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Laue HE, Bonham KS, Coker MO, Moroishi Y, Pathmasiri W, McRitchie S, Sumner S, Hoen AG, Karagas MR, Klepac-Ceraj V, Madan JC. Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium. Mol Autism 2024; 15:21. [PMID: 38760865 PMCID: PMC11101342 DOI: 10.1186/s13229-024-00597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors. METHODS Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects. RESULTS Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use. LIMITATIONS The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD. CONCLUSIONS Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.
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Affiliation(s)
- Hannah E Laue
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Kevin S Bonham
- Department of Biological Sciences, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA
| | - Modupe O Coker
- School of Dental Medicine, Rutgers University, Newark, NJ, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan McRitchie
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA.
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
- Departments of Pediatrics and Psychiatry, One Medical Center Drive, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA.
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52
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Xiao Z, Zhang Y, Zhang W, Zhang A, Wang G, Chen C, Ullah H, Ayaz T, Li S, Zhaxi D, Yan Q, Kang J, Xu X. Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas. Int Microbiol 2024:10.1007/s10123-024-00531-9. [PMID: 38758414 DOI: 10.1007/s10123-024-00531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/05/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood. METHODS Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants. RESULTS The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses. CONCLUSION The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.
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Affiliation(s)
- Zhen Xiao
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Wei Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Aiqin Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Taj Ayaz
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Duoji Zhaxi
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaoguang Xu
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China.
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
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53
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Norenhag J, Edfeldt G, Stålberg K, Garcia F, Hugerth LW, Engstrand L, Fransson E, Du J, Schuppe-Koistinen I, Olovsson M. Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia. Sci Rep 2024; 14:11183. [PMID: 38755259 PMCID: PMC11099171 DOI: 10.1038/s41598-024-61942-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024] Open
Abstract
Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.
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Affiliation(s)
- Johanna Norenhag
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.
| | - Gabriella Edfeldt
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Karin Stålberg
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Fabricio Garcia
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Luisa Warchavchik Hugerth
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Emma Fransson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Matts Olovsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
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Phan J, Calvo DC, Nair D, Jain S, Montagne T, Dietsche S, Blanchard K, Treadwell S, Adams J, Krajmalnik-Brown R. Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder. mSystems 2024; 9:e0050324. [PMID: 38661344 PMCID: PMC11097633 DOI: 10.1128/msystems.00503-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms. IMPORTANCE Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.
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Affiliation(s)
- Joann Phan
- Sun Genomics, Inc., San Diego, California, USA
| | - Diana C. Calvo
- Department of Civil Engineering, Construction Management, and Environmental Engineering, Northern Arizona University, Flagstaff, Arizona, USA
| | - Divya Nair
- Sun Genomics, Inc., San Diego, California, USA
| | - Suneer Jain
- Sun Genomics, Inc., San Diego, California, USA
| | | | | | | | | | - James Adams
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, USA
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55
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Oh S, Gravel-Pucillo K, Ramos M, Davis S, Carey V, Morgan M, Waldron L. AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. RESEARCH SQUARE 2024:rs.3.rs-4370115. [PMID: 38798429 PMCID: PMC11118690 DOI: 10.21203/rs.3.rs-4370115/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. Here we present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflowsimplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflowfor three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. While some limitations exist around workflow customization, AnVILWorkflowlowers the barrier to taking advantage of AnVIL's resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).
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Affiliation(s)
- Sehyun Oh
- City University of New York School of Public Health
| | | | - Marcel Ramos
- City University of New York School of Public Health
| | - Sean Davis
- University of Colorado Anschutz School of Medicine
| | | | | | - Levi Waldron
- City University of New York School of Public Health
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56
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Xiao L, Zhou T, Zuo Z, Sun N, Zhao F. Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders. Sci Bull (Beijing) 2024; 69:1275-1285. [PMID: 38388298 DOI: 10.1016/j.scib.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The microbiome of females undergoes extensive remodeling during pregnancy, which is likely to have an impact on the health of both mothers and offspring. Nevertheless, large-scale integrated investigations characterizing microbiome dynamics across key body habitats are lacking. Here, we performed an extensive meta-analysis that compiles and analyzes microbiome profiles from >10,000 samples across the gut, vagina, and oral cavity of pregnant women from diverse geographical regions. We have unveiled unexpected variations in the taxonomic, functional, and ecological characteristics of microbial communities throughout the course of pregnancy. The gut microbiota showed distinct trajectories between Western and non-Western populations. The vagina microbiota exhibited fluctuating transitions at the genus level across gestation, while the oral microbiota remained relatively stable. We also identified distinctive microbial signatures associated with prevalent pregnancy-related disorders, including opposite variations in the oral and gut microbiota of patients with gestational diabetes and disrupted microbial networks in preterm birth. This study establishes a comprehensive atlas of the pregnancy microbiome by integrating multidimensional datasets and offers foundational insights into the intricate interplay between microbes and host factors that underlie reproductive health.
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Affiliation(s)
- Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Ningxia Sun
- Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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57
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Uthaman S, Parvinroo S, Mathew AP, Jia X, Hernandez B, Proctor A, Sajeevan KA, Nenninger A, Long MJ, Park IK, Chowdhury R, Phillips GJ, Wannemuehler MJ, Bardhan R. Inhibiting the cGAS-STING Pathway in Ulcerative Colitis with Programmable Micelles. ACS NANO 2024; 18:12117-12133. [PMID: 38648373 DOI: 10.1021/acsnano.3c11257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Ulcerative colitis is a chronic condition in which a dysregulated immune response contributes to the acute intestinal inflammation of the colon. Current clinical therapies often exhibit limited efficacy and undesirable side effects. Here, programmable nanomicelles were designed for colitis treatment and loaded with RU.521, an inhibitor of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. STING-inhibiting micelles (SIMs) comprise hyaluronic acid-stearic acid conjugates and include a reactive oxygen species (ROS)-responsive thioketal linker. SIMs were designed to selectively accumulate at the site of inflammation and trigger drug release in the presence of ROS. Our in vitro studies in macrophages and in vivo studies in a murine model of colitis demonstrated that SIMs leverage HA-CD44 binding to target sites of inflammation. Oral delivery of SIMs to mice in both preventive and delayed therapeutic models ameliorated colitis's severity by reducing STING expression, suppressing the secretion of proinflammatory cytokines, enabling bodyweight recovery, protecting mice from colon shortening, and restoring colonic epithelium. In vivo end points combined with metabolomics identified key metabolites with a therapeutic role in reducing intestinal and mucosal inflammation. Our findings highlight the significance of programmable delivery platforms that downregulate inflammatory pathways at the intestinal mucosa for managing inflammatory bowel diseases.
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Affiliation(s)
- Saji Uthaman
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
| | - Shadi Parvinroo
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Ansuja Pulickal Mathew
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
| | - Xinglin Jia
- Department of Mathematics, Iowa State University, Ames, Iowa 50011, United States
| | - Belen Hernandez
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Alexandra Proctor
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Karuna Anna Sajeevan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
| | - Ariel Nenninger
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Mary-Jane Long
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
| | - In-Kyu Park
- Department of Biomedical Sciences and BioMedical Sciences Graduate Program (BMSGP), Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Ratul Chowdhury
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
| | - Gregory J Phillips
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Michael J Wannemuehler
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Rizia Bardhan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Nanovaccine Institute, Iowa State University, Ames, Iowa 50012, United States
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58
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Bermingham KM, Linenberg I, Polidori L, Asnicar F, Arrè A, Wolf J, Badri F, Bernard H, Capdevila J, Bulsiewicz WJ, Gardner CD, Ordovas JM, Davies R, Hadjigeorgiou G, Hall WL, Delahanty LM, Valdes AM, Segata N, Spector TD, Berry SE. Effects of a personalized nutrition program on cardiometabolic health: a randomized controlled trial. Nat Med 2024:10.1038/s41591-024-02951-6. [PMID: 38714898 DOI: 10.1038/s41591-024-02951-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/26/2024] [Indexed: 05/15/2024]
Abstract
Large variability exists in people's responses to foods. However, the efficacy of personalized dietary advice for health remains understudied. We compared a personalized dietary program (PDP) versus general advice (control) on cardiometabolic health using a randomized clinical trial. The PDP used food characteristics, individual postprandial glucose and triglyceride (TG) responses to foods, microbiomes and health history, to produce personalized food scores in an 18-week app-based program. The control group received standard care dietary advice (US Department of Agriculture Guidelines for Americans, 2020-2025) using online resources, check-ins, video lessons and a leaflet. Primary outcomes were serum low-density lipoprotein cholesterol and TG concentrations at baseline and at 18 weeks. Participants (n = 347), aged 41-70 years and generally representative of the average US population, were randomized to the PDP (n = 177) or control (n = 170). Intention-to-treat analysis (n = 347) between groups showed significant reduction in TGs (mean difference = -0.13 mmol l-1; log-transformed 95% confidence interval = -0.07 to -0.01, P = 0.016). Changes in low-density lipoprotein cholesterol were not significant. There were improvements in secondary outcomes, including body weight, waist circumference, HbA1c, diet quality and microbiome (beta-diversity) (P < 0.05), particularly in highly adherent PDP participants. However, blood pressure, insulin, glucose, C-peptide, apolipoprotein A1 and B, and postprandial TGs did not differ between groups. No serious intervention-related adverse events were reported. Following a personalized diet led to some improvements in cardiometabolic health compared to standard dietary advice. ClinicalTrials.gov registration: NCT05273268 .
