Microbiome最新文献

{"title":"Porcine nasal organoids to model interactions between the swine nasal microbiota and the host.","authors":"Laura Bonillo-Lopez, Noelia Carmona-Vicente, Ferran Tarrés-Freixas, Karl Kochanowski, Jorge Martínez, Mònica Perez, Marina Sibila, Florencia Correa-Fiz, Virginia Aragon","doi":"10.1186/s40168-025-02088-9","DOIUrl":"10.1186/s40168-025-02088-9","url":null,"abstract":"<p><strong>Background: </strong>Interactions between the nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. Currently, there is a lack of experimental models to study such interactions under defined in vitro conditions. Here, we developed a porcine nasal organoid (PNO) system from nasal tissue of pigs as well as from cytological brushes.</p><p><strong>Results: </strong>PNOs exhibited similar structure and cell types to the nasal mucosa, as evaluated by immunostaining. PNOs were inoculated with porcine commensal strains of Moraxella pluranimalium, Rothia nasimurium, and the pathobiont Glaesserella parasuis for examining host-commensal-pathogen interactions. All strains adhered to the PNOs, although at different levels. M. pluranimalium and G. parasuis strains stimulated the production of proinflammatory cytokines, whereas R. nasimurium induced the production of IFNγ and diminished the proinflammatory effect of the other strains.</p><p><strong>Conclusions: </strong>Overall, PNOs mimic the in vivo nasal mucosa and can be useful to perform host-microbe interaction studies. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"131"},"PeriodicalIF":13.8,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128139","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":"Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.","authors":"Teng Teng, Fang Huang, Ming Xu, Xuemei Li, Lige Zhang, Bangmin Yin, Yuping Cai, Fei Chen, Luman Zhang, Jushuang Zhang, Aoyi Geng, Chengzhi Chen, Xiaofei Yu, Jing Sui, Zheng-Jiang Zhu, Kai Guo, Chenhong Zhang, Xinyu Zhou","doi":"10.1186/s40168-025-02122-w","DOIUrl":"10.1186/s40168-025-02122-w","url":null,"abstract":"<p><strong>Background: </strong>Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.</p><p><strong>Results: </strong>We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M² = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.</p><p><strong>Conclusions: </strong>Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"128"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102129","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":"Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces.","authors":"Tianyu Sun, Hongwei Liu, Ningqi Wang, Mingcong Huang, Samiran Banerjee, Alexandre Jousset, Yangchun Xu, Qirong Shen, Shimei Wang, Xiaofang Wang, Zhong Wei","doi":"10.1186/s40168-025-02120-y","DOIUrl":"10.1186/s40168-025-02120-y","url":null,"abstract":"<p><strong>Background: </strong>Streptomyces spp. are known for producing bioactive compounds that suppress phytopathogens. However, previous studies have largely focused on their direct interactions with pathogens and plants, often neglecting their interactions with the broader soil microbiome. In this study, we hypothesized that these interactions are critical for effective pathogen control. We investigated a diverse collection of Streptomyces strains to select those with strong protective capabilities against tomato wilt disease caused by Ralstonia solanacearum. Leveraging a synthetic community (SynCom) established in our lab, alongside multiple in planta and in vitro co-cultivation experiments, as well as transcriptomic and metabolomic analyses, we explored the synergistic inhibitory mechanisms underlying bacterial wilt resistance facilitated by both Streptomyces and the soil microbiome.</p><p><strong>Results: </strong>Our findings indicate that direct antagonism by Streptomyces is not sufficient for their biocontrol efficacy. Instead, the efficacy was associated with shifts in the rhizosphere microbiome, particularly the promotion of two native keystone taxa, CSC98 (Stenotrophomonas maltophilia) and CSC13 (Paenibacillus cellulositrophicus). In vitro co-cultivation experiments revealed that CSC98 and CSC13 did not directly inhibit the pathogen. Instead, the metabolite of CSC13 significantly enhanced the inhibition efficiency of Streptomyces R02, a highly effective biocontrol strain in natural soil. Transcriptomic and metabolomic analyses revealed that CSC13's metabolites induced the production of Erythromycin E in Streptomyces R02, a key compound that directly suppressed R. solanacearum, as demonstrated by our antagonism tests.