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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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2
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Zia T, Khan K, Aghayeva S, Uddin R. Breaking resistance: in silico subtractive and comparative genomics approaches for drug targeting in Bacteroides fragilis. Biotechnol Lett 2024:10.1007/s10529-024-03537-5. [PMID: 39424748 DOI: 10.1007/s10529-024-03537-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 09/16/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024]
Abstract
The purpose of this study was to identify potential novel drug targets for Bacteroides fragilis infections using bioinformatics techniques, such as subtractive and comparative genomics. Bacteroides fragilis is a frequently isolated anaerobic pathogen, particularly in the human digestive tract, where its pathogenesis and persistence are influenced by various virulence factors. By understanding these factors, the study aims to explore alternative therapeutic strategies and provide insights for the development of treatments against B. fragilis infections, particularly as alternatives to antibiotic therapy. A comparative subtractive genomic analysis was performed against the B. fragilis (strain CL07T12C05) to identify unique drug targets. The analysis includes the identification of non-paralogous, non-homologous, essential, and drug target like proteins. Moreover, a comprehensive structural analysis of the protein was conducted utilizing structure modeling and validation techniques, along with network topology analysis. Furthermore, a library comprising approximately 9000 FDA-approved compounds accessible in the DrugBank database was employed to conduct virtual screenings for compounds effective against the designated drug target. The top shortlisted compounds were further studied by employing MD simulations using GROMACS. This approach was chosen due to the established safety, efficacy, pharmacokinetics, and toxicity profiles of these compounds. As a result, B. fragilis (strain CL07T12C05) was found to possess 4595 proteins. Among these, 3518 were identified as non-homologous, 1508 deemed essential for bacterial viability, 348 exhibited drug-like properties, 203 were implicated in virulence, and 135 displayed antibiotic resistance. Following an extensive literature review, the protein Sialic acid O-acetyltransferase was chosen through a hierarchical shortlisting process as a potential therapeutic target. The ongoing research facilitated the repurposing of drug compounds: DB12411, DB02112, DB03591, and DB00192, as cost-effective medications against B. fragilis related infections. MD simulations analysis showed that DB12411 may be a potential drug candidate against Sialic acid O-acetyltransferase from B. fragilis. Through subtractive and comparative genomic analysis, Sialic acid O-acetyltransferase was identified as a promising drug target against Bacteroides fragilis. The findings indicate that compounds targeting this protein could potentially be effective in treating B. fragilis infections. However, further experimental validation is required to conclusively confirm their efficacy.
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Affiliation(s)
- Tehreem Zia
- Baqai Institute of Information Technology, Baqai Medical University, Karachi, Pakistan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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3
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Karwowska Z, Szczerbiak P, Kosciolek T. Microbiome time series data reveal predictable patterns of change. Microbiol Spectr 2024; 12:e0410923. [PMID: 39162505 PMCID: PMC11448390 DOI: 10.1128/spectrum.04109-23] [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: 12/05/2023] [Accepted: 07/05/2024] [Indexed: 08/21/2024] Open
Abstract
The human gut microbiome is crucial in health and disease. Longitudinal studies are becoming increasingly important compared to traditional cross-sectional approaches, as precision medicine and individualized interventions are coming to the forefront. Investigating the temporal dynamics of the microbiome is essential for comprehending its function and impact on health. This knowledge has implications for targeted therapeutic strategies, such as personalized diets or probiotic therapy. In this study, we focused on developing and implementing methods specifically designed for analyzing gut microbiome time series. Our statistical framework provides researchers with tools to examine the temporal behavior of the gut microbiome. Key features of our framework include statistical tests for time series properties, predictive modeling, classification of bacterial species based on stability and noise, and clustering analyses to identify groups of bacteria with similar temporal patterns. We analyzed dense amplicon sequencing time series from four generally healthy subjects. Using our developed statistical framework, we analyzed both the overall community dynamics and the behavior of individual bacterial species. We showed six longitudinal regimes within the gut microbiome and discussed their features. Additionally, we explored whether specific bacterial clusters undergo similar fluctuations, suggesting potential functional relationships and interactions within the microbiome. Our development of specialized methods for analyzing human gut microbiome time series significantly enhances the understanding of its dynamic nature and implications for human health. The guidelines and tools provided by our framework support scientists in studying the complex dynamics of the gut microbiome, fostering further research and advancements in microbiome analysis. The gut microbiome is integral to human health, influencing various diseases. Longitudinal studies offer deeper insights into its temporal dynamics compared to cross-sectional approaches. In this study, we developed a statistical framework for analyzing the time series of the human gut microbiome. This framework provides robust tools for examining microbial community dynamics over time. It includes statistical tests for time series properties, predictive modeling, classification of bacterial species based on stability and noise, and clustering analyses. Our approach significantly enhances the methodologies available to researchers, promoting further exploration and innovation in microbiome analysis. IMPORTANCE This project developed innovative methods to analyze gut microbiome time series data, offering fresh insights into its dynamic nature. Unlike many studies that focus on static snapshots, we found that the healthy gut microbiome is predictably stable over time, with only a small subset of bacteria showing significant changes. By identifying groups of bacteria with diverse temporal behaviors and clusters that change together, we pave the way for more effective probiotic therapies and dietary interventions, addressing the overlooked dynamic aspects of gut microbiome changes.
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Affiliation(s)
- Zuzanna Karwowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Paweł Szczerbiak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Tomasz Kosciolek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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Shukla V, Singh S, Verma S, Verma S, Rizvi AA, Abbas M. Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates. Clin Nutr ESPEN 2024; 63:813-820. [PMID: 39178987 DOI: 10.1016/j.clnesp.2024.08.005] [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: 09/22/2023] [Revised: 07/15/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024]
Abstract
The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.
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Affiliation(s)
- Vani Shukla
- Department of Food and Nutrition, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Shikha Singh
- Department of Food and Nutrition, Era University, Lucknow 226003, Uttar Pradesh, India.
| | - Shrikant Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Sushma Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Aliya Abbas Rizvi
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Mohammad Abbas
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
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5
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Cheng M, Xu Y, Cui X, Wei X, Chang Y, Xu J, Lei C, Xue L, Zheng Y, Wang Z, Huang L, Zheng M, Luo H, Leng Y, Jiang C. Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness. Nat Commun 2024; 15:8361. [PMID: 39333527 PMCID: PMC11436904 DOI: 10.1038/s41467-024-52713-8] [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: 02/14/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.
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Affiliation(s)
- Minghui Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Cui
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Yundi Chang
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Jun Xu
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Lei Xue
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Yifan Zheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Zhang Wang
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Lingtong Huang
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Yuxin Leng
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China.
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6
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Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Signal Transduct Target Ther 2024; 9:237. [PMID: 39307902 PMCID: PMC11418828 DOI: 10.1038/s41392-024-01946-6] [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: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/26/2024] Open
Abstract
The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.
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Affiliation(s)
- Ziqi Ma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Ashraf Yusuf Rangrez
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
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7
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Demehri S, Vardar S, Godoy C, Lopez JV, Samuel P, Kawai T, Ozga AT. Supragingival Plaque Microbiomes in a Diverse South Florida Population. Microorganisms 2024; 12:1921. [PMID: 39338595 PMCID: PMC11434252 DOI: 10.3390/microorganisms12091921] [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: 07/26/2024] [Revised: 08/31/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies.
