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Schoultz I, Claesson MJ, Dominguez‐Bello MG, Fåk Hållenius F, Konturek P, Korpela K, Laursen MF, Penders J, Roager H, Vatanen T, Öhman L, Jenmalm MC. Gut microbiota development across the lifespan: Disease links and health-promoting interventions. J Intern Med 2025; 297:560-583. [PMID: 40270478 PMCID: PMC12087861 DOI: 10.1111/joim.20089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2025]
Abstract
The gut microbiota plays a pivotal role in human life and undergoes dynamic changes throughout the human lifespan, from infancy to old age. During our life, the gut microbiota influences health and disease across life stages. This review summarizes the discussions and presentations from the symposium "Gut microbiota development from infancy to old age" held in collaboration with the Journal of Internal Medicine. In early infancy, microbial colonization is shaped by factors such as mode of delivery, antibiotic exposure, and milk-feeding practices, laying the foundation for subsequent increased microbial diversity and maturation. Throughout childhood and adolescence, microbial maturation continues, influencing immune development and metabolic health. In adulthood, the gut microbiota reaches a relatively stable state, influenced by genetics, diet, and lifestyle. Notably, disruptions in gut microbiota composition have been implicated in various inflammatory diseases-including inflammatory bowel disease, Type 1 diabetes, and allergies. Furthermore, emerging evidence suggests a connection between gut dysbiosis and neurodegenerative disorders such as Alzheimer's disease. Understanding the role of the gut microbiota in disease pathogenesis across life stages provides insights into potential therapeutic interventions. Probiotics, prebiotics, and dietary modifications, as well as fecal microbiota transplantation, are being explored as promising strategies to promote a healthy gut microbiota and mitigate disease risks. This review focuses on the gut microbiota's role in infancy, adulthood, and aging, addressing its development, stability, and alterations linked to health and disease across these critical life stages. It outlines future research directions aimed at optimizing the gut microbiota composition to improve health.
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Affiliation(s)
- Ida Schoultz
- School of Medical SciencesFaculty of Medicine and Health Örebro UniversityOrebroSweden
| | | | - Maria Gloria Dominguez‐Bello
- Department of Biochemistry & Microbiology and of AnthropologyRutgers University–New BrunswickNew BrunswickNew JerseyUSA
| | - Frida Fåk Hållenius
- Department of Food Technology, Engineering and NutritionLund UniversityLundSweden
| | - Peter Konturek
- Department of Medicine, Thuringia Clinic SaalfeldTeaching Hospital of the University JenaJenaGermany
| | - Katri Korpela
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | | | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School for Nutrition and Translational Research in MetabolismMaastricht University Medical CenterMaastrichtthe Netherlands
| | - H. Roager
- Department of Nutrition, Exercise and SportsUniversity of CopenhagenFrederiksbergDenmark
| | - Tommi Vatanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Department of Microbiology, Faculty of Agriculture and ForestryUniversity of HelsinkiHelsinkiFinland
- Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Liggins InstituteUniversity of AucklandAucklandNew Zealand
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Maria C. Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
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Dörr AK, Imangaliyev S, Karadeniz U, Schmidt T, Meyer F, Kraiselburd I. Distinguishing critical microbial community shifts from normal temporal variability in human and environmental ecosystems. Sci Rep 2025; 15:16934. [PMID: 40374711 DOI: 10.1038/s41598-025-01781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 05/08/2025] [Indexed: 05/17/2025] Open
Abstract
Differentiating significant microbial community changes from normal fluctuations is vital for understanding microbial dynamics in human and environmental ecosystems. This knowledge could enable early warning systems to monitor critical changes affecting human or environmental health. We applied 16S rRNA gene sequencing and time-series analysis to model bacterial abundance trajectories in human gut and wastewater microbiomes. We evaluated various model architectures using datasets from two human studies and five wastewater settings. Long short-term memory (LSTM) models consistently outperformed other models in predicting bacterial abundances and detecting outliers, as measured by multiple metrics. Prediction intervals for each genus allowed us to identify significant changes and signaling shifts in community states. This study proposes a machine learning model capable of monitoring microbial communities and providing insights into their responses to internal and external factors in medical and environmental settings.