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Affiliation(s)
- Kate M Bermingham
- Department of Nutritional Sciences, King's College London, London, UK
- Zoe Ltd, London, UK
| | - Inbar Linenberg
- Department of Nutritional Sciences, King's College London, London, UK
- Zoe Ltd, London, UK
| | | | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | | | | | | | | | | | | | - Jose M Ordovas
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
- IMDEA Food Institute, Campus of International Excellence, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Universidad Camilo José Cela, Madrid, Spain
| | | | | | - Wendy L Hall
- Department of Nutritional Sciences, King's College London, London, UK
| | - Linda M Delahanty
- Diabetes Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana M Valdes
- School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham National Institute for Health and Care Research Biomedical Research Centre, Nottingham, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Tim D Spector
- Department of Nutritional Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK.
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59
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Hansen ZA, Schilmiller AL, Guzior DV, Rudrik JT, Quinn RA, Vasco KA, Manning SD. Shifts in the functional capacity and metabolite composition of the gut microbiome during recovery from enteric infection. Front Cell Infect Microbiol 2024; 14:1359576. [PMID: 38779558 PMCID: PMC11109446 DOI: 10.3389/fcimb.2024.1359576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
While enteric pathogens have been widely studied for their roles in causing foodborne infection, their impacts on the gut microbial community have yet to be fully characterized. Previous work has identified notable changes in the gut microbiome related to pathogen invasion, both taxonomically and genetically. Characterization of the metabolic landscape during and after enteric infection, however, has not been explored. Consequently, we investigated the metabolome of paired stools recovered from 60 patients (cases) during and after recovery from enteric bacterial infections (follow-ups). Shotgun metagenomics was applied to predict functional microbial pathways combined with untargeted metametabolomics classified by Liquid Chromatography Mass Spectrometry. Notably, cases had a greater overall metabolic capacity with significantly higher pathway richness and evenness relative to the follow-ups (p<0.05). Metabolic pathways related to central carbon metabolism, amino acid metabolism, and lipid and fatty acid biosynthesis were more highly represented in cases and distinct signatures for menaquinone production were detected. By contrast, the follow-up samples had a more diverse metabolic landscape with enhanced richness of polar metabolites (p<0.0001) and significantly greater richness, evenness, and overall diversity of nonpolar metabolites (p<0.0001). Although many metabolites could not be annotated with existing databases, a marked increase in certain clusters of metabolites was observed in the follow-up samples when compared to the case samples and vice versa. These findings suggest the importance of key metabolites in gut health and recovery and enhance understanding of metabolic fluctuations during enteric infections.
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Affiliation(s)
- Zoe A. Hansen
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
| | - Anthony L. Schilmiller
- Research Technology Support Facility, Mass Spectrometry and Metabolomics Core, Michigan State University E., Lansing, MI, United States
| | - Douglas V. Guzior
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University E., Lansing, MI, United States
| | - James T. Rudrik
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, United States
| | - Robert A. Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University E., Lansing, MI, United States
| | - Karla A. Vasco
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
| | - Shannon D. Manning
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
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Su Q, Lau RI, Liu Q, Li MKT, Yan Mak JW, Lu W, Lau ISF, Lau LHS, Yeung GTY, Cheung CP, Tang W, Liu C, Ching JYL, Cheong PK, Chan FKL, Ng SC. The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome. Cell Host Microbe 2024; 32:651-660.e4. [PMID: 38657605 DOI: 10.1016/j.chom.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.
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Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Raphaela I Lau
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Moses K T Li
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Joyce Wing Yan Mak
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ivan S F Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Louis H S Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Giann T Y Yeung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y L Ching
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pui Kuan Cheong
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
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61
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Veschetti L, Paiella S, Carelli M, Zotti F, Secchettin E, Malleo G, Signoretto C, Zulianello G, Nocini R, Crovetto A, Salvia R, Bassi C, Malerba G. Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection. Appl Microbiol Biotechnol 2024; 108:319. [PMID: 38709303 DOI: 10.1007/s00253-024-13152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/03/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Maria Carelli
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Francesca Zotti
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy
| | - Erica Secchettin
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Giuseppe Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Caterina Signoretto
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giorgia Zulianello
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Riccardo Nocini
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy
| | - Anna Crovetto
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Giovanni Malerba
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy.
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62
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Yahara H, Yanamoto S, Takahashi M, Hamada Y, Asaka T, Kitagawa Y, Moridera K, Noguchi K, Maruoka Y, Yahara K. Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis. PLoS One 2024; 19:e0302569. [PMID: 38709734 PMCID: PMC11073694 DOI: 10.1371/journal.pone.0302569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial osteomyelitis. Although previous studies have investigated the association between these diseases and the oral microbiome, the specific taxa associated with each disease remain unknown. In this study, we conducted shotgun metagenome sequencing (≥10 Gb from ≥66,395,670 reads per sample) of bulk DNA extracted from saliva obtained from patients with chronic bacterial osteomyelitis (N = 5) and chronic nonbacterial osteomyelitis (N = 10). We then compared the taxonomic composition of the metagenome in terms of both taxonomic and sequence abundances with that of healthy controls (N = 5). Taxonomic profiling revealed a statistically significant increase in both the taxonomic and sequence abundance of Mogibacterium in cases of chronic bacterial osteomyelitis; however, such enrichment was not observed in chronic nonbacterial osteomyelitis. We also compared a previously reported core saliva microbiome (59 genera) with our data and found that out of the 74 genera detected in this study, 47 (including Mogibacterium) were not included in the previous meta-analysis. Additionally, we analyzed a core-genome tree of Mogibacterium from chronic bacterial osteomyelitis and healthy control samples along with a reference complete genome and found that Mogibacterium from both groups was indistinguishable at the core-genome and pan-genome levels. Although limited by the small sample size, our study provides novel evidence of a significant increase in Mogibacterium abundance in the chronic bacterial osteomyelitis group. Moreover, our study presents a comparative analysis of the taxonomic and sequence abundances of all genera detected using deep salivary shotgun metagenome data. The distinct enrichment of Mogibacterium suggests its potential as a marker to distinguish between patients with chronic nonbacterial osteomyelitis and chronic bacterial osteomyelitis, particularly at the early stages when differences are unclear.