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Affiliation(s)
- Sharlene Demehri
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA; (S.D.); (S.V.)
| | - Saynur Vardar
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA; (S.D.); (S.V.)
| | - Cristina Godoy
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Department of Public Health, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jose V. Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
| | - Paisley Samuel
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
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Torres MDT, Brooks EF, Cesaro A, Sberro H, Gill MO, Nicolaou C, Bhatt AS, de la Fuente-Nunez C. Mining human microbiomes reveals an untapped source of peptide antibiotics. Cell 2024; 187:5453-5467.e15. [PMID: 39163860 DOI: 10.1016/j.cell.2024.07.027] [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: 08/08/2023] [Revised: 05/09/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024]
Abstract
Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin F Brooks
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA
| | - Angela Cesaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hila Sberro
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA
| | - Matthew O Gill
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Cosmos Nicolaou
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA
| | - Ami S Bhatt
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Garcia-Santamarina S, Kuhn M, Devendran S, Maier L, Driessen M, Mateus A, Mastrorilli E, Brochado AR, Savitski MM, Patil KR, Zimmermann M, Bork P, Typas A. Emergence of community behaviors in the gut microbiota upon drug treatment. Cell 2024:S0092-8674(24)00966-8. [PMID: 39321801 DOI: 10.1016/j.cell.2024.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/26/2024] [Accepted: 08/20/2024] [Indexed: 09/27/2024]
Abstract
Pharmaceuticals can directly inhibit the growth of gut bacteria, but the degree to which such interactions manifest in complex community settings is an open question. Here, we compared the effects of 30 drugs on a 32-species synthetic community with their effects on each community member in isolation. While most individual drug-species interactions remained the same in the community context, communal behaviors emerged in 26% of all tested cases. Cross-protection during which drug-sensitive species were protected in community was 6 times more frequent than cross-sensitization, the converse phenomenon. Cross-protection decreased and cross-sensitization increased at higher drug concentrations, suggesting that the resilience of microbial communities can collapse when perturbations get stronger. By metabolically profiling drug-treated communities, we showed that both drug biotransformation and bioaccumulation contribute mechanistically to communal protection. As a proof of principle, we molecularly dissected a prominent case: species expressing specific nitroreductases degraded niclosamide, thereby protecting both themselves and sensitive community members.
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Affiliation(s)
- Sarela Garcia-Santamarina
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany; European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany
| | - Saravanan Devendran
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany
| | - Lisa Maier
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany
| | - Marja Driessen
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany
| | - Eleonora Mastrorilli
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany
| | - Kiran R Patil
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany.
| | - Michael Zimmermann
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany.
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology, Heidelberg, Germany; European Molecular Biology Laboratory, Structural and Computational Biology, Heidelberg, Germany.
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10
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Pilling OA, Sundararaman SA, Brisson D, Beiting DP. Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment. PLoS Pathog 2024; 20:e1012418. [PMID: 39264872 PMCID: PMC11392400 DOI: 10.1371/journal.ppat.1012418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.
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Affiliation(s)
- Olivia A Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sesh A Sundararaman
- Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Pennsylvania, United States of America
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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11
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Hu JC, Sethi S. New methods to detect bacterial or viral infections in patients with chronic obstructive pulmonary disease. Expert Rev Respir Med 2024; 18:693-707. [PMID: 39175157 DOI: 10.1080/17476348.2024.2396413] [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] [Revised: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 08/24/2024]
Abstract
INTRODUCTION Patients with chronic obstructive pulmonary disease (COPD) are frequently colonized and infected by respiratory pathogens. Identifying these infectious etiologies is critical for understanding the microbial dynamics of COPD and for the appropriate use of antimicrobials during exacerbations. AREAS COVERED Traditional methods, such as bacterial and viral cultures, have been standard in diagnosing respiratory infections. However, these methods have significant limitations, including lack of sensitivity and prolonged turnaround time. Modern molecular approaches offer rapid, sensitive, and specific detection, though they also come with their own challenges. This review explores and evaluates the clinical utility of the latest advancements in detecting bacterial and viral respiratory infections in COPD, encompassing molecular techniques, biomarkers, and emerging technologies. EXPERT OPINION In the evolving landscape of COPD management, integrating molecular diagnostics and emerging technologies holds great promise. The enhanced sensitivity of molecular techniques has significantly advanced our understanding of the role of microbes in COPD. However, many of these technologies have primarily been developed for pneumonia diagnosis or research applications, and their clinical utility in managing COPD requires further evaluation.
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Affiliation(s)
- John C Hu
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Sanjay Sethi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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12
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Lei S, Khan I, Zhang X, Chen T, Xie X, Zheng X, Jianye Z, Li Z. Assessing oral and toothbrush microbial profiles among high-altitude individuals with and without periodontal disease: a case-control study. BMC Oral Health 2024; 24:993. [PMID: 39182077 PMCID: PMC11344349 DOI: 10.1186/s12903-024-04603-0] [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: 12/08/2023] [Accepted: 07/15/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Periodontitis is the sixth-most common disease worldwide. The oral microbiome composition and its association with Periodontal disease (PD) have been largely explored; however, limited studies have explored the microbial profiles of both oral and toothbrushes in patients with PD. Thus, this study aimed to ascertain the oral and toothbrushes microbial composition in high-altitude populations, hypothesizing that their correlation with periodontal health would differ from those at lower altitudes, potentially indicating links between environmental factors, microbial colonization patterns, and periodontal health in distinct geographic contexts. METHODS In the present study, we enrolled 35 individuals including 21 healthy and 14 diagnosed with PD from the Lhasa region of Tibet, China. Saliva and toothbrush samples were collected from each participant to assess the association between toothbrush usage and oral microbiome with PD using 16 S rRNA gene-specific V3-V4 regions sequencing. To assess the oral and toothbrush microbiome composition and diversity and its possible link to PD. RESULTS Significantly higher Alpha diversity (Shannon index) was observed between the PD group and PD toothbrushes (p = 0.00021) and between the PD group and Healthy toothbrushes (p = 0.00041). The predominant species were Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Fusobacteria, with genera Pseudomonas, Veillonella, Neisseria, Acinetobacter, and Haemophilus. In addition, PICRUST2 analysis unveiled 44 significant pathways differentiating the disease and healthy groups, along with 29 pathways showing significant differences between their respective toothbrush microbial profiles. The distinct oral and toothbrush microbial composition among high-altitude populations suggests potential adaptations to the challenges of high-altitude environments. CONCLUSION This study emphasizes the importance of tailored dental care strategies, accounting for altitude and racial factors, to effectively manage periodontal health in these communities. Further research is warranted to investigate the specific microbial mechanisms and develop targeted interventions for optimizing oral health in populations across varying altitudes.
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Affiliation(s)
- Shengnan Lei
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China.
- Northwest MINZU University, Lanzhou, Gansu, 730030, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Lab of Oral Diseases of Gansu Province, Northwest Minzu University, Lanzhou, 730030, China.
| | - Ikram Khan
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xu Zhang
- General Hospital of Xizang Military Region, Lhasa, 850007, China
| | - Tuo Chen
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xin Zheng
- Northwest MINZU University, Lanzhou, Gansu, 730030, China
- Key Lab of Oral Diseases of Gansu Province, Northwest Minzu University, Lanzhou, 730030, China
| | - Zhou Jianye
- Northwest MINZU University, Lanzhou, Gansu, 730030, China
- Key Lab of Oral Diseases of Gansu Province, Northwest Minzu University, Lanzhou, 730030, China
| | - Zhiqiang Li
- Northwest MINZU University, Lanzhou, Gansu, 730030, China.
