Microbiome最新文献

{"title":"Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits.","authors":"Zishu Liu, Xiangwu Yao, Chengyi Chen, Yuxiang Zhao, Chifei Dong, Lingtao Sun, Junxian Zhao, Baofeng Zhang, Zhendi Yu, Dongqing Cheng, Lizhong Zhu, Baolan Hu","doi":"10.1186/s40168-024-02005-6","DOIUrl":"10.1186/s40168-024-02005-6","url":null,"abstract":"<p><strong>Background: </strong>The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.</p><p><strong>Results: </strong>Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.</p><p><strong>Conclusion: </strong>The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"8"},"PeriodicalIF":13.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979125","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":"Correction: Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.","authors":"Zhibin He, Yarong Hou, Ying Li, Qicheng Bei, Xin Li, Yong-Guan Zhu, Werner Liesack, Matthias C Rillig, Jingjing Peng","doi":"10.1186/s40168-025-02036-7","DOIUrl":"10.1186/s40168-025-02036-7","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"7"},"PeriodicalIF":13.8,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11724588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971498","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 microbiota of cork and yellow stain as a model for a new route for the synthesis of chlorophenols and chloroanisoles from the microbial degradation of suberin and/or lignin.","authors":"Marina Ruiz-Muñoz, Ignacio Ontañón, Rebeca Cobos, Carla Calvo-Peña, Rebeca Otero-Suárez, Vicente Ferreira, Jordi Roselló, Juan José R Coque","doi":"10.1186/s40168-024-02003-8","DOIUrl":"https://doi.org/10.1186/s40168-024-02003-8","url":null,"abstract":"<p><strong>Background: </strong>The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that destroys the organoleptic properties of wine and results in enormous economic losses for wineries and cork industries. Cork can exhibit a defect known as yellow stain, which is associated with high levels of 2,4,6-trichloroanisole. We describe how the microbiota of cork and yellow stain define a novel mechanism that explains the formation of chlorophenols and chloroanisoles (including 2,4,6-trichloroanisole) from p-hydroxybenzoate produced during lignin and/or suberin breakdown.</p><p><strong>Results: </strong>Electron microscopy revealed that cork affected by yellow stain exhibited significant structural degradation. This deterioration was attributed to the presence of higher microbial populations compared to those found in standard cork. Cork microbiota is rich in filamentous fungi able to metabolize lignin. A metataxonomic analysis confirmed that yellow stain contained significantly greater populations of fungal species belonging to Absidia, Geomyces, Mortierella, Mucor, Penicillium, Pseudogymnoascus, Talaromyces, and Umbelopsis. It also contained significantly greater amounts of bacteria belonging to Enterobacterales, Streptosporangiales, Tepidisphaerales, Pseudomonas, and several members of Burkholderiaceae, particularly species of the Burkholderia-Caballeronia-Paraburkholderia group. The extraction of aromatic compounds from cork samples allowed the identification of several compounds typically observed following lignin depolymerization. Notably, p-hydroxybenzoic acid and phenol were detected. Two strains of the genus Streptomyces isolated from yellow stain were able to biotransform p-hydroxybenzoate into phenol in resting cell assays. Phenol could be efficiently chlorinated in vitro to produce 2,4,6-trichlorophenol by a fungal chloroperoxidase, an enzymatic activity commonly found in filamentous fungi isolated from cork. Finally, as has been widely demonstrated before, 2,4,6-trichlorophenol can be efficiently O-methylated to 2,4,6-trichloroanisole by many of fungi that inhabit cork.</p><p><strong>Conclusions: </strong>Chlorophenols and chloroanisoles can be produced de novo in cork from p-hydroxybenzoate generated by the microbial biodegradation of lignin and/or suberin through the participation of different types of microorganisms present in cork. The natural origin of these compounds, which are of great interest for the chlorine cycle and represent a new source of environmental contamination that differs from that caused by human activity, is described. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"6"},"PeriodicalIF":13.8,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11724547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055980","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":"Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.","authors":"Diana Samodova, Evelina Stankevic, Mathilde Sonne Søndergaard, Naiyu Hu, Tarunveer S Ahluwalia, Daniel R Witte, Daniel Belstrøm, Anniek Frederike Lubberding, Pratik D Jagtap, Torben Hansen, Atul S Deshmukh","doi":"10.1186/s40168-024-01997-5","DOIUrl":"10.1186/s40168-024-01997-5","url":null,"abstract":"<p><strong>Background: </strong>Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.</p><p><strong>Results: </strong>We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.</p><p><strong>Conclusions: </strong>This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"5"},"PeriodicalIF":13.