</p><p><strong>Conclusions: </strong>Collectively, our study reveals how beneficial microbes engage with the native soil microbiome to combat pathogens, suggesting the potential of leveraging microbial interactions to enhance biocontrol efficiency. These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"126"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102126","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":"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.","authors":"Hanpeng Liao, Chang Wen, Dan Huang, Chen Liu, Tian Gao, Qiyao Du, Qiu-E Yang, Ling Jin, Feng Ju, Mengting Maggie Yuan, Xiang Tang, Pingfeng Yu, Shungui Zhou, Pedro J Alvarez, Ville-Petri Friman","doi":"10.1186/s40168-025-02117-7","DOIUrl":"10.1186/s40168-025-02117-7","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.</p><p><strong>Results: </strong>Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.</p><p><strong>Conclusion: </strong>Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"127"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102121","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":"Tissue-resident microbiota signature in nasopharyngeal carcinoma.","authors":"Xi-Rong Tan, Han Qiao, Ying-Qing Li, Wei Jiang, Sheng-Yan Huang, Sha Gong, Wen-Fei Li, Ling-Long Tang, Guan-Qun Zhou, Ye-Lin Liang, Hui Li, Qing-Mei He, Jie-Wen Bai, Ming-Liang Ye, Jing-Yun Wang, Sai-Wei Huang, Jun-Yan Li, Chun-Qiao Gan, Ying-Qin Li, Yin Zhao, Ying Sun, Jun Ma, Na Liu","doi":"10.1186/s40168-025-02114-w","DOIUrl":"10.1186/s40168-025-02114-w","url":null,"abstract":"<p><strong>Background: </strong>Emerging evidence reveals that microbiota plays a crucial role in multiple cancers. Nasopharyngeal carcinoma (NPC) tissues harbour microbiota, highlighting the need to investigate the clinical implications of tissue-resident microbiota in the development of NPC. Here, we aim to clarify the specific profile of tissue-resident microbiota and its influence on NPC outcomes.</p><p><strong>Results: </strong>This retrospective study included 491 NPC patients from Sun Yat-sen University Cancer Center (Guangzhou, China) and the Affiliated Hospital of Guilin Medical College (Guilin, China). We profiled the microbial composition of 343 NPC and 36 normal nasopharyngeal tissues through sequencing of the genes encoding the 16S rRNA subunit of bacterial ribosomes. There were significant differences in microbial composition, alpha diversity (Shannon index, P = 0.007; Simpson index, P = 0.036), and beta diversity (Bray-Curtis distance: R² = 0.016, F = 5.187, P = 0.001; unweighted UniFrac distance: R² = 0.017, F = 5.373, P = 0.001) between NPC and normal nasopharyngeal tissues. A bacterial signature comprising four risk bacterial genera, including Bacteroides, Alloprevotella, Parvimonas, and Dialister, was constructed in the training cohort (n = 171). Patients in the high-risk group had shorter disease-free (HR 2.80, 95% CI 1.51-5.18, P < 0.001), distant metastasis-free (HR 4.00, 95% CI 1.77-9.01, P < 0.001), and overall survival (HR 3.45, 95% CI 1.77-6.72, P < 0.001) than those of patients in the low-risk group. Similar results were yielded in the internal validation (n = 172) and external validation (n = 148) cohorts. Integrated multi-omics analysis revealed that NPC tissues harbouring abundant risk bacteria were characterised by deficient immune infiltration, which was verified by multiplex immunohistochemistry.</p><p><strong>Conclusions: </strong>This study developed and validated the applicability of a four-bacteria signature as a prognostic tool for NPC prognostication. Integrated multi-omics analysis further uncovered that the tumour immune microenvironment was perturbed by tissue-resident microbiota, which might pave the way towards the era of microbiota-targeted precision medicine for NPC. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"125"},"PeriodicalIF":13.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094178","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":"Multi-omics analysis reveals that Bacillus spp. enhance mucosal antiviral immunity in teleost fish by mediating diglyceride production through lipid metabolism.","authors":"Gaofeng Cheng, Weiguang Kong, Ruiqi Lin, Zhihao Jiang, Xinyou Wang, Xueying Qin, Yong Shi, Peng Yang, Xiaoyun Chen, Lu Xia, Zhen Xu","doi":"10.1186/s40168-025-02124-8","DOIUrl":"10.1186/s40168-025-02124-8","url":null,"abstract":"<p><strong>Background: </strong>Symbiotic microbiota in vertebrates play critical roles in establishing and enhancing host resistance to pathogenic infections as well as maintaining host homeostasis. The interactions and mechanisms of commensal microbiota-mediated mucosal immune systems have been extensively studied in mammals and, to a lesser extent, in birds. However, despite several studies emphasizing the role of mucosal microbiota in controlling pathogen infections in teleost fish, limited knowledge exists regarding the core microbiota and the mechanisms by which they contribute to resistance against viral infections.