- Key Lab of Oral Diseases of Gansu Province, Northwest Minzu University, Lanzhou, 730030, China.
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Tan ZC, Meyer AS. The structure is the message: Preserving experimental context through tensor decomposition. Cell Syst 2024; 15:679-693. [PMID: 39173584 PMCID: PMC11366223 DOI: 10.1016/j.cels.2024.07.004] [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: 03/03/2024] [Revised: 06/25/2024] [Accepted: 07/22/2024] [Indexed: 08/24/2024]
Abstract
Recent biological studies have been revolutionized in scale and granularity by multiplex and high-throughput assays. Profiling cell responses across several experimental parameters, such as perturbations, time, and genetic contexts, leads to richer and more generalizable findings. However, these multidimensional datasets necessitate a reevaluation of the conventional methods for their representation and analysis. Traditionally, experimental parameters are merged to flatten the data into a two-dimensional matrix, sacrificing crucial experiment context reflected by the structure. As Marshall McLuhan famously stated, "the medium is the message." In this work, we propose that the experiment structure is the medium in which subsequent analysis is performed, and the optimal choice of data representation must reflect the experiment structure. We review how tensor-structured analyses and decompositions can preserve this information. We contend that tensor methods are poised to become integral to the biomedical data sciences toolkit.
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Affiliation(s)
- Zhixin Cyrillus Tan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
| | - Aaron S Meyer
- Bioinformatics Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Department of Bioengineering, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
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14
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Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus). mSystems 2024; 9:e0010824. [PMID: 38975760 PMCID: PMC11334461 DOI: 10.1128/msystems.00108-24] [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: 01/26/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change. IMPORTANCE Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
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Affiliation(s)
- Cassandra Tang-Wing
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Katherine Makowski
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Daira Melendez
- Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Keith Jenné
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
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15
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Salazar-Jaramillo L, de la Cuesta-Zuluaga J, Chica LA, Cadavid M, Ley RE, Reyes A, Escobar JS. Gut microbiome diversity within Clostridia is negatively associated with human obesity. mSystems 2024; 9:e0062724. [PMID: 39012154 PMCID: PMC11334427 DOI: 10.1128/msystems.00627-24] [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: 05/03/2024] [Accepted: 06/06/2024] [Indexed: 07/17/2024] Open
Abstract
Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production. IMPORTANCE The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.
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Affiliation(s)
- Laura Salazar-Jaramillo
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | | | - Luis A. Chica
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
| | - María Cadavid
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alejandro Reyes
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
- Department of Pathology and Immunology, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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16
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Liu H, Yin J, Huang X, Zang C, Zhang Y, Cao J, Gong M. Mosquito Gut Microbiota: A Review. Pathogens 2024; 13:691. [PMID: 39204291 PMCID: PMC11357333 DOI: 10.3390/pathogens13080691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 09/03/2024] Open
Abstract
Mosquitoes are vectors of many important human diseases. The prolonged and widespread use of insecticides has led to the development of mosquito resistance to these insecticides. The gut microbiota is considered the master of host development and physiology; it influences mosquito biology, disease pathogen transmission, and resistance to insecticides. Understanding the role and mechanisms of mosquito gut microbiota in mosquito insecticide resistance is useful for developing new strategies for tackling mosquito insecticide resistance. We searched online databases, including PubMed, MEDLINE, SciELO, Web of Science, and the Chinese Science Citation Database. We searched all terms, including microbiota and mosquitoes, or any specific genera or species of mosquitoes. We reviewed the relationships between microbiota and mosquito growth, development, survival, reproduction, and disease pathogen transmission, as well as the interactions between microbiota and mosquito insecticide resistance. Overall, 429 studies were included in this review after filtering 8139 search results. Mosquito gut microbiota show a complex community structure with rich species diversity, dynamic changes in the species composition over time (season) and across space (environmental setting), and variation among mosquito species and mosquito developmental stages (larval vs. adult). The community composition of the microbiota plays profound roles in mosquito development, survival, and reproduction. There was a reciprocal interaction between the mosquito midgut microbiota and virus infection in mosquitoes. Wolbachia, Asaia, and Serratia are the three most studied bacteria that influence disease pathogen transmission. The insecticide resistance or exposure led to the enrichment or reduction in certain microorganisms in the resistant mosquitoes while enhancing the abundance of other microorganisms in insect-susceptible mosquitoes, and they involved many different species/genera/families of microorganisms. Conversely, microbiota can promote insecticide resistance in their hosts by isolating and degrading insecticidal compounds or altering the expression of host genes and metabolic detoxification enzymes. Currently, knowledge is scarce about the community structure of mosquito gut microbiota and its functionality in relation to mosquito pathogen transmission and insecticide resistance. The new multi-omics techniques should be adopted to find the links among environment, mosquito, and host and bring mosquito microbiota studies to the next level.
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Affiliation(s)
- Hongmei Liu
- Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China;
- Digestive Disease Hospital of Shandong First Medical University, Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining 272000, China; (X.H.); (C.Z.); (Y.Z.)
- World Health Organization Collaborating Centre for Tropical Diseases, Shanghai 200025, China
| | - Jianhai Yin
- Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China;
- World Health Organization Collaborating Centre for Tropical Diseases, Shanghai 200025, China
| | - Xiaodan Huang
- Digestive Disease Hospital of Shandong First Medical University, Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining 272000, China; (X.H.); (C.Z.); (Y.Z.)
| | - Chuanhui Zang
- Digestive Disease Hospital of Shandong First Medical University, Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining 272000, China; (X.H.); (C.Z.); (Y.Z.)
| | - Ye Zhang
- Digestive Disease Hospital of Shandong First Medical University, Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining 272000, China; (X.H.); (C.Z.); (Y.Z.)
| | - Jianping Cao
- Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China;
- World Health Organization Collaborating Centre for Tropical Diseases, Shanghai 200025, China
| | - Maoqing Gong
- Digestive Disease Hospital of Shandong First Medical University, Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining 272000, China; (X.H.); (C.Z.); (Y.Z.)
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17
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Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nat Commun 2024; 15:6618. [PMID: 39103350 DOI: 10.1038/s41467-024-50124-3] [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: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron. From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D-glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.
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Affiliation(s)
- Yolanda Y Huang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Hung
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Omree Gal-Oz
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Christopher W Smith
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Davian Ho
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Héloïse Carion
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA.
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18
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Nayak RR, Orellana DA. The impact of the human gut microbiome on the treatment of autoimmune disease. Immunol Rev 2024; 325:107-130. [PMID: 38864582 PMCID: PMC11338731 DOI: 10.1111/imr.13358] [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] [Indexed: 06/13/2024]
Abstract
Autoimmune (or rheumatic) diseases are increasing in prevalence but selecting the best therapy for each patient proceeds in trial-and-error fashion. This strategy can lead to ineffective therapy resulting in irreversible damage and suffering; thus, there is a need to bring the promise of precision medicine to patients with autoimmune disease. While host factors partially determine the therapeutic response to immunosuppressive drugs, these are not routinely used to tailor therapy. Thus, non-host factors likely contribute. Here, we consider the impact of the human gut microbiome in the treatment of autoimmunity. We propose that the gut microbiome can be manipulated to improve therapy and to derive greater benefit from existing therapies. We focus on the mechanisms by which the human gut microbiome impacts treatment response, provide a framework to interrogate these mechanisms, review a case study of a widely-used anti-rheumatic drug, and discuss challenges with studying multiple complex systems: the microbiome, the human immune system, and autoimmune disease. We consider open questions that remain in the field and speculate on the future of drug-microbiome-autoimmune disease interactions. Finally, we present a blue-sky vision for how the microbiome can be used to bring the promise of precision medicine to patients with rheumatic disease.
