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Yu W, Wang J, Xiong Y, Liu J, Baranenko D, Zhang Y, Lu W. In vivo absorption, in vitro simulated digestion, and fecal fermentation properties of Imperata cylindrica polysaccharides and their effects on gut microbiota. Food Chem 2024; 461:140773. [PMID: 39154459 DOI: 10.1016/j.foodchem.2024.140773] [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: 03/29/2024] [Revised: 06/18/2024] [Accepted: 08/04/2024] [Indexed: 08/20/2024]
Abstract
Recently we have investigated polysaccharide from Imperata cylindrica (ICP) for its physicochemical structure and biological activities. However, the digestion characteristics have yet to be understood. This study investigated the digestion and metabolism characteristics of ICP through in vivo fluorescence tracking, in vitro simulated digestion, fecal fermentation experiments, and microbial sequencing. The results showed that ICP significant distribution in the gastrointestinal tract and kidneys. ICP underwent slight degradation during simulated gastric and intestinal digestion. During fecal fermentation, the utilization degree of ICP and the concentration of short-chain fatty acids (SCFAs) increased. ICP promoted the increase of beneficial microbial abundance. To understand the impact of ICP on the integrity and health of intestinal tissues, molecular docking was employed to preliminarily predict the interaction between ICP and key proteins. The results revealed that ICP could recognize and bind to key proteins through high-affinity targeting binding sites.
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Affiliation(s)
- Wenchen Yu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China; National and Local Joint Engineering Laboratory for Synthesis, Harbin Institute of Technology, Harbin, China; School of Medicine and Health, Harbin Institute of Technology, Harbin, China; Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
| | - Junwen Wang
- National and Local Joint Engineering Laboratory for Synthesis, Harbin Institute of Technology, Harbin, China; School of Medicine and Health, Harbin Institute of Technology, Harbin, China; Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
| | - Yi Xiong
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China; National and Local Joint Engineering Laboratory for Synthesis, Harbin Institute of Technology, Harbin, China; School of Medicine and Health, Harbin Institute of Technology, Harbin, China; Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
| | - Jiaren Liu
- School of Medicine and Health, Harbin Institute of Technology, Harbin, China
| | - Denis Baranenko
- School of Life Sciences, Faculty of Ecotechnologies, ITMO University, St. Petersburg. 197101, Russia
| | - Yingchun Zhang
- National and Local Joint Engineering Laboratory for Synthesis, Harbin Institute of Technology, Harbin, China; School of Medicine and Health, Harbin Institute of Technology, Harbin, China; Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China; Zhengzhou Research Institute, Harbin Institute of Technology, Zhengzhou, China.
| | - Weihong Lu
- National and Local Joint Engineering Laboratory for Synthesis, Harbin Institute of Technology, Harbin, China; School of Medicine and Health, Harbin Institute of Technology, Harbin, China; Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China; Zhengzhou Research Institute, Harbin Institute of Technology, Zhengzhou, China.
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2
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Wu J, Zhang J, Huang G, Zhong Y, Yang Y, Deng P. Evidence from mendelian randomization identifies several causal relationships between primary membranous nephropathy and gut microbiota. Ren Fail 2024; 46:2349136. [PMID: 38770992 PMCID: PMC11110878 DOI: 10.1080/0886022x.2024.2349136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Research has showcased a correlation between disruptions in gut microbiota and primary membranous nephropathy (pMN), giving rise to the concept of the 'gut-kidney axis'. However, the precise relationship between gut microbiota and pMN remains elusive. Hence, this study endeavors to investigate whether a causal relationship exists between gut microbiota and pMN utilizing Mendelian randomization (MR) analysis. METHODS The primary method employed for MR analysis is the inverse variance weighting method, supplemented by MR-Egger and the weighted median method, to infer causality. This approach was validated within the pMN cohort across two distinct populations. RESULTS At the species level, the abundance of Bifidobacterium bifidum and Alistipes indistinctus was negatively correlated with the risk of pMN. Conversely, pMN was positively associated with Bacilli abundance at the class level, Lachnospiraceae abundance at the family level, and Dialister abundance at the genus level. Specifically, at the species level, pMN was positively correlated with the abundance of Ruminococcus lactaris, Dialister invisus, and Coprococcus_sp_ART55_1. CONCLUSION These findings lay the groundwork for future research exploring the interplay between pMN and the gut microbiota, with substantial implications for the prevention and treatment of pMN and its associated complications.
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Affiliation(s)
- Jianwei Wu
- Department of Medical Technology, Gannan Healthcare Vocational College, Ganzhou, China
| | - Jing Zhang
- Department of Medical Technology, Gannan Healthcare Vocational College, Ganzhou, China
| | - Gang Huang
- Department of Laboratory, GanZhou Cancer Hospital, Ganzhou, China
| | - Yinglian Zhong
- Department of Blood Transfusion, Ganzhou Fifth People’s Hospital, Ganzhou, China
| | - Yi Yang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Deng
- Department of Endocrinology, Department of Nephrology, Ganzhou Fifth People’s Hospital, Ganzhou, China
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3
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Qiu T, Fang Q, Tian X, Cao Y, Fan X, Li Y, Tu Y, Liu L, Chen Z, Wei Y, Bai J, Huang J, Liu Y. Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124705. [PMID: 39134171 DOI: 10.1016/j.envpol.2024.124705] [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: 02/27/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024]
Abstract
The infant gut microbiome matures greatly in the first year of life. Ambient air pollution (AAP) exposure is associated with the infant gut microbiome. However, whether time-varying AAP influences infant gut microbiome variation is rarely investigated. This study aimed to investigate the effects of PM2.5, PM10, and O3 on infant gut microbiome variation longitudinally. Demographic information, stool samples, and AAP exposure concentrations were collected at 6, 12, 24 months from infants. Gut microbiome was processed and analyzed using 16S rRNA V3-V4 gene regions. AAP exposure concentrations were calculated using the China High Air Pollutants (CHAP) database. Multiple pollutant models were used to assess the mixed effects of PM2.5, PM10, and O3 on infant gut microbiome variation. Infants' gut microbiomes at 6, 12, 24 months old had significant differences in alpha diversity, beta diversity, and community composition. PM2.5 and O3 respectively explained 6.3% and 5.3% of the differences in community composition for 24-month-old infants. Single pollutant exposure and multiple pollutant exposure in different periods were both associated with alpha diversity indices and specific gut microbial phyla and genera. AAP was more associated with infant gut microbial alpha diversity indices, phyla variations, and genera variations at 12-24 months than 6-12 months. Multiple pollutant exposure in 0-2 lag months showed negative correlations with 12-24 months variation in Escherichia-Shigella (β = -0.854, 95%CI: 1.398 to -0.310) and Enterococcus (β = -0.979, 95%CI: 1.429 to -0.530). This study highlighted that time-varying PM2.5, PM10, and O3 synergistically influenced the variation of alpha diversity and abundance of gut microbial taxa in infants. Further research is needed to explore the effects and mechanisms of other environmental exposures on infant gut microbiome variation.
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Affiliation(s)
- Tianlai Qiu
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Qingbo Fang
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Xuqi Tian
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Yanan Cao
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Xiaoxiao Fan
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Yanting Li
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Yiming Tu
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Linxia Liu
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Zitong Chen
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Yi Wei
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Jinbing Bai
- Emory University Nell Hodgson Woodruff School of Nursing, 1520 Clifton Road, Atlanta, GA, 30322, USA
| | - Jing Huang
- Department of Occupational and Environmental Health Sciences, Peking University School of Public Health, Beijing, 100191, China
| | - Yanqun Liu
- Wuhan University School of Nursing, Wuhan University, 169 Donghu Road, Wuhan, 430071, China; Research Center for Lifespan Health, Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
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4
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Plomp N, Harmsen HJM. Description of Faecalibacterium wellingii sp. nov. and two Faecalibacterium taiwanense strains, aiding to the reclassification of Faecalibacterium species. Anaerobe 2024; 89:102881. [PMID: 38925221 DOI: 10.1016/j.anaerobe.2024.102881] [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: 04/05/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVES The genus Faecalibacterium is one of the most important butyrate producers in the human intestinal tract and has been widely linked to health. Recently, several different species have been described, but still more phylogroups have been identified, suggesting that additional species may exist. Four strains HTF-FT, HTF-128, HTF-75H and HTF-76H, representing two different phylogenetic clusters, are evaluated in this study. METHODS Phylogenomic analysis was performed using whole-genome sequences and 16S rRNA gene sequences. Chemotaxonomic analysis was done based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Physiological and phenotypical characteristics of these strains were also determined. All characteristics of these strains were compared with other validly published species within the genus Faecalibacterium. RESULTS On a genomic level, the strains HTF-FT and HTF-128 shared an average nucleotide identity (ANI) of <95.0 % and digital DNA-DNA hybridization (dDDH) of <70.0 with other Faecalibacterium species, while between HTF-FT and HTF-128 the ANI-value was 97.18 % and the dDDH was 76.8 %. HTF-75H and HTF-76H had an ANI and dDDH value of 100 % (99.96 %) and 100 % (99.99 %) respectively. Both HTF-75H and HTF-76H were closely related to Faecalibacterium taiwanense HLW78T. 16S rRNA gene and chemotaxonomic analysis were in accordance with the genomic data, confirming that HTF-FT and HTF-128 represent a novel Faecalibacterium species and HTF-75H and HTF-76H belong to F. taiwanense. CONCLUSIONS Faecalibacterium strains HTF-FT (=DSM 117771T = NCIMB 15531T) and HTF-128 represent a novel species. The name Faecalibacterium wellingii with HTF-FT as type strain is proposed. Two novel isolates HTF-75H (=DSM 17770 = NCIMB 15530) and HTF-76H are described in this study and belong to the recently described Faecalibacterium taiwanense.
