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Wang Y, Jin C, Li H, Liang X, Zhao C, Wu N, Yue M, Zhao L, Yu H, Wang Q, Ge Y, Huo M, Lv X, Zhang L, Zhao G, Gai Z. Gut microbiota-metabolite interactions meditate the effect of dietary patterns on precocious puberty. iScience 2024; 27:109887. [PMID: 38784002 PMCID: PMC11112371 DOI: 10.1016/j.isci.2024.109887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Precocious puberty, a pediatric endocrine disorder classified as central precocious puberty (CPP) or peripheral precocious puberty (PPP), is influenced by diet, gut microbiota, and metabolites, but the specific mechanisms remain unclear. Our study found that increased alpha-diversity and abundance of short-chain fatty acid-producing bacteria led to elevated levels of luteinizing hormone and follicle-stimulating hormone, contributing to precocious puberty. The integration of specific microbiota and metabolites has potential diagnostic value for precocious puberty. The Prevotella genus-controlled interaction factor, influenced by complex carbohydrate consumption, mediated a reduction in estradiol levels. Interactions between obesity-related bacteria and metabolites mediated the beneficial effect of seafood in reducing luteinizing hormone levels, reducing the risk of obesity-induced precocious puberty, and preventing progression from PPP to CPP. This study provides valuable insights into the complex interplay between diet, gut microbiota and metabolites in the onset, development and clinical classification of precocious puberty and warrants further investigation.
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Affiliation(s)
- Ying Wang
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Chuandi Jin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hongying Li
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Xiangrong Liang
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Changying Zhao
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Nan Wu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Min Yue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lu Zhao
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Central Laboratory, Weifang People’s Hospital/The First Affiliated Hospital of Shandong Second Medical university, Weifang 261000, China
- Shandong Laibo Biotechnology Co., Ltd., Jinan 250101, China
| | - Han Yu
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Qian Wang
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Yongsheng Ge
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Meiling Huo
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Xin Lv
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Lehai Zhang
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
| | - Guoping Zhao
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Zhongtao Gai
- Children’s Hospital Affiliated to Shandong University, Shandong University, Jinan 250022, China
- Jinan Children’s Hospital, Jinan 250022, China
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2
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Wang T, Shi Z, Ren H, Xu M, Lu J, Yang F, Ye C, Wu K, Chen M, Xu X, Liu D, Kong L, Zheng R, Zheng J, Li M, Xu Y, Zhao Z, Chen Y, Yang H, Wang J, Ning G, Li J, Zhong H, Bi Y, Wang W. Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nat Med 2024:10.1038/s41591-024-03038-y. [PMID: 38844795 DOI: 10.1038/s41591-024-03038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/30/2024] [Indexed: 06/13/2024]
Abstract
Insight into associations between the gut microbiome with metabolism and aging is crucial for tailoring interventions to promote healthy longevity. In a discovery cohort of 10,207 individuals aged 40-93 years, we used 21 metabolic parameters to classify individuals into five clusters, termed metabolic multimorbidity clusters (MCs), that represent different metabolic subphenotypes. Compared to the cluster classified as metabolically healthy (MC1), clusters classified as 'obesity-related mixed' (MC4) and 'hyperglycemia' (MC5) exhibited an increased 11.1-year cardiovascular disease (CVD) risk by 75% (multivariable-adjusted hazard ratio (HR): 1.75, 95% confidence interval (CI): 1.43-2.14) and by 117% (2.17, 1.72-2.74), respectively. These associations were replicated in a second cohort of 9,061 individuals with a 10.0-year follow-up. Based on analysis of 4,491 shotgun fecal metagenomes from the discovery cohort, we found that gut microbial composition was associated with both MCs and age. Next, using 55 age-specific microbial species to capture biological age, we developed a gut microbial age (MA) metric, which was validated in four external cohorts comprising 4,425 metagenomic samples. Among individuals aged 60 years or older, the increased CVD risk associated with MC4 or MC5, as compared to MC1, MC2 or MC3, was exacerbated in individuals with high MA but diminished in individuals with low MA, independent of age, sex and other lifestyle and dietary factors. This pattern, in which younger MA appears to counteract the CVD risk attributable to metabolic dysfunction, implies a modulating role of MA in cardiovascular health for metabolically unhealthy older people.
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Affiliation(s)
- Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhun Shi
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Huahui Ren
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Chaojie Ye
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kui Wu
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen, China
| | - Mingling Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xun Xu
- BGI Research, Shenzhen, China
| | - Dong Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijie Kong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruizhi Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Huanzi Zhong
- BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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3
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Rook GAW. Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES). Neurosci Biobehav Rev 2024; 161:105653. [PMID: 38582194 DOI: 10.1016/j.neubiorev.2024.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.
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Affiliation(s)
- Graham A W Rook
- Centre for Clinical Microbiology, Department of infection, UCL (University College London), London, UK.
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4
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Adamberg S, Adamberg K. Prevotella enterotype associates with diets supporting acidic faecal pH and production of propionic acid by microbiota. Heliyon 2024; 10:e31134. [PMID: 38779015 PMCID: PMC11109898 DOI: 10.1016/j.heliyon.2024.e31134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 03/21/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolism of dietary fibres by colon microbiota plays an important role for human health. Personal data from a nutrition study (57 subjects) were analysed to elucidate quantitative associations between the diet, faecal microbiome, organic acid concentrations and pH. Ratios of the predominant acids acetate, butyrate and propionate ranged from 1:0.67:0.27 to 1:0.17:0.36. Pectin-rich diets resulted in higher faecal acetate concentrations. Negative correlation between faecal pH and BSS was observed. Higher faecal pH and lower acid concentrations were related to the higher abundance of amino acid degrading Clostridium, Odoribacter and Eubacterium coprostanoligenes, which are weak carbohydrate fermenting taxa. Propionic acid correlated especially to high abundance of Prevotella and low abundance of proteobacteria. The acetate to propionate ratio of the Prevotella enterotype was about half of that of the Bacteroides enterotype. Based on the results we suggest the measurement of faecal pH and organic acid composition for research and diagnostic purposes.
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Affiliation(s)
- Signe Adamberg
- Tallinn University of Technology, Department of Chemistry and Biotechnology, 12618, Tallinn, Estonia
| | - Kaarel Adamberg
- Tallinn University of Technology, Department of Chemistry and Biotechnology, 12618, Tallinn, Estonia
- Center of Food and Fermentation Technologies, 12618, Tallinn, Estonia
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5
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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6
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Hs A. The Impact of Prevotella on Neurobiology in Aging: Deciphering Dendritic Cell Activity and Inflammatory Dynamics. Mol Neurobiol 2024:10.1007/s12035-024-04156-x. [PMID: 38613648 DOI: 10.1007/s12035-024-04156-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/29/2024] [Indexed: 04/15/2024]
Abstract
Prevotella species, notably Prevotella copri, significantly populate the human gut. In particular, P. copri is prevalent among non-Western populations with diets high in fiber. These species show complex relationships with diverse health aspects, associating with beneficial outcomes, including reduced visceral fat and improved glucose tolerance. Studies implicate various Prevotella species in specific diseases. Prevotella nigrescens and Porphyromonas gingivalis were linked to periodontal disease, promoting immune responses and influencing T helper type 17 (Th17) cells. Prevotella bivia was associated with bacterial vaginosis and a specific increase in activated cells in the vaginal mucosa. In contrast, they have shown substantial potential for inducing connective tissue degradation and alveolar bone resorption. Prevotella's role in neuroinflammatory disorders and autoinflammatory conditions such as Alzheimer's disease and Parkinson's disease has also been noted. The complex relationship between Prevotella and age-related conditions further extends to neurobiological changes in aging, with varying associations with Alzheimer's, Parkinson's, and other inflammatory conditions. Studies have also identified Prevotella to be implicated in cognitive decline in middle aged and the elderly. Future directions in this research area are anticipated to explore Prevotella-associated inflammatory mechanisms and therapeutic interventions. Investigating specific drug targets and immunomodulatory measures could lead to novel therapeutic strategies. Understanding how Prevotella-induced inflammation interacts with aging diseases would offer promising insights for treatments and interventions. This review urges ongoing research to discover therapeutic targets and mechanisms for moderating Prevotella-associated inflammation to further enhance our understanding and improve health outcomes.
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Affiliation(s)
- Ahmed Hs
- Bangalore Medical College and Research Institute, K.R Road, Bangalore, 560002, Karnataka, India.
