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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes 2024; 73:1391-1410. [PMID: 38912690 DOI: 10.2337/dbi24-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Suzanne Devkota
- Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
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2
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Anthony WE, Allison SD, Broderick CM, Chavez Rodriguez L, Clum A, Cross H, Eloe-Fadrosh E, Evans S, Fairbanks D, Gallery R, Gontijo JB, Jones J, McDermott J, Pett-Ridge J, Record S, Rodrigues JLM, Rodriguez-Reillo W, Shek KL, Takacs-Vesbach T, Blanchard JL. From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. ENVIRONMENTAL MICROBIOME 2024; 19:56. [PMID: 39095861 PMCID: PMC11295382 DOI: 10.1186/s40793-024-00599-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
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Affiliation(s)
| | - Steven D Allison
- University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Caitlin M Broderick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | | | - Alicia Clum
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hugh Cross
- National Ecological Observatory Network - Battelle, Boulder, CO, USA
| | | | - Sarah Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Dawson Fairbanks
- University of California Riverside, Riverside, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | | | | | - Jennifer Jones
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Jason McDermott
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA
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3
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Herrera G, Castañeda S, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile. Microbiol Res 2024; 285:127739. [PMID: 38763016 DOI: 10.1016/j.micres.2024.127739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Clostridioides difficile may have a negative impact on gut microbiota composition in terms of diversity and abundance, thereby triggering functional changes supported by the differential presence of genes involved in significant metabolic pathways, such as short-chain fatty acids (SCFA). This work has evaluated shotgun metagenomics data regarding 48 samples from four groups classified according to diarrhea acquisition site (community- and healthcare facility-onset) and positive or negative Clostridioides difficile infection (CDI) result. The metagenomic-assembled genomes (MAGs) obtained from each sample were taxonomically assigned for preliminary comparative analysis concerning differences in composition among groups. The predicted genes involved in metabolism, transport, and signaling remained constant in microbiota members; characteristic patterns were observed in MAGs and genes involved in SCFA butyrate and acetate metabolic pathways for each study group. A decrease in genera and species, as well as relative MAG abundance with the presence of the acetate metabolism-related gene, was evident in the HCFO/- group. Increased antibiotic resistance markers (ARM) were observed in MAGs along with the genes involved in acetate metabolism. The results highlight the need to explore the role of acetate in greater depth as a potential protector of the imbalances produced by CDI, as occurs in other inflammatory intestinal diseases.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia; Grupo de Fundamentos y Enseñanza de la Física y las Sistemas Dinámicas, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E Pérez-Jaramillo
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia; Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia.
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Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kazanov MD, Leyn SA, Kent JE, Sejane K, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602360. [PMID: 39005317 PMCID: PMC11245093 DOI: 10.1101/2024.07.06.602360] [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
Bifidobacteria are among the earliest colonizers of the human gut, conferring numerous health benefits. While multiple Bifidobacterium strains are used as probiotics, accumulating evidence suggests that the individual responses to probiotic supplementation may vary, likely due to a variety of factors, including strain type(s), gut community composition, dietary habits of the consumer, and other health/lifestyle conditions. Given the saccharolytic nature of bifidobacteria, the carbohydrate composition of the diet is one of the primary factors dictating the colonization efficiency of Bifidobacterium strains. Therefore, a comprehensive understanding of bifidobacterial glycan metabolism at the strain level is necessary to rationally design probiotic or synbiotic formulations that combine bacterial strains with glycans that match their nutrient preferences. In this study, we systematically reconstructed 66 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 565 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 2973 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs). Our analysis uncovered substantial heterogeneity in the predicted glycan utilization capabilities at the species and strain level and revealed the presence of a yet undescribed phenotypically distinct subspecies-level clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Predicted carbohydrate utilization phenotypes were experimentally characterized and validated. Our large-scale genomic analysis considerably expands the knowledge of carbohydrate metabolism in bifidobacteria and provides a foundation for rationally designing single- or multi-strain probiotic formulations of a given bifidobacterial species as well as synbiotic combinations of bifidobacterial strains matched with their preferred carbohydrate substrates.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey, 34956
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - James E Kent
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kristija Sejane
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
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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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6
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Jia M, Zhu S, Xue MY, Chen H, Xu J, Song M, Tang Y, Liu X, Tao Y, Zhang T, Liu JX, Wang Y, Sun HZ. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat Microbiol 2024; 9:1884-1898. [PMID: 38866938 DOI: 10.1038/s41564-024-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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Affiliation(s)
- Minghui Jia
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jinghong Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaohan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Company, Shanghai, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China.