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Affiliation(s)
- Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, California, USA
- Veterans Affairs Medical Center, San Francisco, California, USA
| | - Diego A Orellana
- Rheumatology Division, Department of Medicine, University of California, San Francisco, California, USA
- Veterans Affairs Medical Center, San Francisco, California, USA
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19
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You M, Chen N, Yang Y, Cheng L, He H, Cai Y, Liu Y, Liu H, Hong G. The gut microbiota-brain axis in neurological disorders. MedComm (Beijing) 2024; 5:e656. [PMID: 39036341 PMCID: PMC11260174 DOI: 10.1002/mco2.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024] Open
Abstract
Previous studies have shown a bidirectional communication between human gut microbiota and the brain, known as the microbiota-gut-brain axis (MGBA). The MGBA influences the host's nervous system development, emotional regulation, and cognitive function through neurotransmitters, immune modulation, and metabolic pathways. Factors like diet, lifestyle, genetics, and environment shape the gut microbiota composition together. Most research have explored how gut microbiota regulates host physiology and its potential in preventing and treating neurological disorders. However, the individual heterogeneity of gut microbiota, strains playing a dominant role in neurological diseases, and the interactions of these microbial metabolites with the central/peripheral nervous systems still need exploration. This review summarizes the potential role of gut microbiota in driving neurodevelopmental disorders (autism spectrum disorder and attention deficit/hyperactivity disorder), neurodegenerative diseases (Alzheimer's and Parkinson's disease), and mood disorders (anxiety and depression) in recent years and discusses the current clinical and preclinical gut microbe-based interventions, including dietary intervention, probiotics, prebiotics, and fecal microbiota transplantation. It also puts forward the current insufficient research on gut microbiota in neurological disorders and provides a framework for further research on neurological disorders.
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Affiliation(s)
- Mingming You
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Nan Chen
- Master of Public HealthSchool of Public HealthXiamen UniversityXiamenChina
| | - Yuanyuan Yang
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Lingjun Cheng
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Hongzhang He
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Yanhua Cai
- Master of Public HealthSchool of Public HealthXiamen UniversityXiamenChina
| | - Yating Liu
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Haiyue Liu
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
| | - Guolin Hong
- Xiamen Key Laboratory of Genetic TestingThe Department of Laboratory MedicineThe First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina
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20
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O'Malley MA. The concept of balance in microbiome research. Bioessays 2024; 46:e2400050. [PMID: 38924108 DOI: 10.1002/bies.202400050] [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: 03/02/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Microbiome research is changing how ecosystems, including animal bodies, are understood. In the case of humans, microbiome knowledge is transforming medical approaches and applications. However, the field is still young, and many conceptual and explanatory issues need resolving. These include how microbiome causality is understood, and how to conceptualize the role microbiomes have in the health status of their hosts and other ecosystems. A key concept that crops up in the medical microbiome literature is "balance." A balanced microbiome is thought to produce health and an imbalanced one disease. Based on a quantitative and qualitative analysis of how balance is used in the microbiome literature, this "think again" essay critically analyses each of the several subconceptions of balance. As well as identifying problems with these uses, the essay suggests some starting points for filling this conceptual gap in microbiome research.
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Affiliation(s)
- Maureen A O'Malley
- School of History and Philosophy of Science, University of Sydney, Sydney, Australia
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21
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Lan J, Zhang Y, Jin C, Chen H, Su Z, Wu J, Ma N, Zhang X, Lu Y, Chen Y, Zeng X, Zhang H, Zheng G, Sun Y, Wang C, Hu Y, Wang Y, Liu Y, Zeng Z, Shi L, He J, Cao A, Wang Y, Pan X, Jin G, Wang Y, Jiang X, Shen H, Tang Q, Xie X, Xiao Y, Zhong X, Zhang X, Zeng L, Ye L, Xie J, Geng L, Li Z, Wu X, Wang Y, Mao R, Zhang S, Huang S, Liu S, Zeng H, Xu W, Gong S, Guo Y, Yang M. Gut Dysbiosis Drives Inflammatory Bowel Disease Through the CCL4L2-VSIR Axis in Glycogen Storage Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309471. [PMID: 38889269 PMCID: PMC11321658 DOI: 10.1002/advs.202309471] [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: 12/05/2023] [Revised: 05/04/2024] [Indexed: 06/20/2024]
Abstract
Patients with glycogen storage disease type Ib (GSD-Ib) frequently have inflammatory bowel disease (IBD). however, the underlying etiology remains unclear. Herein, this study finds that digestive symptoms are commonly observed in patients with GSD-Ib, presenting as single or multiple scattered deep round ulcers, inflammatory pseudo-polyps, obstructions, and strictures, which differ substantially from those in typical IBD. Distinct microbiota profiling and single-cell clustering of colonic mucosae in patients with GSD are conducted. Heterogeneous oral pathogenic enteric outgrowth induced by GSD is a potent inducer of gut microbiota immaturity and colonic macrophage accumulation. Specifically, a unique population of macrophages with high CCL4L2 expression is identified in response to pathogenic bacteria in the intestine. Hyper-activation of the CCL4L2-VSIR axis leads to increased expression of AGR2 and ZG16 in epithelial cells, which mediates the unique progression of IBD in GSD-Ib. Collectively, the microbiota-driven pathomechanism of IBD is demonstrated in GSD-Ib and revealed the active role of the CCL4L2-VSIR axis in the interaction between the microbiota and colonic mucosal immunity. Thus, targeting gut dysbiosis and/or the CCL4L2-VISR axis may represent a potential therapy for GSD-associated IBD.
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22
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Stapleton TE, Lindsey LM, Sundar H, Dearing MD. Rodents consuming the same toxic diet harbor a unique functional core microbiome. Anim Microbiome 2024; 6:43. [PMID: 39080711 PMCID: PMC11289948 DOI: 10.1186/s42523-024-00330-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.S. desert southwest from 20 populations (~ 150 individuals) with differential ingestion of creosote bush and analyzed three gut regions (foregut, cecum, hindgut) using16S sequencing and shotgun metagenomics. In each gut region sampled, we found a distinctive set of microbes in individuals feeding on creosote bush that were more abundant than other ASVs, enriched in creosote feeding woodrats, and occurred more frequently than would be predicted by chance. Creosote core members were from microbial families e.g., Eggerthellaceae, known to metabolize plant secondary compounds and three of the identified core KEGG orthologs (4-hydroxybenzoate decarboxylase, benzoyl-CoA reductase subunit B, and 2-pyrone-4, 6-dicarboxylate lactonase) coded for enzymes that play important roles in metabolism of plant secondary compounds. The results support the hypothesis that the ingestion of creosote bush sculpts the microbiome across all major gut regions to select for functional characteristics associated with the degradation of the PSCs in this unique diet.