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Affiliation(s)
- Niels Plomp
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
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5
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Ioannou M, Borkent J, Andreu-Sánchez S, Wu J, Fu J, Sommer IEC, Haarman BCM. Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study. Brain Behav Immun 2024; 121:165-175. [PMID: 39032544 DOI: 10.1016/j.bbi.2024.07.009] [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: 01/12/2024] [Revised: 05/30/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders. METHODS In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol. RESULTS The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use. CONCLUSIONS Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.
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Affiliation(s)
- Magdalini Ioannou
- University of Groningen and University Medical Center Groningen, Department of Psychiatry, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands.
| | - Jenny Borkent
- University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Jiafei Wu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Iris E C Sommer
- University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands
| | - Bartholomeus C M Haarman
- University of Groningen and University Medical Center Groningen, Department of Psychiatry, Groningen, the Netherlands
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6
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Zhou L, Song W, Liu T, Yan T, He Z, He W, Lv J, Zhang S, Dai X, Yuan L, Shi L. Multi-omics insights into anti-colitis benefits of the synbiotic and postbiotic derived from wheat bran arabinoxylan and Limosilactobacillus reuteri. Int J Biol Macromol 2024; 278:134860. [PMID: 39163956 DOI: 10.1016/j.ijbiomac.2024.134860] [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: 04/30/2024] [Revised: 08/08/2024] [Accepted: 08/17/2024] [Indexed: 08/22/2024]
Abstract
Exploring nutritional therapies that manipulate tryptophan metabolism to activate AhR signaling represents a promising approach for mitigating chronic colitis. Arabinoxylan is a bioactive constituent abundant in wheat bran. Here, we comprehensively investigated anti-colitis potentials of wheat bran arabinoxylan (WBAX), its synbiotic and postbiotic derived from WBAX and Limosilactobacillus reuteri WX-94 (i.e., a probiotic strain exhibiting tryptophan metabolic activity). WBAX fueled L. reuteri and promoted microbial conversion of tryptophan to AhR ligands during in vitro fermentation in the culture medium and in the fecal microbiota from type 2 diabetes. The WBAX postbiotic outperformed WBAX and its synbiotic in augmenting efficacy of tryptophan in restoring DSS-disturbed serum immune markers, colonic tight junction proteins and gene profiles involved in amino acid metabolism and FoxO signaling. The WBAX postbiotic remodeled gut microbiota and superiorly enhanced AhR ligands (i.e., indole metabolites and bile acids), alongside with elevation in colonic AhR and IL-22. Associations between genera and metabolites modified by the postbiotic and colitis in human were verified and strong binding capacities between metabolites and colitis-related targets were demonstrated by molecular docking. Our study advances the novel perspective of WBAX in manipulating tryptophan metabolism and anti-colitis potentials of WBAX postbiotic via promoting gut microbiota-dependent AhR signaling.
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Affiliation(s)
- Lanqi Zhou
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Wei Song
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Tianqi Liu
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Tao Yan
- School of Food Science and Engineering, South China University of Technology, Guangdong 510641, China
| | - Ziyan He
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Weitai He
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710062, China
| | - Jiayao Lv
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Shiyi Zhang
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Xiaoshuang Dai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Xbiome, Scientific Research Building, Room 907, Tsinghua High-Tech Park, Shenzhen, China
| | - Li Yuan
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Lin Shi
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China.
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7
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Schneider KM, Kummen M, Trivedi PJ, Hov JR. Role of microbiome in autoimmune liver diseases. Hepatology 2024; 80:965-987. [PMID: 37369002 PMCID: PMC11407779 DOI: 10.1097/hep.0000000000000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/25/2023] [Indexed: 06/29/2023]
Abstract
The microbiome plays a crucial role in integrating environmental influences into host physiology, potentially linking it to autoimmune liver diseases, such as autoimmune hepatitis, primary biliary cholangitis, and primary sclerosing cholangitis. All autoimmune liver diseases are associated with reduced diversity of the gut microbiome and altered abundance of certain bacteria. However, the relationship between the microbiome and liver diseases is bidirectional and varies over the course of the disease. This makes it challenging to dissect whether such changes in the microbiome are initiating or driving factors in autoimmune liver diseases, secondary consequences of disease and/or pharmacological intervention, or alterations that modify the clinical course that patients experience. Potential mechanisms include the presence of pathobionts, disease-modifying microbial metabolites, and more nonspecific reduced gut barrier function, and it is highly likely that the effect of these change during the progression of the disease. Recurrent disease after liver transplantation is a major clinical challenge and a common denominator in these conditions, which could also represent a window to disease mechanisms of the gut-liver axis. Herein, we propose future research priorities, which should involve clinical trials, extensive molecular phenotyping at high resolution, and experimental studies in model systems. Overall, autoimmune liver diseases are characterized by an altered microbiome, and interventions targeting these changes hold promise for improving clinical care based on the emerging field of microbiota medicine.
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Affiliation(s)
| | - Martin Kummen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Palak J Trivedi
- National Institute for Health and Care Research Birmingham Biomedical Research Centre, Centre for Liver and Gastroenterology Research, University of Birmingham, UK
- Liver Unit, University Hospitals Birmingham Queen Elizabeth, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, UK
- Institute of Applied Health Research, University of Birmingham, UK
| | - Johannes R Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
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8
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Hickman B, Salonen A, Ponsero AJ, Jokela R, Kolho KL, de Vos WM, Korpela K. Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants. Nat Commun 2024; 15:8323. [PMID: 39333099 DOI: 10.1038/s41467-024-52561-6] [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: 03/04/2024] [Accepted: 09/10/2024] [Indexed: 09/29/2024] Open
Abstract
The human gut microbiota is central in regulating all facets of host physiology, and in early life it is thought to influence the host's immune system and metabolism, affecting long-term health. However, longitudinally monitored cohorts with parallel analysis of faecal samples and health data are scarce. In our observational study we describe the gut microbiota development in the first 2 years of life and create a gut microbiota wellbeing index based on the microbiota development and health data in a cohort of nearly 1000 infants using clustering and trajectory modelling. We show that infants' gut microbiota development is highly predictable, following one of five trajectories, dependent on infant exposures, and predictive of later health outcomes. We characterise the natural healthy gut microbiota trajectory and several different dysbiotic trajectories associated with different health outcomes. Bifidobacterium and Bacteroides appear as early keystone organisms, directing microbiota development and consistently predicting positive health outcomes. A microbiota wellbeing index, based on the healthy development trajectory, is predictive of general health over the first 5 years. The results indicate that gut microbiota succession is part of infant physiological development, predictable, and malleable. This information can be utilised to improve the predictions of individual health risks.
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Affiliation(s)
- Brandon Hickman
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Roosa Jokela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children's Hospital, University of Helsinki, Stenbäckinkatu 11, FI-00029, HUS, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Schmartz GP, Rehner J, Schuff MJ, Molano LAG, Becker SL, Krawczyk M, Tagirdzhanov A, Gurevich A, Francke R, Müller R, Keller V, Keller A. Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes. Nat Commun 2024; 15:8263. [PMID: 39327429 DOI: 10.1038/s41467-024-52669-9] [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: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.
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Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Miriam J Schuff
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | | | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, 66421 Saarland University, Homburg, Germany
| | - Azat Tagirdzhanov
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
- Department of Computer Science, Saarland University, 66123, Saarbrücken, Germany
| | | | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany.
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10
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Boverhoff D, Kool J, Pijnacker R, Ducarmon QR, Zeller G, Shetty S, Sie S, Mulder AC, van der Klis F, Franz E, Mughini-Gras L, van Baarle D, Fuentes S. Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands. Cell Rep 2024; 43:114729. [PMID: 39264809 DOI: 10.1016/j.celrep.2024.114729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/23/2024] [Accepted: 08/22/2024] [Indexed: 09/14/2024] Open
Abstract
Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.
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Affiliation(s)
- David Boverhoff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Quinten R Ducarmon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sudarshan Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephan Sie
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Annemieke Christine Mulder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Fiona van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Debbie van Baarle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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11
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Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Signal Transduct Target Ther 2024; 9:237. [PMID: 39307902 PMCID: PMC11418828 DOI: 10.1038/s41392-024-01946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/26/2024] Open
Abstract
The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.
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Affiliation(s)
- Ziqi Ma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Ashraf Yusuf Rangrez
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
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12
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Mardinoglu A, Palsson BØ. Genome-scale models in human metabologenomics. Nat Rev Genet 2024:10.1038/s41576-024-00768-0. [PMID: 39300314 DOI: 10.1038/s41576-024-00768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/22/2024]
Abstract
Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs - from cells and tissues to microbiomes and the whole body - have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.