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Affiliation(s)
- Ann-Kathrin Dörr
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Sultan Imangaliyev
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Utku Karadeniz
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Tina Schmidt
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, 45128, Essen, Germany
| | - Folker Meyer
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Ivana Kraiselburd
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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3
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Kehrmann J, Dostmohammadi A, Stumpf AL, Best L, Consten L, Sievert H, Maischack F, Sammet S, Albayrak-Rena S, Doerr AK, Bohlen K, von Velsen O, Kraiselburd I, Karsten CB, Farahpour F, Meyer F, Esser S, Buer J. Gut microbiota differences linked to weight gain and ART in people living with HIV are enterotype specific and minor compared to the large differences linked to sexual behavior. Front Cell Infect Microbiol 2025; 15:1568352. [PMID: 40406514 PMCID: PMC12095285 DOI: 10.3389/fcimb.2025.1568352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 04/03/2025] [Indexed: 05/26/2025] Open
Abstract
Introduction Specific antiretroviral therapy (ART) regimens are associated with weight gain in people living with HIV (PLWH). Gut microbiota is involved in weight gain in humans and animals. Human gut microbiota can be classified into enterotypes with distinct microbial and functional profiles. Methods In a cohort of 118 PLWH, we analyzed the gut microbiome in relation to weight gain and ART regimen using 16S rRNA gene sequencing, taking enterotype classification into account. Results The enterotype was strongly associated with sexual orientation. Of the 67 individuals forming a Prevotella-dominated enterotype cluster in principal coordinates analysis, 93% were men who had sex with men (MSM), while 31% of individuals in the Bacteroides-dominated enterotype cluster were MSM and 69% were non-MSM. Forty-nine genera differed significantly between the MSM and non-MSM individuals. When stratified by dominant genus, only six taxa were associated with weight gain. Of these, five were restricted to Bacteroides-dominated individuals. Among them, the class Actinobacteria and genus Bifidobacterium differed between individuals gaining more than 5% weight and less than 5% weight 1 year after ART switch. Additionally, three taxa were significantly different between 15% of individuals with the highest weight gain (≥6.3%) and the highest weight loss (≤3.19%) 1 year after ART switch, including the phyla Firmicutes, Verrucomicrobia, and Synergistetes. Distinct functional properties in Bacteroides, but not Prevotella-dominated enterotype individuals, linked to weight gain were observed, particularly for glycan and lipid metabolism. Additionally, ART regimen-associated differences were observed for the phylum Actinobacteria, although this was limited to Prevotella-dominated enterotype individuals. Discussion Differences in the composition and functional characteristics of the gut microbiome associated with weight gain and ART regimens were enterotype-specific and relatively small compared with differences linked to sexual orientation. Due to the substantial differences in gut microbiome structure among many MSM, categorization into enterotypes is useful for identifying differences in microbiome composition associated with variables such as weight gain or ART, which may be limited to a single enterotype. This may further advance the identification of microbes that contribute to weight gain or alter the gut microbiome composition in the context of the enterotype.
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Affiliation(s)
- Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alireza Dostmohammadi
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Anna-Lena Stumpf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lara Best
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Leah Consten
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hannah Sievert
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Felix Maischack
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefanie Sammet
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sarah Albayrak-Rena
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Doerr
- Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Katharina Bohlen
- Department of Gastroenterology, Hepatology and Transplantational Medicine, University Hospital Essen, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Otgonzul von Velsen
- Institute of Medical Informatics, Biometrics, and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Clinical Trials, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ivana Kraiselburd
- Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christina B. Karsten
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Farnoush Farahpour
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
- Institute of Cell Biology (Tumor Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Folker Meyer
- Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefan Esser
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Wang M, Zhang L, Liu Z, Guo A, Yang G, Yu T. Host-Microbiota Interactions in the Pathogenesis of Porcine Fetal Mummification. Microorganisms 2025; 13:1052. [PMID: 40431225 PMCID: PMC12113762 DOI: 10.3390/microorganisms13051052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 04/25/2025] [Accepted: 04/28/2025] [Indexed: 05/29/2025] Open
Abstract
The number of mummies (MUM) in pigs is a major factor affecting sow reproductive performance. Reducing the incidence of MUM can effectively improve sow utilization efficiency. However, the complex mechanisms by which the host genome, gut microbiome, and metabolome interact to influence sow MUM remain unclear. Based on the current research landscape, this study systematically reveals the regulatory mechanisms of the host genome-gut microbiome-metabolome interaction network on sow MUM. By conducting a multi-omics analysis on the intestinal contents of Yorkshire sows during late gestation across different parities, we constructed a dynamic atlas of the gut microbiota and identified 385 core microbial taxa. Through multi-model MWAS and meta-analysis, we screened six key microbial taxa significantly associated with MUM, including Bacteroidales_RF16_group, Prevotellaceae_Ga6A1_group, Comamonas, Paraprevotella, Dorea, and Gallicola. An mGWAS analysis further identified Bacteroidales_RF16_group as regulated by host genetics, as well as candidate genes such as EGF, ENPEP, and CASP6, and important SNP loci such as rs345237235 and rs3475666995. The study found that the abundance of Proteobacteria in the sow's gut increased progressively from the first parity, providing a theoretical basis for pathogen suppression mechanisms. By integrating fecal metabolomics data, we constructed a four-dimensional regulatory network of host gene-gut microbiota-metabolite-host phenotype. This study innovatively combines quantitative genetics with multi-omics approaches, not only providing a theoretical foundation for understanding host-microbiota interaction mechanisms but also offering critical scientific guidance for reducing sow MUM incidence and improving reproductive efficiency.