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Affiliation(s)
- Tess E Stapleton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.
| | - LeAnn M Lindsey
- School of Computing, University of Utah, 50 Central Campus Dr, Salt Lake City, UT, 84112, USA
| | - Hari Sundar
- School of Computing, University of Utah, 50 Central Campus Dr, Salt Lake City, UT, 84112, USA
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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23
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Han N, Peng X, Zhang T, Qiang Y, Li X, Zhang W. Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health. Front Microbiol 2024; 15:1414000. [PMID: 39044948 PMCID: PMC11265296 DOI: 10.3389/fmicb.2024.1414000] [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: 04/08/2024] [Accepted: 06/12/2024] [Indexed: 07/25/2024] Open
Abstract
The concept of "enterotypes" in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbiota was investigated, based on the metagenomic method. First, 239 fecal samples from individuals across four regions of China revealed a bimodal distribution, highlighting the abundance and variability in Prevotella spp. within the Chinese population. Second, the longitudinal cohort study included 184 fecal samples from 52 time points collected from seven individuals who demonstrated either the outbreaks or disappearances of Prevotella spp., emphasizing the transient nature of Prevotella abundance levels and suggesting shifts in Prevotella "enterotypes." Furthermore, a turnover of the dominant Prevotella spp. was observed, indicating the potential presence of diverse subtypes of Prevotella enterotype. Notably, the genomic analysis demonstrated the persistence of specific Prevotella strains within individuals over extended periods, highlighting the enduring presence of Prevotella in the human gut. In conclusion, by integrating the temporal and geographical scales in our research, we gained deeper insights into the dynamics of Prevotella, emphasizing the importance of considering the dynamics at the time and species level in gut microbiota studies and their implications on human health.
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Affiliation(s)
- Na Han
- 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, China
| | - Xianhui Peng
- 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, China
| | - Tingting Zhang
- 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, China
| | - Yujun Qiang
- 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, China
| | - Xiuwen Li
- 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, China
| | - Wen Zhang
- 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, China
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24
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BMC Biol 2024; 22:148. [PMID: 38965531 PMCID: PMC11225191 DOI: 10.1186/s12915-024-01937-7] [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: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. RESULTS To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. CONCLUSIONS The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.
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Affiliation(s)
- Sanasar G Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
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25
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Ryu EP, Gautam Y, Proctor DM, Bhandari D, Tandukar S, Gupta M, Gautam GP, Relman DA, Shibl AA, Sherchand JB, Jha AR, Davenport ER. Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601557. [PMID: 39005279 PMCID: PMC11244963 DOI: 10.1101/2024.07.01.601557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called 'vanishing microbiomes' potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Conclusion Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.
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Affiliation(s)
- Erica P. Ryu
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Yoshina Gautam
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Diana M. Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- School of Public Health, University of Adelaide, South Australia, Australia
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- Organization for Public Health and Environment Management, Lalitpur, Bagmati, Nepal
| | - Meera Gupta
- Department of Biology, Pennsylvania State University, University Park, PA
| | | | - David A. Relman
- Departments of Medicine, and of Microbiology & Immunology, Stanford University, Stanford, CA
- Section of Infectious Diseases, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Emily R. Davenport
- Department of Biology, Pennsylvania State University, University Park, PA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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26
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Kim N, Ma J, Kim W, Kim J, Belenky P, Lee I. Genome-resolved metagenomics: a game changer for microbiome medicine. Exp Mol Med 2024; 56:1501-1512. [PMID: 38945961 PMCID: PMC11297344 DOI: 10.1038/s12276-024-01262-7] [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: 12/13/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 07/02/2024] Open
Abstract
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.
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Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Wonjong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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27
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Siguenza N, Brevi A, Zhang JT, Pabani A, Bhushan A, Das M, Ding Y, Hasty J, Ghosh P, Zarrinpar A. Engineered bacterial therapeutics for detecting and treating CRC. Trends Cancer 2024; 10:588-597. [PMID: 38693003 PMCID: PMC11392429 DOI: 10.1016/j.trecan.2024.04.001] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024]
Abstract
Despite an overall decrease in occurrence, colorectal cancer (CRC) remains the third most common cause of cancer deaths in the USA. Detection of CRC is difficult in high-risk groups, including those with genetic predispositions, with disease traits, or from certain demographics. There is emerging interest in using engineered bacteria to identify early CRC development, monitor changes in the adenoma and CRC microenvironment, and prevent cancer progression. Novel genetic circuits for cancer therapeutics or functions to enhance existing treatment modalities have been tested and verified in vitro and in vivo. Inclusion of biocontainment measures would prepare strains to meet therapeutic standards. Thus, engineered bacteria present an opportunity for detection and treatment of CRC lesions in a highly sensitive and specific manner.
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Affiliation(s)
- Nicole Siguenza
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Arianna Brevi
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Joanna T Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Arman Pabani
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Jennifer Moreno Department of Veterans Affairs, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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28
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Kim H, Nzabarushimana E, Huttenhower C, Chan AT, Nguyen LH. Altered Microbial Transcription in Long-term Proton Pump Inhibitor Use: Findings From a United States Cohort Study. Gastroenterology 2024; 167:405-408.e3. [PMID: 38521094 PMCID: PMC11193639 DOI: 10.1053/j.gastro.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Hanseul Kim
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Etienne Nzabarushimana
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts; The Harvard Chan Microbiome in Public Health Center, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts; Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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29
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Zakis DR, Brandt BW, van der Waal SV, Keijser BJF, Crielaard W, van der Plas DW, Volgenant CM, Zaura E. The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study. J Oral Microbiol 2024; 16:2369350. [PMID: 38919384 PMCID: PMC11198155 DOI: 10.1080/20002297.2024.2369350] [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: 02/01/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome. Methods A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18-55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured. Results Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1). No significant changes were observed for the secondary outcomes. Conclusion The effects on the oral microbiota were sweetener dependant with the most pronounced effect on plaque microbiota. Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required.
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Affiliation(s)
- Davis R. Zakis
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Bernd W. Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Suzette V. van der Waal
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Bart J. F. Keijser
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Research Group Microbiology and Systems Biology, TNO, Leiden, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Derek W.K. van der Plas
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Catherine M.C. Volgenant
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
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30
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Weaver L, Troester A, Jahansouz C. The Impact of Surgical Bowel Preparation on the Microbiome in Colon and Rectal Surgery. Antibiotics (Basel) 2024; 13:580. [PMID: 39061262 PMCID: PMC11273680 DOI: 10.3390/antibiotics13070580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Preoperative bowel preparation, through iterations over time, has evolved with the goal of optimizing surgical outcomes after colon and rectal surgery. Although bowel preparation is commonplace in current practice, its precise mechanism of action, particularly its effect on the human gut microbiome, has yet to be fully elucidated. Absent intervention, the gut microbiota is largely stable, yet reacts to dietary influences, tissue injury, and microbiota-specific byproducts of metabolism. The routine use of oral antibiotics and mechanical bowel preparation prior to intestinal surgical procedures may have detrimental effects previously thought to be negligible. Recent evidence highlights the sensitivity of gut microbiota to antibiotics, bowel preparation, and surgery; however, there is a lack of knowledge regarding specific causal pathways that could lead to therapeutic interventions. As our understanding of the complex interactions between the human host and gut microbiota grows, we can explore the role of bowel preparation in specific microbiome alterations to refine perioperative care and improve outcomes. In this review, we outline the current fund of information regarding the impact of surgical bowel preparation and its components on the adult gut microbiome. We also emphasize key questions pertinent to future microbiome research and their implications for patients undergoing colorectal surgery.