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Luangphiphat W, Prombutara P, Muangsillapasart V, Sukitpunyaroj D, Eeckhout E, Taweechotipatr M. Exploring of gut microbiota features in dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography. Front Microbiol 2024; 15:1384146. [PMID: 38646625 PMCID: PMC11026706 DOI: 10.3389/fmicb.2024.1384146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Chronic coronary syndrome (CCS) has a high mortality rate, and dyslipidemia is a major risk factor. Atherosclerosis, a cause of CCS, is influenced by gut microbiota dysbiosis and its metabolites. The objective of this study was to study the diversity and composition of gut microbiota and related clinical parameters among CCS patients undergoing coronary angiography and dyslipidemia patients in comparison to healthy volunteers in Thailand. CCS patients had more risk factors and higher inflammatory markers, high-sensitivity C-reactive protein (hs-CRP) than others. The alpha diversity was lower in dyslipidemia and CCS patients than in the healthy group. A significant difference in the composition of gut microbiota was observed among the three groups. The relative abundance of Proteobacteria, Fusobacteria, Enterobacteriaceae, Prevotella, and Streptococcus was significantly increased while Roseburia, Ruminococcus, and Faecalibacterium were lower in CCS patients. In CCS patients, Lachnospiraceae, Peptostreptococcaceae, and Pediococcus were positively correlated with hs-CRP. In dyslipidemia patients, Megasphaera was strongly positively correlated with triglyceride (TG) level and negatively correlated with high-density lipoprotein cholesterol (HDL-C). The modification of gut microbiota was associated with changes in clinical parameters involved in the development of coronary artery disease (CAD) in CCS patients.
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Affiliation(s)
- Wongsakorn Luangphiphat
- Innovative Anatomy Program, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Mod Gut Co., Ltd., Bangkok, Thailand
| | - Viroj Muangsillapasart
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Damrong Sukitpunyaroj
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Eric Eeckhout
- Service of Cardiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Malai Taweechotipatr
- Center of Excellence in Probiotics, Srinakharinwirot University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
- Clinical Research Center, Faculty of Medicine, Srinakharinwirot University, Ongkharak, Thailand
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Schmidt N, Van Den Ham K, Bower L, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton P. Susceptibility to febrile malaria is associated with an inflammatory gut microbiome. RESEARCH SQUARE 2024:rs.3.rs-3974068. [PMID: 38645126 PMCID: PMC11030534 DOI: 10.21203/rs.3.rs-3974068/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii, Ruminococcus torques, Dorea formicigenerans, Dorea longicatena, Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii, Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.
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Zhou Y, Tang J, Du W, Zhang Y, Ye BC. Screening potential biomarkers associated with insulin resistance in high-fat diet-fed mice by integrating metagenomics and untargeted metabolomics. Microbiol Spectr 2024; 12:e0409423. [PMID: 38411058 PMCID: PMC10986473 DOI: 10.1128/spectrum.04094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024] Open
Abstract
Insulin resistance is the primary pathophysiological basis for metabolic syndrome and type 2 diabetes. Gut microbiota and microbiota-derived metabolites are pivotal in insulin resistance. However, identifying the specific microbes and key metabolites with causal roles is a challenging task, and the underlying mechanisms require further exploration. Here, we successfully constructed a model of insulin resistance in mice induced by a high-fat diet (HFD) and screened potential biomarkers associated with insulin resistance by integrating metagenomics and untargeted metabolomics. Our findings showed a significant increase in the abundance of 30 species of Alistipes in HFD mice compared to normal diet (ND) mice, while the abundance of Desulfovibrio and Candidatus Amulumruptor was significantly lower in HFD mice than in ND mice. Non-targeted metabolomics analysis identified 21 insulin resistance-associated metabolites, originating from the microbiota or co-metabolized by both the microbiota and the host. These metabolites were primarily enriched in aromatic amino acid metabolism (tryptophan metabolism, tyrosine metabolism, and phenylalanine metabolism) and arginine biosynthesis. Further analysis revealed a significant association between the three distinct genera and 21 differentiated metabolites in the HFD and ND mice. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of representative genomes from 12 species of the three distinct genera further revealed the functional potential in aromatic amino acid metabolism and arginine biosynthesis. This study lays the groundwork for future investigations into the mechanisms through which the gut microbiota and its metabolites impact insulin resistance. IMPORTANCE In this study, we aim to identify the microbes and metabolites linked to insulin resistance, some of which have not been previously reported in insulin resistance-related studies. This adds a complementary dimension to existing research. Furthermore, we establish a correlation between alterations in the gut microbiota and metabolite levels. These findings serve as a foundation for identifying the causal bacterial species and metabolites. They also offer insights that guide further exploration into the mechanisms through which these factors influence host insulin resistance.
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Affiliation(s)
- Yunyan Zhou
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Jiahui Tang
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Wei Du
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong Zhang
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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10
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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [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: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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11
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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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12
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Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N. Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.580813. [PMID: 38464031 PMCID: PMC10925137 DOI: 10.1101/2024.02.19.580813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences (~94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.
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Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Italy
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Andrea Silverj
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | | | - Omar Rota-Stabelli
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | - Jordan Jensen
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sagun Maharjan
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric Franzosa
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK
| | - Alessia Visconti
- Center for Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | | | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Hiroaki Kitano
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- The Systems Biology Institute (SBI), Tokyo, Japan
- IOM Bioworks Pvt. Ltd., Centre for Cellular and Molecular Platforms (C-CAMP), GKVK Post, Bellary Rd, Bengaluru, Karnataka-560065, India
| | - Takuji Yamada
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Metagen, Inc., Yamagata, Japan
- Metagen Therapeutics, Inc., Yamagata, Japan
- digzyme, Inc., Tokyo, Japan
| | - Nicola Segata
- Department CIBIO, University of Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
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13
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Yunusbaeva M, Borodina L, Terentyeva D, Bogdanova A, Zakirova A, Bulatov S, Altinbaev R, Bilalov F, Yunusbayev B. Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients. Front Cell Infect Microbiol 2024; 14:1331521. [PMID: 38440790 PMCID: PMC10910113 DOI: 10.3389/fcimb.2024.1331521] [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: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction The link between gut microbiota and host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host's immunity. Methods We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the gut microbiome's metabolic capacity and strain/species-level content. Results We show that the systematic depletion of the commensal flora of the large intestine, Bacteroidetes, and an increase in Actinobacteria, Firmicutes, and Proteobacteria such as Streptococcaceae, Erysipelotrichaceae, Lachnospiraceae, and Enterobacteriaceae explains the strong taxonomic divergence of the gut community in TB patients. The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia. Discussion Excessive fermentation and lactic acidosis likely characterize TB patients' disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus. If confirmed, gut acidosis may be a novel potential host-directed treatment target to augment traditional TB treatment.
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Affiliation(s)
- Milyausha Yunusbaeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Liliya Borodina
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Darya Terentyeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, Saint Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Anna Bogdanova
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
| | - Aigul Zakirova
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Shamil Bulatov
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Radick Altinbaev
- Laboratory of Neurophysiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - Fanil Bilalov
- Laboratory of Molecular Genetics, Republic Medical Genetic Centre, Ufa, Russia
- Department of Public Health and Health Organization with a course of ICPE, Bashkir State Medical University, Ufa, Russia
| | - Bayazit Yunusbayev
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
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14
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Xiao X, Le HH, Lee MT, Lamm D, Johnson EL, Brito IL. Prevotella copri variants among a single host diverge in sphingolipid production. mBio 2024; 15:e0240923. [PMID: 38236049 PMCID: PMC10865984 DOI: 10.1128/mbio.02409-23] [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: 09/05/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, Bacteroides species have been identified as major producers of sphingolipids, and Bacteroides-produced sphingolipids have been shown to be modulators of host immune and metabolic functions. While Bacteroides species are a prominent feature of the gut microbiomes of populations living in industrialized countries, Prevotella copri, a member of the same phyla, albeit a different family, is the dominant feature across the remainder of the global population, although their sphingolipid-producing capabilities have not been as thoroughly investigated. To fill this gap, we examined the genomes of over 60 diverse isolates of P. copri and identified several key enzymes involved in sphingolipid synthesis in P. copri. Combining bioorthogonal labeling and liquid chromatography-mass spectrometry (LC-MS) based lipidomics, we functionally characterized the first step in P. copri de novo sphingolipid synthesis in addition to profiling the sphingolipidomes of P. copri strains, identifying key enzymes that may play roles in producing a diverse set of P. copri sphingolipids. Given the limited genetic engineering tools amenable for use in P. copri, our approach takes advantage of comparative genomics and phenotypic profiling to explore sphingolipid production in these understudied, yet highly prevalent, organisms.IMPORTANCESphingolipids are important signaling molecules for maintaining metabolic and immune homeostasis in the host. These lipids are also produced by gut commensals, most notably by Bacteroides species. Despite the global prevalence of Prevotella copri in gut microbiomes of individuals, little is known about the types of sphingolipids they produce and whether they are similar in composition and structure to those produced by Bacteroides. Given the varied associations of P. copri with diverse sphingolipid-related health outcomes, such as rheumatoid arthritis and glucose intolerance, it is important to first characterize the specific sphingolipids produced by individual strains of P. copri and to identify the genes involved in their pathways of production. This characterization of P. copri-derived sphingolipids provides further insight into how bacterial sphingolipid production can serve as a mechanism for microbial modulation of host phenotypes.