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Affiliation(s)
- Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK.
| | - Bernhard Ø Palsson
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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13
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Dong W, Fan X, Guo Y, Wang S, Jia S, Lv N, Yuan T, Pan Y, Xue Y, Chen X, Xiong Q, Yang R, Zhao W, Zhu B. An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. Nat Commun 2024; 15:8084. [PMID: 39278950 PMCID: PMC11402979 DOI: 10.1038/s41467-024-51864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024] Open
Abstract
Virulence factor genes (VFGs) play pivotal roles in bacterial infections and have been identified within the human gut microbiota. However, their involvement in chronic diseases remains poorly understood. Here, we establish an expanded VFG database (VFDB 2.0) consisting of 62,332 nonredundant orthologues and alleles of VFGs using species-specific average nucleotide identity ( https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases ). We further develop the MetaVF toolkit, facilitating the precise identification of pathobiont-carried VFGs at the species level. A thorough characterization of VFGs for 5452 commensal isolates from healthy individuals reveals that only 11 of 301 species harbour these factors. Further analyses of VFGs within the gut microbiomes of nine chronic diseases reveal both common and disease-specific VFG features. Notably, in type 2 diabetes patients, long HiFi sequencing confirms that shared VF features are carried by pathobiont strains of Escherichia coli and Klebsiella pneumoniae. These findings underscore the critical importance of identifying and understanding VFGs in microbiome-associated diseases.
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Affiliation(s)
- Wanting Dong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinyue Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqiong Guo
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Siyi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulei Jia
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Yuan
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Xue
- National Engineering and Technology Research Center for Fruits and Vegetables, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xi Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Xiong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Weigang Zhao
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China.
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
- Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing, 100101, China.
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14
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Yao S, Han JZ, Guo J, Wang X, Qian L, Wu H, Shi W, Zhu RJ, Wang JH, Dong SS, Cui LL, Wang Y, Guo Y, Yang TL. The Causal Relationships Between Gut Microbiota, Brain Volume, and Intelligence: A Two-Step Mendelian Randomization Analysis. Biol Psychiatry 2024; 96:463-472. [PMID: 38432522 DOI: 10.1016/j.biopsych.2024.02.1012] [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: 10/10/2023] [Revised: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Growing evidence indicates that dynamic changes in gut microbiome can affect intelligence; however, whether these relationships are causal remains elusive. We aimed to disentangle the poorly understood causal relationship between gut microbiota and intelligence. METHODS We performed a 2-sample Mendelian randomization (MR) analysis using genetic variants from the largest available genome-wide association studies of gut microbiota (N = 18,340) and intelligence (N = 269,867). The inverse-variance weighted method was used to conduct the MR analyses complemented by a range of sensitivity analyses to validate the robustness of the results. Considering the close relationship between brain volume and intelligence, we applied 2-step MR to evaluate whether the identified effect was mediated by regulating brain volume (N = 47,316). RESULTS We found a risk effect of the genus Oxalobacter on intelligence (odds ratio = 0.968 change in intelligence per standard deviation increase in taxa; 95% CI, 0.952-0.985; p = 1.88 × 10-4) and a protective effect of the genus Fusicatenibacter on intelligence (odds ratio = 1.053; 95% CI, 1.024-1.082; p = 3.03 × 10-4). The 2-step MR analysis further showed that the effect of genus Fusicatenibacter on intelligence was partially mediated by regulating brain volume, with a mediated proportion of 33.6% (95% CI, 6.8%-60.4%; p = .014). CONCLUSIONS Our results provide causal evidence indicating the role of the microbiome in intelligence. Our findings may help reshape our understanding of the microbiota-gut-brain axis and development of novel intervention approaches for preventing cognitive impairment.
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Affiliation(s)
- Shi Yao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ji-Zhou Han
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jing Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Long Qian
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ren-Jie Zhu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia-Hao Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Li-Li Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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15
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Hashuel R, Gutman E, Litvak Y. Genomic sequencing of 10 spore-forming Bacilli strains isolated from zoo-dwelling mice. Microbiol Resour Announc 2024; 13:e0044624. [PMID: 39083689 PMCID: PMC11385446 DOI: 10.1128/mra.00446-24] [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: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024] Open
Abstract
We present the genomic sequences of 10 spore-forming bacteria from the Bacillaceae family isolated from fecal samples of mice residing in the Tisch Family Biblical Zoo, Jerusalem. These isolates suggest Bacillus bacteria are a native component of rodent gut flora, facilitating further research into gut colonization and microbiome diversity.
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Affiliation(s)
- Rachel Hashuel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Eran Gutman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Yael Litvak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
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16
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Gu W, Zhang H, Zhang Z, Xu M, Li X, Han Z, Fu X, Li X, Wang X, Zhang C. Continuous Oral Administration of the Superantigen Staphylococcal Enterotoxin C2 Activates Intestinal Immunity and Modulates the Gut Microbiota in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405039. [PMID: 39248343 DOI: 10.1002/advs.202405039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/28/2024] [Indexed: 09/10/2024]
Abstract
Staphylococcal Enterotoxin C2 (SEC2), a classical superantigen, is an antitumor immunotherapy agent. However, the injectable formulation of SEC2 limits its clinical application. Here, it is reported that oral administration of SEC2 activates the intestinal immune system and benefits intestinal health in a mouse model. These results indicate that intact SEC2 is detected in the stomach, intestine, and serum after oral administration. Continuous oral administration of SEC2 activates immune cells in gut-associated lymphoid tissues, promoting extensive differentiation and proliferation of CD4+ and CD8+ T cells and CD19+ B cells, leading to increased production of cytokines and secretory immunoglobulin A. SEC2 also enhances intestinal barrier function, as demonstrated by an increased villus length/crypt depth ratio and elevated expression of mucins and tight junction proteins. Additionally, SEC2 indirectly influenced gut microbiota, reinforcing potential probiotics and short-chain fatty acid synthesis. Enhanced differentiation of T and B cells in the spleen, coupled with elevated serum interleukin-2 levels, suggests systemic immune enhancement following oral administration of SEC2. These findings provide a scientific basis for the development of SEC2 as an oral immunostimulant for immune enhancement and anti-tumor immunotherapy.
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Affiliation(s)
- Wu Gu
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing, 101408, P. R. China
| | - Huiwen Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Best Health (Guangdong) Bio-Technology Co., Ltd., Center Building, Minke Park, Xinhui Economic Development Zone, Jiangmen, 529100, P. R. China
| | - Zhichun Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing, 101408, P. R. China
| | - Mingkai Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
| | - Xiang Li
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
| | - Zhiyang Han
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing, 101408, P. R. China
| | - Xuanhe Fu
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
- Department of Immunology, Shenyang Medical College, No. 146 Huanghe North Street, Shenyang, 110034, P. R. China
| | - Xu Li
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
| | - Xiujuan Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
| | - Chenggang Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 WenHua Road, Shenyang, 110016, P. R. China
- Key Laboratory of Superantigen Research of Liao Ning Province, No. 72 WenHua Road, Shenyang, 110016, P. R. China
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17
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Swarte JC, Zhang S, Nieuwenhuis LM, Gacesa R, Knobbe TJ, De Meijer VE, Damman K, Verschuuren EAM, Gan TC, Fu J, Zhernakova A, Harmsen HJM, Blokzijl H, Bakker SJL, Björk JR, Weersma RK. Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients. Gut 2024; 73:1650-1661. [PMID: 38955400 DOI: 10.1136/gutjnl-2023-331441] [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: 11/01/2023] [Accepted: 05/12/2024] [Indexed: 07/04/2024]
Abstract
OBJECTIVE Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, the relationship with overall survival in specific diseases has not been extensively studied. In the current study, we present results from an in-depth analysis of the relationship between gut dysbiosis and all-cause and cause-specific mortality in the setting of solid organ transplant recipients (SOTR). DESIGN We analysed 1337 metagenomes derived from faecal samples of 766 kidney, 334 liver, 170 lung and 67 heart transplant recipients part of the TransplantLines Biobank and Cohort-a prospective cohort study including extensive phenotype data with 6.5 years of follow-up. To analyze gut dysbiosis, we included an additional 8208 metagenomes from the general population of the same geographical area (northern Netherlands). Multivariable Cox regression and a machine learning algorithm were used to analyse the association between multiple indicators of gut dysbiosis, including individual species abundances, and all-cause and cause-specific mortality. RESULTS We identified two patterns representing overall microbiome community variation that were associated with both all-cause and cause-specific mortality. The gut microbiome distance between each transplantation recipient to the average of the general population was associated with all-cause mortality and death from infection, malignancy and cardiovascular disease. A multivariable Cox regression on individual species abundances identified 23 bacterial species that were associated with all-cause mortality, and by applying a machine learning algorithm, we identified a balance (a type of log-ratio) consisting of 19 out of the 23 species that were associated with all-cause mortality. CONCLUSION Gut dysbiosis is consistently associated with mortality in SOTR. Our results support the observations that gut dysbiosis is associated with long-term survival. Since our data do not allow us to infer causality, more preclinical research is needed to understand mechanisms before we can determine whether gut microbiome-directed therapies may be designed to improve long-term outcomes.