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Affiliation(s)
| | | | | | | | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Taiyong Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
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Hu M, Zhu X, Huang X, Hua L, Lin X, Zhang H, Hu Y, Tong T, Li L, Xuan B, Zhao Y, Zhou Y, Ding J, Ma Y, Jiang Y, Ning L, Zhang Y, Wang Z, Fang JY, Zhang Y, Xiao X, Hong J, Chen H, Li J, Chen H. Optimizing anti-PD-1/PD-L1 therapy efficacy and fecal microbiota transplantation donor selection through gut mycobiome-based enterotype. Cell Rep 2025; 44:115589. [PMID: 40257861 DOI: 10.1016/j.celrep.2025.115589] [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: 08/01/2024] [Revised: 01/06/2025] [Accepted: 03/28/2025] [Indexed: 04/23/2025] Open
Abstract
Immunotherapy has revolutionized cancer treatment, but response variability remains a challenge. The gut microbiome's role in therapeutic efficacy is well established, but the impact of the gut mycobiome is less understood. Using unsupervised clustering, we identify two gut mycobiome-based enterotypes, favorable type and unfavorable type, characterized by distinct microbial compositions linked to immunotherapy outcomes. Favorable-type enterotypes exhibit higher fungal and bacterial alpha diversity, enriched butyrate-producing bacteria, and metabolic pathways related to butyric acid and sugar/starch metabolism. External validation confirms their predictive value in assessing immunotherapy efficacy. Multi-omics analysis reveals increased CD8+ T cell infiltration in the tumor microenvironment of favorable-type patients. Fecal microbiota transplantation (FMT) from favorable-type donors enhances anti-PD-1 sensitivity, promotes CD8+ T cell infiltration, and boosts butyrate production in vivo. These findings highlight the gut mycobiome's role in immunotherapy response and support FMT from favorable-type donors as a potential strategy for improving treatment outcomes and patient stratification.
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Affiliation(s)
- Muni Hu
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Xiaoqiang Zhu
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China; Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Xiaowen Huang
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Li Hua
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaolin Lin
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Hu
- Department of Gastroenterology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Tianying Tong
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Lingxi Li
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Baoqin Xuan
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Ying Zhao
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Yilu Zhou
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Jinmei Ding
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Yanru Ma
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Yi Jiang
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Lijun Ning
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Yue Zhang
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Zhenyu Wang
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou 221009, China
| | - Xiuying Xiao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Hong
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Huimin Chen
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China.
| | - Jiantao Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Haoyan Chen
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China.
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Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R. Clinical translation of microbiome research. Nat Med 2025; 31:1099-1113. [PMID: 40217076 DOI: 10.1038/s41591-025-03615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Accepted: 02/26/2025] [Indexed: 04/18/2025]
Abstract
The landscape of clinical microbiome research has dramatically evolved over the past decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the past 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.