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Affiliation(s)
- Hiroko Yahara
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Souichi Yanamoto
- Department of Oral Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Miho Takahashi
- Department of Oral and Maxillofacial Surgery, Tokai University Hachioji Hospital, Tokyo, Japan
| | - Yuji Hamada
- Department of Oral and Maxillofacial Surgery, Tokai University Hachioji Hospital, Tokyo, Japan
| | - Takuya Asaka
- Department of Oral Diagnosis and Medicine, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Yoshimasa Kitagawa
- Department of Oral Diagnosis and Medicine, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Kuniyasu Moridera
- Department of Oral and Maxillofacial Surgery, School of Medicine, Hyogo Medical University, Hyogo, Japan
| | - Kazuma Noguchi
- Department of Oral and Maxillofacial Surgery, School of Medicine, Hyogo Medical University, Hyogo, Japan
| | - Yutaka Maruoka
- Department of Oral and Maxillofacial Surgery, Center Hospital of the National Center for Global Health and Medicine, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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63
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Braun T, Feng R, Amir A, Levhar N, Shacham H, Mao R, Hadar R, Toren I, Algavi Y, Abu-Saad K, Zhuo S, Efroni G, Malik A, Picard O, Yavzori M, Agranovich B, Liu TC, Stappenbeck TS, Denson L, Kalter-Leibovici O, Gottlieb E, Borenstein E, Elinav E, Chen M, Ben-Horin S, Haberman Y. Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. Nat Commun 2024; 15:3764. [PMID: 38704361 PMCID: PMC11069498 DOI: 10.1038/s41467-024-48106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Rui Feng
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, Guangxi, China
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hila Shacham
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ren Mao
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Itamar Toren
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yadid Algavi
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kathleen Abu-Saad
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Shuoyu Zhuo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Alona Malik
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Orit Picard
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Miri Yavzori
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Bella Agranovich
- Laura and Isaac Perlmutter Metabolomics Center, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ofra Kalter-Leibovici
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Eyal Gottlieb
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Elhanan Borenstein
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM, USA
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Microbiome & Cancer Division, German National Cancer Center (DKFZ), Heidelberg, Germany
| | - Minhu Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel.
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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64
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Li B, Chen J, Ou X, Liu X, Xu Z, Xiang X, Yang Y, Wang Q. In-depth multiomic characterization of the effects of obesity in high-fat diet-fed mice. FEBS Open Bio 2024; 14:771-792. [PMID: 38479983 PMCID: PMC11073502 DOI: 10.1002/2211-5463.13788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 05/07/2024] Open
Abstract
High-fat diet (HFD)-fed mice have been widely used in the clinical investigation of obesity. However, the long-term effect of HFD on gut microbiota and metabolites, plasma and liver metabolomics, colonic and liver transcriptomics remain largely unknown. In this study, 6-week-old C57BL/6J male mice fed with HFD for 14 weeks showed increased obesity-related indexes including alanine aminotransferase, aspartate aminotransferase, total cholesterol, total triglyceride, free fatty acids, lipopolysaccharides, IL-6, and TNFα. Furthermore, microbial diversity and richness were also significantly decreased. In the colon, genes involved in tryptophan metabolism, PPAR signaling pathway, cholesterol metabolism, and lipid localization and transport, were upregulated. While in the liver, MAPK signaling and unsaturated fatty acid biosynthesis were upregulated. Metabolomic analyses revealed decreased levels of glycerophospholipids and fatty acyl, but increased amino acids, coenzymes and vitamins, and organic acids in the colon, suggesting high absorption of oxidized lipids, while acyl-carnitine, lysophosphatidylcholine, lysophosphatidylethanolamine, and oxidized lipids were reduced in the liver, suggesting a more active lipid metabolism. Finally, correlation analyses revealed a positive correlation between gut microbiota and metabolites and the expression of genes associated with lipid localization, absorption, and transport in the colon, and nutrients and energy metabolism in the liver. Taken together, our results provide a comprehensive characterization of long-term HFD-induced obesity in mice.
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Affiliation(s)
- Boping Li
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Medicine, Longdong University, Qingyang, China
| | - Juanjuan Chen
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Xiaobin Ou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Xiuli Liu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Zaoxu Xu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Xuesong Xiang
- Element Nutrition of National Health Commission, National Institute of Nutrition and Health, China CDC, Beijing, China
| | - Yan Yang
- Department of Endocrinology and Metabolism, Lanzhou University Second Hospital, Lanzhou, China
| | - Qi Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
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65
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Choi J, Thänert R, Reske KA, Nickel KB, Olsen MA, Hink T, Thänert A, Wallace MA, Wang B, Cass C, Barlet MH, Struttmann EL, Iqbal ZH, Sax SR, Fraser VJ, Baker AW, Foy KR, Williams B, Xu B, Capocci-Tolomeo P, Lautenbach E, Burnham CAD, Dubberke ER, Dantas G, Kwon JH. Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study. EClinicalMedicine 2024; 71:102490. [PMID: 38813445 PMCID: PMC11133793 DOI: 10.1016/j.eclinm.2024.102490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/31/2024] Open
Abstract
Background Urinary tract infections (UTI) affect approximately 250 million people annually worldwide. Patients often experience a cycle of antimicrobial treatment and recurrent UTI (rUTI) that is thought to be facilitated by a gut reservoir of uropathogenic Escherichia coli (UPEC). Methods 125 patients with UTI caused by an antibiotic-resistant organism (ARO) were enrolled from July 2016 to May 2019 in a longitudinal, multi-center cohort study. Multivariate statistical models were used to assess the relationship between uropathogen colonization and recurrent UTI (rUTI), controlling for clinical characteristics. 644 stool samples and 895 UPEC isolates were interrogated for taxonomic composition, antimicrobial resistance genes, and phenotypic resistance. Cohort UTI gut microbiome profiles were compared against published healthy and UTI reference microbiomes, as well as assessed within-cohort for timepoint- and recurrence-specific differences. Findings Risk of rUTI was not independently associated with clinical characteristics. The UTI gut microbiome was distinct from healthy reference microbiomes in both taxonomic composition and antimicrobial resistance gene (ARG) burden, with 11 differentially abundant taxa at the genus level. rUTI and non-rUTI gut microbiomes in the cohort did not generally differ, but gut microbiomes from urinary tract colonized patients were elevated in E. coli abundance 7-14 days post-antimicrobial treatment. Corresponding UPEC gut isolates from urinary tract colonizing lineages showed elevated phenotypic resistance against 11 of 23 tested drugs compared to non-colonizing lineages. Interpretation The gut microbiome is implicated in UPEC urinary tract colonization during rUTI, serving as an ARG-enriched reservoir for UPEC. UPEC can asymptomatically colonize the gut and urinary tract, and post-antimicrobial blooms of gut E. coli among urinary tract colonized patients suggest that cross-habitat migration of UPEC is an important mechanism of rUTI. Thus, treatment duration and UPEC populations in both the urinary and gastrointestinal tract should be considered in treating rUTI and developing novel therapeutics. Funding This work was supported in part by awards from the U.S. Centers for Disease Control and Prevention Epicenter Prevention Program (grant U54CK000482; principal investigator, V.J.F.); to J.H.K. from the Longer Life Foundation (an RGA/Washington University partnership), the National Center for Advancing Translational Sciences (grants KL2TR002346 and UL1TR002345), and the National Institute of Allergy and Infectious Diseases (NIAID) (grant K23A1137321) of the National Institutes of Health (NIH); and to G.D. from NIAID (grant R01AI123394) and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (grant R01HD092414) of NIH. R.T.'s research was funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; grant 402733540). REDCap is Supported by Clinical and Translational Science Award (CTSA) Grant UL1 TR002345 and Siteman Comprehensive Cancer Center and NCI Cancer Center Support Grant P30 CA091842. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.
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Affiliation(s)
- JooHee Choi
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Katelin B. Nickel
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Margaret A. Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Margaret H. Barlet
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily L. Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Zainab Hassan Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Steven R. Sax
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Victoria J. Fraser
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Arthur W. Baker
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
| | - Katherine R. Foy
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
| | - Brett Williams
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, IL, USA
| | - Ben Xu
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, IL, USA
| | - Pam Capocci-Tolomeo
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ebbing Lautenbach
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jennie H. Kwon
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - CDC Prevention Epicenters Program
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, IL, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
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Adeniyi-Ipadeola GO, Hoffman KL, Yang H, Javornik Cregeen SJ, Preidis GA, Ramani S, Hair AB. Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study. Pediatr Res 2024; 95:1564-1571. [PMID: 38228744 DOI: 10.1038/s41390-023-02948-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/09/2023] [Accepted: 11/18/2023] [Indexed: 01/18/2024]
Abstract
BACKGROUND In very low birth weight (VLBW) infants, human milk cream added to standard human milk fortification is used to improve growth. This study aimed to evaluate the impact of cream supplement on the intestinal microbiome of VLBW infants. METHODS Whole genome shotgun sequencing was performed on stool (n = 57) collected from a cohort of 23 infants weighing 500-1250 grams (control = 12, cream = 11). Both groups received an exclusive human milk diet (mother's own milk, donor human milk, and donor human milk-derived fortifier) with the cream group receiving an additional 2 kcal/oz cream at 100 mL/kg/day of fortified feeds and then 4 kcal/oz if poor growth. RESULTS While there were no significant differences in alpha diversity, infants receiving cream significantly differed from infants in the control group in beta diversity. Cream group samples had significantly higher prevalence of Proteobacteria and significantly lower Firmicutes compared to control group. Klebsiella species dominated the microbiota of cream-exposed infants, along with bacterial pathways involved in lipid metabolism and metabolism of cofactors and amino acids. CONCLUSIONS Cream supplementation significantly altered composition of the intestinal microbiome of VLBW infants to favor increased prevalence of Proteobacteria and functional gene content associated with these bacteria. IMPACT We report changes to the intestinal microbiome associated with administration of human milk cream; a novel supplement used to improve growth rates of preterm very low birth weight infants. Since little is known about the impact of cream on intestinal microbiota composition of very low birth weight infants, our study provides valuable insight on the effects of diet on the microbiome of this population. Dietary supplements administered to preterm infants in neonatal intensive care units have the potential to influence the intestinal microbiome composition which may affect overall health status of the infant.