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Affiliation(s)
- J Casper Swarte
- Gastroenterology and Hepatology, University Medical Centre, Groningen, Netherlands
| | - Shuyan Zhang
- Gastroenterology and Hepatology, University Medical Centre, Groningen, Netherlands
| | | | - Ranko Gacesa
- Gastroenterology and Hepatology, University Medical Centre, Groningen, Netherlands
- Department of Genetics, University of Groningen, University Medical Center, Groningen, Netherlands
| | - Tim J Knobbe
- University Medical Centre, Groningen, Netherlands
| | | | - Kevin Damman
- University Medical Centre, Groningen, Netherlands
| | | | - Tji C Gan
- University Medical Centre, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center, Groningen, Netherlands
- Department of Pediatrics, University Medical Center, Groningen, Netherlands
| | | | - Hermie J M Harmsen
- Medical Microbiology, University of Groningen, University Medical Center, Groningen, Netherlands
| | | | | | - Johannes R Björk
- Gastroenterology and Hepatology, University Medical Centre, Groningen, Netherlands
| | - Rinse K Weersma
- Gastroenterology and Hepatology, University Medical Centre, Groningen, Netherlands
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18
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Govender P, Ghai M. Population-specific differences in the human microbiome: Factors defining the diversity. Gene 2024; 933:148923. [PMID: 39244168 DOI: 10.1016/j.gene.2024.148923] [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: 05/24/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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19
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Xiang L, Zhuo S, Luo W, Tian C, Xu S, Li X, Zhu Y, Feng R, Chen M. Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites. Food Res Int 2024; 192:114852. [PMID: 39147529 DOI: 10.1016/j.foodres.2024.114852] [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: 05/31/2024] [Revised: 07/12/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.
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Affiliation(s)
- Liyuan Xiang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuyu Zhuo
- Department of Nutrition, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wanrong Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Chunyang Tian
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaozhi Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yijun Zhu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning 530022, China.
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
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20
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Kullberg RFJ, Wikki I, Haak BW, Kauko A, Galenkamp H, Peters-Sengers H, Butler JM, Havulinna AS, Palmu J, McDonald D, Benchraka C, Abdel-Aziz MI, Prins M, Maitland van der Zee AH, van den Born BJ, Jousilahti P, de Vos WM, Salomaa V, Knight R, Lahti L, Nieuwdorp M, Niiranen T, Wiersinga WJ. Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies. THE LANCET. MICROBE 2024; 5:100864. [PMID: 38909617 DOI: 10.1016/s2666-5247(24)00079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/20/2024] [Accepted: 03/14/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND Microbiota alterations are common in patients hospitalised for severe infections, and preclinical models have shown that anaerobic butyrate-producing gut bacteria protect against systemic infections. However, the relationship between microbiota disruptions and increased susceptibility to severe infections in humans remains unclear. We investigated the relationship between gut microbiota and the risk of future infection-related hospitalisation in two large population-based cohorts. METHODS In this observational microbiome study, gut microbiota were characterised using 16S rRNA gene sequencing in independent population-based cohorts from the Netherlands (HELIUS study; derivation cohort) and Finland (FINRISK 2002 study; validation cohort). HELIUS was conducted in Amsterdam, Netherlands, and included adults (aged 18-70 years at inclusion) who were randomly sampled from the municipality register of Amsterdam. FINRISK 2002 was conducted in six regions in Finland and is a population survey that included a random sample of adults (aged 25-74 years). In both cohorts, participants completed questionnaires, underwent a physical examination, and provided a faecal sample at inclusion (Jan 3, 2013, to Nov 27, 2015, for HELIUS participants and Jan 21 to April 19, 2002, for FINRISK participants. For inclusion in our study, a faecal sample needed to be provided and successfully sequenced, and national registry data needed to be available. Primary predictor variables were microbiota composition, diversity, and relative abundance of butyrate-producing bacteria. Our primary outcome was hospitalisation or mortality due to any infectious disease during 5-7-year follow-up after faecal sample collection, based on national registry data. We examined associations between microbiota and infection risk using microbial ecology and Cox proportional hazards. FINDINGS We profiled gut microbiota from 10 699 participants (4248 [39·7%] from the derivation cohort and 6451 [60·3%] from the validation cohort). 602 (5·6%) participants (152 [3·6%] from the derivation cohort; 450 [7·0%] from the validation cohort) were hospitalised or died due to infections during follow-up. Gut microbiota composition of these participants differed from those without hospitalisation for infections (derivation p=0·041; validation p=0·0002). Specifically, higher relative abundance of butyrate-producing bacteria was associated with a reduced risk of hospitalisation for infections (derivation cohort cause-specific hazard ratio 0·75 [95% CI 0·60-0·94] per 10% increase in butyrate producers, p=0·013; validation cohort 0·86 [0·77-0·96] per 10% increase, p=0·0077). These associations remained unchanged following adjustment for demographics, lifestyle, antibiotic exposure, and comorbidities. INTERPRETATION Gut microbiota composition, specifically colonisation with butyrate-producing bacteria, was associated with protection against hospitalisation for infectious diseases in the general population across two independent European cohorts. Further studies should investigate whether modulation of the microbiome can reduce the risk of severe infections. FUNDING Amsterdam UMC, Porticus, National Institutes of Health, Netherlands Organisation for Health Research and Development (ZonMw), and Leducq Foundation.
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Affiliation(s)
- Robert F J Kullberg
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
| | - Irina Wikki
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Bastiaan W Haak
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Anni Kauko
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Institute for Molecular Medicine Finland, FIMM-HiLIFE, Finland
| | - Joonatan Palmu
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | | | - Mahmoud I Abdel-Aziz
- Department of Pulmonary Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Maria Prins
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, Netherlands; Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Bert-Jan van den Born
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Internal Medicine, Division of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands; Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Max Nieuwdorp
- Department of Internal Medicine, Division of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Teemu Niiranen
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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21
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Crothers H, Ferguson J, Quraishi MN, Cooney R, Iqbal TH, Trivedi PJ. Past, current, and future trends in the prevalence of primary sclerosing cholangitis and inflammatory bowel disease across England (2015-2027): a nationwide, population-based study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 44:101002. [PMID: 39099647 PMCID: PMC11296053 DOI: 10.1016/j.lanepe.2024.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024]
Abstract
Background Primary sclerosing cholangitis (PSC) is one of the leading indications for liver transplantation in Europe, and a major risk factor for cancer in inflammatory bowel disease (IBD). However, it is not known how the epidemiology of PSC will change as that of IBD evolves. The aim of this study is to provide nationwide statistics on the past and current prevalence of PSC and IBD across England, and forecast how this is likely to change over time. Methods We accessed and analysed a nationwide population-based administrative healthcare registry, which houses prospectively accrued data since April 1st 2001. In so doing, the past and current prevalence of PSC-IBD and IBD alone was determined among 18-60-year-olds in England, alongside average annual percentage change rates (AAPC), between the 1st of January 2015 and 2020. Past and current prevalence data, alongside trends in incidence and event-free survival rates, were then used to forecast future prevalence between 2021 and 2027. Findings In 2015, the prevalence of PSC with prior IBD diagnosis was 5.0 per 100,000 population, rising to 5.7 when including those with IBD diagnosed after PSC. In 2020, prevalence increased to 7.6 (8.6 accounting for IBD developing after PSC), yielding an AAPC of 8.8. In 2027, PSC-IBD prevalence is forecast to be 11.7 (95% prediction interval [PI]: 10.8-12.7), and 13.3 when accounting for IBD developing after PSC (AAPC: 6.4; 95% PI: 5.3-7.5). Comparatively, the prevalence of IBD alone rose among 18-60-year-olds from 384.3 in 2015 to 538.7 in 2020 (AAPC 7.0), and forecast to increase to 742.5 by 2027 (95% PI: 736.4-748.0; AAPC: 4.7, 95% PI: 4.6-4.8). Interpretation The rate of growth in PSC-IBD is predicted to exceed IBD-alone. Further research is needed to understand changes in disease epidemiology, including aetiological drivers of developing (invariably progressive) liver disease in IBD, and the implications of rising case burden on health care resources. Funding This study was supported by an unrestricted grant provided by Gilead Sciences.
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Affiliation(s)
- Hannah Crothers
- Research and Development, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - James Ferguson
- Liver Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
- National Institute for Health and Social Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Mohammed Nabil Quraishi
- National Institute for Health and Social Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Rachel Cooney
- National Institute for Health and Social Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Tariq H. Iqbal
- National Institute for Health and Social Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Palak J. Trivedi
- Liver Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
- National Institute for Health and Social Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
- Institute of Applied Health Research, University of Birmingham, B15 2TT, UK
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22
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Light SH, Nagler CR. Regulation of immune responses to food by commensal microbes. Immunol Rev 2024; 326:203-218. [PMID: 39285525 DOI: 10.1111/imr.13396] [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: 09/28/2024]
Abstract
The increasing prevalence of immune-mediated non-communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co-evolved host-microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome-based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.
