Microbiome最新文献

{"title":"Modeling microbiome-trait associations with taxonomy-adaptive neural networks.","authors":"Yifan Jiang, Matthew Aton, Qiyun Zhu, Yang Young Lu","doi":"10.1186/s40168-025-02080-3","DOIUrl":"10.1186/s40168-025-02080-3","url":null,"abstract":"<p><p>The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"87"},"PeriodicalIF":13.8,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743646","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":"Culturomics of the pig tonsil microbiome identifies new species and an untapped source of novel antimicrobials.","authors":"Isabela Maria Fernandes de Oliveira, Simen Fredriksen, Marcela Fernández Gutiérrez, Hermie J M Harmsen, Jos Boekhorst, Peter van Baarlen, Jerry M Wells","doi":"10.1186/s40168-025-02064-3","DOIUrl":"10.1186/s40168-025-02064-3","url":null,"abstract":"<p><strong>Background: </strong>In humans and pigs, altered composition of the microbiota associated with the epithelium of the palatine tonsils has been associated with bacterial or viral infection and lymphoid tissue inflammation. Tonsil lymphoid tissue is important for immunity and considered an important portal of entry for pathogens such as Streptococcus suis. Little is known about correlations between tonsil-associated microbiota, tonsillar infections, and the species that might confer colonization resistance against pathogens. Here, we describe a large collection of representative bacterial species from the tonsil surface biofilm and used genome mining and in vitro assays to assess their potential as probiotics to reduce infections by S. suis and other pathogens.</p><p><strong>Results: </strong>Data on tonsil microbiota composition from over 100 piglets from 11 farms and 3 countries revealed a core microbiota comprising Actinobacillus, Streptococcus, and Moraxella and 11 other less abundant but prevalent genera. To establish a collection of culturable core species, we plated 5 tonsil swabs taken from healthy piglets on different farms and countries on 8 different media and isolated 518 pure cultures belonging to 23 genera. To identify candidate probiotic strains, we tested for antagonistic activity against a panel of pathogens and in silico genome mining to find biosynthetic gene clusters (BGCs) in isolates that might produce antimicrobial compounds. We identified two novel species with potential probiotic activities: a Brevibacterium species and Corynebacterium species producing a heat and proteolytically stable lanthipeptide variant of flavucin, inhibiting in vitro growth of the opportunistic pathogens S. suis and Staphylococcus aureus.</p><p><strong>Conclusions: </strong>We defined the core tonsil microbiota of piglets and cultured representative single bacterial isolates for research on microbiota-host interactions in the oral cavity. Several isolates inhibiting the growth of bacterial pathogens that might be exploited as probiotics to promote colonization resistance were deposited in publicly available strain repositories. Our mining of genomes from cultured isolates suggests that the tonsil microbiota is an untapped source of novel antimicrobials Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"86"},"PeriodicalIF":13.8,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743639","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":"Lactiplantibacillus plantarum FRT4 protects against fatty liver hemorrhage syndrome: regulating gut microbiota and FoxO/TLR-4/NF-κB signaling pathway in laying hens.","authors":"Daojie Li, Kun Meng, Guohua Liu, Zhiguo Wen, Yunsheng Han, Weiwei Liu, Xin Xu, Liye Song, Hongying Cai, Peilong Yang","doi":"10.1186/s40168-025-02083-0","DOIUrl":"10.1186/s40168-025-02083-0","url":null,"abstract":"<p><strong>Background: </strong>Fatty liver hemorrhage syndrome (FLHS) has become one of the major factors leading to the death of laying hen in caged egg production. FLHS is commonly associated with lipid peroxidation, hepatocyte injury, decreased antioxidant capacity, and inflammation. However, there are limited evidences regarding the preventive effect of Lactiplantibacillus plantarum on FLHS in laying hens and its mechanisms. Our previous results showed that Lp. plantarum FRT4 alleviated FLHS by regulating lipid metabolism, but did not focus on its antioxidant and anti-inflammatory functions and mechanisms. Therefore, this study aimed to investigate the preventive mechanisms of Lp. plantarum FRT4 in alleviating FLHS, with a focus on its role in antioxidant activity and inflammation regulation.