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Affiliation(s)
- Xieyue Xiao
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
| | - Henry H. Le
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
| | - Min-Ting Lee
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
| | - Daniel Lamm
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
| | - Elizabeth L. Johnson
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Ilana L. Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
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15
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Yuan H, Wu X, Wang X, Zhou JY, Park S. Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype. Int J Mol Sci 2024; 25:2183. [PMID: 38396863 PMCID: PMC10889285 DOI: 10.3390/ijms25042183] [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: 12/28/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is characterized by hepatic fat accumulation by metabolic dysfunction. The rising prevalence of MAFLD, especially among Asians, may be associated with changes in gut microbiota. We investigated gut microbiota characteristics and potential mechanisms leading to MAFLD development according to enterotypes. Case-control studies examining the gut microbiota composition between MAFLD and non-MAFLD participants were searched in public databases until July 2023. Gut microbiota was categorized into two enterotypes by principal component analysis. According to the enterotypes, LEfSe, ALDEx2, XGBoost, and DCiPatho were utilized to identify differential abundances and pathogenic microbes in the gut between the MAFLD and non-MAFLD groups. We analyzed microbial community networks with the SprCC module and predicted microbial functions. In the Prevotella enterotype (ET-P), 98.6% of Asians and 65.1% of Caucasians were associated with MAFLD (p = 0.049). MAFLD incidence was correlated with enterotype, age, obesity, and ethnicity (p < 0.05). Asian MAFLD patients exhibited decreased Firmicutes and Akkermansia muciniphila and increased Bacteroidetes and P. copri. The pathogenicity scores were 0.006 for A. muciniphila and 0.868 for P. copri. The Asian MAFLD group showed decreased stability and complexity in the gut microbiota network. Metagenome function analysis revealed higher fructose metabolism and lipopolysaccharide (LPS) biosynthesis and lower animal proteins and α-linolenic acid metabolism in Asians with MAFLD compared with the non-MAFLD group. LPS biosynthesis was positively correlated with P. copri (p < 0.05). In conclusion, P. copri emerged as a potential microbial biomarker for MAFLD. These findings enhance our understanding of the pathological mechanisms of MAFLD mediated through the gut microbiota, providing insights for future interventions.
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Affiliation(s)
- Heng Yuan
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Xuangao Wu
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Xichun Wang
- Department of Computer and Data Analysis, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jun-Yu Zhou
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Sunmin Park
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan 31499, Republic of Korea
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16
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Valentino V, Magliulo R, Farsi D, Cotter PD, O'Sullivan O, Ercolini D, De Filippis F. Fermented foods, their microbiome and its potential in boosting human health. Microb Biotechnol 2024; 17:e14428. [PMID: 38393607 PMCID: PMC10886436 DOI: 10.1111/1751-7915.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.
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Affiliation(s)
- Vincenzo Valentino
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Raffaele Magliulo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
| | - Dominic Farsi
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
| | - Paul D. Cotter
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Orla O'Sullivan
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Danilo Ercolini
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
| | - Francesca De Filippis
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
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17
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Rozwalak P, Barylski J, Wijesekara Y, Dutilh BE, Zielezinski A. Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nat Commun 2024; 15:495. [PMID: 38263397 PMCID: PMC10805732 DOI: 10.1038/s41467-023-44370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
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Affiliation(s)
- Piotr Rozwalak
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
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18
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature 2024; 625:157-165. [PMID: 38093016 PMCID: PMC10764277 DOI: 10.1038/s41586-023-06838-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.
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Affiliation(s)
- Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Nikita P Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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19
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Hao QY, Yan J, Wei JT, Zeng YH, Feng LY, Que DD, Li SC, Guo JB, Fan Y, Ding YF, Zhang XL, Yang PZ, Gao JW, Li ZH. Prevotella copri promotes vascular calcification via lipopolysaccharide through activation of NF-κB signaling pathway. Gut Microbes 2024; 16:2351532. [PMID: 38727248 DOI: 10.1080/19490976.2024.2351532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
Emerging evidence indicates that alteration of gut microbiota plays an important role in chronic kidney disease (CKD)-related vascular calcification (VC). We aimed to investigate the specific gut microbiota and the underlying mechanism involved in CKD-VC. We identified an increased abundance of Prevotella copri (P. copri) in the feces of CKD rats (induced by using 5/6 nephrectomy followed by a high calcium and phosphate diet) with aortic calcification via amplicon sequencing of 16S rRNA genes. In patients with CKD, we further confirmed a positive correlation between abundance of P. copri and aortic calcification scores. Moreover, oral administration of live P. copri aggravated CKD-related VC and osteogenic differentiation of vascular smooth muscle cells in vivo, accompanied by intestinal destruction, enhanced expression of Toll-like receptor-4 (TLR4), and elevated lipopolysaccharide (LPS) levels. In vitro and ex vivo experiments consistently demonstrated that P. copri-derived LPS (Pc-LPS) accelerated high phosphate-induced VC and VSMC osteogenic differentiation. Mechanistically, Pc-LPS bound to TLR4, then activated the nuclear factor κB (NF-κB) and nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) inflammasome signals during VC. Inhibition of NF-κB reduced NLRP3 inflammasome and attenuated Pc-LPS-induced VSMC calcification. Our study clarifies a novel role of P. copri in CKD-related VC, by the mechanisms involving increased inflammation-regulating metabolites including Pc-LPS, and activation of the NF-κB/NLRP3 signaling pathway. These findings highlight P. copri and its-derived LPS as potential therapeutic targets for VC in CKD.
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MESH Headings
- Animals
- Vascular Calcification/metabolism
- Vascular Calcification/pathology
- NF-kappa B/metabolism
- Lipopolysaccharides/metabolism
- Rats
- Renal Insufficiency, Chronic/metabolism
- Renal Insufficiency, Chronic/microbiology
- Renal Insufficiency, Chronic/chemically induced
- Renal Insufficiency, Chronic/pathology
- Signal Transduction
- Humans
- Male
- Toll-Like Receptor 4/metabolism
- Toll-Like Receptor 4/genetics
- Gastrointestinal Microbiome
- Prevotella/metabolism
- Rats, Sprague-Dawley
- Myocytes, Smooth Muscle/metabolism
- Osteogenesis/drug effects
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- Feces/microbiology
- Inflammasomes/metabolism
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Affiliation(s)
- Qing-Yun Hao
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Yan
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jin-Tao Wei
- Department of Cardiology, Dongguan Hospital of Southern Medical University, Southern Medical University, Dongguan, China
| | - Yu-Hong Zeng
- Medical Apparatus and Equipment Deployment, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Li-Yun Feng
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Dong-Dong Que
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shi-Chao Li
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Bin Guo
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Fan
- Department of Cardiology, Dongguan Hospital of Southern Medical University, Southern Medical University, Dongguan, China
| | - Yun-Fa Ding
- Department of General Surgery, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiu-Li Zhang
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ping-Zhen Yang
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Wei Gao
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Hua Li
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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20
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Jennings A, Kühn T, Bondonno NP, Waniek S, Bang C, Franke A, Kassubek J, Müller HP, Both M, Weber KS, Lieb W, Cassidy A. The gut microbiome modulates associations between adherence to a Mediterranean-style diet, abdominal adiposity, and C-reactive protein in population-level analysis. Am J Clin Nutr 2024; 119:136-144. [PMID: 37926191 PMCID: PMC10808821 DOI: 10.1016/j.ajcnut.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Adherence to a Mediterranean-style dietary pattern is likely to have variable effects on body composition, but the impact of gut microbiome on this relationship is unknown. OBJECTIVES To examine the potential mediating effect of the gut microbiome on the associations between Alternate Mediterranean Diet (aMed) scores, abdominal adiposity, and inflammation in population-level analysis. DESIGN In a community-based sample aged 25 to 83 y (n = 620; 41% female) from Northern Germany, we assessed the role of the gut microbiome, sequenced from 16S rRNA genes, on the associations between aMed scores, estimated using validated food-frequency questionnaires, magnetic resonance imaging-determined visceral (VAT) and subcutaneous (SAT) adipose tissue and C-reactive protein (CRP). RESULTS Higher aMed scores were associated with lower SAT (-0.86 L (95% CI: -1.56, -0.17), P = 0.01), VAT (-0.65 L (95% CI: -1.03,-0.27), P = 0.01) and CRP concentrations (-0.35 mg/L; β: -20.1% (95% CI: 35.5, -1.09), P = 0.04) in the highest versus lowest tertile after multivariate adjustment. Of the taxa significantly associated with aMed scores, higher abundance of Porphyromonadaceae mediated 11.6%, 9.3%, and 8.7% of the associations with lower SAT, VAT, and CRP, respectively. Conversely, a lower abundance of Peptostreptococcaceae mediated 13.1% and 18.2% of the association with SAT and CRP levels. Of the individual components of the aMed score, moderate alcohol intake was associated with lower VAT (-0.2 (95% CI: -0.4, -0.1), P =0.01) with a higher abundance of Oxalobacteraceae and lower abundance of Burkholderiaceae explaining 8.3% and 9.6% of this association, respectively. CONCLUSION These novel data suggest that abundance of specific taxa in the Porphyromonadaceae and Peptostreptococcaceae families may contribute to the association between aMed scores, lower abdominal adipose tissue, and inflammation.