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Affiliation(s)
- Grace O Adeniyi-Ipadeola
- Graduate Program in Immunology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi L Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Heeju Yang
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Sara J Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Amy B Hair
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA.
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Ghorbani M, Khoshdoozmasouleh N. Distinct oral DNA viral signatures in rheumatoid arthritis: a Pilot study. J Oral Microbiol 2024; 16:2348260. [PMID: 38698892 PMCID: PMC11064737 DOI: 10.1080/20002297.2024.2348260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
Background Despite evidence linking viruses and oral microbiome to rheumatoid arthritis (RA), limited whole genome sequencing research has been conducted on the oral virome (a viral component of the microbiome) of untreated RA patients. This pilot research seeks to address this knowledge gap by comparing the oral virome of untreated rheumatoid arthritis patients (RAs) and healthy individuals (HCs). Method Whole genome DNA sequence of saliva samples from 45 participants including 21 RAs and 24 age and gender matched HCs was obtained from the BioProject: PRJEB6997. Metaphlan3 pipeline and LEfSe analysis were used for the viral signature detection. Wilcoxon pairwise test and ROC analysis were used to validate and predict signatures. Results RA exhibits higher alpha diversity compared to HCs. Callitrichine gammaherpesvirus 3, Human gammaherpesvirus 4 (EBV), Murid betaherpesvirus 8, and Suid alphaherpesvirus 1 were enriched in RAs, while Aotine betaherpesvirus 1 from the Cytomegalovirus genus was enriched in HCs. In addition, Saccharomyces cerevisiae killer virus M1 (ScV-M1) was found to be enriched in RAs, whereas bacteriophage Hk97virus (Siphoviridae) and Cd119virus (Myoviridae) were enriched in HCs. Conclusion This study identifies significant DNA oral viral signatures at species level as potential biomarkers for the early detection and diagnosis of rheumatoid arthritis.
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Affiliation(s)
- Mahin Ghorbani
- Department of Dental Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Nooshin Khoshdoozmasouleh
- Department of Molecular Medicine, University of Padova, Padova, Italy
- Roswell Park Comprehensive Cancer Center, Department of Cancer Genomics, Buffalo, NY, USA
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Zhang QZ, Zhang JR, Li X, Yin JL, Jin LM, Xun ZR, Xue H, Yang WQ, Zhang H, Qu J, Xing ZK, Wang XM. Fangyukangsuan granules ameliorate hyperuricemia and modulate gut microbiota in rats. Front Immunol 2024; 15:1362642. [PMID: 38745649 PMCID: PMC11091346 DOI: 10.3389/fimmu.2024.1362642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Hyperuricaemia (HUA) is a metabolic disorder characterised by high blood uric acid (UA) levels; moreover, HUA severity is closely related to the gut microbiota. HUA is also a risk factor for renal damage, diabetes, hypertension, and dyslipidaemia; however, current treatments are associated with detrimental side effects. Alternatively, Fangyukangsuan granules are a natural product with UA-reducing properties. To examine their efficacy in HUA, the binding of small molecules in Fangyukangsuan granules to xanthine oxidase (XOD), a key factor in UA metabolism, was investigated via molecular simulation, and the effects of oral Fangyukangsuan granule administration on serum biochemical indices and intestinal microorganisms in HUA-model rats were examined. Overall, 24 small molecules in Fangyukangsuan granules could bind to XOD. Serum UA, creatinine, blood urea nitrogen, and XOD levels were decreased in rats treated with Fangyukangsuan granules compared to those in untreated HUA-model rats. Moreover, Fangyukangsuan granules restored the intestinal microbial structure in HUA-model rats. Functional analysis of the gut microbiota revealed decreased amino acid biosynthesis and increased fermentation of pyruvate into short-chain fatty acids in Fangyukangsuan granule-treated rats. Together, these findings demonstrate that Fangyukangsuan granules have anti-hyperuricaemic and regulatory effects on the gut microbiota and may be a therapeutic candidate for HUA.
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Affiliation(s)
- Qing-zheng Zhang
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Ji-rui Zhang
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Xue Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Jin-long Yin
- Department of Food Science and Engineering, Jilin Business and Technology College, Changchun, Jilin, China
| | - Li-ming Jin
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, China
| | - Zhuo-ran Xun
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Hao Xue
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Wan-qi Yang
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Hua Zhang
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Jingyong Qu
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Zhi-kai Xing
- College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Xu-min Wang
- College of Life Sciences, Yantai University, Yantai, Shandong, China
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Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
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Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
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Ma W, Wang Y, Nguyen LH, Mehta RS, Ha J, Bhosle A, Mclver LJ, Song M, Clish CB, Strate LL, Huttenhower C, Chan AT. Gut microbiome composition and metabolic activity in women with diverticulitis. Nat Commun 2024; 15:3612. [PMID: 38684664 PMCID: PMC11059386 DOI: 10.1038/s41467-024-47859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.
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Affiliation(s)
- Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yiqing Wang
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raaj S Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jane Ha
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Amrisha Bhosle
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lauren J Mclver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa L Strate
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Meng X, Xv C, Lv J, Zhang S, Ma C, Pang X. Optimizing Akkermansia muciniphila Isolation and Cultivation: Insights into Gut Microbiota Composition and Potential Growth Promoters in a Chinese Cohort. Microorganisms 2024; 12:881. [PMID: 38792711 PMCID: PMC11124125 DOI: 10.3390/microorganisms12050881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The study aims to analyze the composition of the gut microbiota in Chinese individuals using metagenomic sequencing technology, with a particular focus on the abundance of Akkermansia muciniphila (Akk). To improve the efficiency of Akk isolation and identification accuracy, modifications were made to the enrichment culture medium and 16S rRNA universal primers. Additionally, potential growth-promoting factors that stimulate Akk growth were explored through in vitro screening. The research results revealed that the abundance of Akk in Chinese fecal samples ranged from 0.004% to 0.4%. During optimization, a type of animal protein peptide significantly enhanced the enrichment efficiency of Akk, resulting in the isolation of three Akk strains from 14 fecal samples. Furthermore, 17 different growth-promoting factors were compared, and four factors, including galactose, sialic acid, lactose, and chitosan, were identified as significantly promoting Akk growth. Through orthogonal experiments, the optimal ratio of these four growth-promoting factors was determined to be 1:1:2:1. After adding 1.25% of this growth-promoting factor combination to the standard culture medium, Akk was cultivated at 37° for 36 h, achieving an OD600nm value of 1.169, thus realizing efficient proliferation and optimized cultivation of Akk. This study provides important clues for a deeper understanding of the gut microbiota composition in Chinese individuals, while also offering effective methods for the isolation and cultivation of Akk, laying the groundwork for its functional and application research in the human body.
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Affiliation(s)
- Xiangyu Meng
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
| | - Chen Xv
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiaping Lv
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
| | - Shuwen Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
| | - Changlu Ma
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
| | - Xiaoyang Pang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.M.); (C.X.); (J.L.); (S.Z.); (C.M.)