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Affiliation(s)
- Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Interdisciplinary Lactation Centre, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin J Blaser
- CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Mariana Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Fransisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Fransisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Hiutung Chu
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines, La Jolla, CA, USA
| | - Lara R Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
- Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Microbiome and Cancer Division, DKFZ, Heidelberg, Germany
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- eScience Institute, University of Washington, Seattle, WA, USA
| | - Katharine E Gilbert
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | | | - Suzanne L Ishaq
- School of Food and Agriculture, University of Maine, Orono, ME, USA
- Microbes and Social Equity working group, Orono, ME, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- ZOE Ltd, London, UK
| | | | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carolina Tropini
- CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA
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7
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Li X, Han X, Yan H, Zhu H, Wang H, Li D, Tian Y, Su Y. From gut microbiota to host genes: A dual-regulatory pathway driving body weight variation in dagu chicken (Gallus gallus domesticus). Poult Sci 2025; 104:105067. [PMID: 40239312 PMCID: PMC12032334 DOI: 10.1016/j.psj.2025.105067] [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: 01/12/2025] [Revised: 03/16/2025] [Accepted: 03/18/2025] [Indexed: 04/18/2025] Open
Abstract
During the growth and development of animals, there is an interaction between the gut microbiota and the host genotype. The host genotype can regulate the microbiota, and in turn, the microbiota can influence host gene expression, thereby affecting the animal's production performance. This study explored the dynamic interplay between the gut microbiota and host gene expression in body weight variation in Dagu chicken, an indigenous poultry genetic resource in China. We characterized mucosa-associated microbiota across four gastrointestinal segments (duodenum, jejunum, ileum, cecum) and ileocecal chyme microbiota in 12-week-old Dagu chickens stratified by divergent body weight phenotypes, while simultaneously quantifying region-specific intestinal epithelial transcriptional regulation. 16S rDNA sequencing was employed to identify Firmicutes as the predominant bacterial phylum, with notable differences in the abundance of specific genera (e.g., Ligilactobacillus and Lactobacillus) being observed between the high- or low-body-weight groups. Enhanced biosynthesis pathways were functionally predicted in heavier roosters, whereas reduced nutrient metabolism pathways were contrasted. A conserved functional concordance was observed between regionally predominant differential microbiota and the physiological specialization of corresponding intestinal niches. Functional analysis revealed that the high-body-weight group demonstrated superior capabilities in microbial biosynthesis, whereas the low-body-weight group exhibited enhanced microbial metabolic activity. NAA80 was identified as the common differentially expressed gene across all intestinal epithelial tissues. The Gene Ontology and KEGG pathway analyses revealed elevated nutrient absorption efficiency in the high-body-weight group, while the low-body-weight group demonstrated accelerated cellular renewal rates and shorter cycles. Correlation analysis identified significant associations between gut microbiota and host genes expression profiles, with the majority of correlations being positive. These results suggest a coordinated interaction between microbial communities and host genetic regulation, potentially driving phenotypic differences in body weight performance.
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Affiliation(s)
- Xiaohan Li
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Xueru Han
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Huan Yan
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Hongyan Zhu
- College of Basic Medical Science, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Hongcai Wang
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Desheng Li
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Yumin Tian
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China
| | - Yuhong Su
- College of Animal Husbandry and Veterinary, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China; Liaoning Provincial Key Laboratory of Animal Product Quality and Safety, Jinzhou Medical University, Jinzhou 121001, Liaoning, PR China.
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Ribeiro G, Schellekens H, Cuesta-Marti C, Maneschy I, Ismael S, Cuevas-Sierra A, Martínez JA, Silvestre MP, Marques C, Moreira-Rosário A, Faria A, Moreno LA, Calhau C. A menu for microbes: unraveling appetite regulation and weight dynamics through the microbiota-brain connection across the lifespan. Am J Physiol Gastrointest Liver Physiol 2025; 328:G206-G228. [PMID: 39811913 DOI: 10.1152/ajpgi.00227.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/14/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]
Abstract
Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior. Therefore, the role of the microbiota-gut-brain axis in appetite and obesity is receiving increased attention. Omics approaches such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics in appetite and weight regulation offer new opportunities for featuring obesity phenotypes. Furthermore, gut-microbiota-targeted approaches such as pre-, pro-, post-, and synbiotic, personalized nutrition, and fecal microbiota transplantation are novel avenues for precision treatments. The aim of this narrative review is 1) to provide an overview of the role of the microbiota-gut-brain axis in appetite regulation across the lifespan and 2) to discuss the potential of omics and gut microbiota-targeted approaches to deepen understanding of appetite regulation and obesity.