</p><p><strong>Results: </strong>Our findings suggest that viral infections shape clinical manifestations of varying severity in infected fish. An increased abundance of Bacillus spp. in the mild phenotype indicates its crucial role in influencing fish immunity during viral infections. To confirm that Bacillus spp. act as a core contributor against viral infection in fish, we isolated a representative strain of Bacillus spp. from largemouth bass (Micropterus salmoides), which was identified as Bacillus velezensis (Bv), and subsequently conducted feeding trials. Our study demonstrated that dietary supplementation with Bv significantly reduced mortality from largemouth bass virus (LMBV) infection in bass by enhancing host immunity and metabolism as well as by regulating the microbial community. Furthermore, multi-omics analysis elucidated the mechanism by which Bacillus spp. confer resistance to viral infections by regulating the production of diglyceride (DG) during lipid metabolism.</p><p><strong>Conclusions: </strong>Our study provides the first evidence that Bacillus spp. are a core microbiota for combating viral infections in teleost fish, shedding light on the conserved functions of probiotics as a core microbiota in regulating microbial homeostasis and mucosal immunity across the vertebrate lineage.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"123"},"PeriodicalIF":13.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086155","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":"Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.","authors":"Shiqi Zhang, Nan Zheng, Shengguo Zhao, Jiaqi Wang","doi":"10.1186/s40168-025-02111-z","DOIUrl":"10.1186/s40168-025-02111-z","url":null,"abstract":"<p><strong>Background: </strong>Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and ¹⁵N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.</p><p><strong>Results: </strong>Allicin was identified as an inhibitor of ruminal urease, with an IC₅₀ of 126.77 ± 1.21 μM. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A ¹⁵N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.</p><p><strong>Conclusion: </strong>Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"124"},"PeriodicalIF":13.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085807","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":"Host taxonomy and environment shapes insectivore viromes and viral spillover risks in Southwestern China.","authors":"Ji-Hu Yang, Chun-Feng Luo, Rong Xiang, Jiu-Meng Min, Zong-Ti Shao, Yi-Lin Zhao, Lu Chen, Lin Huang, Yun Zhang, Shun-Shuai Liu, Yu-Qiong Li, En-Nian Pu, Wen-Qiang Shi, Hai-Feng Pan, Wei-Jun Chen, Chun-Hong Du, Jia-Fu Jiang","doi":"10.1186/s40168-025-02115-9","DOIUrl":"10.1186/s40168-025-02115-9","url":null,"abstract":"<p><strong>Background: </strong>Zoonotic viruses originating from small mammals pose significant challenges to public health on a global scale. Insectivores, serving as natural reservoirs for a diverse array of zoonotic viruses, are known to carry a multitude of viral species. However, compared to the extensive research conducted on rodents (Rodentia) and bats (Chiroptera), the role of insectivores in harboring and transmitting unknown pathogens remains underexplored, which may lead to a severe underestimation of their contributions and impact to global public health.</p><p><strong>Results: </strong>This study employed a meta-transcriptomic approach to profile the viromes of 214 individual insectivores, encompassing 13 species from the families Soricidae, Erinaceidae, and Talpidae, collected across 12 counties in Yunnan Province, a recognized zoonotic hotspot. Based on virus reads, the analysis identified 42 viral families associated with vertebrates, highlighting significant virome diversity and host-specific viral tropisms among shrews, hedgehogs, and moles, along with notable geographic and environmental specificity of the viruses. Shrews exhibited greater viral richness and abundance compared to hedgehogs and moles, with variations influenced predominantly by host taxonomy, altitude, and geographic location. A total of 114 RNA-dependent RNA polymerase sequences were obtained, leading to the identification of 68 viruses, including 57 novel species. Instances of host jumping were observed in 11 viruses, with potential pathogenic viruses related to Mojiang paramyxovirus and members of the Hantaviridae family. Cross-species transmission was predominantly observed in viruses carried by shrews, while moles may play a pivotal role in facilitating viral transmission among insectivores.