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11720885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142965703","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":"Regional antimicrobial resistance gene flow among the One Health sectors in China.","authors":"Yuqing Feng, Xin Lu, Jiayong Zhao, Hongmin Li, Jialiang Xu, Zhenpeng Li, Mengyu Wang, Yao Peng, Tian Tian, Gailing Yuan, Yuan Zhang, Jiaqi Liu, Meihong Zhang, A La Teng Zhu La, Geruo Qu, Yujiao Mu, Wanshen Guo, Yongning Wu, Yuyu Zhang, Dexiang Wang, Yongfei Hu, Biao Kan","doi":"10.1186/s40168-024-01983-x","DOIUrl":"https://doi.org/10.1186/s40168-024-01983-x","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.</p><p><strong>Results: </strong>In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.</p><p><strong>Conclusions: </strong>Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"3"},"PeriodicalIF":13.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11705761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951289","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":"Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis.","authors":"Cláudia Ferreira, Ilia Burgsdorf, Tzipora Perez, Gustavo Ramírez, Maya Lalzar, Dorothée Huchon, Laura Steindler","doi":"10.1186/s40168-024-01963-1","DOIUrl":"https://doi.org/10.1186/s40168-024-01963-1","url":null,"abstract":"<p><strong>Background: </strong>Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are still being elucidated. To understand these genetic adaptations, we conducted a comparative genomics analysis on 350 genomes of Actinobacteriota, a phylum commonly associated with sponges.</p><p><strong>Results: </strong>Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. Analyses of a broader set of microbes showed that members of the GPP34 family are also found in sponge symbionts across 16 additional bacterial phyla. While GPP34 proteins were thought to be restricted to eukaryotes, our phylogenetic analysis shows that the GPP34 domain is found in all three domains of life, suggesting its ancient origin. We also show that the GPP34 family includes genes with two main structures: a short form that includes only the GPP34 domain and a long form that encompasses a GPP34 domain coupled with a cytochrome P450 domain, which is exclusive to sponge symbiotic bacteria.</p><p><strong>Conclusions: </strong>Given previous studies showing that GPP34 is a phosphatidylinositol-4-phosphate (PI4P)-binding protein in eukaryotes and that other PI4P-binding proteins from bacterial pathogens can interfere with phagolysosome maturation, we propose that symbionts employ GPP34 to modulate phagocytosis to colonize and persist within sponge hosts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"4"},"PeriodicalIF":13.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951287","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":"Effects of data transformation and model selection on feature importance in microbiome classification data.","authors":"Zuzanna Karwowska, Oliver Aasmets, Tomasz Kosciolek, Elin Org","doi":"10.1186/s40168-024-01996-6","DOIUrl":"10.1186/s40168-024-01996-6","url":null,"abstract":"<p><strong>Background: </strong>Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.</p><p><strong>Results: </strong>Our analysis of over 8500 samples from 24 shotgun metagenomic datasets showed that it is possible to classify healthy and diseased individuals using microbiome data with minimal dependence on the choice of algorithm or transformation. Presence-absence transformations performed comparably to abundance-based transformations, and only a small subset of predictors is necessary for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlights the need to reevaluate machine learning-based biomarker detection.</p><p><strong>Conclusions: </strong>Microbiome data transformations can significantly influence feature selection but have a limited effect on classification accuracy. Our findings suggest that while classification is robust across different transformations, the variation in feature selection necessitates caution when using machine learning for biomarker identification. This research provides valuable insights for applying machine learning to microbiome data and identifies important directions for future work.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"2"},"PeriodicalIF":13.8,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927494","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":"A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population.","authors":"Tindaro Bongiovanni, Marina Santiago, Kinga Zielinska, Jonathan Scheiman, Carolina Barsa, Ralf Jäger, Daniela Pinto, Fabio Rinaldi, Giammaria Giuliani, Tullio Senatore, Aleksandar D Kostic","doi":"10.1186/s40168-024-01936-4","DOIUrl":"10.1186/s40168-024-01936-4","url":null,"abstract":"<p><strong>Background: </strong>The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness. Here, we conducted the first large-scale investigation into the influence of a novel elite athlete-derived probiotic, consisting of a multi-strain Lactobacillus consortium, on sleep quality, exercise recovery, and gut microbiome composition in both elite athletes (n = 11) and the general population (n = 257).