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7
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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetologia 2024:10.1007/s00125-024-06198-1. [PMID: 38910152 DOI: 10.1007/s00125-024-06198-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne Devkota
- Cedars-Sinai Medical Center, Human Microbiome Research Institute, Los Angeles, CA, USA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain.
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
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8
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Huang P, Dong Q, Wang Y, Tian Y, Wang S, Zhang C, Yu L, Tian F, Gao X, Guo H, Yi S, Li M, Liu Y, Zhang Q, Lu W, Wang G, Yang B, Cui S, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Ma B, Wu T, Zou H, Shi J, Zhang H, Fan D, Sheng Y, Zhao J, Tang L, Zhang H, Sun W, Chen W, Kong X, Chen L, Zhai Q. Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects. CELL GENOMICS 2024; 4:100559. [PMID: 38740021 PMCID: PMC11228888 DOI: 10.1016/j.xgen.2024.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.
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Affiliation(s)
- Pan Huang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yunfan Tian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Guo
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyang Li
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yang Liu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Gang Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Yuwen Jiao
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Beining Ma
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Tang
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China.
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9
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Xie Y, Liu F. The role of the gut microbiota in tumor, immunity, and immunotherapy. Front Immunol 2024; 15:1410928. [PMID: 38903520 PMCID: PMC11188355 DOI: 10.3389/fimmu.2024.1410928] [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: 04/02/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
In recent years, with the deepening understanding of the gut microbiota, it has been recognized to play a significant role in the development and progression of diseases. Particularly in gastrointestinal tumors, the gut microbiota influences tumor growth by dysbiosis, release of bacterial toxins, and modulation of host signaling pathways and immune status. Immune checkpoint inhibitors (ICIs) have greatly improved cancer treatment efficacy by enhancing immune cell responses. Current clinical and preclinical studies have demonstrated that the gut microbiota and its metabolites can enhance the effectiveness of immunotherapy. Furthermore, certain gut microbiota can serve as biomarkers for predicting immunotherapy responses. Interventions targeting the gut microbiota for the treatment of gastrointestinal diseases, especially colorectal cancer (CRC), include fecal microbiota transplantation, probiotics, prebiotics, engineered bacteria, and dietary interventions. These approaches not only improve the efficacy of ICIs but also hold promise for enhancing immunotherapy outcomes. In this review, we primarily discuss the role of the gut microbiota and its metabolites in tumors, host immunity, and immunotherapy.
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Affiliation(s)
| | - Fang Liu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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10
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Wu L, Lin H, Zhang L, Kiet TQ, Liu P, Song J, Duan Y, Hu C, Yang H, Duan W, Yang X. Construction of high-quality genomes and gene catalogue for culturable microbes of sugarcane (Saccharum spp.). Sci Data 2024; 11:534. [PMID: 38789459 PMCID: PMC11126615 DOI: 10.1038/s41597-024-03379-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies.
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Affiliation(s)
- Liang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Haidong Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Lijun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, 650221, China
| | - Ta Quang Kiet
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Peng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Jinkang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yong Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Chunyu Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Hao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences / Sugarcane Research Center, Chinese Academy of Agricultural Sciences / Guangxi Key Laboratory of Sugarcane Genetic Improvement / Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning, Guangxi, 530007, China.