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Affiliation(s)
- Samuel H Light
- Biological Sciences Division, Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Cathryn R Nagler
- Biological Sciences Division, Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
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23
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Henares D, Monsalvez V, Brotons P, Machado ML, Capilla S, Gomila-Grange A, Bierge P, Cubero M, Q Pich O, Requena-Méndez A, Muñoz-Almagro C, Gasch O. Human gut microbiota composition associated with international travels. Travel Med Infect Dis 2024; 61:102747. [PMID: 39094984 DOI: 10.1016/j.tmaid.2024.102747] [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: 03/27/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
OBJECTIVE The objective of this study was to evaluate whether long stays in non-European countries influence the composition, diversity, and dynamics of gut microbiota, considering the potential impact of travelling, close contact with new people, and consumption of water and food. METHODS Two prospective cohorts were analyzed: (i) A longitudinal cohort comprising long-term travellers who provided fecal samples before and after their travels. (ii) A cohort consisting of long-term travellers and recently arrived migrants from non-European countries, which was compared with non-traveller controls. Each participant self-collected fecal samples and provided demographic and epidemiological data. Microbiota was characterized through 16 S rRNA gene sequencing. RESULTS The longitudinal cohort comprised 17 subjects. A trend toward higher bacterial diversity was observed after travelling (Shannon index 3.12vs3.26). When comparing 84 travellers/migrants with 97 non-travellers, a confirmed association of higher diversity levels with travelling was observed (Phylogenetic diversity: 22.1vs20.9). Specific genera enriched in travellers' gut microbiota were identified, including Escherichia/Shigella, Bacteroides, and Parabacteroides. The analysis revealed three major clusters with profound differences in their bacterial composition, which exhibited differential distribution between travellers and non-travellers (Adonis P < 0.001; R2 = 30.6 %). Two clusters were more frequently observed in travellers: The first cluster, characterized by dominance of Escherichia/Shigella, exhibited the lowest levels of richness and diversity. The second cluster, dominated by Faecalibacterium and Bacteroides, displayed the highest richness and diversity patterns. CONCLUSION These findings highlight the diverse impact of international travel on gut microbiota composition and underscore the importance of considering microbiota resilience and diversity in understanding the health implications.
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Affiliation(s)
- D Henares
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950, Esplugues de Llobregat, Barcelona, Spain; CIBER Center for Epidemiology (CIBER) and Public Health, Carlos III Health Institute (CIBERESP, ISCIII), Avenida Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - V Monsalvez
- Department of Infectious Diseases, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Pedro Brotons
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950, Esplugues de Llobregat, Barcelona, Spain; CIBER Center for Epidemiology (CIBER) and Public Health, Carlos III Health Institute (CIBERESP, ISCIII), Avenida Monforte de Lemos, 3-5, 28029, Madrid, Spain; Department of Medicine, Universitat Internacional de Catalunya, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Maria Luisa Machado
- Department of Infectious Diseases, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Silvia Capilla
- Department of microbiology, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Aina Gomila-Grange
- Department of Infectious Diseases, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Meritxell Cubero
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ana Requena-Méndez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Carrer Roselló 132, 08036, Barcelona, Spain; Biomedical Research Networking Center (CIBER) of Infectious Diseases, Carlos III Health Institute (CIBERINFEC, ISCIII), Carrer Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Department of Medicine Solna, Karolinska Institutet, Solnavägen 1, 17177, Solna, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Solnavägen 1, 17177, Solna, Stockholm, Sweden
| | - C Muñoz-Almagro
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950, Esplugues de Llobregat, Barcelona, Spain; CIBER Center for Epidemiology (CIBER) and Public Health, Carlos III Health Institute (CIBERESP, ISCIII), Avenida Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - O Gasch
- Department of Infectious Diseases, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.
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24
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Su Q, Wong OWH, Lu W, Wan Y, Zhang L, Xu W, Li MKT, Liu C, Cheung CP, Ching JYL, Cheong PK, Leung TF, Chan S, Leung P, Chan FKL, Ng SC. Multikingdom and functional gut microbiota markers for autism spectrum disorder. Nat Microbiol 2024; 9:2344-2355. [PMID: 38977906 DOI: 10.1038/s41564-024-01739-1] [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: 08/01/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024]
Abstract
Associations between the gut microbiome and autism spectrum disorder (ASD) have been investigated although most studies have focused on the bacterial component of the microbiome. Whether gut archaea, fungi and viruses, or function of the gut microbiome, is altered in ASD is unclear. Here we performed metagenomic sequencing on faecal samples from 1,627 children (aged 1-13 years, 24.4% female) with or without ASD, with extensive phenotype data. Integrated analyses revealed that 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes and 12 metabolic pathways were altered in children with ASD. Machine learning using single-kingdom panels showed area under the curve (AUC) of 0.68 to 0.87 in differentiating children with ASD from those that are neurotypical. A panel of 31 multikingdom and functional markers showed a superior diagnostic accuracy with an AUC of 0.91, with comparable performance for males and females. Accuracy of the model was predominantly driven by the biosynthesis pathways of ubiquinol-7 or thiamine diphosphate, which were less abundant in children with ASD. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiota markers as non-invasive diagnostic tools in ASD.
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Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yating Wan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenye Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Moses K T Li
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | | | - Ting Fan Leung
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Patrick Leung
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China.
- The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Chang D, Gupta VK, Hur B, Cobo-López S, Cunningham KY, Han NS, Lee I, Kronzer VL, Teigen LM, Karnatovskaia LV, Longbrake EE, Davis JM, Nelson H, Sung J. Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles. Nat Commun 2024; 15:7447. [PMID: 39198444 PMCID: PMC11358288 DOI: 10.1038/s41467-024-51651-9] [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: 09/25/2023] [Accepted: 08/09/2024] [Indexed: 09/01/2024] Open
Abstract
Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.
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Affiliation(s)
- Daniel Chang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Vinod K Gupta
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Benjamin Hur
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sergio Cobo-López
- Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Kevin Y Cunningham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Department of Food Science and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | - Insuk Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Vanessa L Kronzer
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Levi M Teigen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | | | | | - John M Davis
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Emeritus, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Jaeyun Sung
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
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26
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Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell 2024; 187:4554-4570.e18. [PMID: 38981480 DOI: 10.1016/j.cell.2024.06.018] [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: 05/12/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.
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Affiliation(s)
- Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alberto Arrè
- Department CIBIO, University of Trento, Trento, Italy; Zoe Ltd, London, UK
| | - Kate M Bermingham
- Zoe Ltd, London, UK; Department of Nutritional Sciences, King's College London, London, UK
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | | | - Emily R Leeming
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Monia Lobina
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tim D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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27
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Mohr AE, Jasbi P, van Woerden I, Chi J, Gu H, Bruening M, Whisner CM. Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort. GUT MICROBES REPORTS 2024; 1:1-23. [PMID: 39221110 PMCID: PMC11361303 DOI: 10.1080/29933935.2024.2387936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.
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Affiliation(s)
- Alex E. Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Personalized Diagnostics, School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | - Irene van Woerden
- Community and Public Health, Idaho State University, Pocatello, ID, USA
| | - Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Meg Bruening
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Nutritional Sciences, College of Health and Human Development, Pennsylvania State University, University Park, PA, USA
| | - Corrie M. Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
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28
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Romaní-Pérez M, Líebana-García R, Flor-Duro A, Bonillo-Jiménez D, Bullich-Vilarrubias C, Olivares M, Sanz Y. Obesity and the gut microbiota: implications of neuroendocrine and immune signaling. FEBS J 2024. [PMID: 39159270 DOI: 10.1111/febs.17249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 06/29/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024]
Abstract
Obesity is a major health challenge due to its high prevalence and associated comorbidities. The excessive intake of a diet rich in fat and sugars leads to a persistent imbalance between energy intake and energy expenditure, which increases adiposity. Here, we provide an update on relevant diet-microbe-host interactions contributing to or protecting from obesity. In particular, we focus on how unhealthy diets shape the gut microbiota and thus impact crucial intestinal neuroendocrine and immune system functions. We describe how these interactions promote dysfunction in gut-to-brain neuroendocrine pathways involved in food intake control and postprandial metabolism and elevate the intestinal proinflammatory tone, promoting obesity and metabolic complications. In addition, we provide examples of how this knowledge may inspire microbiome-based interventions, such as fecal microbiota transplants, probiotics, and biotherapeutics, to effectively combat obesity-related disorders. We also discuss the current limitations and gaps in knowledge of gut microbiota research in obesity.
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Affiliation(s)
- Marina Romaní-Pérez
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Rebeca Líebana-García
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Alejandra Flor-Duro
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Daniel Bonillo-Jiménez
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Clara Bullich-Vilarrubias
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
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29
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Pan Y, Jiao FY. Link between childhood obesity and gut microbiota. World J Gastroenterol 2024; 30:3560-3563. [PMID: 39193569 PMCID: PMC11346147 DOI: 10.3748/wjg.v30.i30.3560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/08/2024] Open
Abstract
Childhood obesity is a critical global health concern with rising prevalence and significant long-term health implications. Recent studies have implicated gut microbiota in the development and progression of obesity. This editorial analyzes the research conducted by Li et al, who utilized 16S rRNA gene sequencing to compare the gut microbiome of overweight and healthy-weight children. The study found significant differences in microbial diversity and composition between the two groups, with potential implications for understanding and managing childhood obesity. We analyzed the study's advantages and drawbacks, proposing potential areas for future research to better understand the connection between gut microbiota and obesity.