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Affiliation(s)
- Gabriela Ribeiro
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Harriët Schellekens
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Cristina Cuesta-Marti
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ivie Maneschy
- Growth, Exercise, Nutrition and Development Research Group, Instituto Agroalimentario de Aragón, University of Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón, University of Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Shámila Ismael
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Amanda Cuevas-Sierra
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- Precision Nutrition and Cardiometabolic Health, IMDEA-Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM+CSIC, Spanish National Research Council, Madrid, Spain
| | - J Alfredo Martínez
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Precision Nutrition and Cardiometabolic Health, IMDEA-Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM+CSIC, Spanish National Research Council, Madrid, Spain
| | - Marta P Silvestre
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Cláudia Marques
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - André Moreira-Rosário
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Ana Faria
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Luis A Moreno
- Growth, Exercise, Nutrition and Development Research Group, Instituto Agroalimentario de Aragón, University of Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón, University of Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Conceição Calhau
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
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Huang L, Huhulea EN, Abraham E, Bienenstock R, Aifuwa E, Hirani R, Schulhof A, Tiwari RK, Etienne M. The Role of Artificial Intelligence in Obesity Risk Prediction and Management: Approaches, Insights, and Recommendations. MEDICINA (KAUNAS, LITHUANIA) 2025; 61:358. [PMID: 40005474 PMCID: PMC11857386 DOI: 10.3390/medicina61020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 02/07/2025] [Accepted: 02/12/2025] [Indexed: 02/27/2025]
Abstract
Greater than 650 million individuals worldwide are categorized as obese, which is associated with significant health, economic, and social challenges. Given its overlap with leading comorbidities such as heart disease, innovative solutions are necessary to improve risk prediction and management strategies. In recent years, artificial intelligence (AI) and machine learning (ML) have emerged as powerful tools in healthcare, offering novel approaches to chronic disease prevention. This narrative review explores the role of AI/ML in obesity risk prediction and management, with a special focus on childhood obesity. We begin by examining the multifactorial nature of obesity, including genetic, behavioral, and environmental factors, and the limitations of traditional approaches to predict and treat morbidity associated obesity. Next, we analyze AI/ML techniques commonly used to predict obesity risk, particularly in minimizing childhood obesity risk. We shift to the application of AI/ML in obesity management, comparing perspectives from healthcare providers versus patients. From the provider's perspective, AI/ML tools offer real-time data from electronic medical records, wearables, and health apps to stratify patient risk, customize treatment plans, and enhance clinical decision making. From the patient's perspective, AI/ML-driven interventions offer personalized coaching and improve long-term engagement in health management. Finally, we address key limitations and challenges, such as the role of social determinants of health, in embracing the role of AI/ML in obesity management, while offering our recommendations based on our literature review.
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Affiliation(s)
- Lillian Huang
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Ellen N. Huhulea
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Elizabeth Abraham
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Raphael Bienenstock
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Esewi Aifuwa
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Rahim Hirani
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
- Graduate School of Biomedical Sciences, New York Medical College, Valhalla, NY 10595, USA
| | - Atara Schulhof
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
| | - Raj K. Tiwari
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
- Graduate School of Biomedical Sciences, New York Medical College, Valhalla, NY 10595, USA
| | - Mill Etienne
- School of Medicine, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY 10595, USA (R.H.)
- Department of Neurology, New York Medical College, Valhalla, NY 10595, USA
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10
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Gong L, Li X, Ji L, Chen G, Han Z, Su L, Wu D. Characterization and comparison of gut microbiota in patients with acute pancreatitis by metagenomics and culturomics. Heliyon 2025; 11:e42243. [PMID: 39931490 PMCID: PMC11808722 DOI: 10.1016/j.heliyon.2025.e42243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/19/2024] [Accepted: 01/23/2025] [Indexed: 02/13/2025] Open
Abstract
Acute pancreatitis (AP) is a common gastrointestinal disorder with a high mortality rate. This study sought to identify the microbial community structure in patients with AP using metagenomics and culturomics. Compared to healthy controls, patients with AP exhibited a significant decrease in alpha diversity; a higher abundance of unclassified Enterococcus species (sp), Enterococcus faecium, and Enterococcus faecalis; and a lower abundance of Eubacterium rectale. A total of 336 isolates from 25 genera and 44 species were obtained by sample cultivation. The dominant species identified in patients with AP were Enterococcus faecium and Klebsiella grimontii, whereas those in the healthy controls were Enterococcus faecium, Escherichia coli, and Bacteroides faecis. Our research has contributed to the expanded understanding of the genome, diversity, and function of the intestinal microbiota in patients with AP and provided some reference for selecting culture medium and sample processing methods.