</p><p><strong>Results: </strong>Supplementation with Lp. plantarum FRT4 enhanced the levels of T-AOC, T-SOD, and GSH-Px, while reducing the levels of TNF-α, IL-1β, IL-8, and NLRP3 in the liver and ovary of laying hens. Additionally, Lp. plantarum FRT4 upregulated the mRNA expressions of SOD1, SOD2, CAT, and GPX1, downregulated the mRNA expressions of pro-inflammatory factors IL-1β, IL-6, and NLRP3, and upregulated the mRNA expressions of anti-inflammatory factors IL-4 and IL-10. Lp. plantarum FRT4 improved the structure and metabolic functions of gut microbiota, and regulated the relative abundances of dominant phyla (Bacteroidetes, Firmicute, and Proteobacteria) and genera (Prevotella and Alistipes). Additionally, it influenced key KEGG pathways, including tryptophan metabolism, amino sugar and nucleotide sugar metabolism, insulin signaling pathway, FoxO signaling pathway. Spearman analysis revealed that the abundance of microbiota at different taxonomic levels was closely related to antioxidant enzymes and inflammatory factors. Furthermore, Lp. plantarum FRT4 modulated the mRNA expressions of related factors in the FoxO/TLR-4/NF-κB signaling pathway by regulating gut microbiota. Moreover, the levels of E₂, FSH, and VTG were significantly increased in the ovary after Lp. plantarum FRT4 intervention.</p><p><strong>Conclusions: </strong>Lp. plantarum FRT4 effectively ameliorates FLHS in laying hens. This efficacy is attributed to its antioxidant and anti-inflammatory properties, which are mediated by modulating the structure and function of gut microbiota, and further intervening in the FoxO/TLR-4/NF-κB signaling pathway. These actions enhance hepatic and ovarian function and increase estrogen levels. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"88"},"PeriodicalIF":13.8,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743643","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":"hTAS2R38 polymorphisms modulate oral microbiota and influence the prevalence and treatment outcome of halitosis.","authors":"Hongxiang Mei, Cai Qi, Jinchi Liu, Sirui Yang, Jiajia Zhou, Yangyu Lu, Liwei Zheng, Juan Li, Lei Zhao, Xin Xu","doi":"10.1186/s40168-025-02087-w","DOIUrl":"10.1186/s40168-025-02087-w","url":null,"abstract":"<p><strong>Background: </strong>The genetic susceptibility of halitosis is unclear, challenging its precise management in high-risk population. Here we investigated the association of hTAS2R38 polymorphisms with the prevalence and treatment outcome of halitosis, with a particular focus on oral microbiota.</p><p><strong>Methods: </strong>A cross-sectional study including 689 participants was conducted to investigate the association between hTAS2R38 polymorphisms and halitosis. A 6-month cohort including 60 halitosis patients was established to explore the relationship between hTAS2R38 polymorphisms and treatment outcome of halitosis. Salivary microbiota was further analyzed and its correlation with hTAS2R38 polymorphisms was investigated.</p><p><strong>Results: </strong>In the cross-sectional study, a higher prevalence of halitosis was observed in individuals with AVI/AVI genotype as compared to non-AVI/AVI genotype (PAV/PAV + PAV/AVI) (OR = 2.380, 95% CI = 1.493-3.807). 16S rRNA sequencing revealed the enrichment of Prevotella in the saliva of AVI/AVI individuals. In the prospective study, halitosis patients with AVI/AVI genotype exhibited poor treatment outcome relative to non-AVI/AVI individuals during the 6-month follow-up after halitosis intervention (RR = 2.077, 95% CI = 1.382-3.339). Tannerella, Filifactor, and Mycoplasma were identified to be the major persistent genus in the saliva of AVI/AVI patients over the 6-month period after treatment. Furthermore, the human gingival fibroblasts with AVI/AVI genotype exhibited reduced inhibition against the growth and volatile sulfur compounds production of periodontal pathogens.</p><p><strong>Conclusions: </strong>Our work demonstrates that hTAS2R38 polymorphisms contribute to the development and treatment outcome of halitosis via modulating oral microbiota, providing new insights to the better management of halitosis. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"85"},"PeriodicalIF":13.