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Affiliation(s)
- Yan Pan
- Department of Pediatrics, The First Affiliated Hospital of Yangtze University, Jingzho 434000, Hubei Province, China
| | - Fu-Yong Jiao
- Shaanxi Kawasaki Disease Diagnosis and Treatment Center, Children's Hospital, Shaanxi Provincial People's Hospital of Xi'an, Jiaotong University, Xi'an 710000, Shaanxi Province, China
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30
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Sinha T, Prins JR, Fernández-Pato A, Kruk M, Dierikx T, de Meij T, de Boer M, de Boer JF, Scherjon S, Kurilshikov A, Zhernakova A. Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome. Cell Host Microbe 2024; 32:1444-1454.e6. [PMID: 39146801 PMCID: PMC11335186 DOI: 10.1016/j.chom.2024.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/09/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
Pregnant women undergoing a cesarean section (CS) typically receive antibiotics prior to skin incision to prevent infections. To investigate if the timing of antibiotics influences the infant gut microbiome, we conducted a randomized controlled trial (NCT06030713) in women delivering via a scheduled CS who received antibiotics either before skin incision or after umbilical cord clamping. We performed a longitudinal analysis on 172 samples from 28 infants at 8 post-birth time points and a cross-sectional analysis at 1 month in 79 infants from 3 cohorts. Although no significant associations with bacterial composition, metabolic pathways, short-chain fatty acids, and bile acids were found, we observed subtle differences between the groups at the bacterial strain level and in the load of antibiotic resistance genes. Rather, feeding mode was a predominant and defining factor impacting infant microbial composition. In conclusion, antibiotic administration during CS has only limited effects on the early-life gut microbiome.
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Affiliation(s)
- Trishla Sinha
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Jelmer R Prins
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Asier Fernández-Pato
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Thomas Dierikx
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Tim de Meij
- Department of Paediatric Gastroenterology, Amsterdam UMC, Emma Children's Hospital, Amsterdam, the Netherlands
| | - Marjon de Boer
- Department of Obstetrics and Gynaecology, Reproduction and Development, Amsterdam UMC Locatie VUmc, Amsterdam, the Netherlands
| | - Jan Freark de Boer
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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31
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Troise D, Mercuri S, Infante B, Losappio V, Cirolla L, Netti GS, Ranieri E, Stallone G. mTOR and SGLT-2 Inhibitors: Their Synergistic Effect on Age-Related Processes. Int J Mol Sci 2024; 25:8676. [PMID: 39201363 PMCID: PMC11354721 DOI: 10.3390/ijms25168676] [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: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
The aging process contributes significantly to the onset of chronic diseases, which are the primary causes of global mortality, morbidity, and healthcare costs. Numerous studies have shown that the removal of senescent cells from tissues extends lifespan and reduces the occurrence of age-related diseases. Consequently, there is growing momentum in the development of drugs targeting these cells. Among them, mTOR and SGLT-2 inhibitors have garnered attention due to their diverse effects: mTOR inhibitors regulate cellular growth, metabolism, and immune responses, while SGLT-2 inhibitors regulate glucose reabsorption in the kidneys, resulting in various beneficial metabolic effects. Importantly, these drugs may act synergistically by influencing senescence processes and pathways. Although direct studies on the combined effects of mTOR inhibition and SGLT-2 inhibition on age-related processes are limited, this review aims to highlight the potential synergistic benefits of these drugs in targeting senescence.
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Affiliation(s)
- Dario Troise
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Renal Medicine and Baxter Novum, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 14152 Stockholm, Sweden
| | - Silvia Mercuri
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Barbara Infante
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Vincenzo Losappio
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Luciana Cirolla
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Giuseppe Stefano Netti
- Unit of Clinical Pathology, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Elena Ranieri
- Unit of Clinical Pathology, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
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32
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Adolph TE, Tilg H. Western diets and chronic diseases. Nat Med 2024; 30:2133-2147. [PMID: 39085420 DOI: 10.1038/s41591-024-03165-6] [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: 03/01/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024]
Abstract
'Westernization', which incorporates industrial, cultural and dietary trends, has paralleled the rise of noncommunicable diseases across the globe. Today, the Western-style diet emerges as a key stimulus for gut microbial vulnerability, chronic inflammation and chronic diseases, affecting mainly the cardiovascular system, systemic metabolism and the gut. Here we review the diet of modern times and evaluate the threat it poses for human health by summarizing recent epidemiological, translational and clinical studies. We discuss the links between diet and disease in the context of obesity and type 2 diabetes, cardiovascular diseases, gut and liver diseases and solid malignancies. We collectively interpret the evidence and its limitations and discuss future challenges and strategies to overcome these. We argue that healthcare professionals and societies must react today to the detrimental effects of the Western diet to bring about sustainable change and improved outcomes in the future.
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Affiliation(s)
- Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
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33
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Wadop YN, Vasquez EL, Mathews JJ, Muhammad JAS, Mavarez RP, Satizabal C, Gonzales MM, Tanner J, Maestre G, Fonteh AN, Seshadri S, Kautz TF, Fongang B. Differential Patterns of Gut and Oral Microbiomes in Hispanic Individuals with Cognitive Impairment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605455. [PMID: 39211240 PMCID: PMC11361189 DOI: 10.1101/2024.07.27.605455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Alzheimer's disease and related dementias (ADRD) have been associated with alterations in both oral and gut microbiomes. While extensive research has focused on the role of gut dysbiosis in ADRD, the contribution of the oral microbiome remains relatively understudied. Furthermore, the potential synergistic interactions between oral and gut microbiomes in ADRD pathology are largely unexplored. This study aims to evaluate distinct patterns and potential synergistic effects of oral and gut microbiomes in a cohort of predominantly Hispanic individuals with cognitive impairment (CI) and without cognitive impairment (NC). We conducted 16S rRNA gene sequencing on stool and saliva samples from 32 participants (17 CI, 15 NC; 62.5% female, mean age = 70.4 ± 6.2 years) recruited in San Antonio, Texas, USA. Correlation analysis through MaAslin2 assessed the relationship between participants' clinical measurements (e.g., fasting glucose and blood cholesterol) and their gut and saliva microbial contents. Differential abundance analysis evaluated taxa with significant differences between CI and NC groups, and alpha and beta diversity metrics assessed within-sample and group compositional differences. Our analyses revealed no significant differences between NC and CI groups in fasting glucose or blood cholesterol levels. However, a clear association was observed between gut microbiome composition and levels of fasting glucose and blood cholesterol. While alpha and beta diversity metrics showed no significant differences between CI and NC groups, differential abundance analysis revealed an increased presence of oral genera such as Dialister , Fretibacterium , and Mycoplasma in CI participants. Conversely, CI individuals exhibited a decreased abundance of gut genera, including Shuttleworthia , Holdemania , and Subdoligranulum , which are known for their anti-inflammatory properties. No evidence was found for synergistic contributions between oral and gut microbiomes in the context of ADRD. Our findings suggest that similar to the gut microbiome, the oral microbiome undergoes significant modifications as individuals transition from NC to CI. Notably, the identified oral microbes have been previously associated with periodontal diseases and gingivitis. These results underscore the necessity for further investigations with larger sample sizes to validate our findings and elucidate the complex interplay between oral and gut microbiomes in ADRD pathogenesis.
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34
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Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL, Christakis NA. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Rep 2024; 43:114442. [PMID: 38968070 PMCID: PMC11290354 DOI: 10.1016/j.celrep.2024.114442] [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: 01/09/2024] [Revised: 04/27/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.
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Affiliation(s)
- Shivkumar Vishnempet Shridhar
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Francesco Beghini
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Marcus Alexander
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Nicholas A Christakis
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
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35
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Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, Poissant J. Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses. Nat Commun 2024; 15:6012. [PMID: 39039075 PMCID: PMC11263349 DOI: 10.1038/s41467-024-49963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.
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Affiliation(s)
- Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sarah A Medill
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD. A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BMC Genomics 2024; 25:708. [PMID: 39033279 DOI: 10.1186/s12864-024-10562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.
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Affiliation(s)
- Pauline Trinh
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Sarah Teichman
- Department of Statistics, University of Washington, Seattle, USA
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Statistics, University of Washington, Seattle, USA.
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Wilde J, Slack E, Foster KR. Host control of the microbiome: Mechanisms, evolution, and disease. Science 2024; 385:eadi3338. [PMID: 39024451 DOI: 10.1126/science.adi3338] [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: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.
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Affiliation(s)
- Jacob Wilde
- Department of Biology, University of Oxford, Oxford, UK
| | - Emma Slack
- Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Basel Institute for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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38
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Lee H, Yang X, Jin PR, Won KJ, Kim CH, Jeong H. The Discovery of Gut Microbial Metabolites as Modulators of Host Susceptibility to Acetaminophen-Induced Hepatotoxicity. Drug Metab Dispos 2024; 52:754-764. [PMID: 38302428 PMCID: PMC11257691 DOI: 10.1124/dmd.123.001541] [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: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
The mammalian gut microbiota plays diverse and essential roles in modulating host physiology. Key mediators determining the outcome of the microbiota-host interactions are the small molecule metabolites produced by the gut microbiota. The liver is a major organ exposed to gut microbial metabolites, and it serves as the nexus for maintaining healthy interactions between the gut microbiota and the host. At the same time, the liver is the primary target of potentially harmful gut microbial metabolites. In this review, we provide an up-to-date list of gut microbial metabolites that have been identified to either increase or decrease host susceptibility to acetaminophen (APAP)-induced liver injury. The signaling pathways and molecular factors involved in the progression of APAP-induced hepatotoxicity are well-established, and we propose that the mouse model of APAP-induced hepatotoxicity serves as a model system for uncovering gut microbial metabolites with previously unknown functions. Furthermore, we envision that gut microbial metabolites identified to alter APAP-induced hepatotoxicity likely have broader implications in other liver diseases. SIGNIFICANCE STATEMENT: This review provides an overview of the role of the gut microbiota in modulating the host susceptibility to acetaminophen (APAP)-induced liver injury. It focuses on the roles of gut bacterial small molecule metabolites as mediators of the interaction between the gut microbiota and the liver. It also illustrates the utility of APAP-induced liver injury as a model to identify gut microbial metabolites with biological function.