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Alexa EA, Cobo-Díaz JF, Renes E, O Callaghan TF, Kilcawley K, Mannion D, Skibinska I, Ruiz L, Margolles A, Fernández-Gómez P, Alvarez-Molina A, Puente-Gómez P, Crispie F, López M, Prieto M, Cotter PD, Alvarez-Ordóñez A. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. MICROBIOME 2024; 12:78. [PMID: 38678226 PMCID: PMC11055350 DOI: 10.1186/s40168-024-01790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. RESULTS Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. CONCLUSION Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
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Affiliation(s)
- Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Erica Renes
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 Y337, Ireland
| | | | - David Mannion
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
| | | | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | | | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
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Chen Q, Huang X, Zhang H, Jiang X, Zeng X, Li W, Su H, Chen Y, Lin F, Li M, Gu X, Jin H, Wang R, Diao D, Wang W, Li J, Wei S, Zhang W, Liu W, Huang Z, Deng Y, Luo W, Liu Z, Zhang B. Characterization of tongue coating microbiome from patients with colorectal cancer. J Oral Microbiol 2024; 16:2344278. [PMID: 38686186 PMCID: PMC11057396 DOI: 10.1080/20002297.2024.2344278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC). Methods Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model. Results We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as Atopobium rimae, Streptococcus sanguinis, and Prevotella oris aided differentiation of CRC patients from healthy participants. Conclusion These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.
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Affiliation(s)
- Qubo Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Xiaoting Huang
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen, Shenzhen, China
| | - Haiyan Zhang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuanting Jiang
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Xuan Zeng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Wanhua Li
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hairong Su
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Chen
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengye Lin
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Man Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Xiangyu Gu
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huihui Jin
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruohan Wang
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dechang Diao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Colorectal surgery of Guangdong Provincial Hospital of TCM, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Wang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Gastrointestinal Surgery Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jin Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Gastrointestinal Surgery Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Sufen Wei
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weizheng Zhang
- Medical Laboratory, Guangzhou Cadre Health Management Center, Guangzhou No.11 People’s Hospital, Guangzhou, China
| | - Wofeng Liu
- Medical Laboratory, Guangzhou Cadre Health Management Center, Guangzhou No.11 People’s Hospital, Guangzhou, China
| | - Zhiping Huang
- Information Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yusheng Deng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Wen Luo
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Zuofeng Liu
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Beiping Zhang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Xu L, Yue XL, Li HZ, Jian SL, Shu WS, Cui L, Xu XW. Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7087-7098. [PMID: 38651173 DOI: 10.1021/acs.est.4c02881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Collge of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Xiao-Lan Yue
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Shu-Ling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Wen-Sheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, P. R. China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
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75
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Liu D, Xie LS, Lian S, Li K, Yang Y, Wang WZ, Hu S, Liu SJ, Liu C, He Z. Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. mSphere 2024; 9:e0081623. [PMID: 38470044 PMCID: PMC11036815 DOI: 10.1128/msphere.00816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications. IMPORTANCE This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.
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Affiliation(s)
- Danping Liu
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Li-Sheng Xie
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shitao Lian
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Kexin Li
- Systems Biology and Bioinformatics (SBI), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Yun Yang
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zilong He
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
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76
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Qin Y, Tong X, Mei WJ, Cheng Y, Zou Y, Han K, Yu J, Jie Z, Zhang T, Zhu S, Jin X, Wang J, Yang H, Xu X, Zhong H, Xiao L, Ding PR. Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nat Commun 2024; 15:3396. [PMID: 38649355 PMCID: PMC11035630 DOI: 10.1038/s41467-024-47523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.
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Affiliation(s)
- Youwen Qin
- BGI Research, Shenzhen, 518083, China.
- BGI Genomics, Shenzhen, 518083, China.
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
| | - Wei-Jian Mei
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Yanshuang Cheng
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Kai Han
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Jiehai Yu
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Zhuye Jie
- BGI Research, Shenzhen, 518083, China
| | - Tao Zhang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, Shenzhen, China
- BGI Research, Wuhan, 430074, China
| | - Shida Zhu
- BGI Genomics, Shenzhen, 518083, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Huanzi Zhong
- BGI Research, Shenzhen, 518083, China
- BGI Genomics, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Pei-Rong Ding
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China.
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77
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Jiang D, Soo N, Tan CY, Dankwa S, Wang HY, Theriot BS, Ardeshir A, Siddiqui NY, Van Rompay KKA, De Paris K, Permar SR, Goswami R, Surana NK. Commensal bacteria inhibit viral infections via a tryptophan metabolite. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.589969. [PMID: 38659737 PMCID: PMC11042330 DOI: 10.1101/2024.04.21.589969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance to infection. We experimentally validated these findings by demonstrating two different Lachnospiraceae isolates, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo. Given the link between tryptophan catabolism and HIV disease severity, we found that an isogenic mutant of C. immunis that lacks the aromatic amino acid aminotransferase (ArAT) gene, which is key to metabolizing tryptophan into 3-indolelactic acid (ILA), no longer inhibits HIV infection. Intriguingly, we confirmed that a second commensal bacterium also inhibited HIV in an ArAT-dependent manner, thus establishing the generalizability of this finding. In addition, we found that purified ILA inhibited HIV infection by agonizing the aryl hydrocarbon receptor (AhR). Given that the AhR has been implicated in the control of multiple viral infections, we demonstrated that C. immunis also inhibited human cytomegalovirus (HCMV) infection in an ArAT-dependent manner. Importantly, metagenomic analysis of individuals at-risk for HIV revealed that those who ultimately acquired HIV had a lower fecal abundance of the bacterial ArAT gene compared to individuals who did not, which indicates our findings translate to humans. Taken together, our results provide mechanistic insights into how commensal bacteria decrease susceptibility to viral infections. Moreover, we have defined a microbiota-driven antiviral pathway that offers the potential for novel therapeutic strategies targeting a broad spectrum of viral pathogens.
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78
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Zhang L, Wang D, Shi P, Li J, Niu J, Chen J, Wang G, Wu L, Chen L, Yang Z, Li S, Meng J, Ruan F, He Y, Zhao H, Ren Z, Wang Y, Liu Y, Shi X, Wang Y, Liu Q, Li J, Wang P, Wang J, Zhu Y, Cheng G. A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes. Science 2024; 384:eadn9524. [PMID: 38669573 DOI: 10.1126/science.adn9524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
The commensal microbiota of the mosquito gut plays a complex role in determining the vector competence for arboviruses. In this study, we identified a bacterium from the gut of field Aedes albopictus mosquitoes named Rosenbergiella sp. YN46 (Rosenbergiella_YN46) that rendered mosquitoes refractory to infection with dengue and Zika viruses. Inoculation of 1.6 × 103 colony forming units (CFUs) of Rosenbergiella_YN46 into A. albopictus mosquitoes effectively prevents viral infection. Mechanistically, this bacterium secretes glucose dehydrogenase (RyGDH), which acidifies the gut lumen of fed mosquitoes, causing irreversible conformational changes in the flavivirus envelope protein that prevent viral entry into cells. In semifield conditions, Rosenbergiella_YN46 exhibits effective transstadial transmission in field mosquitoes, which blocks transmission of dengue virus by newly emerged adult mosquitoes. The prevalence of Rosenbergiella_YN46 is greater in mosquitoes from low-dengue areas (52.9 to ~91.7%) than in those from dengue-endemic regions (0 to ~6.7%). Rosenbergiella_YN46 may offer an effective and safe lead for flavivirus biocontrol.
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Affiliation(s)
- Liming Zhang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Daxi Wang
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Peibo Shi
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juzhen Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Jichen Niu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Jielong Chen
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Gang Wang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linjuan Wu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Chen
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenxing Yang
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan 650000, China
| | - Susheng Li
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan 650000, China
| | - Jinxin Meng
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan 650000, China
| | - Fangchao Ruan
- Kunming Medical University, Kunming, Yunnan 650000, China
| | - Yuwen He
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan 650000, China
| | - Hailong Zhao
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Zirui Ren
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Yibaina Wang
- China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - Yang Liu
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiaolu Shi
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Yunfu Wang
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Junhua Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Jinglin Wang
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan 650000, China
| | - Yibin Zhu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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79
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Dean CJ, Peña-Mosca F, Ray T, Wehri TJ, Sharpe K, Antunes, Jr. AM, Doster E, Fernandes L, Calles VF, Bauman C, Godden S, Heins B, Pinedo P, Machado VS, Caixeta LS, Noyes NR. Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives. Appl Environ Microbiol 2024; 90:e0223423. [PMID: 38497641 PMCID: PMC11022539 DOI: 10.1128/aem.02234-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/04/2024] [Indexed: 03/19/2024] Open
Abstract
The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26). IMPORTANCE Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.