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Affiliation(s)
- Amy Jennings
- Institute for Global Food Security, Queen's University Belfast, Northern Ireland
| | - Tilman Kühn
- Institute for Global Food Security, Queen's University Belfast, Northern Ireland; Heidelberg Institute of Global Health (HIGH), Faculty of Medicine and University Hospital, Heidelberg, Germany
| | - Nicola P Bondonno
- Institute for Nutrition Research, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia; The Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - Sabina Waniek
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Kassubek
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Marcus Both
- Department of Radiology and Neuroradiology, University Hospital of Schleswig-Holstein, Arnold-Heller-Straße 3, 24105, Kiel, Germany
| | - Katharina S Weber
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel Germany
| | - Aedín Cassidy
- Institute for Global Food Security, Queen's University Belfast, Northern Ireland.
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21
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Su J, Lin X, Li D, Yang C, Lv S, Chen X, Yang X, Pan B, Xu R, Ren L, Zhang Y, Xie Y, Chen Q, Xia C. Prevotella copri exhausts intrinsic indole-3-pyruvic acid in the host to promote breast cancer progression: inactivation of AMPK via UHRF1-mediated negative regulation. Gut Microbes 2024; 16:2347757. [PMID: 38773738 PMCID: PMC11123460 DOI: 10.1080/19490976.2024.2347757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Emerging evidence has revealed the novel role of gut microbiota in the development of cancer. The characteristics of function and composition in the gut microbiota of patients with breast cancer patients has been reported, however the detailed causation between gut microbiota and breast cancer remains uncertain. In the present study, 16S rRNA sequencing revealed that Prevotella, particularly the dominant species Prevotella copri, is significantly enriched and prevalent in gut microbiota of breast cancer patients. Prior-oral administration of P. copri could promote breast cancer growth in specific pathogen-free mice and germ-free mice, accompanied with sharp reduction of indole-3-pyruvic acid (IPyA). Mechanistically, the present of excessive P. copri consumed a large amount of tryptophan (Trp), thus hampering the physiological accumulation of IPyA in the host. Our results revealed that IPyA is an intrinsic anti-cancer reagent in the host at physiological level. Briefly, IPyA directly suppressed the transcription of UHRF1, following by the declined UHRF1 and PP2A C in nucleus, thus inhibiting the phosphorylation of AMPK, which is just opposite to the cancer promoting effect of P. copri. Therefore, the exhaustion of IPyA by excessive P. copri strengthens the UHRF1-mediated negative control to inactivated the energy-controlling AMPK signaling pathway to promote tumor growth, which was indicated by the alternation in pattern of protein expression and DNA methylation. Our findings, for the first time, highlighted P. copri as a risk factor for the progression of breast cancer.
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Affiliation(s)
- Jiyan Su
- Scientific Research Center, Foshan Maternity & Child Healthcare Hospital, Foshan, P. R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiaojie Lin
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Dan Li
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangzhou, P. R. China
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Guangzhou, P. R. China
| | - Chunmin Yang
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Shumei Lv
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangzhou, P. R. China
| | - Xiaohong Chen
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangzhou, P. R. China
- Department of Basic Medical Science, Xiamen Medical College, Xiamen, P. R. China
| | - Xiujuan Yang
- Scientific Research Center, Foshan Maternity & Child Healthcare Hospital, Foshan, P. R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Botao Pan
- Scientific Research Center, Foshan Maternity & Child Healthcare Hospital, Foshan, P. R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Rui Xu
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Liping Ren
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Yanfang Zhang
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Yizhen Xie
- Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangzhou, P. R. China
- R&D Department, Guangdong Yuewei Edible Fungi Technology Co. Ltd, Guangzhou, P. R. China
| | - Qianjun Chen
- Breast Department, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. China
| | - Chenglai Xia
- Scientific Research Center, Foshan Maternity & Child Healthcare Hospital, Foshan, P. R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, P. R. China
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22
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Tsai CY, Liu PY, Huang MC, Chang CI, Chen HY, Chou YH, Tsai CN, Lin CH. Abundance of Prevotella copri in gut microbiota is inversely related to a healthy diet in patients with type 2 diabetes. J Food Drug Anal 2023; 31:599-608. [PMID: 38526814 PMCID: PMC10962673 DOI: 10.38212/2224-6614.3484] [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: 06/11/2023] [Revised: 11/24/2023] [Accepted: 11/13/2023] [Indexed: 03/27/2024] Open
Abstract
While the gut microbiota is known to be influenced by habitual food intake, this relationship is seldom explored in type 2 diabetes patients. This study aims to investigate the relationship between dietary patterns and gut microbial species abundance in 113 type 2 diabetes patients (mean age, 58 years; body mass index, 29.1; glycohemoglobin [HbA1c], 8.1%). We analyzed the gut microbiota using 16S amplicon sequencing, and all patients were categorized into either the Bacteroides enterotype (57.5%, n = 65) or the Prevotella enterotype (42.5%, n = 48) using the partitioning around medoids clustering algorithm, based on the most representative genera. Patients with the Bacteroides enterotype showed better glycemic control with a 2.71 odds of HbA1c ≤ 7.0% compared to the Prevotella enterotype (95% confidence interval, 1.02-7.87; P, 0.034). Dietary habits and the nutrient composition of all patients were assessed using a validated food frequency questionnaire. It was observed that the amounts of dietary fiber consumed were suboptimal, with an average intake of 16 g per day. Additionally, we extracted four dietary patterns through factor analysis: eating-out, high-sugar foods, fish-vegetable, and fermented foods patterns. Patients with the Bacteroides enterotype had higher scores for the fish-vegetable pattern compared to the Prevotella enterotype (0.17 ± 0.13 versus -0.23 ± 0.09; P, 0.010). We further investigated the relationship between the microbiota and the four dietary patterns and found that only the fish-vegetable dietary pattern scores were correlated with principal coordinate values. A lower pattern score was associated with the accumulated abundance of the 31 significant microbial features. Among these features, Prevotella copri was identified as the most significant by using a random forest model, with an area under the receiver operating characteristic of 0.93 (95% confidence interval, 0.88-0.98). To validate these results, we conducted a custom quantitative polymerase chain reaction assay. This assay confirmed the presence of P. copri (sensitivity, 0.96; specificity, 0.97) in our cohort, with a prevalence of 47.8%, and a mean relative abundance of 21.0% in subjects harboring P. copri. In summary, type 2 diabetes patients with the Prevotella enterotype demonstrated poorer glycemic control and deviations from a healthy dietary pattern. The abundance of P. copri, as a major contributing microbial feature, was associated with the severity in the deficiency in dietary fish and vegetables. Emphasis should be placed on promoting a healthy dietary pattern and understanding the microbial correlations.
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Affiliation(s)
- Chih-Yiu Tsai
- Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung,
Taiwan
| | - Meng-Chuan Huang
- Department of Nutrition and Dietetics, Kaohsiung Medical University Hospital, Kaohsiung,
Taiwan
- Department of Public Health and Environmental Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung,
Taiwan
| | - Chiao-I Chang
- Department of Public Health and Environmental Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung,
Taiwan
| | - Hsin-Yun Chen
- Department of Nutrition Therapy, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Yu-Hsien Chou
- Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Surgery, New Taipei Municipal Tucheng Hospital, New Taipei City,
Taiwan
| | - Chia-Hung Lin
- Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- Department of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
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23
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Baud GLC, Prasad A, Ellegaard KM, Engel P. Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers. Genome Biol 2023; 24:283. [PMID: 38066630 PMCID: PMC10704631 DOI: 10.1186/s13059-023-03131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood. RESULTS Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states. CONCLUSIONS Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.