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Affiliation(s)
- Liang Gong
- Department of Gastroenterology, Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, No. 1 Shuaifuyuan, 100730, Beijing, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 100021, Beijing, China
| | - Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 100021, Beijing, China
| | - Li Ji
- Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Department of Geriatrics, 210008, Nanjing, Jiangsu, China
| | - Guorong Chen
- Department of Gastroenterology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Peking Union Medical College, Chinese Academy of Medical Sciences, 100029, Beijing, China
| | - Ziying Han
- Department of Gastroenterology, Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, No. 1 Shuaifuyuan, 100730, Beijing, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 100021, Beijing, China
| | - Dong Wu
- Department of Gastroenterology, Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, No. 1 Shuaifuyuan, 100730, Beijing, China
- Department of Gastroenterology, The People's Hospital of Tibetan Autonomous Region, Lhasa, 850000, China
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11
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Pinto S, Šajbenová D, Benincà E, Nooij S, Terveer EM, Keller JJ, van der Meulen–de Jong AE, Bogaards JA, Steyerberg EW. Dynamics of Gut Microbiota After Fecal Microbiota Transplantation in Ulcerative Colitis: Success Linked to Control of Prevotellaceae. J Crohns Colitis 2025; 19:jjae137. [PMID: 39225490 PMCID: PMC11836888 DOI: 10.1093/ecco-jcc/jjae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/21/2024] [Accepted: 09/02/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an experimental treatment for ulcerative colitis (UC). We aimed to study microbial families associated with FMT treatment success. METHODS We analyzed stools from 24 UC patients treated with 4 FMTs weekly after randomization for pretreatment during 3 weeks with budesonide (n = 12) or placebo (n = 12). Stool samples were collected 9 times pre-, during, and post-FMT. Clinical and endoscopic response was assessed 14 weeks after initiation of the study using the full Mayo score. Early withdrawal due to worsening of UC symptoms was classified as non-response. RESULTS Nine patients (38%) reached remission at week 14, and 15 patients had a partial response or non-response at or before week 14. With a Dirichlet multinomial mixture model, we identified 5 distinct clusters based on the microbiota composition of 180 longitudinally collected patient samples and 27 donor samples. A Prevotellaceae-dominant cluster was associated with poor response to FMT treatment. Conversely, the families Ruminococcaceae and Lachnospiraceae were associated with a successful clinical response. These associations were already visible at the start of the treatment for a subgroup of patients and were retained in repeated measures analyses of family-specific abundance over time. Responders were also characterized by a significantly lower Simpson dominance compared to non-responders. CONCLUSIONS The success of FMT treatment of UC patients appears to be associated with specific gut microbiota families, such as control of Prevotellaceae. Monitoring the dynamics of these microbial families could potentially be used to inform treatment success early during FMT. CLINICAL TRIAL REGISTRATION NUMBER The study was registered in the Netherlands Trial Register, with reference number NL9858.
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Affiliation(s)
- Susanne Pinto
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dominika Šajbenová
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisa Benincà
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sam Nooij
- Leiden University Center for Infectious Diseases (LUCID) Research, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth M Terveer
- Leiden University Center for Infectious Diseases (LUCID) Research, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Donor Feces Bank, LUCID Medical Microbiology & Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - Josbert J Keller
- Netherlands Donor Feces Bank, LUCID Medical Microbiology & Infection Control, Leiden University Medical Center, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Gastroenterology, Haaglanden Medisch Centrum, The Hague, The Netherlands
| | | | - Johannes A Bogaards
- Department of Epidemiology and Data Science, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity (AI&I), Amsterdam UMC, Amsterdam, The Netherlands
| | - Ewout W Steyerberg
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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12
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Bhosle A, Jackson MI, Walsh AM, Franzosa EA, Badri DV, Huttenhower C. Response of the gut microbiome and metabolome to dietary fiber in healthy dogs. mSystems 2025; 10:e0045224. [PMID: 39714168 PMCID: PMC11748496 DOI: 10.1128/msystems.00452-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 10/21/2024] [Indexed: 12/24/2024] Open
Abstract
Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects. IMPORTANCE Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Aaron M. Walsh
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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13
