Animal microbiome最新文献

{"title":"Correction: Bovine ocular microbiome: the next frontier in managing pinkeye in cattle.","authors":"Justine Kilama, Shafinul Islam, Samat Amat","doi":"10.1186/s42523-025-00438-4","DOIUrl":"10.1186/s42523-025-00438-4","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"69"},"PeriodicalIF":4.9,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12182683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340746","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":"Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.","authors":"Mary N Chege, Pamela Ferretti, Shasta Webb, Rosaline W Macharia, George Obiero, Joseph Kamau, Susan C Alberts, Jenny Tung, Mercy Y Akinyi, Elizabeth A Archie","doi":"10.1186/s42523-025-00436-6","DOIUrl":"10.1186/s42523-025-00436-6","url":null,"abstract":"<p><strong>Background: </strong>Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.</p><p><strong>Results: </strong>We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).</p><p><strong>Conclusions: </strong>Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"70"},"PeriodicalIF":4.9,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12182654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340747","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 impact of florfenicol treatment on the microbial populations present in the gill, intestine, and skin of channel catfish (Ictalurus punctatus).","authors":"Hongye Wang, Lina Sheng, Zeinab Yazdi, Xiran Li, Zhuosheng Liu, Sushumna Canakapalli, Yi Zhou, Chao Liao, Shiva Emami, Anita M Kelly, Luke A Roy, Esteban Soto, Luxin Wang","doi":"10.1186/s42523-025-00433-9","DOIUrl":"10.1186/s42523-025-00433-9","url":null,"abstract":"<p><strong>Background: </strong>Florfenicol is a broad-spectrum antimicrobial approved in many countries for treating bacterial infections in production animals. Although florfenicol has been widely used in the US catfish industry, its impact on the native microbiota within catfish tissues remains largely unknown. Florfenicol treatment is followed by a mandatory withdrawal period to ensure drug residues fall below regulatory limits before harvest. This interval also allows for the potential recovery of the native microbiota. In particular, the skin and gill microbiota have often been overlooked in aquaculture microbiome research. Moreover, the dynamics of microbial communities and resistome profiles following drug withdrawal are still poorly understood, despite their ecological significance.</p><p><strong>Results: </strong>A significant increase in intestinal microbial diversity was observed at the end of the withdrawal period. The highest alpha diversity (Shannon index) was observed in catfish intestines. This increase indicated the restoration of the normal microbiota in catfish intestine. The predominant bacterial phyla shared among catfish gill, intestine, and skin are Proteobacteria (62%), Bacteroidetes (18%), Actinobacteriota (12%), Firmicutes (3%), Patescibacteria (2%), and Verrucomicrobiota (1%). Florfenicol application can have lasting effects through the withdrawal period, particularly altering the intestinal microbial community.</p><p><strong>Conclusion: </strong>The result of this study underscores the impact of florfenicol treatment on the bacterial landscape and antibiotic resistance in catfish, highlighting significant changes in microbial composition in the catfish intestine and at the end of the withdrawal period. These findings address the need for monitoring and managing antibiotic resistance in fish farming environments.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"68"},"PeriodicalIF":4.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337294","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":"Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.","authors":"Nahidur Rahman, Taylor McCullough, Daniel Flores Orozco, Sean Walkowiak, Abdolvahab Farzan, Shahrokh Shekarriz, Michael G Surette, Nazim Cicek, Hooman Derakhshani","doi":"10.1186/s42523-025-00432-w","DOIUrl":"10.1186/s42523-025-00432-w","url":null,"abstract":"<p><strong>Introduction: </strong>The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.</p><p><strong>Results: </strong>We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.</p><p><strong>Conclusion: </strong>Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"66"},"PeriodicalIF":4.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327929","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 traits and environmental variation shape gut microbiota diversity in wild threespine stickleback.","authors":"Andreas Härer, Emma Kurstjens, Diana J Rennison","doi":"10.1186/s42523-025-00404-0","DOIUrl":"10.1186/s42523-025-00404-0","url":null,"abstract":"<p><strong>Background: </strong>Despite the growing recognition of the importance of gut microbiota in host ecology and evolution, our understanding of the relative contributions of host-associated and environmental factors shaping gut microbiota composition within and across wild populations remains limited. Here, we investigate how host morphology, sex, genetic divergence, and environmental characteristics influence the gut microbiota of threespine stickleback fish populations from 20 lakes on Vancouver Island, Canada.