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Affiliation(s)
- Gilles L C Baud
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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24
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Abdelsalam NA, Hegazy SM, Aziz RK. The curious case of Prevotella copri. Gut Microbes 2023; 15:2249152. [PMID: 37655441 PMCID: PMC10478744 DOI: 10.1080/19490976.2023.2249152] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
Prevotella copri is an abundant member of the human gastrointestinal microbiome, whose relative abundance has curiously been associated with positive and negative impacts on diseases, such as Parkinson's disease and rheumatoid arthritis. Yet, the verdict is still out on the definitive role of P. copri in human health, and on the effect of different diets on its relative abundance in the gut microbiome. The puzzling discrepancies among P. copri studies have only recently been attributed to the diversity of its strains, which substantially differ in their encoded metabolic patterns from the commonly used reference strain. However, such strain differences cannot be resolved by common 16S rRNA amplicon profiling methods. Here, we scrutinize P. copri, its versatile metabolic potential, and the hypotheses behind the conflicting observations on its association with diet and human health. We also provide suggestions for designing studies and bioinformatics pipelines to better research P. copri.
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Affiliation(s)
| | - Shaimaa M. Hegazy
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ramy K. Aziz
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
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25
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Lim MY, Nam YD. Gut microbiome in healthy aging versus those associated with frailty. Gut Microbes 2023; 15:2278225. [PMID: 37968837 PMCID: PMC10730223 DOI: 10.1080/19490976.2023.2278225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
As the proportion of older people in the world's population steadily increases, there is an urgent need to identify ways to support healthy aging. The gut microbiome has been proposed to be involved in aging-related diseases and has become an attractive target for improving health in older people. Herein, we cover the relationship between the gut microbiome and chronological age in adults, and then, we discuss the gut microbiome features associated with frailty, as a hallmark of unhealthy aging in older people. Furthermore, we describe the effects of microbiome-targeted interventions, such as dietary patterns and consumption of probiotics, prebiotics, and synbiotics, on modulating the gut microbiome composition and further promoting healthy aging. Further studies are needed to explore the underlying mechanisms of gut microbiome-induced aging complications and to develop personalized microbiome-based strategies for reducing the severity of frailty or preventing the onset of frailty in older adults.
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Affiliation(s)
- Mi Young Lim
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| | - Young-Do Nam
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
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26
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Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep 2023; 42:113233. [PMID: 38510311 PMCID: PMC10954246 DOI: 10.1016/j.celrep.2023.113233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no-MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
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Affiliation(s)
- Rebecca H. Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolé cules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
- Lead contact
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27
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Hugon AM, Deblois CL, Simmons HA, Mejia A, Schotzo ML, Czuprynski CJ, Suen G, Golos TG. Listeria monocytogenes infection in pregnant macaques alters the maternal gut microbiome†. Biol Reprod 2023; 109:618-634. [PMID: 37665249 PMCID: PMC10651077 DOI: 10.1093/biolre/ioad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
OBJECTIVES The bacterium Listeria monocytogenes (Lm) is associated with adverse pregnancy outcomes. Infection occurs through consumption of contaminated food that is disseminated to the maternal-fetal interface. The influence on the gastrointestinal microbiome during Lm infection remains unexplored in pregnancy. The objective of this study was to determine the impact of listeriosis on the gut microbiota of pregnant macaques. METHODS A non-human primate model of listeriosis in pregnancy has been previously described. Both pregnant and non-pregnant cynomolgus macaques were inoculated with Lm and bacteremia and fecal shedding were monitored for 14 days. Non-pregnant animal tissues were collected at necropsy to determine bacterial burden, and fecal samples from both pregnant and non-pregnant animals were evaluated by 16S rRNA next-generation sequencing. RESULTS Unlike pregnant macaques, non-pregnant macaques did not exhibit bacteremia, fecal shedding, or tissue colonization by Lm. Dispersion of Lm during pregnancy was associated with a significant decrease in alpha diversity of the host gut microbiome, compared to non-pregnant counterparts. The combined effects of pregnancy and listeriosis were associated with a significant loss in microbial richness, although there were increases in some genera and decreases in others. CONCLUSIONS Although pregnancy alone is not associated with gut microbiome disruption, we observed dysbiosis with listeriosis during pregnancy. The macaque model may provide an understanding of the roles that pregnancy and the gut microbiota play in the ability of Lm to establish intestinal infection and disseminate throughout the host, thereby contributing to adverse pregnancy outcomes and risk to the developing fetus.
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Affiliation(s)
- Anna Marie Hugon
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Courtney L Deblois
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - Heather A Simmons
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Michele L Schotzo
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Charles J Czuprynski
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin–Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin–Madison, Madison, WI, USA
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28
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Mah JC, Lohmueller KE, Garud N. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566454. [PMID: 38014007 PMCID: PMC10680615 DOI: 10.1101/2023.11.09.566454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.
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29
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Peng Y, Tun HM. Meet the extended Segatella copri complex. Cell Host Microbe 2023; 31:1766-1769. [PMID: 37944487 DOI: 10.1016/j.chom.2023.10.009] [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: 10/06/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
The Segatella copri complex contains key members of the human gut microbiome, but their genetic diversity and associations with health are incompletely understood. In this issue of Cell Host & Microbe, Blanco-Míguez et al. expand the S. copri complex to 13 species and reveal species-specific associations with lifestyle and health.
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Affiliation(s)
- Ye Peng
- Microbiota I-Center (MagIC), Hong Kong, China; Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong, China; Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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30
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Blanco-Míguez A, Gálvez EJC, Pasolli E, De Filippis F, Amend L, Huang KD, Manghi P, Lesker TR, Riedel T, Cova L, Punčochář M, Thomas AM, Valles-Colomer M, Schober I, Hitch TCA, Clavel T, Berry SE, Davies R, Wolf J, Spector TD, Overmann J, Tett A, Ercolini D, Segata N, Strowig T. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions. Cell Host Microbe 2023; 31:1804-1819.e9. [PMID: 37883976 PMCID: PMC10635906 DOI: 10.1016/j.chom.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.
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Affiliation(s)
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Linda Cova
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | | | | | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Technical University of Braunschweig, Braunschweig, Germany
| | - Adrian Tett
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Wien, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
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31
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Caputo M, Pigni S, Antoniotti V, Agosti E, Caramaschi A, Antonioli A, Aimaretti G, Manfredi M, Bona E, Prodam F. Targeting microbiota in dietary obesity management: a systematic review on randomized control trials in adults. Crit Rev Food Sci Nutr 2023; 63:11449-11481. [PMID: 35708057 DOI: 10.1080/10408398.2022.2087593] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Obesity is an alarming public health problem. Tailored nutritional therapy is advisable since emerging evidence on complex cross-talks among multifactorial agents. In this picture, the gut microbiota is highly individualized and intricately dependent on dietary patterns, with implications for obesity management. Most of the papers on the topic are observational and often conflicting. This review aimed to systematically organize the body of evidence on microbiota deriving from dietary trials in adult obesity giving the most certain phylogenetic, and metabolomic signatures in relation to both the host metabolism and phenotype changes published until now. We retrieved 18 randomized control trials on 1385 subjects with obesity who underwent several dietary interventions, including standard diet and healthy dietary regimens. Some phyla and species were more related to diets rich in fibers and others to healthy diets. Weight loss, metabolism improvements, inflammatory markers decrease were specifically related to different microorganisms or functions. The Prevotella/Bacteroides ratio was one of the most reported predictors. People with the burden of obesity comorbidities had the most significant taxonomic changes in parallel with a general improvement. These data emphasize the possibility of using symbiotic approaches involving tailored diets, microbiota characteristics, and maybe drugs to treat obesity and metabolic disorders. We encourage Authors to search for specific phylogenetic associations beyond a too generally reported Firmicutes/Bacteroides ratio.