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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11
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Da Silva Morais E, Grimaud GM, Warda A, Stanton C, Ross P. Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus. Sci Rep 2024; 14:10109. [PMID: 38698002 PMCID: PMC11066082 DOI: 10.1038/s41598-024-59148-7] [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: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.
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Affiliation(s)
- Emilene Da Silva Morais
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Ghjuvan Micaelu Grimaud
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Alicja Warda
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- Microbiology Department, University College Cork, Co. Cork, Ireland.
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12
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Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
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Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
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13
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Paller AS, Scharschmidt TC, Kezic S, Irvine AD. Preclinical Atopic Dermatitis Skin in Infants: An Emerging Research Area. J Invest Dermatol 2024; 144:1001-1009. [PMID: 38573278 DOI: 10.1016/j.jid.2024.02.021] [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: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
Whereas clinically apparent atopic dermatitis (AD) can be confirmed by validated diagnostic criteria, the preclinical phenotype of infants who eventually develop AD is less well-characterized. Analogous to unaffected or nonlesional skin in established AD, clinically normal-appearing skin in infants who will develop clinical AD has distinct changes. Prospective studies have revealed insights into this preclinical AD phenotype. In this study, we review the structural, immunologic, and microbiome nature of the preclinical AD phenotype. Determination of markers that predict the development of AD will facilitate targeting of interventions to prevent the development or reduce the severity of AD in infants.
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Affiliation(s)
- Amy S Paller
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
| | - Tiffany C Scharschmidt
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Sanja Kezic
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Alan D Irvine
- Clinical Medicine, Trinity College Dublin, Dublin, Ireland
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14
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Xu X, Feng Q, Zhang T, Gao Y, Cheng Q, Zhang W, Wu Q, Xu K, Li Y, Nguyen N, Taft DH, Mills DA, Lemay DG, Zhu W, Mao S, Zhang A, Xu K, Liu J. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. IMETA 2024; 3:e169. [PMID: 38882494 PMCID: PMC11170968 DOI: 10.1002/imt2.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R 2 = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.
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Affiliation(s)
- Xinming Xu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition Fudan University Shanghai China
| | - Qingying Feng
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Biological Engineering Division Massachusetts Institute of Technology (MIT) Cambridge Massachusetts USA
| | - Tao Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Yunlong Gao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wanqiu Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qinglong Wu
- Department of Pathology and Immunology Baylor College of Medicine Houston Texas USA
| | - Ke Xu
- Department of Statistics University of Chicago Chicago Illinois
| | - Yucan Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute Fudan University Shanghai China
| | - Nhu Nguyen
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - Diana H Taft
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - David A Mills
- Department of Food Science and Technology University of California, Davis Davis California USA
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science University of California, Davis Davis California USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center Davis California USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences Sichuan University Chengdu China
| | - Kelin Xu
- Department of Biostatistics, Key Laboratory of Public Health Safety, NHC Key Laboratory of Health Technology Assessment, School of Public Health Fudan University Shanghai China
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
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15
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Jin MK, Zhang Q, Xu N, Zhang Z, Guo HQ, Li J, Ding K, Sun X, Yang XR, Zhu D, Su X, Qian H, Zhu YG. Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4476-4486. [PMID: 38382547 DOI: 10.1021/acs.est.3c05741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.
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Affiliation(s)
- Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Hong-Qin Guo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400715, China
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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16
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Zeng S, Almeida A, Li S, Ying J, Wang H, Qu Y, Paul Ross R, Stanton C, Zhou Z, Niu X, Mu D, Wang S. A metagenomic catalog of the early-life human gut virome. Nat Commun 2024; 15:1864. [PMID: 38424077 PMCID: PMC10904392 DOI: 10.1038/s41467-024-45793-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.
