dysbiosis significantly contributes to increased susceptibility to enteric infections in postweaning pigs. While Fe, Zn and Cu are essential micronutrients for bacteria including pathogens, the exact effects of transition metal restriction and excessive exposure on gut dysbiosis and pathogen virulence during weaning transition remain unclear. This study investigated how dietary iron and pharmacological levels of zinc and copper affect dynamic changes of gut microbiota in postweaning piglets experimentally challenged with enteric pathogen. RESULTS: Fifty weanling pigs were stratified and randomized to five dietary treatments for 24 days (d). The experimental diets included a control diet (Con) containing 25, 139, and 141 mg/kg of Cu, Fe, and Zn, respectively, a low-iron diet (19 mg Fe/kg, LFe), a high-iron diet (1219 mg Fe/kg, HFe), a high-copper diet (257 mg Cu/kg, HCu), and a high-zinc diet (2631 mg Zn/kg with 2490 mg/kg from ZnO, HZn). The Con diet meets all nutrient requirements of nursery pigs, and the other diets were formulated based on the Con diet by removing or supplementing respective metals in mineral premix. All pigs were orally administered with enterotoxigenic E. coli (ETEC) once daily on d13–d16. Fecal microbiome was analyzed through 16 S rRNA sequencing on d1, 6, 12, 15, 18 and 24. Although the overall clinical signs of ETEC infection was moderate, the HFe and HCu pigs had lower diarrheal frequency than the Con pigs (P < 0.05). Fecal shedding of pathogen did not differ across treatments. Fecal microbiome showed the least changes in Shannon diversity in LFe pigs compared to the HFe and HCu groups over time (P < 0.05), while the HZn group showed the lowest Shannon diversity relative to groups Con, HFe, and HCu (P < 0.05). The β-diversity differed between LFe and HFe groups only at d24, whereas HZn reduced both α- and β-diversity beginning at d12 and d6, respectively (P < 0.05). Differential abundance analysis revealed greater abundance of Campilobacteria and Escherichia-Shigella in LFe pigs compared with the HFe group (P < 0.05), while HZn treatment was associated with Bacteroidota dominance and broad reductions in many taxa (P < 0.05). CONCLUSIONS: The pharmacological level of ZnO has profound effects on gut microbiome characterized by reduced diversity and Bacteroidota dominance. Despite moderate clinical signs, these results highlight the role of dietary iron and metal-based growth promoters in shaping gut microbiota and modulating resilience to infection. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663269","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}