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Yoo Y, Kim S, Lee W, Kim J, Son B, Lee KJ, Shin H. The prebiotic potential of dietary onion extracts: shaping gut microbial structures and promoting beneficial metabolites. mSystems 2025; 10:e0118924. [PMID: 39714164 PMCID: PMC11748487 DOI: 10.1128/msystems.01189-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 11/23/2024] [Indexed: 12/24/2024] Open
Abstract
Onions are well-known vegetables that offer various health benefits. This study explores the impact of onion extracts on gut microbiome using an in vitro fecal incubation model and metabolome analysis. Fecal samples were collected from 19 healthy donors and incubated in the presence or absence of onion extracts for 24 h. To reduce inter-individual variability in the gut microbiome, we employed enterotyping based on baseline fecal microbiota: 14 subjects with a Bacteroides-dominant type (enterotype B) and 5 subjects with Prevotella-dominant type (enterotype P). Alpha diversity was significantly reduced in the onion-treated group compared to the non-treated control group in both Bacteroides- and Prevotella-dominant types. However, significant structural differences in bacterial communities were observed based on weighted UniFrac distance. Notably, short-chain fatty acid (SCFA)-producing bacteria, such as Bifidobacterium_388775, Feacalibacterium, and Fusicatenibacter, were overrepresented in response to onion extracts in enterotype B. Furthermore, genes related to butyrate production were significantly overrepresented in the onion-treated group within enterotype B. Consistent with the enriched taxa and the predicted metabolic pathways, SCFAs and their related metabolites were significantly enriched in the onion-treated group. Additionally, tryptophan metabolism-derived metabolites, including indolelactate (ILA) and indolepropionate (IPA), were elevated by 4- and 32-fold, respectively, in the onion-treated group compared to the control group. In vitro growth assays showed an increase in lactobacilli strains in the presence of onion extracts. These results provide evidence that onion extracts could serve as promising prebiotics by altering gut microbial structure and promoting the production of beneficiary metabolites, including SCFAs and indole derivatives, and enhancing the growth of probiotics.IMPORTANCEThis study is significant as it provides compelling evidence that onion extracts have the potential to serve as effective prebiotics. Utilizing an in vitro fecal incubation model and enterotyping to reduce inter-individual variability, the research demonstrates how onion extracts can alter gut microbial structure and promote the production of beneficial metabolites, including SCFAs and indole derivatives like ILA and IPA. Additionally, onion extract treatment enhances the growth of beneficial probiotics. The findings underscore the potential of onion extracts to improve gut health by enriching specific beneficial bacteria and metabolic pathways, thereby supporting the development of functional foods aimed at improving gut microbiota composition and metabolic health.
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Affiliation(s)
- Yebeen Yoo
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Seongok Kim
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul, South Korea
| | - WonJune Lee
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul, South Korea
| | - Jinwoo Kim
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul, South Korea
| | - Bokyung Son
- Department of Food Biotechnology, Dong-A University, Busan, Republic of Korea
| | - Kwang Jun Lee
- Division of Zoonotic and Vector Borne Diseases Research, Center for Infectious Diseases Research, National Institute of Health, Cheongju, South Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul, South Korea
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14
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Nikola L, Iva L. Gut microbiota as a modulator of type 1 diabetes: A molecular perspective. Life Sci 2024; 359:123187. [PMID: 39488260 DOI: 10.1016/j.lfs.2024.123187] [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: 05/22/2024] [Revised: 10/04/2024] [Accepted: 10/24/2024] [Indexed: 11/04/2024]
Abstract
Type 1 diabetes (T1D) is defined as an autoimmune metabolic disorder, characterized by destruction of pancreatic β-cells and high blood sugar levels. If left untreated, T1D results in severe health complications, including cardiovascular and kidney disease, as well as nerve damage, with ultimately grave consequences. Besides the role of genetic and certain environmental factors in T1D development, in the last decade, one new player emerged to affect T1D pathology as well, and that is a gut microbiota. Dysbiosis of gut bacteria can contribute to T1D by gut barrier disruption and the activation of autoimmune response, leading to the destruction of insulin producing cells, causing the development and aggravation of T1D symptoms. The relationship between gut microbiota and diabetes is complex and varies between individuals and additional research is needed to fully understand the effects of gut microbiome alternations in T1D pathogenesis. Therefore, the goal of this review is to understand the current knowledge in underlying molecular mechanism of gut microbiota effects, which leads to the new approaches for further studies in the prevention and treatment of T1D.
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Affiliation(s)
- Lukic Nikola
- Laboratory for Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Lukic Iva
- Laboratory for Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", National Institute of the Republic of Serbia, University of Belgrade, Serbia.