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Affiliation(s)
- Shuqin Zeng
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Shiping Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Junjie Ying
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hua Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yi Qu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Zhemin Zhou
- Pasteurien College, Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Dezhi Mu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Shaopu Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
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17
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Ding Y, Jiang X, Wu J, Wang Y, Zhao L, Pan Y, Xi Y, Zhao G, Li Z, Zhang L. Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome. mSphere 2024; 9:e0060823. [PMID: 38112433 PMCID: PMC10826358 DOI: 10.1128/msphere.00608-23] [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: 10/21/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which Klebsiella pneumoniae, Enterobacter hormaechei_A, and Escherichia coli_D played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.IMPORTANCEThe transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota. K. pneumoniae, E. hormaechei_A, and E. coli_D were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.
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Affiliation(s)
- Yanwen Ding
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xin Jiang
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiacheng Wu
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yihui Wang
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lanlan Zhao
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yingmiao Pan
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yaxuan Xi
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guoping Zhao
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong University, State Key Laboratory of Microbial Technology, Qingdao, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, China National Institute of Health, Shanghai, China
| | - Ziyun Li
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lei Zhang
- Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong University, State Key Laboratory of Microbial Technology, Qingdao, China
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18
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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19
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Steinke K, Pamp SJ, Munk P. MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis. BMC Genomics 2024; 25:55. [PMID: 38216924 PMCID: PMC10785454 DOI: 10.1186/s12864-023-09912-2] [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: 07/28/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for single-isolate genomes. As result quality depends on sequence quality, performance of tools for single-isolate genomes on MAGs should be tested beforehand. Bioinformatics can be leveraged to quickly create varied synthetic test sets with known composition for this purpose. RESULTS We present MAGICIAN, a flexible, user-friendly pipeline for the simulation of MAGs. MAGICIAN combines a synthetic metagenome simulator with a metagenomic assembly and binning pipeline to simulate MAGs based on user-supplied input genomes, allowing users to test performance of tools on MAGs while having a ground truth to compare results to. Using MAGICIAN, we found that even very slight (1%) changes in depth of coverage can drastically affect whether a genome can be recovered. We also demonstrate the use of simulated MAGs by evaluating the suitability of such genomes obtained with MAGICIAN's current default pipeline for analysis with the antimicrobial resistance gene identification tool ResFinder. CONCLUSIONS Using MAGICIAN, it is possible to simulate MAGs which, while generally high in quality, reflect issues encountered with real-world data, thus providing realistic best-case data. Evaluating the results of ResFinder analysis of these genomes revealed a risk for plausible-looking false positives, which underlines the need for pipeline validation so that researchers are aware of the potential issues when interpreting real-world data. Furthermore, the effects of fluctuations in depth of coverage on genome recovery in our simulated "random sequencing" warrant further investigation and indicate random subsampling of reads may affect discovery of more genomes.
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Affiliation(s)
- Kat Steinke
- Center for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800, Kongens Lyngby, Denmark
- Department of Clinical Microbiology, Odense University Hospital, J. B. Winsløws Vej 21, 5000, Odense, Denmark
| | - Sünje J Pamp
- Center for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800, Kongens Lyngby, Denmark
| | - Patrick Munk
- Center for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800, Kongens Lyngby, Denmark.
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20
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Sanchez FB, Sato Guima SE, Setubal JC. How to Obtain and Compare Metagenome-Assembled Genomes. Methods Mol Biol 2024; 2802:135-163. [PMID: 38819559 DOI: 10.1007/978-1-0716-3838-5_6] [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: 06/01/2024]
Abstract
Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.
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Affiliation(s)
- Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Suzana Eiko Sato Guima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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21
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Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024; 16:2297837. [PMID: 38217470 PMCID: PMC10793692 DOI: 10.1080/19490976.2023.2297837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024] Open
Abstract
Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.
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Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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22
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Shen Z, Robert L, Stolpman M, Che Y, Allen KJ, Saffery R, Walsh A, Young A, Eckert J, Deming C, Chen Q, Conlan S, Laky K, Li JM, Chatman L, Kashaf SS, Kong HH, Frischmeyer-Guerrerio PA, Perrett KP, Segre JA. A genome catalog of the early-life human skin microbiome. Genome Biol 2023; 24:252. [PMID: 37946302 PMCID: PMC10636849 DOI: 10.1186/s13059-023-03090-w] [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: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. RESULTS Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants. CONCLUSIONS Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.