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Affiliation(s)
- Marina Caputo
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
- Endocrinology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Stella Pigni
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Valentina Antoniotti
- SCDU of Pediatrics, Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Emanuela Agosti
- Endocrinology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Alice Caramaschi
- Department of Sustainable Development and Ecological Transition, Università del Piemonte Orientale, Vercelli, Italy
- Center for Translational Research on Autoimmune and Allergic Disease, Università del Piemonte Orientale, Novara, Italy
| | - Alessandro Antonioli
- Endocrinology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Gianluca Aimaretti
- Endocrinology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Marcello Manfredi
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease, Università del Piemonte Orientale, Novara, Italy
| | - Elisa Bona
- Department of Sustainable Development and Ecological Transition, Università del Piemonte Orientale, Vercelli, Italy
- Center for Translational Research on Autoimmune and Allergic Disease, Università del Piemonte Orientale, Novara, Italy
| | - Flavia Prodam
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
- Endocrinology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
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32
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Huttenhower C, Finn RD, McHardy AC. Challenges and opportunities in sharing microbiome data and analyses. Nat Microbiol 2023; 8:1960-1970. [PMID: 37783751 DOI: 10.1038/s41564-023-01484-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Microbiome data, metadata and analytical workflows have become 'big' in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Following best practices for data deposition requires substantial effort, with sometimes little obvious reward. Gaps remain where microbiome-specific resources for data sharing or reproducibility do not yet exist. We outline available best practices, challenges to their adoption and opportunities in data sharing in microbiome research. We showcase examples of best practices and advocate for their enforcement and incentivization for data sharing. This includes recognition of data curation and sharing endeavours by individuals, institutions, journals and funders. Opportunities for progress include enabling microbiome-specific databases to incorporate future methods for data analysis, integration and reuse.
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Affiliation(s)
- Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Departments of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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33
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Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023; 41:1633-1644. [PMID: 36823356 PMCID: PMC10635831 DOI: 10.1038/s41587-023-01688-w] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
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Affiliation(s)
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelsey N Thompson
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | - William A Nickols
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | | | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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34
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You L, Jin H, Kwok LY, Lv R, Zhao Z, Bilige M, Sun Z, Liu W, Zhang H. Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem. Sci Bull (Beijing) 2023; 68:2405-2417. [PMID: 37718237 DOI: 10.1016/j.scib.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Menghe Bilige
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Zhang P, Wang X, Li S, Cao X, Zou J, Fang Y, Shi Y, Xiang F, Shen B, Li Y, Fang B, Zhang Y, Guo R, Lv Q, Zhang L, Lu Y, Wang Y, Yu J, Xie Y, Wang R, Chen X, Yu J, Zhang Z, He J, Zhan J, Lv W, Nie Y, Cai J, Xu X, Hu J, Zhang Q, Gao T, Jiang X, Tan X, Xue N, Wang Y, Ren Y, Wang L, Zhang H, Ning Y, Chen J, Zhang L, Jin S, Ren F, Ehrlich SD, Zhao L, Ding X. Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease. Genome Biol 2023; 24:226. [PMID: 37828586 PMCID: PMC10571392 DOI: 10.1186/s13059-023-03056-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of the gut ecosystem and its functional capacity in such patients, which is still lacking. RESULTS Herein, we explore the gut microbiome of 378 hemodialytic ESRD patients and 290 healthy volunteers from two independent cohorts via deep metagenomic sequencing and metagenome-assembled-genome-based characterization of their feces. Our findings reveal fundamental alterations in the ESRD microbiome, characterized by a panel of 348 differentially abundant species, including ESRD-elevated representatives of Blautia spp., Dorea spp., and Eggerthellaceae, and ESRD-depleted Prevotella and Roseburia species. Through functional annotation of the ESRD-associated species, we uncover various taxon-specific functions linked to the disease, such as antimicrobial resistance, aromatic compound degradation, and biosynthesis of small bioactive molecules. Additionally, we show that the gut microbial composition can be utilized to predict serum uremic toxin concentrations, and based on this, we identify the key toxin-contributing species. Furthermore, our investigation extended to 47 additional non-dialyzed chronic kidney disease (CKD) patients, revealing a significant correlation between the abundance of ESRD-associated microbial signatures and CKD progression. CONCLUSION This study delineates the taxonomic and functional landscapes and biomarkers of the ESRD microbiome. Understanding the role of gut microbiota in ESRD could open new avenues for therapeutic interventions and personalized treatment approaches in patients with this condition.
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Affiliation(s)
- Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Xifan Wang
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Xuesen Cao
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jianzhou Zou
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yi Fang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yiqin Shi
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Fangfang Xiang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Bo Shen
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yixuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Liwen Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yufei Lu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yaqiong Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jinbo Yu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yeqing Xie
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Ran Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Xiaohong Chen
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jiawei Yu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Zhen Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jingjing He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Jing Zhan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Wenlv Lv
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yuxin Nie
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jieru Cai
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jiachang Hu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Qi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Ting Gao
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Xiaotian Jiang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Xiao Tan
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Ning Xue
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yimei Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yimei Ren
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Li Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Han Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Yichun Ning
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Jing Chen
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Lin Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Shi Jin
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China
| | - Fazheng Ren
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China
| | - Stanislav Dusko Ehrlich
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3RX, UK.
| | - Liang Zhao
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing, 100190, China.
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University; Hemodialysis Quality Control Center of Shanghai; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Institute for Kidney and Dialysis; Shanghai Clinical Medical Center for Kidney Disease, Shanghai, 200032, China.
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36
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Mayur O, Martinez R, Yi JZ, Chung HJ, McGee JS. A pilot study profiling the gut microbiome in acne patients of different racial backgrounds: Experimental considerations and pitfalls. Exp Dermatol 2023; 32:1864-1866. [PMID: 37183311 DOI: 10.1111/exd.14833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Omkar Mayur
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Rebeca Martinez
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Julie Z Yi
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Hye Jin Chung
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jean S McGee
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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37
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Gomes-Neto JC, Pavlovikj N, Korth N, Naberhaus SA, Arruda B, Benson AK, Kreuder AJ. Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs. Front Vet Sci 2023; 10:1186554. [PMID: 37781286 PMCID: PMC10537282 DOI: 10.3389/fvets.2023.1186554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023] Open
Abstract
Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S. Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson's and Shannon's indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.
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Affiliation(s)
- Joao Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Natasha Pavlovikj
- Holland Computing Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nate Korth
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Samantha A. Naberhaus
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Bailey Arruda
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Andrew K. Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda J. Kreuder
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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38
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Zeriouh M, Raskov H, Kvich L, Gögenur I, Bennedsen ALB. Checkpoint inhibitor responses can be regulated by the gut microbiota - A systematic review. Neoplasia 2023; 43:100923. [PMID: 37603952 PMCID: PMC10465958 DOI: 10.1016/j.neo.2023.100923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Evidence suggests that the human gut microbiota modulates the treatment response of immune checkpoint inhibitors (ICI) in cancer. Thus, finding predictive biomarkers in the fecal gut microbiota of patients who are less likely to respond to ICI would be valuable. This systematic review aimed to investigate the association between fecal gut microbiota composition and ICI-treatment response in patients with cancer. METHODS EMBASE, Medline, and Cochrane Library databases were searched using the "Participants, Interventions, Comparisons, and Outcomes" (PICO) process to locate studies including participants with solid cancers treated with ICI intervention. The comparator was the gut microbiota, and the outcomes were oncological outcomes such as response rates and progression-free survival. Study data were synthesized qualitatively in a systematic narrative synthesis, and the risk of bias in the studies was assessed. RESULTS Two reviewers screened 2092 abstracts independently, and 140 studies were read as full-text reports and assessed for eligibility. Eighteen studies were included with 775 patients with different types of solid cancers who received anti-PD-1, anti-PD-L1, or anti-CTLA-4 therapy. Distinct patterns were observed in the patients' fecal samples. Some bacterial species were reported to be present in responders and non-responders, while others were present only in one group. The most reported species associated with better prognosis were Faecalibacterium prausnitzii, Streptococcus parasanguinis, Bacteroides caccae, and Prevotella copri. In contrast, the most reported species associated with poor prognosis were Blautia obeum and Bacteroides ovatus. CONCLUSION Distinct microbiota features were associated with good and poor prognoses in ICI-treated patients with cancer.
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Affiliation(s)
- Mariam Zeriouh
- Department of Surgery, Center for Surgical Science, Zealand University Hospital, Lykkebækvej 1, Køge 4600, Denmark
| | - Hans Raskov
- Department of Surgery, Center for Surgical Science, Zealand University Hospital, Lykkebækvej 1, Køge 4600, Denmark
| | - Lasse Kvich
- Department of Surgery, Center for Surgical Science, Zealand University Hospital, Lykkebækvej 1, Køge 4600, Denmark; Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Ismail Gögenur
- Department of Surgery, Center for Surgical Science, Zealand University Hospital, Lykkebækvej 1, Køge 4600, Denmark
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39
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for malnourished children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293998. [PMID: 37645824 PMCID: PMC10462212 DOI: 10.1101/2023.08.14.23293998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that two Prevotella copri MAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i) in vitro growth of Bangladeshi P. copri strains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship between P. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.