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Affiliation(s)
- Hyunwoo Lee
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Xiaotong Yang
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Pei-Ru Jin
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Kyoung-Jae Won
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Chang H Kim
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Hyunyoung Jeong
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
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Chen W, Li Y, Wang W, Gao S, Hu J, Xiang B, Wu D, Jiao N, Xu T, Zhi M, Zhu L, Zhu R. Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. Cell Rep Med 2024; 5:101624. [PMID: 38942021 PMCID: PMC11293350 DOI: 10.1016/j.xcrm.2024.101624] [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: 11/04/2023] [Revised: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.
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Affiliation(s)
- Wanning Chen
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Yichen Li
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Wenxia Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Jun Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Bingjie Xiang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Tao Xu
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China
| | - Min Zhi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China.
| | - Lixin Zhu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China.
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China.
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Park CE, Jo YJ, Jung DR, Park HC, Shin JH. Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation. Microorganisms 2024; 12:1419. [PMID: 39065187 PMCID: PMC11278867 DOI: 10.3390/microorganisms12071419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future.
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Affiliation(s)
- Chang-Eon Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Young-Jae Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Hee-Cheon Park
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
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Sun J, Teng M, Zhu W, Zhao X, Zhao L, Li Y, Zhang Z, Liu Y, Bi S, Wu F. MicroRNA and Gut Microbiota Alter Intergenerational Effects of Paternal Exposure to Polyethylene Nanoplastics. ACS NANO 2024; 18:18085-18100. [PMID: 38935618 DOI: 10.1021/acsnano.4c06298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Nanoplastics (NPs), as emerging contaminants, have been shown to cause testicular disorders in mammals. However, whether paternal inheritance effects on offspring health are involved in NP-induced reproductive toxicity remains unclear. In this study, we developed a mouse model where male mice were administered 200 nm polyethylene nanoparticles (PE-NPs) at a concentration of 2 mg/L through daily gavage for 35 days to evaluate the intergenerational effects of PE-NPs in an exclusive male-lineage transmission paradigm. We observed that paternal exposure to PE-NPs significantly affected growth phenotypes and sex hormone levels and induced histological damage in the testicular tissue of both F0 and F1 generations. In addition, consistent changes in sperm count, motility, abnormalities, and gene expression related to endoplasmic reticulum stress, sex hormone synthesis, and spermatogenesis were observed across paternal generations. The upregulation of microRNA (miR)-1983 and the downregulation of miR-122-5p, miR-5100, and miR-6240 were observed in both F0 and F1 mice, which may have been influenced by reproductive signaling pathways, as indicated by the RNA sequencing of testis tissues and quantitative real-time polymerase chain reaction findings. Furthermore, alterations in the gut microbiota and subsequent Spearman correlation analysis revealed that an increased abundance of Desulfovibrio (C21_c20) and Ruminococcus (gnavus) and a decreased abundance of Allobaculum were positively associated with spermatogenic dysfunction. These findings were validated in a fecal microbiota transplantation trial. Our results demonstrate that changes in miRNAs and the gut microbiota caused by paternal exposure to PE-NPs mediated intergenerational effects, providing deeper insights into mechanisms underlying the impact of paternal inheritance.
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Affiliation(s)
- Jiaqi Sun
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Miaomiao Teng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lihui Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yunxia Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zixuan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yunjie Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Bi
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Fengchang Wu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Di Paola FJ, Alquati C, Conti G, Calafato G, Turroni S, D'Amico F, Ceccarelli C, Buttitta F, Bernardi A, Cuicchi D, Poggioli G, Turchetti D, Ferrari S, Cannizzaro R, Realdon S, Brigidi P, Ricciardiello L. Interplay between WNT/PI3K-mTOR axis and the microbiota in APC-driven colorectal carcinogenesis: data from a pilot study and possible implications for CRC prevention. J Transl Med 2024; 22:631. [PMID: 38970018 PMCID: PMC11227240 DOI: 10.1186/s12967-024-05305-5] [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: 03/07/2024] [Accepted: 05/16/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Wnt/β-catenin signalling impairment accounts for 85% of colorectal cancers (CRCs), including sporadic and familial adenomatous polyposis (FAP) settings. An altered PI3K/mTOR pathway and gut microbiota also contribute to CRC carcinogenesis. We studied the interplay between the two pathways and the microbiota composition within each step of CRC carcinogenesis. METHODS Proteins and target genes of both pathways were analysed by RT-qPCR and IHC in tissues from healthy faecal immunochemical test positive (FIT+, n = 17), FAP (n = 17) and CRC (n = 15) subjects. CRC-related mutations were analysed through NGS and Sanger. Oral, faecal and mucosal microbiota was profiled by 16 S rRNA-sequencing. RESULTS We found simultaneous hyperactivation of Wnt/β-catenin and PI3K/mTOR pathways in FAP-lesions compared to CRCs. Wnt/β-catenin molecular markers positively correlated with Clostridium_sensu_stricto_1 and negatively with Bacteroides in FAP faecal microbiota. Alistipes, Lachnospiraceae, and Ruminococcaceae were enriched in FAP stools and adenomas, the latter also showing an overabundance of Lachnoclostridium, which positively correlated with cMYC. In impaired-mTOR-mutated CRC tissues, p-S6R correlated with Fusobacterium and Dialister, the latter also confirmed in the faecal-ecosystem. CONCLUSIONS Our study reveals an interplay between Wnt/β-catenin and PI3K/mTOR, whose derangement correlates with specific microbiota signatures in FAP and CRC patients, and identifies new potential biomarkers and targets to improve CRC prevention, early adenoma detection and treatment.
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Affiliation(s)
| | - Chiara Alquati
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Gabriele Conti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Calafato
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Federica D'Amico
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claudio Ceccarelli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | - Alice Bernardi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Dajana Cuicchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Gilberto Poggioli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Daniela Turchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Simona Ferrari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Renato Cannizzaro
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Stefano Realdon
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Luigi Ricciardiello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
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Sandys O, Stokkers PCF, Te Velde AA. DAMP-ing IBD: Extinguish the Fire and Prevent Smoldering. Dig Dis Sci 2024:10.1007/s10620-024-08523-5. [PMID: 38963463 DOI: 10.1007/s10620-024-08523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
In inflammatory bowel diseases (IBD), the most promising therapies targeting cytokines or immune cell trafficking demonstrate around 40% efficacy. As IBD is a multifactorial inflammation of the intestinal tract, a single-target approach is unlikely to solve this problem, necessitating an alternative strategy that addresses its variability. One approach often overlooked by the pharmaceutically driven therapeutic options is to address the impact of environmental factors. This is somewhat surprising considering that IBD is increasingly viewed as a condition heavily influenced by such factors, including diet, stress, and environmental pollution-often referred to as the "Western lifestyle". In IBD, intestinal responses result from a complex interplay among the genetic background of the patient, molecules, cells, and the local inflammatory microenvironment where danger- and microbe-associated molecular patterns (D/MAMPs) provide an adjuvant-rich environment. Through activating DAMP receptors, this array of pro-inflammatory factors can stimulate, for example, the NLRP3 inflammasome-a major amplifier of the inflammatory response in IBD, and various immune cells via non-specific bystander activation of myeloid cells (e.g., macrophages) and lymphocytes (e.g., tissue-resident memory T cells). Current single-target biological treatment approaches can dampen the immune response, but without reducing exposure to environmental factors of IBD, e.g., by changing diet (reducing ultra-processed foods), the adjuvant-rich landscape is never resolved and continues to drive intestinal mucosal dysregulation. Thus, such treatment approaches are not enough to put out the inflammatory fire. The resultant smoldering, low-grade inflammation diminishes physiological resilience of the intestinal (micro)environment, perpetuating the state of chronic disease. Therefore, our hypothesis posits that successful interventions for IBD must address the complexity of the disease by simultaneously targeting all modifiable aspects: innate immunity cytokines and microbiota, adaptive immunity cells and cytokines, and factors that relate to the (micro)environment. Thus the disease can be comprehensively treated across the nano-, meso-, and microscales, rather than with a focus on single targets. A broader perspective on IBD treatment that also includes options to adapt the DAMPing (micro)environment is warranted.
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Affiliation(s)
- Oliver Sandys
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands
| | - Pieter C F Stokkers
- Department of Gastroenterology and Hepatology, OLVG West, Amsterdam, The Netherlands
| | - Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands.