</p><p><strong>Results: </strong>Our findings reveal substantial variation in gut microbiota composition and diversity among populations, with host traits exerting a relatively stronger influence on bacterial alpha diversity than environmental characteristics. Previous studies have suggested a link between stickleback body shape and niche specialization, and our results indicate that aspects of host morphology may be associated with gut microbiota divergence among populations, though whether this is related to trophic ecology remains to be explored. Within and across populations, we only observed a weakly defined core microbiota and limited sharing of amplicon sequence variants (ASVs) among hosts, indicating that gut microbiota composition is individualized. Additionally, we detected sex-dependent differences in microbial diversity, opening avenues for future research into the mechanisms driving this variation.</p><p><strong>Conclusions: </strong>In sum, our study emphasizes the need to consider both host-associated and environmental factors in shaping gut microbiota dynamics and highlights the complex interplay between host organisms, their associated microbial communities, and the environment in natural settings. Ultimately, these insights add to our understanding of the eco-evolutionary implications of host-microbiota interactions while underscoring the need for further investigation into the underlying mechanisms.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"67"},"PeriodicalIF":4.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12177961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327930","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 surveillance of antimicrobial resistance in the pig gut microbiome.","authors":"Judith Guitart-Matas, Arturo Vera-Ponce de León, Phillip B Pope, Torgeir R Hvidsten, Lorenzo Fraile, Maria Ballester, Yuliaxis Ramayo-Caldas, Lourdes Migura-Garcia","doi":"10.1186/s42523-025-00418-8","DOIUrl":"10.1186/s42523-025-00418-8","url":null,"abstract":"<p><strong>Background: </strong>High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment.</p><p><strong>Results: </strong>The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis.</p><p><strong>Conclusions: </strong>Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"65"},"PeriodicalIF":4.9,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318828","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":"Prospecting microbiota of Adriatic fish: Bacillus velezensis as a potential probiotic candidate.","authors":"Jerko Hrabar, Ivana Babić, Slaven Jozić, Željka Trumbić, Adele Pioppi, Lasse Johan Dyrbye Nielsen, Ana Maravić, Tina Tomašević, Ákos T Kovacs, Ivona Mladineo","doi":"10.1186/s42523-025-00429-5","DOIUrl":"10.1186/s42523-025-00429-5","url":null,"abstract":"<p><strong>Background: </strong>Aquaculture is one of the fastest growing sectors of food production and covers more than half of the market demand for fish and fishery products. However, aquaculture itself faces numerous challenges, such as infectious disease outbreaks, which are one of the limiting factors for the growth and environmental sustainability of modern aquaculture. Understanding the composition and diversity of the gut microbiota of fish is important to elucidate its role in host health and aquaculture management. In addition, the gut microbiota represents a valuable source of bacteria with probiotic potential for farmed fish.</p><p><strong>Results: </strong>In this study, we analysed the intestinal microbiota of two economically important fish species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), using 16S rRNA gene amplicon sequencing. The taxonomic analysis identified 462 amplicon sequence variants at a similarity level of 99 and showed similar alpha diversity indices between seabass and gilthead seabream. Beta diversity analysis showed no significant differentiation in gut microbiota between fish species or aquaculture sites. Among the culturable isolates, a high proportion of Photobacterium damselae and Bacillus spp. was detected. We selected a single Bacillus velezensis isolate and further characterised its biosynthetic potential by performing whole genome sequencing. Its genome contains biosynthetic gene clusters for most of the common secondary metabolites typical of B. velezensis. Antibiotic susceptibility testing showed the sensitivity of the selected isolates to several antibiotics according to EFSA recommendations. Furthermore, stimulation of peripheral blood leukocytes (PBL) with B. velezensis resulted in a strong pro-inflammatory response, with a pronounced upregulation of cytokines il1b, il6, tnfa and il10 observed over time.