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Affiliation(s)
- 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
| | - Daniel M. Webber
- 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
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Suzanne Henrissat
- 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
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- 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
| | - Cyrus Zhou
- 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
| | - Hannah M. Lynn
- 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
| | - Yi Wang
- 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
| | - Hao-Wei Chang
- 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
| | - Evan M. Lee
- 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
| | - Janaki Lelwala-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
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Semen A. Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering),
Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University,
Jeddah, Saudi Arabia
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Nikita P. Bacalzo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Ye Chen
- 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 Chemistry, University of California, Davis, CA
95616, USA
| | | | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - 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
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - 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
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Liao H, Ji Y, Sun Y. High-resolution strain-level microbiome composition analysis from short reads. MICROBIOME 2023; 11:183. [PMID: 37587527 PMCID: PMC10433603 DOI: 10.1186/s40168-023-01615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 07/07/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities. Metagenomic sequencing has become the major means for probing the microbial composition in host-associated or environmental samples. Although there are a plethora of composition analysis tools, they are not optimized to address the challenges in strain-level analysis: highly similar strain genomes and the presence of multiple strains under one species in a sample. Thus, this work aims to provide a high-resolution and more accurate strain-level analysis tool for short reads. RESULTS In this work, we present a new strain-level composition analysis tool named StrainScan that employs a novel tree-based k-mers indexing structure to strike a balance between the strain identification accuracy and the computational complexity. We tested StrainScan extensively on a large number of simulated and real sequencing data and benchmarked StrainScan with popular strain-level analysis tools including Krakenuniq, StrainSeeker, Pathoscope2, Sigma, StrainGE, and StrainEst. The results show that StrainScan has higher accuracy and resolution than the state-of-the-art tools on strain-level composition analysis. It improves the F1 score by 20% in identifying multiple strains at the strain level. CONCLUSIONS By using a novel k-mer indexing structure, StrainScan is able to provide strain-level analysis with higher resolution than existing tools, enabling it to return more informative strain composition analysis in one sample or across multiple samples. StrainScan takes short reads and a set of reference strains as input and its source codes are freely available at https://github.com/liaoherui/StrainScan . Video Abstract.
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Affiliation(s)
- Herui Liao
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, China
| | - Yongxin Ji
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, China.
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G-Santoyo I, Ramírez-Carrillo E, Sanchez JD, López-Corona O. Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle. J Dev Orig Health Dis 2023; 14:469-480. [PMID: 37222148 DOI: 10.1017/s2040174423000144] [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: 05/25/2023]
Abstract
Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.
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Affiliation(s)
- Isaac G-Santoyo
- Neuroecology Lab, Department of Psychology, UNAM, México, 04510
- Unidad de Investigación en Psicobiología y Neurociencias, Department of Psychology, UNAM, México, 04510
| | | | | | - Oliver López-Corona
- Investigadores por México (IxM)-CONACyT, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas (IIMAS), UNAM, México, 04510
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de la Rubia Ortí JE, Moneti C, Serrano-Ballesteros P, Castellano G, Bayona-Babiloni R, Carriquí-Suárez AB, Motos-Muñoz M, Proaño B, Benlloch M. Liposomal Epigallocatechin-3-Gallate for the Treatment of Intestinal Dysbiosis in Children with Autism Spectrum Disorder: A Comprehensive Review. Nutrients 2023; 15:3265. [PMID: 37513683 PMCID: PMC10383799 DOI: 10.3390/nu15143265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is characterized by varying degrees of difficulty in social interaction and communication. These deficits are often associated with gastrointestinal symptoms, indicating alterations in both intestinal microbiota composition and metabolic activities. The intestinal microbiota influences the function and development of the nervous system. In individuals with ASD, there is an increase in bacterial genera such as Clostridium, as well as species involved in the synthesis of branched-chain amino acids (BCAA) like Prevotella copri. Conversely, decreased amounts of Akkermansia muciniphila and Bifidobacterium spp. are observed. Epigallocatechin-3-gallate (EGCG) is one of the polyphenols with the greatest beneficial activity on microbial growth, and its consumption is associated with reduced psychological distress. Therefore, the objective of this review is to analyze how EGCG and its metabolites can improve the microbial dysbiosis present in ASD and its impact on the pathology. The analysis reveals that EGCG inhibits the growth of pathogenic bacteria like Clostridium perfringens and Clostridium difficile. Moreover, it increases the abundance of Bifidobacterium spp. and Akkermansia spp. As a result, EGCG demonstrates efficacy in increasing the production of metabolites involved in maintaining epithelial integrity and improving brain function. This identifies EGCG as highly promising for complementary treatment in ASD.
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Affiliation(s)
| | - Costanza Moneti
- Doctoral School, Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
| | | | - Gloria Castellano
- Centro de Investigación Traslacional San Alberto Magno (CITSAM), Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - Raquel Bayona-Babiloni
- Department of Basic Medical Sciences, Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - Ana Belén Carriquí-Suárez
- Department of Basic Medical Sciences, Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - María Motos-Muñoz
- Department of Personality Psychology, Treatment and Methodology, Catholic University of Valencia San Vicente Mártir, 46100 Valencia, Spain
- Child Neurorehabilitation Unit, Manises Hospital, 46940 Valencia, Spain
| | - Belén Proaño
- Department of Basic Medical Sciences, Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - María Benlloch
- Department of Basic Medical Sciences, Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
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43
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Hugon AM, Golos TG. Listeria monocytogenes infection in intestinal epithelial Caco-2 cells with exposure to progesterone and estradiol-17beta in a gestational infection model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550068. [PMID: 37503025 PMCID: PMC10370168 DOI: 10.1101/2023.07.21.550068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Listeria monocytogenes (Lm) is a food-borne pathogen associated with serious pregnancy complications, including miscarriage, stillbirth, preterm birth, neonatal sepsis, and meningitis. Although Lm infection within the gastrointestinal (GI) tract is well studied, little is known about the influence sex hormones may have on listeriosis. Estradiol (E2) and progesterone (P4) not only have receptors within the GI tract but are significantly increased during pregnancy. The presence of these hormones may play a role in susceptibility to listeriosis during pregnancy. Caco-2 cell monolayers were grown on trans-well inserts in the presence of E2, P4, both E2 and P4, or no hormones (control). Cells were inoculated with Lm for 1 hour, before rinsing with gentamycin and transfer to fresh media. Trans-epithelial resistance was recorded hourly, and bacterial burden of the apical media, intracellular lysates, and basal media were assessed at 6 hours post inoculation. There were no significant differences in bacterial replication when directly exposed to sex steroids, and Caco-2 cell epithelial barrier function was not impacted during culture with Lm. Addition of P4 significantly reduced intracellular bacterial burden compared to E2 only and no hormone controls. Interestingly, E2 only treatment was associated with significantly increased Lm within the basal compartment, compared to reduction in the intracellular and apical layers. These data indicate that increased circulating sex hormones alone do not significantly impact intestinal epithelial barrier integrity during listeriosis, but that addition of P4 and E2, alone or in combination, was associated with reduced epithelial cell bacterial burden and apical release of Lm.
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Affiliation(s)
- Anna Marie Hugon
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
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Morgado MC, Sousa M, Marques C, Coelho AB, Costa JA, Seabra A. Effects of Physical Activity and Nutrition Education on the Gut Microbiota in Overweight and Obese Children. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1242. [PMID: 37508739 PMCID: PMC10378599 DOI: 10.3390/children10071242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Childhood obesity continues to represent a growing challenge, and it has been associated with gut microbiota dysbiosis. This study examines the gut microbiota composition in overweight and obese school children and assesses whether a 12-week multidisciplinary intervention can induce changes in the gut microbiota. The intervention, which combined recreational football and nutritional education, was implemented among 15 school children, aged 7-10 years, with a Body Mass Index ≥ 85th percentile. The children were assigned into two groups: Football Group (n = 9) and Nutrition and Football Group (n = 6). Faecal samples were collected at the beginning and end of the program and analysed by sequencing the 16S rRNA gene. Over the intervention, a significant decrease was found collectively for Bifidobacterium genera (p = 0.011) and for Roseburia genera in the Football Group (p = 0.021). The relative abundance of Roseburia (p = 0.002) and Roseburia faecis (p = 0.009) was negatively correlated with moderate to vigorous physical activity (MVPA), while Prevotella copri was positively correlated with MVPA (p = 0.010) and with the daily intake of protein (p = 0.008). Our findings suggest that a multidisciplinary intervention was capable of inducing limited but significant positive changes in the gut microbiota composition in overweight and obese school children.