</p><p><strong>Results: </strong>Our two-phase study design, which included an open-label study followed by a controlled longitudinal study in a professional soccer team, allowed us to identify key interactions between probiotics, the gut microbiome, and the host. In the placebo-controlled study, we observed significant improvements in self-reported sleep quality by 69%, energy levels by 31%, and bowel movements by 37% after probiotic intervention relative to after placebo. These improvements were associated with a significant decrease in D-ROMS (a marker of oxidative stress) and a significantly higher free-testosterone/cortisol ratio. Multi-omics analyses revealed specific changes in microbiome composition and function, potentially providing mechanistic insights into these observed effects.</p><p><strong>Conclusion: </strong>This study provides novel insights into how a multi-strain Lactobacillus probiotic modulates sleep quality, exercise recovery, and gut microbiome composition in both the general population and elite athletes, and introduces potential mechanisms through which this probiotic could be influencing overall health. Our results emphasize the untapped potential of tailored probiotic interventions derived from extremely fit and healthy individuals in improving several aspects of health and performance directly in humans. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"1"},"PeriodicalIF":13.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922046","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":"Live Akkermansia muciniphila boosts dendritic cell retinoic acid synthesis to modulate IL-22 activity and mitigate colitis in mice.","authors":"Hongbin Liu, Ruo Huang, Binhai Shen, Chongyang Huang, Qian Zhou, Jiahui Xu, Shengbo Chen, Xinlong Lin, Jun Wang, Xinmei Zhao, Yandong Guo, Xiuyun Ai, Yangyang Liu, Ye Wang, Wendi Zhang, Fachao Zhi","doi":"10.1186/s40168-024-01995-7","DOIUrl":"10.1186/s40168-024-01995-7","url":null,"abstract":"<p><strong>Background: </strong>The interplay between gut microbiota and immune responses is crucial in ulcerative colitis (UC). Though Akkermansia muciniphila (Akk) shows therapeutic potential, the mechanisms remain unclear. This study sought to investigate differences in therapeutic efficacy among different forms or strains of Akk and elucidate the underlying mechanisms.</p><p><strong>Results: </strong>Employing a dextran sulfate sodium (DSS)-induced colitis mouse model, we assessed Akk's impact on colitis using cellular cytokine analysis, immune phenotyping, proteomics, and biochemical methods. Our results suggest that treatment with live Akk effectively reduced colitis in the DSS-induced model, whereas heat-inactivated Akk did not yield the same results. Notably, Akk exhibited protective properties by promoting the secretion of IL-22 by Group 3 innate lymphoid cells (ILC3s), as evidenced by the absence of protection in IL-22 knockout mice. Additionally, Akk augmented the population of CD103⁺CD11b^- dendritic cells (DCs) and enhanced their retinoic acid (RA) synthesis through the modulation of RALDH2, a crucial enzyme in RA metabolism. The depletion of RALDH2 in DCs diminished Akk's protective properties and impaired IL-22-mediated mucosal healing. Mechanistically, Akk activated RA production in DCs by enhancing the JAK2-STAT3 signaling pathway. Additionally, various strains of Akk may exhibit differing abilities to alleviate colitis, with the novel strain Am06 derived from breast milk showing consistent efficacy similar to the reference strain.</p><p><strong>Conclusions: </strong>In summary, our findings indicate that certain strains of Akk may mitigate colitis through the promotion of RA synthesis and IL-22 secretion, underscoring the potential efficacy of Akk as a therapeutic intervention for the management of UC. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"275"},"PeriodicalIF":13.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903376","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":"Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.","authors":"Lei Liang, Cheng Kong, Jinming Li, Guang Liu, Jinwang Wei, Guan Wang, Qinying Wang, Yongzhi Yang, Debing Shi, Xinxiang Li, Yanlei Ma","doi":"10.1186/s40168-024-01987-7","DOIUrl":"10.1186/s40168-024-01987-7","url":null,"abstract":"<p><strong>Background: </strong>Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota, and metabolites to explain the site-specific difference.</p><p><strong>Methods: </strong>Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC, and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC, and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing, and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.</p><p><strong>Results: </strong>We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with the accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5, and AC079354.1.</p><p><strong>Conclusion: </strong>Our findings identify previously unknown links between intestinal microbiota alterations, metabolites, and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"274"},"PeriodicalIF":13.8,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895781","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}