Microbiome最新文献

{"title":"Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.","authors":"Zachary J Lewis, Angela Scott, Christopher Madden, Dean Vik, Ahmed A Zayed, Garrett J Smith, Sheryl S Justice, Adam Rudinsky, Jessica Hokamp, Vanessa L Hale","doi":"10.1186/s40168-025-02191-x","DOIUrl":"https://doi.org/10.1186/s40168-025-02191-x","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.</p><p><strong>Results: </strong>In relation to urine sample volume, ≥ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.</p><p><strong>Conclusions: </strong>Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"199"},"PeriodicalIF":12.7,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental variability drives functional plasticity in the gill-associated microbiome of Lithodes santolla: a meta-transcriptomic perspective.","authors":"Alexandra Brante, Paulina Bustos, Claudio Ortega-Muñoz, Eliana Paola Acuña Gómez, Vicenzo Brante, Rodolfo Farlora","doi":"10.1186/s40168-025-02215-6","DOIUrl":"10.1186/s40168-025-02215-6","url":null,"abstract":"<p><strong>Background: </strong>Environmental variability shapes microbial community composition and function, yet its influence on microbial gene expression and host-microbiome interactions in sub-Antarctic regions remains poorly understood. Gills serve as the primary interface between aquatic organisms and their environment, harboring diverse and dynamic microbial communities that play a fundamental role in host physiology. Using a metatranscriptomic approach, this research aims to explore the influence of abiotic fluctuations in Patagonian fjords on the functional profile of the gill-associated microbiome in the southern king crab (Lithodes santolla) holobiont. By assessing shifts in microbial composition and gene expression, this research aims to uncover functional pathways linked to microbial metabolic adjustments and the host's resilience. The findings provide insights into microbiome-driven functional responses in marine species and may inform conservation strategies under environmental change.</p><p><strong>Results: </strong>Microbial gene expression profiles from individuals collected at two environmentally distinct locations, Ballena Sound and Choiseul Bay, revealed slight differences in microbial composition, with Proteobacteria dominating at both sites. Functional annotation identified key metabolic pathways involved in energy production, stress response, and microbial interactions, highlighting distinct adaptive mechanisms to environmental fluctuations. Differential expression analysis revealed shifts in carbon fixation, ion transport, and oxidative stress responses, suggesting that these physiological responses could be modeled by environmental conditions. Additionally, host-associated transcripts showed differential enrichment in immune regulation and metabolic homeostasis pathways, suggesting microbiome-mediated effects on host physiology.</p><p><strong>Conclusions: </strong>These findings offer first insights into the dynamic relationship between environmental factors and microbial functionality in L. santolla, highlighting the significance of gill-associated microbiome plasticity in adapting to changing habitats. These results improve our understanding of microbiome-driven functional responses to sub-Antarctic environments, offering valuable perspectives for assessing holobiont resilience in these fluctuating ecosystems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"197"},"PeriodicalIF":12.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145199769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding the genetic drivers of marine bacterial blooms through comparative genomics.","authors":"Xavier Rey-Velasco, Adrià Auladell, Ona Deulofeu-Capo, Daniel Lundin, Jarone Pinhassi, Isabel Ferrera, Olga Sánchez, Josep M Gasol","doi":"10.1186/s40168-025-02182-y","DOIUrl":"10.1186/s40168-025-02182-y","url":null,"abstract":"<p><strong>Background: </strong>While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as \"bloomers,\" have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.</p><p><strong>Results: </strong>We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.</p><p><strong>Conclusions: </strong>In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"198"},"PeriodicalIF":12.