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Affiliation(s)
- Micaela C Morgado
- Research Centre in Physical Activity, Health and Leisure (CIAFEL), Faculty of Sport, University of Porto, 4200-450 Porto, Portugal
- Portugal Football School, Portuguese Football Federation (FPF), 1495-433 Cruz Quebrada, Portugal
| | - Mónica Sousa
- CINTESIS@RISE, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - Cláudia Marques
- CINTESIS@RISE, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - André B Coelho
- Faculty of Sports Science and Physical Education, University of Coimbra, 3040-248 Coimbra, Portugal
| | - Júlio A Costa
- Portugal Football School, Portuguese Football Federation (FPF), 1495-433 Cruz Quebrada, Portugal
| | - André Seabra
- Research Centre in Physical Activity, Health and Leisure (CIAFEL), Faculty of Sport, University of Porto, 4200-450 Porto, Portugal
- Portugal Football School, Portuguese Football Federation (FPF), 1495-433 Cruz Quebrada, Portugal
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Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 2023; 31:1111-1125.e6. [PMID: 37339626 DOI: 10.1016/j.chom.2023.05.024] [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: 01/26/2023] [Revised: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
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Affiliation(s)
- Clémence Frioux
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK; Inria, University of Bordeaux, INRAE, 33400 Talence, France.
| | - Rebecca Ansorge
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Ezgi Özkurt
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | | | - Joachim Fritscher
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Christopher Quince
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo 0318, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA 94148, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Falk Hildebrand
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK.
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RAH, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W, Manne U. Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients. Heliyon 2023; 9:e18035. [PMID: 37483698 PMCID: PMC10362239 DOI: 10.1016/j.heliyon.2023.e18035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
Purpose Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicities demonstrate distinct clinical behaviors. Thus, we investigated microbiome dysbiosis in Egyptian, African American (AA), and European American (EA) CRC patients. Patients and methods CRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. DNA was isolated from frozen tissues, and the microbiome composition was analyzed by 16S rRNA sequencing. Differential microbial abundance, diversity, and metabolic pathways were identified using linear discriminant analysis (LDA) effect size analyses. Additionally, we compared these profiles with our previously published microbiome data derived from Kenyan CRC patients. Results Differential microbiome analysis of CRCs across all racial/ethnic groups showed dysbiosis. There were high abundances of Herbaspirillum and Staphylococcus in CRCs of Egyptians, Leptotrichia in CRCs of AAs, Flexspiria and Streptococcus in CRCs of EAs, and Akkermansia muciniphila and Prevotella nigrescens in CRCs of Kenyans (LDA score >4, adj. p-value <0.05). Functional analyses showed distinct microbial metabolic pathways in CRCs compared to normal tissues within the racial/ethnic groups. Egyptian CRCs, compared to normal tissues, showed lower l-methionine biosynthesis and higher galactose degradation pathways. Conclusions Our findings showed altered mucosa-associated microbiome profiles of CRCs and their metabolic pathways across racial/ethnic groups. These findings provide a basis for future studies to link racial/ethnic microbiome differences with distinct clinical behaviors in CRC.
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Affiliation(s)
- Amr Elkholy
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Nagavardhini Avuthu
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mohammed Abdalla
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Michael Behring
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Prachi Bajpai
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Hyung-Gyoon Kim
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Doaa Header
- Department of Gastroenterology, Faculty of Medicine, University of Alexandria, Egypt
| | - Reham AH. Abo Elwafa
- Department of Clinical Pathology, Faculty of Medicine, University of Alexandria, Egypt
| | - Hesham Saed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Amira Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Nefertiti El-Nikhely
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Sarah Obuya
- Moi Teaching and Referral Hospital, Moi University, Kesses, Kenya
| | - Mostafa Mohamed
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Ahmed Ashour Badawy
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, University of Alexandria, Egypt
| | - Ahmed Nawar
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, University of Alexandria, Egypt
| | - Farrukh Afaq
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Laura Q. Rogers
- Division of Preventive Medicine, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sejong Bae
- Division of Preventive Medicine, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James M. Shikany
- Division of Preventive Medicine, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lori Brand Bateman
- Division of Preventive Medicine, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mona Fouad
- Division of Preventive Medicine, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mansoor Saleh
- Department of Hematology-Oncology, Aga Khan University, Nairobi, Kenya
| | - Temesgen Samuel
- Tuskegee University College of Veterinary Medicine Tuskegee, AL, USA
| | - Sooryanarayana Varambally
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Waleed Arafat
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, University of Alexandria, Egypt
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
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Holman DB, Gzyl KE, Kommadath A. The gut microbiome and resistome of conventionally vs. pasture-raised pigs. Microb Genom 2023; 9:mgen001061. [PMID: 37439777 PMCID: PMC10438820 DOI: 10.1099/mgen.0.001061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.
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Affiliation(s)
- Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Katherine E. Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
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Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci 2023:10.1038/s41593-023-01361-0. [PMID: 37365313 DOI: 10.1038/s41593-023-01361-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed a Bayesian differential ranking algorithm to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles. We found a functional architecture along the GBA that correlates with heterogeneity of ASD phenotypes, and it is characterized by ASD-associated amino acid, carbohydrate and lipid profiles predominantly encoded by microbial species in the genera Prevotella, Bifidobacterium, Desulfovibrio and Bacteroides and correlates with brain gene expression changes, restrictive dietary patterns and pro-inflammatory cytokine profiles. The functional architecture revealed in age-matched and sex-matched cohorts is not present in sibling-matched cohorts. We also show a strong association between temporal changes in microbiome composition and ASD phenotypes. In summary, we propose a framework to leverage multi-omic datasets from well-defined cohorts and investigate how the GBA influences ASD.
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Affiliation(s)
- James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dong-Min Jin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gibraan Rahman
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julie Carmel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Sandra Martin-Brevet
- Laboratory for Research in Neuroimaging, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Berding
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Brittany D Needham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - María Fernanda Zurita
- Microbiology Institute and Health Science College, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maude David
- Departments of Microbiology & Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Olga V Averina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Antonio Noto
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
- Microbiome Therapy Center, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ellen Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stony Brook University, Stony Brook, NY, USA
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Vassilios Fanos
- Neonatal Intensive Care Unit and Neonatal Pathology, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dennis P Wall
- Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Paúl Cárdenas
- Institute of Microbiology, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Manuel E Baldeón
- Facultad de Ciencias Médicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Sébastien Jacquemont
- Sainte Justine Hospital Research Center, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sharon M Donovan
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Bob Carpenter
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Prescient Design, a Genentech Accelerator, New York, NY, USA
| | - Gaspar Taroncher-Oldenburg
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
- Simons Foundation Autism Research Initiative, Simons Foundation, New York, NY, USA.
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Dai L, Mafra D, Shiels PG, Hackeng TM, Stenvinkel P, Schurgers LJ. Vitamin K and Hallmarks of Ageing: Focus on Diet and Gut Microbiome. Nutrients 2023; 15:2727. [PMID: 37375631 DOI: 10.3390/nu15122727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Vitamin K and vitamin K-dependent proteins have been reported to be associated with a large spectrum of age-related diseases. While most of these associations have been deduced from observational studies, solid evidence for the direct impact of vitamin K on cellular senescence remains to be proven. As vitamin K status reflects the complexity of interactions between dietary intake, gut microbiome activity and health, we will demonstrate the pivotal role of the diet-microbiome-health axis in human ageing and exemplify how vitamin K is implicated therein. We propose that food quality (i.e., food pattern) should be highlighted beyond the quantity of total vitamin K intake. Instead of focusing on a single nutrient, exploring a healthy diet containing vitamin K may be more strategic. As such, healthy eating patterns can be used to make dietary recommendations for the public. Emerging evidence suggests that dietary vitamin K is a modulator of the diet-microbiome-health axis, and this needs to be incorporated into the investigation of the impact of vitamin K on gut microbial composition and metabolic activities, along with host health outcomes. In addition, we highlight several critical caveats that need to be acknowledged regarding the interplay between diet, vitamin K, gut microbiome and host health that is pivotal for elucidating the role of vitamin K in ageing and responding to the urgent call of healthy eating concerning public health.
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Affiliation(s)
- Lu Dai
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17165 Stockholm, Sweden
- Department of Clinical Science, Division of Renal Medicine, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Denise Mafra
- Graduate Program in Nutrition Sciences, Fluminense Federal University, Niterói 24020-141, RJ, Brazil
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow G12 8QQ, UK
| | - Paul G Shiels
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, Glasgow G12 8QQ, UK
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Peter Stenvinkel
- Department of Clinical Science, Division of Renal Medicine, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Leon J Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6211 LK Maastricht, The Netherlands
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, 52056 Aachen, Germany
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