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Affiliation(s)
- Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lukian Robert
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Milan Stolpman
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - You Che
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Katrina J Allen
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Audrey Walsh
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Angela Young
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jana Eckert
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Qiong Chen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jenny Min Li
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Lindsay Chatman
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | | | - Kirsten P Perrett
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Allergy and Immunology, Royal Children's Hospital, Parkville, VIC, Australia
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
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23
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Shaw J, Yu YW. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat Methods 2023; 20:1661-1665. [PMID: 37735570 PMCID: PMC10630134 DOI: 10.1038/s41592-023-02018-3] [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: 02/07/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani ( https://github.com/bluenote-1577/skani ), a method for determining average nucleotide identity (ANI) via sparse approximate alignments. skani outperforms FastANI in accuracy and speed (>20× faster) for fragmented, incomplete MAGs. skani can query genomes against >65,000 prokaryotic genomes in seconds and 6 GB memory. skani unlocks higher-resolution insights for extensive, noisy metagenomic datasets.
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Affiliation(s)
- Jim Shaw
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
| | - Yun William Yu
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
- Computer and Mathematical Sciences, University of Toronto at Scarborough, Toronto, Ontario, Canada.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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24
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Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA. Expanded microbiome niches of RAG-deficient patients. Cell Rep Med 2023; 4:101205. [PMID: 37757827 PMCID: PMC10591041 DOI: 10.1016/j.xcrm.2023.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
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Affiliation(s)
- Ryan A Blaustein
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - ShihQueen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Glenna Banania
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Keisuke Nagao
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Dimana Dimitrova
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jennifer A Kanakry
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Helen Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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25
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Almanza-Aguilera E, Cano A, Gil-Lespinard M, Burguera N, Zamora-Ros R, Agudo A, Farràs M. Mediterranean diet and olive oil, microbiota, and obesity-related cancers. From mechanisms to prevention. Semin Cancer Biol 2023; 95:103-119. [PMID: 37543179 DOI: 10.1016/j.semcancer.2023.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/02/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
Olive oil (OO) is the main source of added fat in the Mediterranean diet (MD). It is a mix of bioactive compounds, including monounsaturated fatty acids, phytosterols, simple phenols, secoiridoids, flavonoids, and terpenoids. There is a growing body of evidence that MD and OO improve obesity-related factors. In addition, obesity has been associated with an increased risk for several cancers: endometrial, oesophageal adenocarcinoma, renal, pancreatic, hepatocellular, gastric cardia, meningioma, multiple myeloma, colorectal, postmenopausal breast, ovarian, gallbladder, and thyroid cancer. However, the epidemiological evidence linking MD and OO with these obesity-related cancers, and their potential mechanisms of action, especially those involving the gut microbiota, are not clearly described or understood. The goals of this review are 1) to update the current epidemiological knowledge on the associations between MD and OO consumption and obesity-related cancers, 2) to identify the gut microbiota mechanisms involved in obesity-related cancers, and 3) to report the effects of MD and OO on these mechanisms.
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Affiliation(s)
- Enrique Almanza-Aguilera
- Unit of Nutrition and Cancer, Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain
| | - Ainara Cano
- Food Research, AZTI, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Astondo Bidea, Edificio 609, 48160, Derio, Spain
| | - Mercedes Gil-Lespinard
- Unit of Nutrition and Cancer, Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain
| | - Nerea Burguera
- Food Research, AZTI, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Astondo Bidea, Edificio 609, 48160, Derio, Spain
| | - Raul Zamora-Ros
- Unit of Nutrition and Cancer, Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain; Department of Nutrition, Food Sciences, and Gastronomy, Food Innovation Network (XIA), Institute for Research on Nutrition and Food Safety (INSA), Faculty of Pharmacy and Food Sciences University of Barcelona, Barcelona, Spain.