</p><p><strong>Conclusions: </strong>This study enhances the understanding of the high diversity of mammalian viruses among insectivores in a relatively confined region and underscores the associations between virome composition and related zoonotic risks, providing a foundation for proactive measures to prevent and control the spillover of emerging zoonotic pathogens and potential future outbreaks. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"122"},"PeriodicalIF":13.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086105","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":"Community differences and potential function along the particle size spectrum of microbes in the twilight zone.","authors":"Yue Zhang, Hongbin Liu, Hongmei Jing","doi":"10.1186/s40168-025-02116-8","DOIUrl":"https://doi.org/10.1186/s40168-025-02116-8","url":null,"abstract":"<p><strong>Background: </strong>The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.</p><p><strong>Results: </strong>Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.</p><p><strong>Conclusion: </strong>Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"121"},"PeriodicalIF":13.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078658","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":"Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain.","authors":"Simone Zuffa, Christophe Lay, Elizabeth A Wimborne, Arabella Hornung Rodriguez, Yi Wu, Franklin L Nobrega, Nana Bartke, Anita C S Hokken-Koelega, Jan Knol, Guus Roeselers, Jonathan R Swann","doi":"10.1186/s40168-025-02106-w","DOIUrl":"10.1186/s40168-025-02106-w","url":null,"abstract":"<p><strong>Background: </strong>The supramolecular structure and composition of milk fat globules in breast milk is complex. Lipid droplets in formula milk are typically smaller compared to human milk and differ in their lipid and protein composition. These droplets play an important role in gut and immune maturation, and their components possess antimicrobial and antiviral properties. Here, the influence of a concept infant formula (IF) containing large milk phospholipid-coated lipid droplets on the maturation of the infant microbiota, metabolome, and weight gain in the first year of life was investigated.</p><p><strong>Results: </strong>Formula-fed infants were randomized to receive either a standard IF (Control) or a Test formula containing large milk phospholipid-coated lipid droplets (Test) until 17 weeks of age. A breast-fed Reference group was also investigated. At 3 months of age, several taxa identified as opportunistic pathogens (e.g., Enterobacter, Klebsiella, Enterococcus, Streptococcus) were less abundant in the Test stools compared to Control, while an enrichment of the butyrate-producing Ruminococcaceae and Lachnospiraceae was observed. These findings indicate that the Test formula resulted in gut microbiota maturation trajectories more comparable to healthy breast-fed infants. This was accompanied by variation in several fecal and plasma metabolites at 3 months of age related to gut microbial metabolism including bile acids, hippurate, phenylacetylglycine, trimethylamine, and various lipids and fatty acids. At 12 months, measures of subcutaneous fat and body mass index (BMI) were significantly higher in infants receiving standard IF compared to those receiving breast milk. However, this weight gain and adiposity was attenuated in the Test group infants.</p><p><strong>Conclusions: </strong>The presence of large phospholipid-coated lipid droplets in formula milk positively influenced the development of the infants' gut microbiota, their metabolomic profiles, and their body composition to more closely resemble breast-fed infants compared to standard IF. These droplets may further enhance the restriction of pathogenic bacteria seen with standard infant formula and suggest a potential impact on infant metabolic programming that may contribute to physiological development. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"120"},"PeriodicalIF":13.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078697","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}