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Affiliation(s)
- C. J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - F. Peña-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. J. Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - K. Sharpe
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - A. M. Antunes, Jr.
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - E. Doster
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L. Fernandes
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - V. F. Calles
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - C. Bauman
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - S. Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B. Heins
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - P. Pinedo
- Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA
| | - V. S. Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - L. S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N. R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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80
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Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG. Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs. Anim Microbiome 2024; 6:18. [PMID: 38627869 PMCID: PMC11022352 DOI: 10.1186/s42523-024-00306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. RESULTS Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. CONCLUSION Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
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Affiliation(s)
- Juan M Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Catherine M Burgess
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Edgar G Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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81
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Li C, Lü F, Peng W, He PJ, Zhang H. Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6659-6669. [PMID: 38557040 DOI: 10.1021/acs.est.4c01227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.
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Affiliation(s)
- Chao Li
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Fan Lü
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Wei Peng
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Pin-Jing He
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Hua Zhang
- Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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82
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Chen See JR, Leister J, Wright JR, Kruse PI, Khedekar MV, Besch CE, Kumamoto CA, Madden GR, Stewart DB, Lamendella R. Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities. Front Microbiol 2024; 15:1398018. [PMID: 38680911 PMCID: PMC11045941 DOI: 10.3389/fmicb.2024.1398018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.
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Affiliation(s)
| | | | - Justin R. Wright
- Juniata College, Huntingdon, PA, United States
- Wright Labs LLC, Huntingdon, PA, United States
| | | | | | | | - Carol A. Kumamoto
- Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
| | - Gregory R. Madden
- University of Virginia School of Medicine, Charlottesville, VA, United States
| | - David B. Stewart
- Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL, United States
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83
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Heppner N, Reitmeier S, Heddes M, Merino MV, Schwartz L, Dietrich A, List M, Gigl M, Meng C, van der Veen DR, Schirmer M, Kleigrewe K, Omer H, Kiessling S, Haller D. Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula. Cell Host Microbe 2024; 32:573-587.e5. [PMID: 38569545 DOI: 10.1016/j.chom.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/13/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
Microbiota assembly in the infant gut is influenced by diet. Breastfeeding and human breastmilk oligosaccharides promote the colonization of beneficial bifidobacteria. Infant formulas are supplemented with bifidobacteria or complex oligosaccharides, notably galacto-oligosaccharides (GOS), to mimic breast milk. To compare microbiota development across feeding modes, this randomized controlled intervention study (German Clinical Trial DRKS00012313) longitudinally sampled infant stool during the first year of life, revealing similar fecal bacterial communities between formula- and breast-fed infants (N = 210) but differences across age. Infant formula containing GOS sustained high levels of bifidobacteria compared with formula containing B. longum and B. breve or placebo. Metabolite and bacterial profiling revealed 24-h oscillations and circadian networks. Rhythmicity in bacterial diversity, specific taxa, and functional pathways increased with age and was strongest following breastfeeding and GOS supplementation. Circadian rhythms in dominant taxa were further maintained ex vivo in a chemostat model. Hence, microbiota rhythmicity develops early in life and is impacted by diet.
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Affiliation(s)
- Nina Heppner
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Reitmeier
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Marjolein Heddes
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Michael Vig Merino
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Leon Schwartz
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Alexander Dietrich
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Gigl
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Daan R van der Veen
- Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Melanie Schirmer
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Hélène Omer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Silke Kiessling
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany; Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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84
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Singh JP, Bottos EM, Van Hamme JD, Fraser LH. Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170996. [PMID: 38369136 DOI: 10.1016/j.scitotenv.2024.170996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.
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Affiliation(s)
- Jay Prakash Singh
- Department of Natural Resource Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Lauchlan H Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
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85
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Schalich KM, Buendia MA, Kaur H, Choksi YA, Washington MK, Codreanu GS, Sherrod SD, McLean JA, Peek, Jr. RM, Acra SA, Townsend SD, Yan F. A human milk oligosaccharide prevents intestinal inflammation in adulthood via modulating gut microbial metabolism. mBio 2024; 15:e0029824. [PMID: 38441000 PMCID: PMC11005405 DOI: 10.1128/mbio.00298-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
Observational evidence suggests that human milk oligosaccharides (HMOs) promote the growth of commensal bacteria in early life and adulthood. However, the mechanisms by which HMOs benefit health through modulation of gut microbial homeostasis remain largely unknown. 2'-fucosyllactose (2'-FL) is the most abundant oligosaccharide in human milk and contributes to the essential health benefits associated with human milk consumption. Here, we investigated how 2'-FL prevents colitis in adulthood through its effects on the gut microbial community. We found that the gut microbiota from adult mice that consumed 2'-FL exhibited an increase in abundance of several health-associated genera, including Bifidobacterium and Lactobacillus. The 2'-FL-modulated gut microbial community exerted preventive effects on colitis in adult mice. By using Bifidobacterium infantis as a 2'-FL-consuming bacterial model, exploratory metabolomics revealed novel 2'-FL-enriched secretory metabolites by Bifidobacterium infantis, including pantothenol. Importantly, pantothenate significantly protected the intestinal barrier against oxidative stress and mitigated colitis in adult mice. Furthermore, microbial metabolic pathway analysis identified 26 dysregulated metabolic pathways in fecal microbiota from patients with ulcerative colitis, which were significantly regulated by 2'-FL treatment in adult mice, indicating that 2'-FL has the potential to rectify dysregulated microbial metabolism in colitis. These findings support the contribution of the 2'-FL-shaped gut microbial community and bacterial metabolite production to the protection of intestinal integrity and prevention of intestinal inflammation in adulthood.IMPORTANCEAt present, neither basic research nor clinical studies have revealed the exact biological functions or mechanisms of action of individual oligosaccharides during development or in adulthood. Thus, it remains largely unknown whether human milk oligosaccharides could serve as effective therapeutics for gastrointestinal-related diseases. Results from the present study uncover 2'-FL-driven alterations in bacterial metabolism and identify novel B. infantis-secreted metabolites following the consumption of 2'-FL, including pantothenol. This work further demonstrates a previously unrecognized role of pantothenate in significantly protecting the intestinal barrier against oxidative stress and mitigating colitis in adult mice. Remarkably, 2'-FL-enhanced bacterial metabolic pathways are found to be dysregulated in the fecal microbiota of ulcerative colitis patients. These novel metabolic pathways underlying the bioactivities of 2'-FL may lay a foundation for applying individual oligosaccharides for prophylactic intervention for diseases associated with impaired intestinal homeostasis.
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Affiliation(s)
- Kasey M. Schalich
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matthew A. Buendia
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Harpreet Kaur
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yash A. Choksi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gabriela S. Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee, USA
| | - Stacy D. Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee, USA
| | - John A. McLean
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M. Peek, Jr.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sari A. Acra
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Steven D. Townsend
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Fang Yan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
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86
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Ovsepian A, Kardaras FS, Skoulakis A, Hatzigeorgiou AG. Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis. Front Microbiol 2024; 15:1383404. [PMID: 38659984 PMCID: PMC11041396 DOI: 10.3389/fmicb.2024.1383404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
The characterization of oral microbial communities and their functional potential has been shaped by metagenomics and metatranscriptomics studies. Here, a meta-analysis of four geographically and technically diverse oral shotgun metatranscriptomics studies of human periodontitis was performed. In total, 54 subgingival plaque samples, 27 healthy and 27 periodontitis, were analyzed. The core microbiota of the healthy and periodontitis group encompassed 40 and 80 species, respectively, with 38 species being common to both microbiota. The differential abundance analysis identified 23 genera and 26 species, that were more abundant in periodontitis. Our results not only validated previously reported genera and species associated with periodontitis with heightened statistical significance, but also elucidated additional genera and species that were overlooked in the individual studies. Functional analysis revealed a significant up-regulation in the transcription of 50 gene families (UniRef-90) associated with transmembrane transport and secretion, amino acid metabolism, surface protein and flagella synthesis, energy metabolism, and DNA supercoiling in periodontitis samples. Notably, the overwhelming majority of the identified gene families did not exhibit differential abundance when examined across individual datasets. Additionally, 4 bacterial virulence factor genes, including TonB dependent receptor from P. gingivalis, surface antigen BspA from T. forsynthia, and adhesin A (PsaA) and Type I glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Streptococcus genus, were also found to be significantly more transcribed in periodontitis group. Microbial co-occurrence analysis demonstrated that the periodontitis microbial network was less dense compared to the healthy network, but it contained more positive correlations between the species. Furthermore, there were discernible disparities in the patterns of interconnections between the species in the two networks, denoting the rewiring of the whole microbial network during the transition to the disease state. In summary, our meta-analysis has provided robust insights into the oral active microbiome and transcriptome in both health and disease.