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743641","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":"The mitigation of spatial constraint in porous environments enhances biofilm phylogenetic and functional diversity.","authors":"Chengxia Fu, Yichao Wu, Søren J Sørensen, Ming Zhang, Ke Dai, Chunhui Gao, Chenchen Qu, Qiaoyun Huang, Peng Cai","doi":"10.1186/s40168-025-02075-0","DOIUrl":"10.1186/s40168-025-02075-0","url":null,"abstract":"<p><strong>Background: </strong>Porous environments constitute ubiquitous microbial habitats across natural, engineered, and medical settings, offering extensive internal surfaces for biofilm development. While the physical structure of the porous environment is known to shape the spatial organization of biofilm inhabitants and their interspecific interactions, its influence on biofilm community structure and functional diversity remains largely unknown. This study employed microfluidic chips with varying micropillar diameters to create distinct pore spaces that impose different levels of spatial constraints on biofilm development. The impact of pore spaces on biofilm architecture, community assembly, and metabolic functions was investigated through in situ visualization and multi-omics technologies.</p><p><strong>Results: </strong>Larger pore sizes were found to increase biofilm thickness and roughness while decreasing biofilm coverage over pore spaces. An increase in pore size resulted in reduced biofilm community evenness and increased phylogenetic diversity. Remarkably, biofilms in 300-μm pore spaces displayed the highest richness and the most complex and interconnected co-occurrence network pattern. The neutral model analysis demonstrated that biofilm assembly within different pore spaces was predominantly governed by stochastic processes, while deterministic processes became more influential as pore space increased. Exometabolomic analyses of effluents from the microfluidic chips further elucidated a significant correlation between the exometabolite profiles and biofilm community structure. The increased community richness in the 300-μm pore space was associated with the significantly higher exometabolome diversity.</p><p><strong>Conclusions: </strong>Collectively, our results indicate that increased pore space, which alleviated spatial constraints on biofilm development, resulted in the formation of thicker biofilms with enhanced phylogenetic and functional diversity. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"84"},"PeriodicalIF":13.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700870","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":"Dietary emulsifier carboxymethylcellulose-induced gut dysbiosis and SCFA reduction aggravate acute pancreatitis through classical monocyte activation.","authors":"Yongpu Feng, Wenjin Chen, Jiayu Chen, Fengyuan Sun, Fanyang Kong, Lei Li, Yating Zhao, Shouxin Wu, Zhaoshen Li, Yiqi Du, Xiangyu Kong","doi":"10.1186/s40168-025-02074-1","DOIUrl":"10.1186/s40168-025-02074-1","url":null,"abstract":"<p><strong>Objective: </strong>Carboxymethylcellulose (CMC), one of the most common emulsifiers used in the food industry, has been reported to promote chronic inflammatory diseases, but its impact on acute inflammatory diseases, e.g., acute pancreatitis (AP), remains unclear. This study investigates the detrimental effects of CMC on AP and the potential for mitigation through Akkermansia muciniphila or butyrate supplementation.</p><p><strong>Design: </strong>C57BL/6 mice were given pure water or CMC solution (1%) for 4 weeks and then subjected to caerulein-induced AP. The pancreas, colon, and blood were sampled for molecular and immune parameters associated with AP severity. Gut microbiota composition was assessed using 16S rRNA gene amplicon sequencing. Fecal microbiota transplantation (FMT) was used to illustrate gut microbiota's role in mediating the effects of CMC on host mice. Additional investigations included single-cell RNA sequencing, monocytes-specific C/EBPδ knockdown, LPS blocking, fecal short-chain fatty acids (SCFAs) quantification, and Akkermansia muciniphila or butyrate supplementation. Finally, the gut microbiota of AP patients with different severity was analyzed.</p><p><strong>Results: </strong>CMC exacerbated AP with gut dysbiosis. FMT from CMC-fed mice transferred such adverse effects to recipient mice, while single-cell analysis showed an increase in classical monocytes in blood. LPS-stimulated C/EBPδ, caused by an impaired gut barrier, drives monocytes towards classical phenotype. LPS antagonist (eritoran), Akkermansia muciniphila or butyrate supplementation ameliorates CMC-induced AP exacerbation. Fecal Akkermansia muciniphila abundance was negatively correlated with AP severity in patients.</p><p><strong>Conclusions: </strong>This study reveals the detrimental impact of CMC on AP due to gut dysbiosis, with Akkermansia muciniphila or butyrate offering potential therapeutic avenues for counteracting CMC-induced AP exacerbation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"83"},"PeriodicalIF":13.