</p><p><strong>Conclusions: </strong>Overall, this study provides an insight into the composition of the intestinal microbiota and the diversity of culturable intestinal bacteria of two economically most important fish species from Adriatic cage culture and sheds light on the autochthonous intestinal B. velezensis as a promising probiotic candidate for Mediterranean aquaculture.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"64"},"PeriodicalIF":4.9,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295423","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":"Microbiome dynamics associated with Hematodinium sp. infection in Norway lobster (Nephrops norvegicus).","authors":"Irene Martin, Ahmed Elsheshtawy, Benjamin Gregory James Clokie, Simon MacKenzie, Kelly Simone Bateman, David Bass, Grant D Stentiford, Amaya Albalat","doi":"10.1186/s42523-025-00416-w","DOIUrl":"https://doi.org/10.1186/s42523-025-00416-w","url":null,"abstract":"<p><strong>Background: </strong>The parasite Hematodinium sp. causes morbidity and seasonal mortality events in more than 40 decapod species globally and therefore, it is now recognised as a significant threat to the future sustainability of shellfish fisheries and aquaculture worldwide. Among these, Norway lobster (Nephrops norvegicus), an important representative of the marine benthos and supporting the most valuable shellfish fishery in the UK, experience yearly seasonal Hematodinium sp. patent infections. Currently, little is known about the N. norvegicus microbiome and potential role during Hematodinium sp.</p><p><strong>Infection: </strong>Therefore, in this study we investigated the microbiome dynamics of N. norvegicus associated with Hematodinium sp. infection and disease progression in the haemolymph and gut. N. norvegicus were sampled from the Clyde Sea Area, Scotland during the peak of the Hematodinium sp. patent infection. The presence and intensity of Hematodinium sp. infection were determined using the body colour method (BCM), pleopod method (PM), histology (heart, gonads, hepatopancreas, gills and muscle) and molecular tools (PCR).</p><p><strong>Results: </strong>Marked shifts in the bacterial richness of the haemolymph and significant alterations in the overall bacterial community composition of both tissues were observed in infected lobsters. These changes, observed even at subpatent levels of infection (only positive by PCR), indicate a prompt and persistent microbiome shift associated with Hematodinium sp.</p><p><strong>Infection: </strong>Furthermore, smaller healthy animals (25.2 ± 1.20 mm CL) known to be particularly susceptible to high severity infection displayed a decreased microbiome richness in the haemolymph suggesting a potential link between the host microbiome and susceptibility to disease progression, a possibility that merits further research.</p><p><strong>Conclusions: </strong>This study offers the first insights into the pathobiome of N. norvegicus due to Hematodinium sp. infection and disease that in turn provides a foundation for further studies on the pathogenesis of this important parasitic disease.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"62"},"PeriodicalIF":4.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12164141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295421","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":"Mitochondrial sirtuin 4 shapes the intestinal microbiota of Drosophila by controlling lysozyme expression.","authors":"Mirjam Knop, Christian Treitz, Stina Bettendorf, Judith Bossen, Jakob von Frieling, Shauni Doms, Abdulgawaad Saboukh, Iris Bruchhaus, Ronald P Kühnlein, John F Baines, Andreas Tholey, Thomas Roeder","doi":"10.1186/s42523-025-00431-x","DOIUrl":"10.1186/s42523-025-00431-x","url":null,"abstract":"<p><strong>Background: </strong>Sirtuins are deacetylases that are highly conserved throughout the animal kingdom. They act as metabolic sensors that coordinate cellular responses, allowing an adapted response to various stressors. Epithelial cells, especially those of the intestine, are directly exposed to a wide range of stressors. Together with the microbiota, they form a complex ecosystem with mutual influences. The significance of sirtuins in this complex system is still waiting to be clarified.