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Affiliation(s)
- Armen Ovsepian
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Filippos S. Kardaras
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anargyros Skoulakis
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Artemis G. Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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87
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Hu X, Yu C, He Y, Zhu S, Wang S, Xu Z, You S, Jiao Y, Liu SL, Bao H. Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity. BMC Microbiol 2024; 24:119. [PMID: 38580930 PMCID: PMC10996249 DOI: 10.1186/s12866-024-03278-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.
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Affiliation(s)
- Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Songling Zhu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shuang Wang
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
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Narrowe AB, Lemons JMS, Mahalak KK, Firrman J, den Abbeele PV, Baudot A, Deyaert S, Li Y, Yu L(L, Liu L. Targeted remodeling of the human gut microbiome using Juemingzi ( Senna seed extracts). Front Cell Infect Microbiol 2024; 14:1296619. [PMID: 38638830 PMCID: PMC11024242 DOI: 10.3389/fcimb.2024.1296619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR® (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.
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Affiliation(s)
- Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | | | | | | | - Yanfang Li
- Department of Nutrition and Food Science, The University of Maryland, College, Park, MD, United States
| | - Liangli (Lucy) Yu
- Department of Nutrition and Food Science, The University of Maryland, College, Park, MD, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
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89
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Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y, Wang Z. Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites. Microbiol Spectr 2024; 12:e0143723. [PMID: 38421192 PMCID: PMC10986621 DOI: 10.1128/spectrum.01437-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
The present study aimed to characterize the gut microbiota and serum metabolome changes associated with sleep deprivation (SD) as well as to explore the potential benefits of multi-probiotic supplementation in alleviating SD-related mental health disorders. Rats were subjected to 7 days of SD, followed by 14 days of multi-probiotics or saline administration. Open-field tests were conducted at baseline, end of SD (day 7), and after 14 days of saline or multi-probiotic gavage (day 21). Metagenomic sequencing was conducted on fecal samples, and serum metabolites were measured by untargeted liquid chromatography tandem-mass spectrometry. At day 7, anxiety-like behaviors, including significant decreases in total movement distance (P = 0.0002) and staying time in the central zone (P = 0.021), were observed. In addition, increased levels of lipopolysaccharide (LPS; P = 0.028) and decreased levels of uridine (P = 0.018) and tryptophan (P = 0.01) were detected in rats after 7 days of SD. After SD, the richness of the gut bacterial community increased, and the levels of Akkermansia muciniphila, Muribaculum intestinale, and Bacteroides caecimuris decreased. The changes in the host metabolism and gut microbiota composition were strongly associated with the anxiety-like behaviors caused by SD. In addition, multi-probiotic supplementation for 14 days modestly improved the anxiety-like behaviors in SD rats but significantly reduced the serum level of LPS (P = 0.045). In conclusion, SD induces changes in the gut microbiota and serum metabolites, which may contribute to the development of chronic inflammatory responses and affect the gut-brain axis, causing anxiety-like behaviors. Probiotic supplementation significantly reduces serum LPS, which may alleviate the influence of chronic inflammation. IMPORTANCE The disturbance in the gut microbiome and serum metabolome induced by SD may be involved in anxiety-like behaviors. Probiotic supplementation decreases serum levels of LPS, but this reduction may be insufficient for alleviating SD-induced anxiety-like behaviors.
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Affiliation(s)
- Nana Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Xuefeng Gao
- Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Integrative Microecology Clinical Center, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
- Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
- The Clinical Innovation & Research Center, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Donghao Li
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Lijuan Xu
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Guanzhou Zhou
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Mengqi Xu
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Lihua Peng
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Gang Sun
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Fei Pan
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Yan Li
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Rongrong Ren
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Ruolan Huang
- Department of Neurology, Shenzhen University Clinical Research Center for Neurological Diseases, Shenzhen University General Hospital, Shenzhen, China
| | - Yunsheng Yang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
| | - Zikai Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, The First Centre of Chinese PLA General Hospital, Beijing, China
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90
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Mahmud B, Vargas RC, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK, Dantas G. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol 2024; 9:1007-1020. [PMID: 38570675 DOI: 10.1038/s41564-024-01639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.
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Affiliation(s)
- Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Liao
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lindsey R Hall
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Akhil Kesaraju
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Erik Kronholm
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Kyle Koshalek
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Jeffrey J VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
- Computational Informatics in Biology and Medicine program, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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91
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Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW. A host-microbiota interactome reveals extensive transkingdom connectivity. Nature 2024; 628:171-179. [PMID: 38509360 DOI: 10.1038/s41586-024-07162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.
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Affiliation(s)
- Nicole D Sonnert
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew R Ghazi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tyler A Rice
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mytien T Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anjelica L Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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92
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Torma F, Kerepesi C, Jókai M, Babszki G, Koltai E, Ligeti B, Kalcsevszki R, McGreevy KM, Horvath S, Radák Z. Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness. Aging Cell 2024; 23:e14101. [PMID: 38414315 PMCID: PMC11019127 DOI: 10.1111/acel.14101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.
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Affiliation(s)
- Ferenc Torma
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
- Sports Neuroscience Division, Advanced Research Initiative for Human High Performance (ARIHHP), Faculty of Health and Sport SciencesUniversity of TsukubaTsukubaIbarakiJapan
- Laboratory of Exercise Biochemistry and Neuroendocrinology, Faculty of Health and Sport SciencesUniversity of TsukubaTsukubaIbarakiJapan
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI)Hungarian Research Network (HUN‐REN)BudapestHungary
| | - Mátyás Jókai
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Gergely Babszki
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Erika Koltai
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Balázs Ligeti
- Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary
| | - Regina Kalcsevszki
- Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary
| | - Kristen M. McGreevy
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Altos Labs, Cambridge Institute of ScienceCambridgeUK
| | - Zsolt Radák
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
- Waseda UniversityTokorozawaJapan
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93
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D’Amico F, Rinaldi M, Pascale R, Fabbrini M, Morelli MC, Siniscalchi A, Laici C, Coladonato S, Ravaioli M, Cescon M, Ambretti S, Viale P, Brigidi P, Turroni S, Giannella M. Gut microbiome dynamics and Enterobacterales infection in liver transplant recipients: A prospective observational study. JHEP Rep 2024; 6:101039. [PMID: 38524669 PMCID: PMC10960129 DOI: 10.1016/j.jhepr.2024.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 03/26/2024] Open
Abstract
Background & Aims The aim of this study was to investigate gut microbiome (GM) dynamics in relation to carbapenem-resistant Enterobacterales (CRE) colonization, CRE infection, and non-CRE infection development within 2 months after liver transplant (LT). Methods A single-center, prospective study was performed in patients undergoing LT from November 2018 to January 2020. The GM was profiled through 16S rRNA amplicon sequencing of a rectal swab taken on the day of transplantation, and fecal samples were collected weekly until 1 month after LT. A subset of samples was subjected to shotgun metagenomics, including resistome dynamics. The primary endpoint was to explore changes in the GM in the following groups: (1) CRE carriers developing CRE infection (CRE_I); (2) CRE carriers not developing infection (CRE_UI); (3) non-CRE carriers developing microbial infection (INF); and (4) non-CRE carriers not developing infection (NEG). Results Overall, 97 patients were enrolled, and 91 provided fecal samples. Of these, five, nine, 22, and 55 patients were classified as CRE_I, CRE_UI, INF, and NEG, respectively. CRE_I patients showed an immediate and sustained post-LT decrease in alpha diversity, with depletion of the GM structure and gradual over-representation of Klebsiella and Enterococcus. The proportions of Klebsiella were significantly higher in CRE_I patients than in NEG patients even before LT, serving as an early marker of subsequent CRE infection. CRE_UI patients had a more stable and diverse GM, whose compositional dynamics tended to overlap with those of NEG patients. Conclusions GM profiling before LT could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis. Impact and implications Little is known about the temporal dynamics of gut microbiome (GM) in liver transplant recipients associated with carbapenem-resistant Enterobacterales (CRE) colonization and infection. The GM structure and functionality of patients colonized with CRE and developing infection appeared to be distinct compared with CRE carriers without infection or patients with other microbial infection or no infection and CRE colonization. Higher proportions of antimicrobial-resistant pathogens and poor representation of bacteria and metabolic pathways capable of promoting overall host health were observed in CRE carriers who developed infection, even before liver transplant. Therefore, pretransplant GM profiling could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.