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Affiliation(s)
- Lauren Weaver
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA; (L.W.); (A.T.)
| | - Alexander Troester
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA; (L.W.); (A.T.)
| | - Cyrus Jahansouz
- Division of Colon & Rectal Surgery, Department of Surgery, University of Minnesota, 420 Delaware St. SE, MMC 450, Minneapolis, MN 55455, USA
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31
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Gawey BJ, Mars RA, Kashyap PC. The role of the gut microbiome in disorders of gut-brain interaction. FEBS J 2024. [PMID: 38922780 DOI: 10.1111/febs.17200] [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: 01/14/2024] [Revised: 04/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Disorders of Gut-Brain Interaction (DGBI) are widely prevalent and commonly encountered in gastroenterology practice. While several peripheral and central mechanisms have been implicated in the pathogenesis of DGBI, a recent body of work suggests an important role for the gut microbiome. In this review, we highlight how gut microbiota and their metabolites affect physiologic changes underlying symptoms in DGBI, with a particular focus on their mechanistic influence on GI transit, visceral sensitivity, intestinal barrier function and secretion, and CNS processing. This review emphasizes the complexity of local and distant effects of microbial metabolites on physiological function, influenced by factors such as metabolite concentration, duration of metabolite exposure, receptor location, host genetics, and underlying disease state. Large-scale in vitro work has elucidated interactions between host receptors and the microbial metabolome but there is a need for future research to integrate such preclinical findings with clinical studies. The development of novel, targeted therapeutic strategies for DGBI hinges on a deeper understanding of these metabolite-host interactions, offering exciting possibilities for the future of treatment of DGBI.
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Affiliation(s)
- Brent J Gawey
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ruben A Mars
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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32
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Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB. Framework for exploring the sensory repertoire of the human gut microbiota. mBio 2024; 15:e0103924. [PMID: 38757952 PMCID: PMC11237719 DOI: 10.1128/mbio.01039-24] [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: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.
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Affiliation(s)
- Patricia A. Ross
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ekaterina Jalomo-Khayrova
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Patrick H. Bradley
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [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: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [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: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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35
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Brandi G, Calabrese C, Tavolari S, Bridonneau C, Raibaud P, Liguori G, Thomas M, Di Battista M, Gaboriau-Routhiau V, Langella P. Intestinal Microbiota Increases Cell Proliferation of Colonic Mucosa in Human-Flora-Associated (HFA) Mice. Int J Mol Sci 2024; 25:6182. [PMID: 38892368 PMCID: PMC11172776 DOI: 10.3390/ijms25116182] [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: 04/29/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Intestinal epithelium renewal strictly depends on fine regulation between cell proliferation, differentiation, and apoptosis. While murine intestinal microbiota has been shown to modify some epithelial cell kinetics parameters, less is known about the role of the human intestinal microbiota. Here, we investigated the rate of intestinal cell proliferation in C3H/HeN germ-free mice associated with human flora (HFA, n = 8), and in germ-free (n = 15) and holoxenic mice (n = 16). One hour before sacrifice, all mice were intraperitoneally inoculated with 5-bromodeoxyuridine (BrdU), and the number of BrdU-positive cells/total cells (labelling index, LI), both in the jejunum and the colon, was evaluated by immunohistochemistry. Samples were also observed by scanning electron microscopy (SEM). Moreover, the microbiota composition in the large bowel of the HFA mice was compared to that of of human donor's fecal sample. No differences in LI were found in the small bowels of the HFA, holoxenic, and germ-free mice. Conversely, the LI in the large bowel of the HFA mice was significantly higher than that in the germ-free and holoxenic counterparts (p = 0.017 and p = 0.048, respectively). In the holoxenic and HFA mice, the SEM analysis disclosed different types of bacteria in close contact with the intestinal epithelium. Finally, the colonic microbiota composition of the HFA mice widely overlapped with that of the human donor in terms of dominant populations, although Bifidobacteria and Lactobacilli disappeared. Despite the small sample size analyzed in this study, these preliminary findings suggest that human intestinal microbiota may promote a high proliferation rate of colonic mucosa. In light of the well-known role of uncontrolled proliferation in colorectal carcinogenesis, these results may deserve further investigation in a larger population study.
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Affiliation(s)
- Giovanni Brandi
- Department of Medical and Surgical Science, University of Bologna, 40138 Bologna, Italy; (C.C.); (G.L.); (M.D.B.)
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Carlo Calabrese
- Department of Medical and Surgical Science, University of Bologna, 40138 Bologna, Italy; (C.C.); (G.L.); (M.D.B.)
| | - Simona Tavolari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Chantal Bridonneau
- INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.B.); (P.R.); (M.T.); (V.G.-R.); (P.L.)
| | - Pierre Raibaud
- INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.B.); (P.R.); (M.T.); (V.G.-R.); (P.L.)
| | - Giuseppina Liguori
- Department of Medical and Surgical Science, University of Bologna, 40138 Bologna, Italy; (C.C.); (G.L.); (M.D.B.)
| | - Muriel Thomas
- INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.B.); (P.R.); (M.T.); (V.G.-R.); (P.L.)
| | - Monica Di Battista
- Department of Medical and Surgical Science, University of Bologna, 40138 Bologna, Italy; (C.C.); (G.L.); (M.D.B.)
| | - Valerie Gaboriau-Routhiau
- INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.B.); (P.R.); (M.T.); (V.G.-R.); (P.L.)
- Laboratory of Intestinal Immunity, Imagine Institute, INSERM UMR1163, Université Paris Cité, 75015 Paris, France
| | - Philippe Langella
- INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.B.); (P.R.); (M.T.); (V.G.-R.); (P.L.)
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Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. TARO: tree-aggregated factor regression for microbiome data integration. Bioinformatics 2024; 40:btae321. [PMID: 38788190 PMCID: PMC11193058 DOI: 10.1093/bioinformatics/btae321] [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: 09/21/2023] [Revised: 03/16/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
MOTIVATION Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns. RESULTS We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the taxonomic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances. AVAILABILITY AND IMPLEMENTATION The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package.
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Affiliation(s)
- Aditya K Mishra
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Christine B Peterson
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
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Bessa MK, Bessa GR, Bonamigo RR. Kefir as a therapeutic agent in clinical research: a scoping review. Nutr Res Rev 2024; 37:79-95. [PMID: 36994828 DOI: 10.1017/s0954422423000070] [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] [Indexed: 03/31/2023]
Abstract
Increasing research has been conducted on the role of probiotics in disease treatment. Kefir, a safe, low-cost probiotic fermented milk drink, has been investigated in many in vitro and animal studies, although parameters for human therapeutic dose or treatment time have not yet been determined. Here we perform a scoping review of clinical studies that have used kefir as a therapeutic agent, compiling the results for perspectives to support and direct further research. This review was based on Joanna Briggs Institute guidelines, including studies on the effects of kefir-fermented milk in humans. Using the term KEFIR, the main international databases were searched for studies published in English, Spanish or Portuguese until 9 March 2022. A total of 5835 articles were identified in the four databases, with forty-four eligible for analysis. The research areas were classified as metabolic syndrome and type 2 diabetes, gastrointestinal health/disorders, maternal/child health and paediatrics, dentistry, oncology, women's and geriatric health, and dermatology. The many study limitations hampered generalisation of the results. The small sample sizes, methodological variation and differences in kefir types, dosage and treatment duration prevented clear conclusions about its benefits for specific diseases. We suggest using a standard therapeutic dose of traditionally prepared kefir in millilitres according to body weight, making routine consumption more feasible. The studies showed that kefir is safe for people without serious illnesses.