</p><p><strong>Results: </strong>Here, we show that a protein-restricted diet strongly increases the intestinal expression of sirtuin 4 (dSirt4), the only mitochondrial sirtuin in Drosophila. To elucidate the effects of deregulated dSirt4 expression in the intestine, we analyzed dSirt4 knockout flies. These flies showed substantial changes in their intestinal proteome and physiological properties. One of the most striking effects was the strong induction of lysozymes in the intestine, with a corresponding increase in lysozyme activity. This effect was organ-autonomous, as it was also observed in flies with dSirt4 knocked out only in intestinal enterocytes. The significant increase in lysozyme abundance in response to tissue-specific dSirt4 knockdown did not reduce the total number of bacteria in the intestine. However, it did affect the microbiota composition by reducing the number of gram-positive bacteria. This effect on microbiota composition can be attributed to dSirt4-dependent lysozyme expression, which is absent in a lysozyme-deficient background. dSirt4 knockout in the enterocytes shortened the lifespan of the flies, as did ectopic lysozyme overexpression in the enterocytes.</p><p><strong>Conclusions: </strong>The only mitochondrial sirtuin in Drosophila, dSirt4, is induced by dietary stress in intestinal epithelial cells, which directly regulates the lysozyme activity of these cells. We could associate this altered lysozyme activity with a shift in the microbiota composition, demonstrating a direct link between stress, nutrition, and the host's microbiota regulation.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"63"},"PeriodicalIF":4.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295422","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":"Inonotus obliquus fermentation product improves growth performance and meat quality probably through intestine and antioxidant capacity enhanced by gut microbes and metabolites regulation in rabbits.","authors":"Lin Zhang, Zhiguo Fei, Yaling Ding, Yajia Zhang, Zhiyong Ding, Yueyan Huang, Junkun Wang, Gongyan Liu, Liya Bai, Jiaqiang Wu","doi":"10.1186/s42523-025-00427-7","DOIUrl":"10.1186/s42523-025-00427-7","url":null,"abstract":"<p><strong>Background: </strong>Inonotus obliquus is a medicinal edible fungus that contains a variety of biologically active ingredients and has multiple physiological effects. When supplemented in avian diet, Inonotus obliquus has proved to be beneficial. However, information regarding these effects on mammals is scanty. The present study aims to investigate the effect of supplementation of Inonotus obliquus fermentation product (IOFP) on the growth performance, antioxidant capacity, meat quality, intestinal function and gut microbiota of rabbit exploratorily, which may act as an important feed additive and also as an antibiotic alternative with its medicinal properties.</p><p><strong>Results: </strong>Dietary supplementation of IOFP increased body weight (P < 0.01) at the initial 21 d and improved feed efficiency throughout the 35 d experimental period when compared to control group. At the same time it was observed that meat quality and carcass parameters improved upon supplementation of IOFP. Additionally, IOFP supplementation resulted in significant increases (P < 0.05) in total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and nitric oxide (NO) activity or concentration in the serum and muscle. The crypt depth decreased significantly, whereas the villus height/crypt depth (V/C) value increased (P < 0.05). The concentration of secrete IgA (sIgA) of the intestine also increased (P < 0.05). IOFP supplementation significantly increased the fold change expression of Claudin 1, Occludin, ZO1, and ZO2 (P < 0.05) when compared to the respective gene expression levels of the duodenum and jejunum tissues of control group. Further study on cecum microbiota revealed that IOFP supplementation increased the microbiota diversity by increasing the number of beneficial bacteria and reducing the numbers of pathological bacteria. It was observed that cecum metabolites produced in the treated group were related to antioxidants, antiinflammation and antidepressive effects. The harmful metabolites related to fat deposition, loss of appetite and cytotoxic conditions decreased. Pearson's correlation studies between different bacteria and metabolites revealed that the metabolites produced were regulated by the beneficial and harmful bacteria respectively.</p><p><strong>Conclusions: </strong>IOFP enhanced intestinal morphology and function, and organismic antioxidant capacity, probably by increasing the concentration of beneficial microbiota and metabolites resulting in improvement of body weight, feed efficiency, and parameters related to meat quality and carcass traits of rabbits.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"61"},"PeriodicalIF":4.9,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12147337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259497","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}