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain
| | - Marta Farràs
- Unit of Nutrition and Cancer, Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain.
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26
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Arikawa K, Hosokawa M. Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics. Comput Struct Biotechnol J 2023; 21:4508-4518. [PMID: 37771751 PMCID: PMC10523443 DOI: 10.1016/j.csbj.2023.09.010] [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: 06/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.
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Affiliation(s)
- Koji Arikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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27
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Han Y, Zhang C, Zhao Z, Peng Y, Liao J, Jiang Q, Liu Q, Shao Z, Dong X. A comprehensive genomic catalog from global cold seeps. Sci Data 2023; 10:596. [PMID: 37684262 PMCID: PMC10491686 DOI: 10.1038/s41597-023-02521-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Cold seeps harbor abundant and diverse microbes with tremendous potential for biological applications and that have a significant influence on biogeochemical cycles. Although recent metagenomic studies have expanded our understanding of the community and function of seep microorganisms, knowledge of the diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic datasets from 16 cold seep sites across the globe to construct a comprehensive gene and genome catalog. The non-redundant gene catalog comprised 147 million genes, and 36% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) were obtained, most of which (94%) belonged to novel species. Of them, 81 ANME species were identified that cover all subclades except ANME-2d, and 23 syntrophic SRB species spanned the Seep-SRB1a, Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAG catalog is a valuable resource that will aid in deepening our understanding of the functions of cold seep microbiomes.
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Affiliation(s)
- Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Zhuoming Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jing Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Qiuyun Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Qing Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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Pan S, Zhao XM, Coelho LP. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. Bioinformatics 2023; 39:i21-i29. [PMID: 37387171 PMCID: PMC10311329 DOI: 10.1093/bioinformatics/btad209] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Metagenomic binning methods to reconstruct metagenome-assembled genomes (MAGs) from environmental samples have been widely used in large-scale metagenomic studies. The recently proposed semi-supervised binning method, SemiBin, achieved state-of-the-art binning results in several environments. However, this required annotating contigs, a computationally costly and potentially biased process. RESULTS We propose SemiBin2, which uses self-supervised learning to learn feature embeddings from the contigs. In simulated and real datasets, we show that self-supervised learning achieves better results than the semi-supervised learning used in SemiBin1 and that SemiBin2 outperforms other state-of-the-art binners. Compared to SemiBin1, SemiBin2 can reconstruct 8.3-21.5% more high-quality bins and requires only 25% of the running time and 11% of peak memory usage in real short-read sequencing samples. To extend SemiBin2 to long-read data, we also propose ensemble-based DBSCAN clustering algorithm, resulting in 13.1-26.3% more high-quality genomes than the second best binner for long-read data. AVAILABILITY AND IMPLEMENTATION SemiBin2 is available as open source software at https://github.com/BigDataBiology/SemiBin/ and the analysis scripts used in the study can be found at https://github.com/BigDataBiology/SemiBin2_benchmark.
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Affiliation(s)
- Shaojun Pan
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
- Zhangjiang Fudan International Innovation Center, Shanghai 201203, China
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China
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Shen Z, Robert L, Stolpman M, Che Y, Walsh A, Saffery R, Allen KJ, Eckert J, Young A, Deming C, Chen Q, Conlan S, Laky K, Li JM, Chatman L, Saheb Kashaf S, Kong HH, Frischmeyer-Guerrerio PA, Perrett KP, Segre JA. A genome catalog of the early-life human skin microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541509. [PMID: 37398010 PMCID: PMC10312837 DOI: 10.1101/2023.05.22.541509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.