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Affiliation(s)
- Milena Klippel Bessa
- Postgraduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, 245, 90050-170, Porto Alegre, RS, Brazil
| | | | - Renan Rangel Bonamigo
- Postgraduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, 245, 90050-170, Porto Alegre, RS, Brazil
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38
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Vomstein K, Krog MC, Wrønding T, Nielsen HS. The microbiome in recurrent pregnancy loss - A scoping review. J Reprod Immunol 2024; 163:104251. [PMID: 38718429 DOI: 10.1016/j.jri.2024.104251] [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: 07/26/2023] [Revised: 12/23/2023] [Accepted: 04/22/2024] [Indexed: 06/03/2024]
Abstract
Recurrent pregnancy loss (RPL) is a troubling condition that affects couples worldwide. Despite extensive research efforts, many RPL cases remain unexplained, highlighting the need for novel approaches to unravel its underlying mechanisms. Recent advances in microbiome research have shed light on the potential role of the microbiome in reproductive health and outcomes. Based on a systematic literature research, this review aims to comprehensively explore the current understanding of the microbiome's involvement in RPL, focusing on the vaginal, endometrial, and gut microbiomes. Evidence from the available studies is examined to explain the relationship between the microbiome and RPL. Furthermore, we discuss the diagnostic potential of the microbiome, therapeutic interventions, and future directions in microbiome research for RPL. Understanding the complex interactions between the microbiome and reproductive health holds promise for developing targeted interventions to help patients today diagnosed as unexplained.
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Affiliation(s)
- Kilian Vomstein
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, Hvidovre & Rigshospitalet, Copenhagen DK-2650, Denmark; Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital Hvidovre, DK-2650, Denmark.
| | - Maria C Krog
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, Hvidovre & Rigshospitalet, Copenhagen DK-2650, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen DK-2100, Denmark
| | - Tine Wrønding
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, Hvidovre & Rigshospitalet, Copenhagen DK-2650, Denmark; Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital Hvidovre, DK-2650, Denmark
| | - Henriette Svarre Nielsen
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, Hvidovre & Rigshospitalet, Copenhagen DK-2650, Denmark; Department of Obstetrics and Gynecology, The Fertility Clinic, Copenhagen University Hospital Hvidovre, DK-2650, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark
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Galeana-Cadena D, Ramirez-Martínez G, Alberto Choreño-Parra J, Silva-Herzog E, Margarita Hernández-Cárdenas C, Soberón X, Zúñiga J. Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity. Heliyon 2024; 10:e31562. [PMID: 38826746 PMCID: PMC11141365 DOI: 10.1016/j.heliyon.2024.e31562] [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: 07/12/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024] Open
Abstract
Background The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome. Methods We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages. Results The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of Lawsonella and Cutibacterium genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of Streptococcus, Actinomyces, Peptostreptococcus, Atopobium, Granulicatella, Mogibacterium, Veillonella, Prevotella_7, Rothia, Gemella, Alloprevotella, and Solobacterium genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of Staphylococcus, Corynebacterium, and Streptococcus. Conclusions Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.
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Affiliation(s)
- David Galeana-Cadena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gustavo Ramirez-Martínez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - José Alberto Choreño-Parra
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Eugenia Silva-Herzog
- Unidad de Vinculación Científica Facultad de Medicina UNAM-INMEGEN, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Carmen Margarita Hernández-Cárdenas
- Unidad de Cuidados Intensivos y Dirección General, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Ciudad de México, Mexico
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
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Yan S, Chen L, Li N, Wei X, Wang J, Dong W, Wang Y, Shi J, Ding X, Peng Y. Effect of Akkermansia muciniphila on pancreatic islet β-cell function in rats with prediabetes mellitus induced by a high-fat diet. BIORESOUR BIOPROCESS 2024; 11:51. [PMID: 38763955 PMCID: PMC11102893 DOI: 10.1186/s40643-024-00766-4] [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: 02/13/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024] Open
Abstract
Prediabetes is an important stage in the development of diabetes. It is necessary to find a safe, effective and sustainable way to delay and reverse the progression of prediabetes. Akkermansia muciniphila (A. muciniphila) is one of the key bacteria associated with glucose metabolism. Recent studies mainly focus on the effect of A. muciniphila on obesity and insulin resistance, but there is no research on the effect of A. muciniphila on pancreatic β-cell function and its mechanism in prediabetes. In this study, we investigated the effects of A. muciniphila on β-cell function, apoptosis and differentiation, as well as its effects on the gut microbiome, intestinal barrier, metaflammation and the expression of Toll-like receptors (TLRs) in a high-fat diet (HFD)-induced prediabetic rat model. The effect of A. muciniphila was compared with dietary intervention. The results showed both A. muciniphila treatment and dietary intervention can reduce metaflammation by repairing the intestinal barrier in rats with prediabetes induced by an HFD and improve β-cell secretory function, apoptosis and differentiation through signaling pathways mediated by TLR2 and TLR4. Additionally, A. muciniphila can further elevate β-cell secretion, attenuate apoptosis and improve differentiation and the TLR signaling pathway on the basis of diet.
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Affiliation(s)
- Shuai Yan
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Lin Chen
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Na Li
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaohui Wei
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jingjing Wang
- Shanghai Key Laboratory for Pancreatic Diseases, Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Weiping Dong
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yufan Wang
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jianxia Shi
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaoying Ding
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Yongde Peng
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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Wang Y, Han Y, Yang C, Bai T, Zhang C, Wang Z, Sun Y, Hu Y, Besenbacher F, Chen C, Yu M. Long-term relapse-free survival enabled by integrating targeted antibacteria in antitumor treatment. Nat Commun 2024; 15:4194. [PMID: 38760364 PMCID: PMC11101653 DOI: 10.1038/s41467-024-48662-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: 05/11/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The role of tumor-resident intracellular microbiota (TRIM) in carcinogenesis has sparked enormous interest. Nevertheless, the impact of TRIM-targeted antibacteria on tumor inhibition and immune regulation in the tumor microenvironment (TME) remains unexplored. Herein, we report long-term relapse-free survival by coordinating antibacteria with antitumor treatment, addressing the aggravated immunosuppression and tumor overgrowth induced by TRIM using breast and prostate cancer models. Combining Ag+ release with a Fenton-like reaction and photothermal conversion, simultaneous bacteria killing and multimodal antitumor therapy are enabled by a single agent. Free of immune-stimulating drugs, the agent restores antitumor immune surveillance and activates immunological responses. Secondary inoculation and distal tumor analysis confirm lasting immunological memory and systemic immune responses. A relapse-free survival of >700 days is achieved. This work unravels the crucial role of TRIM-targeted antibacteria in tumor inhibition and unlocks an unconventional route for immune regulation in TME and a complete cure for cancer.