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145199766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From gut to gamete: how the microbiome influences fertility and preconception health.","authors":"Sarah K Munyoki, Natalie Vukmer, Julie M Rios, Amanda Kallen, Eldin Jašarević","doi":"10.1186/s40168-025-02230-7","DOIUrl":"10.1186/s40168-025-02230-7","url":null,"abstract":"<p><p>Global fertility rates continue to decline despite advancements in assisted reproductive technologies, highlighting a significant gap in our understanding of the mechanisms underlying preconception physiology. In this commentary, we review a growing body of work demonstrating that the microbiome plays a crucial yet underexplored role in women's reproductive health. This work has shown that microbial communities produce substrates that support metabolic, immune, and hormonal functions during this critical period, affecting fertility, pregnancy outcomes, and offspring health. Women with reproductive disorders, including endometriosis, polycystic ovarian syndrome, primary ovarian insufficiency, and recurrent pregnancy loss, harbor distinct microbial signatures. Animal studies provide key mechanistic insights, showing that disruption of microbiota accelerates ovarian aging, but translating these findings to human preconception health requires careful consideration. While these findings are compelling, this emerging field currently lacks a clear understanding of how microbial signals affect reproductive tissues through metabolites, immune responses, or hormonal pathways. We outline criteria for establishing microbial causation in preconception health, including sufficiency, necessity, specificity, and timing. Moving beyond correlations involves selecting appropriate models, focusing on key developmental windows, conducting longitudinal studies before conception, and investigating how specific microbial metabolites influence reproductive outcomes. Incorporating microbiome research into preconception care could lead to the development of new therapies and interventions. While the principles outlined here primarily address preconception reproductive health, they also offer a framework for microbiome research in general, emphasizing the need for a mechanistic understanding, timely interventions, and progress from association to causation in this rapidly evolving field.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"195"},"PeriodicalIF":12.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome in heritage: how maternal microbiome transmission impacts next generation health.","authors":"Clara Delaroque, Benoit Chassaing","doi":"10.1186/s40168-025-02186-8","DOIUrl":"10.1186/s40168-025-02186-8","url":null,"abstract":"<p><p>After birth, the infant's intestine is colonized by microorganisms, initiating a period of rapid microbial expansion and major compositional maturation influenced by both maternal and environmental factors. Simultaneously, the host's intestinal environment exhibits unique characteristics that facilitate critical interactions with the developing microbiome during this early-life window. These early biological events have lasting effects on health, fostering immune tolerance to environmental exposures or, conversely, increasing susceptibility to noncommunicable diseases-such as allergies, obesity, and inflammatory bowel disease-if microbiome development is disrupted. In this review, we summarize recent advances in understanding the key stages of microbiome development after birth and explore how changes in the maternal environment-especially diet-as well as maternal intestinal bacteria and their derived molecules shape the microbiome's composition and function in early-life, ultimately influencing long-term health and disease risk. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"196"},"PeriodicalIF":12.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.","authors":"Shasha Wang, Zhuoming Zhao, Ruolin Cheng, Liang Cui, Jun Wang, Maxim Rubin-Blum, Yao Zhang, Bolin Liu, Xing Chen, Federico Baltar, Xiaxing Cao, Xuezhe Wen, Karine Alain, Zhen Chen, Jing Liao, Lijing Jiang, Zongze Shao","doi":"10.1186/s40168-025-02177-9","DOIUrl":"10.1186/s40168-025-02177-9","url":null,"abstract":"<p><strong>Background: </strong>Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.</p><p><strong>Results: </strong>Our results showed that the DCF rates ranged from 0.02 to 3.27 mmol C m^-2 day^-1 in all samples, showing a depth-dependent spatial variation. These rates of DCF were closely related to the environmental factors such as DIC, TS, AVS, NH₄⁺, NO₃^-, and NO₂^-. Metagenomic analysis revealed six carbon-fixing pathways, with the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway being predominant. Further analysis of MAGs revealed that Gammaproteobacteria, Desulfobacteria, and Campylobacteria were the most abundant carbon-fixing groups. Intriguingly, some new lineages were found to have carbon-fixing potential, including two candidatus taxa JAJVIF01 and BMS3Abin14. Metatranscriptomic analyses confirmed that these carbon-fixing microbes were active in situ and occupied different niches. In the surface layers, Gammaproteobacteria with the CBB cycle played an important role in DCF, mainly driven by sulfur and hydrogen oxidation with oxygen reduction; in the deeper layers, Campylobacteria with the reductive tricarboxylic acid (rTCA) cycle and Desulfobacteria with the WL pathway were active members for DCF, mainly through sulfur, hydrogen, and CO oxidation. While in the deepest layers of 18-20 cm, methane-producing archaea Methanosarcinia was the essential member driving DCF. In addition, most taxa containing the WL pathway displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies.</p><p><strong>Conclusions: </strong>Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"194"},"PeriodicalIF":12.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12400630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maternal Faecalibacterium pathobionts and low-fiber diets synergize to impact offspring health: implications for atopic dermatitis.","authors":"Dongju Lee, Jongwook Park, Song-Yi Park, Junghyun Hwang, Sewon Kim, Sun-Ho Kee, Heenam Stanley Kim","doi":"10.1186/s40168-025-02194-8","DOIUrl":"https://doi.org/10.1186/s40168-025-02194-8","url":null,"abstract":"<p><strong>Background: </strong>The incidence of atopic dermatitis (AD) has increased globally in recent decades. A recent study identified enrichment of Faecalibacterium subspecies in young AD patients, implicating these gut bacteria in disease pathogenesis. This was unexpected, as Faecalibacterium is widely recognized as one of the most beneficial bacteria in the human gut.</p><p><strong>Results: </strong>We tested the bacteria in female mice and observed their effect on the gut microbiome and overall health, which subsequently influenced the health of their offspring. These effects were markedly exacerbated when female mice were fed a low-fiber diet, leading to heightened systemic inflammation, skin damage, and hair loss in their offspring. Offspring of female mice receiving a low-fiber diet without pathobiont administration exhibited reduced symptom severity, which was further mitigated bythe administration of the beneficial strain A2-165.</p><p><strong>Conclusions: </strong>These findings provide compelling evidence that maternalFaecalibacterium pathobionts play a critical role in the development of systemic conditions in offspring, offering valuable insights into the etiology of AD. Furthermore, the synergistic effect of gut microbiota dysbiosis and low fiber intake highlights the potential impact of modern dietary trends on the rising prevalence of AD and other chronic conditions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"192"},"PeriodicalIF":12.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global biogeography of airborne viruses in public transit systems and their host interactions.","authors":"Huaxin Lei, Shicong Du, Xinzhao Tong, Wing Lam Chan, Marcus H Y Leung, Kari O Bøifot, Daniela Bezdan, Daniel J Butler, David C Danko, David C Green, Mark T Hernandez, Frank J Kelly, Alexander G Lucaci, Cem Meydan, Marina Nieto-Caballero, Krista Ryon, Braden Tierney, Klas I Udekwu, Benjamin G Young, Christopher E Mason, Marius Dybwad, Patrick K H Lee","doi":"10.1186/s40168-025-02173-z","DOIUrl":"https://doi.org/10.1186/s40168-025-02173-z","url":null,"abstract":"<p><strong>Background: </strong>There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses' taxonomy, functional potential, and microbial hosts were determined. The study also investigated correlations between virus and host abundances, the coevolution of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems and anti-CRISPR (Acr) proteins, and the potential impacts of auxiliary metabolic genes (AMGs) on hosts.</p><p><strong>Results: </strong>Airborne viruses in global BEs exhibited biogeographical variations in diversity, composition, function, and virus-host interactions. Nearly half of the vOTUs analyzed were from the Caulimoviridae family, while 31.8% of them could not be taxonomically classified. Diverse functions were identified within the vOTUs, together with antimicrobial resistance genes with the potential to confer resistance to various antibiotics and antimicrobial agents. Strong correlations were observed between vOTU and host abundances, with clear distinctions between virulent and temperate viruses. However, there was limited co-evolution of CRISPR-Cas systems and Acr proteins, which was likely due to the oligotrophic and physical conditions in the BEs and the dominance of vOTUs with a virulent lifestyle. Phage-encoded AMGs appeared to have the potential to enhance host fitness. These findings highlight biogeographical variations in airborne viruses in BEs and that physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution.</p><p><strong>Conclusion: </strong>There are biogeographical variations in airborne viruses in BEs in global cities, as physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution. Moreover, the characteristics of airborne viruses in BEs are distinct from those of viruses found in other, more nutrient-rich ecosystems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"193"},"PeriodicalIF":12.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mobilome-mediated transcriptional activation of biosynthetic gene clusters and its impact on strain competitiveness in food fermentation microbiomes.","authors":"Lei Xu, Jian-Yu Jiao, Chen Ling, Ru-Bing Du, Qun Wu, Yan Xu, Wen-Jun Li","doi":"10.1186/s40168-025-02180-0","DOIUrl":"https://doi.org/10.1186/s40168-025-02180-0","url":null,"abstract":"<p><strong>Background: </strong>Microbial interactions are critical for maintaining the stability of food fermentation microbiomes, and mobile genetic elements (MGEs) significantly influence these interactions by horizontal gene transfer events. Although MGEs are known to facilitate horizontal gene transfer, their distribution among microorganisms and specific effects on microbial interactions remain poorly understood.</p><p><strong>Results: </strong>We analyzed 590 metagenomic and 42 metatranscriptomic samples from food fermentations, recovering 1133 metagenome-assembled genomes (MAGs). Our analysis revealed that MGEs were widely distributed in food fermentation microbiomes, with higher occurrence rates in Firmicutes (Bacillota: 0.71 ~ 11.85%) and Proteobacteria (Pseudomonadota: 0.47 ~ 11.05%). MGEs tended to be located adjacent to functional genes, particularly biosynthetic gene clusters (BGCs), with co-occurrence rates ranging from 9.41 to 23.99%. Furthermore, the transcriptional activity of BGCs was significantly correlated with the number of MGEs that were co-located with BGCs, which might enhance the competitiveness of strains. Variability in the diversity of MGEs that were co-located with BGCs was also evident at the strain level. Using Lactiplantibacillus plantarum as a case, we revealed that the strain-level differences in MGEs that were co-located with BGCs are positively correlated with the transcription of BGCs and competitiveness of strains within the species.</p><p><strong>Conclusions: </strong>This study highlighted the role of MGEs in enhancing transcription of BGCs and facilitating strain competitiveness, providing new insights into how MGEs enhance the adaptability of microbial communities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"191"},"PeriodicalIF":12.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12392511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.","authors":"Yujie Zhang, Yen-Te Liao, Fang Liu, Robert W Li, Vivian C H Wu","doi":"10.1186/s40168-025-02163-1","DOIUrl":"https://doi.org/10.1186/s40168-025-02163-1","url":null,"abstract":"<p><strong>Background: </strong>In the United States beef industry, grain-feeding and grass-feeding are the two most common types of cattle feeding. Different feeding methods are likely to affect gut microbiota compositions and subsequently change microbial adaptation and cattle metabolism. However, there is limited information regarding the impact of diet on cattle gastrointestinal virome. This study examined the composition of fecal virome from grain-fed and grass-fed beef cattle and identified unique virome features to understand the relationship between these two feeding types.</p><p><strong>Results: </strong>Six grain-fed and six grass-fed Angus beef cattle were weighed, and their fecal samples were collected for further viral metagenomic sequencing. The difference in animal growth revealed a significantly higher post-weaning weight in grain-fed cattle than in grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the order Cremeviriles and Petitvirales. At the family level, 13 and 16 different viral families were detected in the grain and grass-fed groups, respectively. The comparison of virome features from the two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome. In contrast, the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, the viruses, belonging to the order Caudovirales and the family Podoviridae, had significantly higher abundances in the grass-fed virome than in the grain-fed virome.</p><p><strong>Conclusions: </strong>The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome can contribute to further understanding of phage-bacterial interactions and their underlying mechanisms in regulating the animal host's metabolism and feed efficiency. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"190"},"PeriodicalIF":12.7,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}