Animal microbiome最新文献

{"title":"Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).","authors":"Ashley G Bell, Emma R Vaughan, Barbara Kasprzyk-Hordern, Jo Cable, Ben Temperton, Charles R Tyler","doi":"10.1186/s42523-025-00434-8","DOIUrl":"10.1186/s42523-025-00434-8","url":null,"abstract":"<p><strong>Background: </strong>The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).</p><p><strong>Results: </strong>A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.</p><p><strong>Conclusion: </strong>This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"73"},"PeriodicalIF":4.9,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593033","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":"Spatiotemporal characterization of the dynamic changes in the intestinal microbiota of Taihe Silky Fowl.","authors":"Wentao Li, Haoneng Guo, Youping Wu, Yizhen Wang, Zeqing Lu","doi":"10.1186/s42523-025-00426-8","DOIUrl":"10.1186/s42523-025-00426-8","url":null,"abstract":"<p><strong>Background: </strong>The aim of this study was to elucidate the dynamic characteristics of the Taihe Silky Fowl (TSF) intestinal microbiota systematically and predict their biological functions from hatching to market through large-scale sampling and 16S rRNA gene sequencing of a total of 288 samples taken at 8 timepoints from 3 intestinal regions to provide a theoretical basis for optimizing the intestinal microbiota to promote growth performance and intestinal health through artificial interventions on the basis of different growth ages and intestinal regions.</p><p><strong>Results: </strong>The alpha and beta diversity of the intestinal microbiota changed significantly with age in different intestinal regions. In terms of alpha diversity, the ACE index and Shannon index followed the order cecum > rectum > duodenum, while the Simpson index followed the order rectum and duodenum > cecum. The PCoA plots revealed significant differences in beta diversity at different ages and in intestinal regions. The core phyla (top 5) in the TSF microbiota were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria. The core genera (top 10) were Lactobacillus, Bacillus, Escherichia-Shigella, Alistipes, norank_o__Clostridia_UCG-014, Bacteroides, Faecalibacterium, norank_f__Ruminococcaceae, Enterococcus and Streptococcus. Additionally, the degree centrality of the cecal microbiota rapidly increased from hatching to 1 week of age, then rapidly decreased from 1 to 2 weeks of age, where it remained relatively stable until 21 weeks of age, whereas the betweenness centrality exhibited the opposite trend; the closeness centrality decreased continuously with age. The functions of the cecal microbiota varied at different ages, and the central functions were nucleic acid metabolism and protein synthesis at 0 weeks of age and carbohydrate metabolism and quorum sensing at 9 weeks of age.</p><p><strong>Conclusions: </strong>In conclusion, the diversity, structure, composition, community relationships and functions of the intestinal microbiota in Taihe Silky Fowl dynamically changed with age in different intestinal regions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"72"},"PeriodicalIF":4.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565487","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 effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.","authors":"Mary Jane Drake, Meghann Pierdon, George DeMers, Scott G Daniel, Kyle Bittinger, Laurel E Redding","doi":"10.1186/s42523-025-00435-7","DOIUrl":"10.1186/s42523-025-00435-7","url":null,"abstract":"<p><p>Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"71"},"PeriodicalIF":4.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546364","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":"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":"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}