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Affiliation(s)
- Yuanlin Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Yaqian Han
- School of Instrumentation Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Chenhui Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Tiancheng Bai
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Chenggang Zhang
- School of Instrumentation Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Zhaotong Wang
- School of Instrumentation Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Ye Sun
- School of Instrumentation Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
| | - Ying Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, 8000, Denmark
| | - Chunying Chen
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
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Xiao W, Weissman JL, Johnson PLF. Ecological drivers of CRISPR immune systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594560. [PMID: 38952799 PMCID: PMC11216370 DOI: 10.1101/2024.05.16.594560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR system. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity. Importance 2Microbes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.
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Wang W, Qiu Z, Li H, Wu X, Cui Y, Xie L, Chang B, Li P, Zeng H, Ding T. Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171703. [PMID: 38490424 DOI: 10.1016/j.scitotenv.2024.171703] [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: 10/16/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.
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Affiliation(s)
- Wan Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Zongyao Qiu
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China
| | - Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lixiang Xie
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Peipei Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China.
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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Zeng MH, Li S, Lv QB, Wang XX, Qadeer A, Mahmoud MH. Modulation of the rat intestinal microbiota in the course of Anisakis pegreffii infection. Front Vet Sci 2024; 11:1403920. [PMID: 38784661 PMCID: PMC11111928 DOI: 10.3389/fvets.2024.1403920] [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: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Background Anisakis are globally distributed, marine parasitic nematodes that can cause human health problems, including symptoms such as vomiting, acute diarrhea, and allergic reactions. As parasitic nematodes that primarily affect the patient's digestive tract, intestinal helminths can interact directly with the host microbiota through physical contact, chemicals, or nutrient competition. It is widely accepted that the host microbiota plays a crucial role in the regulation of immunity. Materials and methods Nematodes collected from the abdominal cavity of marine fish were identified by molecular biology and live worms were artificially infected in rats. Infection was determined by indirect ELISA based on rat serum and worm extraction. Feces were collected for 16S rDNA-based analysis of microbiota diversity. Results Molecular biology identification based on ITS sequences identified the collected nematodes as A. pegreffii. The success of the artificial infection was determined by indirect ELISA based on serum and worm extraction from artificially infected rats. Microbiota diversity analysis showed that a total of 773 ASVs were generated, and PCoA showed that the infected group was differentiated from the control group. The control group contained five characterized genera (Prevotellaceae NK3B31 group, Turicibacter, Clostridium sensu stricto 1, Candidatus Stoquefichus, Lachnospira) and the infected group contained nine characterized genera (Rodentibacter, Christensenella, Dubosiella, Streptococcus, Anaeroplasma, Lactococcus, Papillibacter, Desulfovibrio, Roseburia). Based on the Wilcoxon test, four processes were found to be significant: bacterial secretion system, bacterial invasion of epithelial cells, bacterial chemotaxis, and ABC transporters. Conclusion This study is the first to analyze the diversity of the intestinal microbiota of rats infected with A. pegreffii and to determine the damage and regulation of metabolism and immunity caused by the infection in the rat gut. The findings provide a basis for further research on host-helminth-microbe correlationships.
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Affiliation(s)
- Min-hao Zeng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shan Li
- Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University, Jiujiang, China
| | - Qing-bo Lv
- Key Laboratory of Zoonosis Research, Institute of Zoonosis, College of Veterinary Medicine, Ministry of Education, Jilin University, Changchun, China
| | - Xiao-xu Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Abdul Qadeer
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Mohamed H. Mahmoud
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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Singh A, Luallen RJ. Understanding the factors regulating host-microbiome interactions using Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230059. [PMID: 38497260 PMCID: PMC10945399 DOI: 10.1098/rstb.2023.0059] [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: 08/16/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Anupama Singh
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Robert J. Luallen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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Baiz MD, Wood AW, Toews DPL. Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone. Proc Biol Sci 2024; 291:20240238. [PMID: 38628125 PMCID: PMC11022011 DOI: 10.1098/rspb.2024.0238] [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: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.
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Affiliation(s)
- Marcella D. Baiz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Andrew W. Wood
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
| | - David P. L. Toews
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
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Wei X, Tsai MS, Liang L, Jiang L, Hung CJ, Jelliffe-Pawlowski L, Rand L, Snyder M, Jiang C. Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process. Cell Rep 2024; 43:114078. [PMID: 38598334 DOI: 10.1016/j.celrep.2024.114078] [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: 09/15/2023] [Revised: 03/01/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.
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Affiliation(s)
- Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ming-Shian Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liuyiqi Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Chia-Jui Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
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Zhang K, Paul K, Jacobs JP, Cockburn MG, Bronstein JM, Del Rosario I, Ritz B. Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study. Environ Health 2024; 23:41. [PMID: 38627687 PMCID: PMC11020204 DOI: 10.1186/s12940-024-01078-y] [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: 01/16/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans. METHODS We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders. RESULTS OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6. CONCLUSION In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.
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Affiliation(s)
- Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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50
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Wan S, You P, Shi Q, Hu H, Zhang L, Chen L, Wu Z, Lin S, Song X, Luo Y, Wang Y, Ju F, Jin D, Chen Y. Gut microbiome changes in mouse, Mongolian gerbil, and hamster models following Clostridioides difficile challenge. Front Microbiol 2024; 15:1368194. [PMID: 38638911 PMCID: PMC11024471 DOI: 10.3389/fmicb.2024.1368194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Clostridioides difficile infection (CDI), as well as its etiology and pathogenesis, have been extensively investigated. However, the absence of suitable CDI animal models that reflect CDI symptoms and the associated gut microbiome changes in humans has limited research progress in this field. Thus, we aimed to investigate whether Mongolian gerbils, which present a range of human pathological conditions, can been used in studies on CDI. Methods: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing. Methods In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing. Results The results obtained showed that C. difficile colonized the gastrointestinal tracts of the three rodents, and after the C. difficile challenge, C57BL/6J mice did not manifest CDI symptoms and their intestines showed no significant pathological changes. However, the hamsters showed explosive intestinal bleeding and inflammation and the Mongolian gerbils presented diarrhea as well as increased infiltration of inflammatory cells, mucus secretion, and epithelial cell shedding in their intestinal tissue. Further, intestinal microbiome analysis revealed significant differences with respect to intestinal flora abundance and diversity. Specifically, after C. difficile challenge, the Firmicutes/Bacteroidetes ratio decreased for C57BL/6J mice, but increased significantly for Mongolian gerbils and hamsters. Furthermore, the abundance of Proteobacteria increased in all three models, especially in hamsters, while that of Verrucomicrobia only increased significantly in C57BL/6J mice and Mongolian gerbils. Our results also indicated that differences in the relative abundances of Lactobacillaceae and Akkermansia were primarily responsible for the observed differences in response to C. difficile challenge. Conclusion Based on the observed responses to C. difficile challenge, we concluded for the first time that the Mongolian gerbil could be used as an animal model for CDI. Additionally, the taxa identified in this study may be used as biomarkers for further studies on CDI and to improve understanding regarding changes in gut microbiome in CDI-related diseases.
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Affiliation(s)
- Shuangshuang Wan
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Peijun You
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Qikai Shi
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Hui Hu
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Lu Zhang
- Environmental Microbiome and Biotechnology Laboratory, School of Engineering, Westlake University, Hangzhou, China
| | - Leyang Chen
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, China
| | - Ziyi Wu
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, China
| | - Shan Lin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Xiaojun Song
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Yongneng Luo
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Yaxuan Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Feng Ju
- Environmental Microbiome and Biotechnology Laboratory, School of Engineering, Westlake University, Hangzhou, China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Yu Chen
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
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