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44
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De Vos WM, Nguyen Trung M, Davids M, Liu G, Rios-Morales M, Jessen H, Fiedler D, Nieuwdorp M, Bui TPN. Phytate metabolism is mediated by microbial cross-feeding in the gut microbiota. Nat Microbiol 2024; 9:1812-1827. [PMID: 38858593 DOI: 10.1038/s41564-024-01698-7] [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: 08/25/2023] [Accepted: 04/04/2024] [Indexed: 06/12/2024]
Abstract
Dietary intake of phytate has various reported health benefits. Previous work showed that the gut microbiota can convert phytate to short-chain fatty acids (SCFAs), but the microbial species and metabolic pathway are unclear. Here we identified Mitsuokella jalaludinii as an efficient phytate degrader, which works synergistically with Anaerostipes rhamnosivorans to produce the SCFA propionate. Analysis of published human gut taxonomic profiles revealed that Mitsuokella spp., in particular M. jalaludinii, are prevalent in human gut microbiomes. NMR spectroscopy using 13C-isotope labelling, metabolomic and transcriptomic analyses identified a complete phytate degradation pathway in M. jalaludinii, including production of the intermediate Ins(2)P/myo-inositol. The major end product, 3-hydroxypropionate, was converted into propionate via a synergistic interaction with Anaerostipes rhamnosivorans both in vitro and in mice. Upon [13C6]phytate administration, various 13C-labelled components were detected in mouse caecum in contrast with the absence of [13C6] InsPs or [13C6]myo-inositol in plasma. Caco-2 cells incubated with co-culture supernatants exhibited improved intestinal barrier integrity. These results suggest that the microbiome plays a major role in the metabolism of this phytochemical and that its fermentation to propionate by M. jalaludinii and A. rhamnosivorans may contribute to phytate-driven health benefits.
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Affiliation(s)
- Willem M De Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institute of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mark Davids
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
| | - Guizhen Liu
- Institute of Organic Chemistry & Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Melany Rios-Morales
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
| | - Henning Jessen
- Institute of Organic Chemistry & Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institute of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands.
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45
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Liu Y, Fachrul M, Inouye M, Méric G. Harnessing human microbiomes for disease prediction. Trends Microbiol 2024; 32:707-719. [PMID: 38246848 DOI: 10.1016/j.tim.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Human Genomics and Evolution Unit, St Vincent's Institute of Medical Research, Victoria, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia; Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Medical Science, Molecular Epidemiology, Uppsala University, Uppsala, Sweden; Department of Cardiovascular Research, Translation, and Implementation, La Trobe University, Melbourne, Victoria, Australia.
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46
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Zhang Q, Schwarz D, Cheng Y, Sohrabi Y. Unraveling host genetics and microbiome genome crosstalk: a novel therapeutic approach. Trends Mol Med 2024:S1471-4914(24)00165-5. [PMID: 38937208 DOI: 10.1016/j.molmed.2024.06.007] [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: 04/17/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024]
Abstract
The ability of the gut microbiome to adapt to a new environment and utilize a new metabolite or dietary compound by inducing structural variations (SVs) in the genome has an important role in human health. Here, we discuss recent data on host genetic regulation of SV induction and its use as a new therapeutic approach.
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Affiliation(s)
- Qian Zhang
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany
| | - Dennis Schwarz
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany; Institute of Experimental Pathology (ExPat), Center for Molecular Biology of Inflammation (ZMBE), University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany
| | - Yumei Cheng
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Yahya Sohrabi
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany; Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czechia.
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47
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Yan Z, Hao T, Yan Y, Zhao Y, Wu Y, Tan Y, Bi Y, Cui Y, Yang R, Zhao Y. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR. Appl Microbiol Biotechnol 2024; 108:396. [PMID: 38922447 PMCID: PMC11208268 DOI: 10.1007/s00253-024-13204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.
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Affiliation(s)
- Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongyu Hao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
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48
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Brenchley JM, Serrano-Villar S. From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy. MICROBIOME 2024; 12:113. [PMID: 38907315 PMCID: PMC11193286 DOI: 10.1186/s40168-024-01825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV. RESULTS Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents. CONCLUSIONS Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, MA, USA.
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, IRYCIS and CIBERInfec, Madrid, Spain.
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49
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Derosa L, Iebba V, Silva CAC, Piccinno G, Wu G, Lordello L, Routy B, Zhao N, Thelemaque C, Birebent R, Marmorino F, Fidelle M, Messaoudene M, Thomas AM, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Sibilot DM, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Bouchard N, Sow C, Darik I, Zoppi S, Ly P, Reni A, Daillère R, Deutsch E, Lee KA, Bolte LA, Björk JR, Weersma RK, Barlesi F, Padilha L, Finzel A, Isaksen ML, Escudier B, Albiges L, Planchard D, André F, Cremolini C, Martinez S, Besse B, Zhao L, Segata N, Wojcik J, Kroemer G, Zitvogel L. Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome. Cell 2024; 187:3373-3389.e16. [PMID: 38906102 DOI: 10.1016/j.cell.2024.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerio Iebba
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | - Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Leonardo Lordello
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Bertrand Routy
- Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Department of Medicine, Montréal, QC, Canada; Centre de Recherche du CHUM (CRCHUM), Montréal, QC, Canada
| | - Naisi Zhao
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Federica Marmorino
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marine Fidelle
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | | | - Gerard Zalcman
- Université Paris Cité, Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | | | - Denis Moro- Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- INSERM U1016-CNRS UMR8104, Paris Cité University, Paris, France; Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France; Centre de Recherche INSERM LNC-UMR1231, Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | | | - Cissé Sow
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Ines Darik
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Silvia Zoppi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Pierre Ly
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Anna Reni
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Section of Oncology, Department of Medicine, University of Verona School of Medicine and Verona University Hospital Trust, Verona, Italy
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Radiation Oncology, Gustave Roussy, Villejuif, France; INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Lucas Padilha
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | - Ana Finzel
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | | | - Bernard Escudier
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fabrice André
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Chiara Cremolini
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Benjamin Besse
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA; State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Centre de Recherche des Cordeliers, Equipe labellisée-Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
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Zhang S, Swarte JC, Gacesa R, Knobbe TJ, Kremer D, Jansen BH, de Borst MH, Harmsen HJM, Erasmus ME, Verschuuren EAM, Bakker SJL, Gan CT, Weersma RK, Björk JR. The gut microbiome in end-stage lung disease and lung transplantation. mSystems 2024; 9:e0131223. [PMID: 38712927 PMCID: PMC11237811 DOI: 10.1128/msystems.01312-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/03/2024] [Indexed: 05/08/2024] Open
Abstract
Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients, but the gut microbiome of lung transplant recipients has not been extensively explored. We assessed the gut microbiome in 64 fecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transplant recipients after transplantation using metagenomic sequencing. To identify dysbiotic microbial signatures, we analyzed 243 fecal samples from age-, sex-, and BMI-matched healthy controls. By unsupervised clustering, we identified five groups of lung transplant recipients using different combinations of immunosuppressants and antibiotics and analyzed them in relation to the gut microbiome. Finally, we investigated the gut microbiome of lung transplant recipients in different chronic lung allograft dysfunction (CLAD) stages and longitudinal gut microbiome changes after transplantation. We found 108 species (58.1%) in end-stage lung disease patients and 139 species (74.7%) in lung transplant recipients that were differentially abundant compared with healthy controls, with several species exhibiting sharp longitudinal increases from before to after transplantation. Different combinations of immunosuppressants and antibiotics were associated with specific gut microbial signatures. We found that the gut microbiome of lung transplant recipients in CLAD stage 0 was more similar to healthy controls compared to those in CLAD stage 1. Finally, the gut microbial diversity of lung transplant recipients remained lower than the average gut microbial diversity of healthy controls up to more than 20 years post-transplantation. Gut dysbiosis, already present before lung transplantation was exacerbated following lung transplantation.IMPORTANCEThis study provides extensive insights into the gut microbiome of end-stage lung disease patients and lung transplant recipients, which warrants further investigation before the gut microbiome can be used for microbiome-targeted interventions that could improve the outcome of lung transplantation.
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Affiliation(s)
- Shuyan Zhang
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - J. Casper Swarte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim J. Knobbe
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Bernadien H. Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Martin H. de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - TransplantLines InvestigatorsAnnemaCobyBakkerStephan J. L.BergerStefan P.BlokzijlHansBodewesFrank A. J. A.de BoerMarieke T.DammanKevinde BorstMartin H.DiepstraArjanDijkstraGerardDouwesRianne M.DoorenbosCaecilia S. E.EisengaMichele F.ErasmusMichiel E.GanC. TjiHakEelkoHepkemaBouke G.KlontFrankKnobbeTim J.KremerDaanLeuveninkHenri G. D.LexmondWillem S.de MeijerVincent E.NiestersHubert G. M.Nieuwenhuis-MoekeGertrude J.van PeltL. JoostPolRobert A.PorteRobert J.RanchorAdelta V.SiebelinkMarion J.SlartRiemer J. H. J. A.SwarteJ. CasperTouwDaan J.van den HeuvelMarius C.van Leer-ButerCorettavan LondenMarcoVerschuurenErik A. M.VosMichel J.WeersmaRinse K.Gomes NetoAntonio W.SandersJan Stephan F.
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Cardiothoracic Surgery, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Medical Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Michiel E. Erasmus
- Department of Cardiothoracic Surgery, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Erik A. M. Verschuuren
- Department of Medical Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Stephan J. L. Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - C. Tji Gan
- Department of Medical Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Johannes R. Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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