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700843","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":"Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.","authors":"Anna L DeVeaux, Carla Hall-Moore, Nurmohammad Shaikh, Meghan Wallace, Carey-Ann D Burnham, David Schnadower, Nathan Kuppermann, Prashant Mahajan, Octavio Ramilo, Phillip I Tarr, Gautam Dantas, Drew J Schwartz","doi":"10.1186/s40168-025-02079-w","DOIUrl":"10.1186/s40168-025-02079-w","url":null,"abstract":"<p><strong>Background: </strong>Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.</p><p><strong>Results: </strong>We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.</p><p><strong>Conclusions: </strong>The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"82"},"PeriodicalIF":13.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700769","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":"Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.","authors":"Shane R Byrne, Michael S DeMott, Yifeng Yuan, Farzan Ghanegolmohammadi, Stefanie Kaiser, James G Fox, Eric J Alm, Peter C Dedon","doi":"10.1186/s40168-025-02071-4","DOIUrl":"10.1186/s40168-025-02071-4","url":null,"abstract":"<p><strong>Background: </strong>Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.</p><p><strong>Results: </strong>Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m⁶dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"81"},"PeriodicalIF":13.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700847","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":"Variety-dependent seed endophytic bacteria enhance stress tolerance to and bioaccumulation of ciprofloxacin in choy sum (Brassica parachinensis).","authors":"Yi-Ze Wang, Hai-Ming Zhao, Xian-Pei Huang, Yu Zhang, Jin-Cheng Ye, Nai-Xian Feng, Yan-Wen Li, Bai-Lin Liu, Quan-Ying Cai, Lei Xiang, Ce-Hui Mo, Qing X Li","doi":"10.1186/s40168-025-02073-2","DOIUrl":"10.1186/s40168-025-02073-2","url":null,"abstract":"<p><strong>Background: </strong>Accumulation of antibiotics in crops threatens human health. However, the mechanisms and effects of microorganisms on the uptake and accumulation of antibiotics in crops remain poorly understood. This study aimed to investigate the impact and underlying mechanisms of seed-borne microbiota in root on ciprofloxacin (CIP) accumulation in two choy sum varieties through amplicon sequencing, multiple statistical analyses, and subsequent validation of key bacteria via isolation and co-culturing with plants.</p><p><strong>Results: </strong>Bacillaceae (mainly Bacillus) was enriched specifically in the roots of CIP high-antibiotic-accumulating variety (HAV) via seed-based vertical transmission activated by the root exudate-derived maleic acid. The relative abundance of Bacillaceae was 9.2 to 27.7 times higher in roots of HAV relative to the low-antibiotic-accumulating variety (LAV). The enrichment of Bacillaceae facilitated a cooperative and beneficial bacterial community formed by the deterministic process. The community in HAV could not only stimulate antioxidase activities and decrease membrane lipid peroxidation via secreting indoleacetic acid and siderophore but also promote its biomass, especially the root length and biomass of HAV, thus greatly improving its tolerance to and absorption of CIP. The variety-specific plant-microbial interactions caused 1.6- to 3.2-fold higher CIP accumulation in shoots of HAV relative to LAV shoots.</p><p><strong>Conclusions: </strong>The findings highlight the crucial roles of the seed-borne microbiota in regulating the uptake and accumulation of antibiotics in crops, giving new understanding on the accumulation of organic pollutants in plants, with an emphasis on plant-microbial interactions Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"80"},"PeriodicalIF":13.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692594","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":"Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.","authors":"Tatiana Demina, Heli Marttila, Igor S Pessi, Minna K Männistö, Bas E Dutilh, Simon Roux, Jenni Hultman","doi":"10.1186/s40168-025-02053-6","DOIUrl":"10.1186/s40168-025-02053-6","url":null,"abstract":"<p><strong>Background: </strong>Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.</p><p><strong>Results: </strong>Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.</p><p><strong>Conclusions: </strong>This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"79"},"PeriodicalIF":13.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670202","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}