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Affiliation(s)
- Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Matteo Rinaldi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Renato Pascale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maria Cristina Morelli
- Internal Medicine Unit for the Treatment of Severe Organ Failure, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Antonio Siniscalchi
- Division of Anesthesiology, Department of Anesthesia and Intensive Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristiana Laici
- Division of Anesthesiology, Department of Anesthesia and Intensive Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Coladonato
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Matteo Ravaioli
- General Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Matteo Cescon
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- General Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Simone Ambretti
- Microbiology Operative Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Pierluigi Viale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maddalena Giannella
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
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94
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Xu J, Xu X, Jiang Y, Fu Y, Shen C. Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning. ENVIRONMENT INTERNATIONAL 2024; 186:108574. [PMID: 38507933 DOI: 10.1016/j.envint.2024.108574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.
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Affiliation(s)
- Jiaqi Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Xin Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yunhan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China.
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95
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Favale N, Farina R, Carrieri A, Simonelli A, Severi M, Sabbioni S, Trombelli L, Scapoli C. Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis. Mol Oral Microbiol 2024; 39:62-79. [PMID: 37257865 DOI: 10.1111/omi.12418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.
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Affiliation(s)
- Nicoletta Favale
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Roberto Farina
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Alberto Carrieri
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Anna Simonelli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Mattia Severi
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnology - Section of Pathology and Applied Microbiology, University of Ferrara, Ferrara, Italy
| | - Leonardo Trombelli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
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96
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Li J, Barnes S, Lefkowitz E, Yarar-Fisher C. Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury. Physiol Genomics 2024; 56:317-326. [PMID: 38344780 DOI: 10.1152/physiolgenomics.00107.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
Accumulating evidence has revealed that alterations in the gut microbiome following spinal cord injury (SCI) exhibit similarities to those observed in metabolic syndrome. Considering the causal role of gut dysbiosis in metabolic syndrome development, SCI-induced gut dysbiosis may be a previously unidentified contributor to the increased risk of cardiometabolic diseases, which has garnered attention. With a cross-sectional design, we evaluated the correlation between gut microbiome composition and functional potential with indicators of metabolic health among 46 individuals with chronic SCI. Gut microbiome communities were profiled using next-generation sequencing techniques. Indices of metabolic health, including fasting lipid profile, glucose tolerance, insulin resistance, and inflammatory markers, were assessed through fasting blood tests and an oral glucose tolerance test. We used multivariate statistical techniques (i.e., regularized canonical correlation analysis) to identify correlations between gut bacterial communities, functional pathways, and metabolic health indicators. Our findings spotlight bacterial species and functional pathways associated with complex carbohydrate degradation and maintenance of gut barrier integrity as potential contributors to improved metabolic health. Conversely, those correlated with detrimental microbial metabolites and gut inflammatory pathways demonstrated associations with poorer metabolic health outcomes. This cross-sectional investigation represents a pivotal initial step toward comprehending the intricate interplay between the gut microbiome and metabolic health in SCI. Furthermore, our results identified potential targets for future research endeavors to elucidate the role of the gut microbiome in metabolic syndrome in this population.NEW & NOTEWORTHY Spinal cord injury (SCI) is accompanied by gut dysbiosis and the impact of this on the development of metabolic syndrome in this population remains to be investigated. Our study used next-generation sequencing and multivariate statistical analyses to explore the correlations between gut microbiome composition, function, and metabolic health indices in individuals with chronic SCI. Our results point to potential gut microbial species and functional pathways that may be implicated in the development of metabolic syndrome.
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Affiliation(s)
- Jia Li
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Columbus, Ohio, United States
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Elliot Lefkowitz
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Ceren Yarar-Fisher
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Columbus, Ohio, United States
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97
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Zimmermann P, Pittet LF, Jakob W, Messina NL, Falquet L, Curtis N. The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial. Pediatr Infect Dis J 2024; 43:378-389. [PMID: 38145402 DOI: 10.1097/inf.0000000000004223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
INTRODUCTION The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome. OBJECTIVE To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age. METHODS Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses. RESULTS The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis . Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis. CONCLUSION BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.
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Affiliation(s)
- Petra Zimmermann
- From the Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laure F Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Nicole L Messina
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
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98
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Erhardt R, Steels E, Harnett JE, Taing MW, Steadman KJ. Effects of a prebiotic formulation on the composition of the faecal microbiota of people with functional constipation. Eur J Nutr 2024; 63:777-784. [PMID: 38165420 DOI: 10.1007/s00394-023-03292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Prebiotics are defined as substances which selectively promote beneficial gut microbes leading to a health benefit for the host. Limited trials have been carried out investigating their effect on the microbiota composition of individuals afflicted by functional constipation with equivocal outcomes. In a 21-day randomised, controlled clinical trial involving 61 adults with functional constipation, a prebiotic formulation with partially hydrolysed guar gum and acacia gum as its main ingredients, significantly increased complete spontaneous bowel motions in the treatment group. This follow-up exploratory analysis investigated whether the prebiotic was associated with changes to the composition, richness, and diversity of the faecal microbiota. METHODS Participants provided a faecal specimen at baseline and on day 21 of the intervention period. Whole genome metagenomic shotgun sequencing comprehensively assessed taxonomic and functional composition of the microbiota. RESULTS Linear mixed effects regression models adjusted for potential confounders showed a significant reduction in species richness of 28.15 species (95% CI - 49.86, - 6.43) and Shannon diversity of 0.29 units (95% CI - 0.56, - 0.02) over the trial period in the prebiotic group. These changes were not observed in the control group, and functional composition was unchanged in both groups. CONCLUSION In adults with functional constipation, the intake of a prebiotic formulation was associated with a decline of species richness and Shannon diversity. Further research regarding the associations between prebiotics and the composition and function of the gut microbiota is warranted.
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Affiliation(s)
- Rene Erhardt
- School of Pharmacy, The University of Queensland, Brisbane, Australia.
- School of Pharmacy, The University of Queensland, 20 Cornwall Street , Woolloongabba, QLD, 4102, Australia.
| | - Elizabeth Steels
- School of Pharmacy, The University of Queensland, Brisbane, Australia
- Evidence Sciences Pty. Ltd., New Farm, Australia
| | | | - Meng-Wong Taing
- School of Pharmacy, The University of Queensland, Brisbane, Australia
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99
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Macey MC. Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13246. [PMID: 38575138 PMCID: PMC10994693 DOI: 10.1111/1758-2229.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
Metagenome assembled genomes (MAGs), generated from sequenced 13C-labelled DNA from 13C-methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger number of higher-quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross-feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol-enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.
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Affiliation(s)
- Michael C. Macey
- AstrobiologyOU, Earth, Environment and Ecosystem SciencesThe Open UniversityMilton KeynesUK
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100
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Abstract
The microbiome represents a hidden world of tiny organisms populating not only our surroundings but also our own bodies. By enabling comprehensive profiling of these invisible creatures, modern genomic sequencing tools have given us an unprecedented ability to characterize these populations and uncover their outsize impact on our environment and health. Statistical analysis of microbiome data is critical to infer patterns from the observed abundances. The application and development of analytical methods in this area require careful consideration of the unique aspects of microbiome profiles. We begin this review with a brief overview of microbiome data collection and processing and describe the resulting data structure. We then provide an overview of statistical methods for key tasks in microbiome data analysis, including data visualization, comparison of microbial abundance across groups, regression modeling, and network inference. We conclude with a discussion and highlight interesting future directions.
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Affiliation(s)
- Christine B Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Satabdi Saha
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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