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Affiliation(s)
- Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Lukian Robert
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Milan Stolpman
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - You Che
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Audrey Walsh
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Katrina J. Allen
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Jana Eckert
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Angela Young
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Qiong Chen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Jenny Min Li
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Lindsay Chatman
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | | | - VITALITY team
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | - Kirsten P. Perrett
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Allergy & Immunology, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
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30
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Ladeira R, Tap J, Derrien M. Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy. MICROBIOME RESEARCH REPORTS 2023; 2:9. [PMID: 38047280 PMCID: PMC10688807 DOI: 10.20517/mrr.2023.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 12/05/2023]
Abstract
Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.
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Affiliation(s)
- Ruben Ladeira
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
| | - Julien Tap
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas 78350, France
| | - Muriel Derrien
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
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31
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Rahman T, Sarwar PF, Potter C, Comstock SS, Klepac-Ceraj V. Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema. Front Pediatr 2023; 11:1090048. [PMID: 37020647 PMCID: PMC10069630 DOI: 10.3389/fped.2023.1090048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.
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Affiliation(s)
- Trisha Rahman
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Prioty F. Sarwar
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassie Potter
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sarah S. Comstock
- Department of Food Science & Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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32
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Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F. Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research. Microbiol Spectr 2023; 11:e0428222. [PMID: 36744896 PMCID: PMC10101064 DOI: 10.1128/spectrum.04282-22] [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: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lu Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Guoqing Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Ze Zhao
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Hui Wang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
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33
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Derrien M, Mikulic N, Uyoga MA, Chenoll E, Climent E, Howard-Varona A, Nyilima S, Stoffel NU, Karanja S, Kottler R, Stahl B, Zimmermann MB, Bourdet-Sicard R. Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides. Gut Microbes 2023; 15:2178793. [PMID: 36794816 PMCID: PMC9980514 DOI: 10.1080/19490976.2023.2178793] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants (n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis (B. infantis) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum. Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III (Se+, Le-) (22%) than in most previously studied populations, with an enrichment in 2'-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis, and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.
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Affiliation(s)
- Muriel Derrien
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France,CONTACT Muriel Derrien Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
| | - Nadja Mikulic
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Mary A Uyoga
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Empar Chenoll
- ADM-Biopolis, ADM, Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | - Eric Climent
- ADM-Biopolis, ADM, Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | - Adrian Howard-Varona
- ADM-Biopolis, ADM, Parc Cientific Universitat de Valencia, Paterna, Valencia, Spain
| | - Suzane Nyilima
- Public and Community Health Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nicole U Stoffel
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Simon Karanja
- Public and Community Health Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Bernd Stahl
- Advanced Health & Science, Danone Nutricia Research, Utrecht, The Netherlands,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Raphaëlle Bourdet-Sicard
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France,Raphaëlle Bourdet-Sicard Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
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Mills DA, German JB, Lebrilla CB, Underwood MA. Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants. Gut Microbes 2023; 15:2192458. [PMID: 37013357 PMCID: PMC10075334 DOI: 10.1080/19490976.2023.2192458] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.
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Affiliation(s)
- David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Department of Viticulture and Enology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - J. Bruce German
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Department of Chemistry, University of California-Davis, Davis, CA, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, CA, United States
| | - Mark A. Underwood
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Division of Neonatology, Department of Pediatrics, University of California-Davis, Sacramento, CA, United States
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Ventura M, van Sinderen D, Turroni F. New research frontiers pertaining to the infant gut microbiota. MICROBIOME RESEARCH REPORTS 2022; 1:24. [PMID: 38046907 PMCID: PMC10688817 DOI: 10.20517/mrr.2022.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2023]
Abstract
The human gut microbiota is believed to be responsible for multiple health-impacting host effects. The influence of gut microorganisms on the human host begins immediately after birth, having long-lasting health effects, while the gut microbiota itself continues to develop throughout the host's entire life. The purported health-associated effects of the gut microbiota have fueled extensive and ongoing research efforts. Nonetheless, the precise mode of action of functionalities exerted by microbial colonizers of the infant intestine is still largely unknown. The current perspective intends to illustrate major future investigative directions concerning the human gut microbiota with a specific focus on infant-associated gut microbes.
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Affiliation(s)
- Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork T12 YT20, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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