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15
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Patloka O, Komprda T, Franke G. Review of the Relationships Between Human Gut Microbiome, Diet, and Obesity. Nutrients 2024; 16:3996. [PMID: 39683390 DOI: 10.3390/nu16233996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 11/15/2024] [Accepted: 11/19/2024] [Indexed: 12/18/2024] Open
Abstract
Obesity is a complex disease that increases the risk of other pathologies. Its prevention and long-term weight loss maintenance are problematic. Gut microbiome is considered a potential obesity modulator. The objective of the present study was to summarize recent findings regarding the relationships between obesity, gut microbiota, and diet (vegetable/animal proteins, high-fat diets, restriction of carbohydrates), with an emphasis on dietary fiber and resistant starch. The composition of the human gut microbiome and the methods of its quantification are described. Products of the gut microbiome metabolism, such as short-chain fatty acids and secondary bile acids, and their effects on the gut microbiota, intestinal barrier function and immune homeostasis are discussed in the context of obesity. The importance of dietary fiber and resistant starch is emphasized as far as effects of the host diet on the composition and function of the gut microbiome are concerned. The complex relationships between human gut microbiome and obesity are finally summarized.
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Affiliation(s)
- Ondřej Patloka
- Department of Food Technology, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Tomáš Komprda
- Department of Food Technology, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Gabriela Franke
- Department of Food Technology, Mendel University in Brno, 61300 Brno, Czech Republic
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Li W, Yang M, Luo Y, Liu W, Wang Z, Ning Z. Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial. Poult Sci 2024; 103:104133. [PMID: 39180778 PMCID: PMC11385426 DOI: 10.1016/j.psj.2024.104133] [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: 06/02/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/26/2024] Open
Abstract
Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.
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Affiliation(s)
- Wen Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Meixue Yang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuxing Luo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Liu
- Zhuozhou Mufeng Poultry Company Limited, Zhuozhou 072750, China
| | - Zhong Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Mancini A, Vitucci D, Lasorsa VA, Lupo C, Brustio PR, Capasso M, Orrù S, Rainoldi A, Schena F, Buono P. Six months of different exercise type in sedentary primary schoolchildren: impact on physical fitness and saliva microbiota composition. Front Nutr 2024; 11:1465707. [PMID: 39512522 PMCID: PMC11542257 DOI: 10.3389/fnut.2024.1465707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 10/15/2024] [Indexed: 11/15/2024] Open
Abstract
Introduction Lifestyle influences microbiota composition. We previously reported a healthier microbiota composition in saliva from active schoolchildren compared to sedentary. In the present study, we evaluated the effects of 6 months of different exercise types on physical fitness and saliva microbiota composition in 8-11-years-old sedentary schoolchildren. Methods Sixty-four sedentary children from five primary schools in Turin, Italy, were divided into three groups: one continued normal curricular activity while two underwent different exercise protocols for 6 months. The Structured Exercise (Sa) group did 2 h per week of muscle activation, strength and coordination exercises supervised by a kinesiologist. The Daily Mile (Dm) group did 1 h per week of Sa plus 15 min of walking/running outdoors four times a week, supervised by a class teacher; control group (Ct) did 2 h a week of curricular exercise supervised by a class teacher. Physical fitness was evaluated before and after the intervention. Saliva samples were collected post-intervention in all participants and analyzed using PCR amplification of 16S rRNA bacterial genes. The Amplicon Sequence Variants were filtered, decontaminated, and phylogenetically classified using DADA2 software. Differential abundance analysis of microbiome taxa and pathway data was conducted using the LEfSe algorithm and PICRUSt. Results The Sa group showed better performances in lower limb power and sprint performance while both the Sa and Dm groups improved in endurance and balance at the end of the intervention; only balance resulted slightly improved in the Ct group. Among the genera differently enriched in saliva after the training intervention, we found that the Prevotella, the Dubosiella and the Family XIII AD3011 group were the most abundant in the Sa group; differently, the Neisseria and the Abiotrophia in Ct group. Four species showed significant the Prevotella melaninogenica and the Prevotella nanceiensis were more abundant in the Sa, conversely, Gemella sanguinis was enriched in Dm and Abiotrophia defectiva in Ct saliva group. Conclusion We demonstrated that Sa and Dm, not curricular exercise, improve the physical fitness components in sedentary schoolchildren correlated to health and promote an enrichment in saliva microbiota species associated to a healthier profile.
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Affiliation(s)
- Annamaria Mancini
- Department of Medicine, Movement Sciences and Wellness, University Parthenope, Naples, Italy
- CEINGE-Biotecnologie Avanzate “Franco Salvatore”, Napoli, Italy
| | - Daniela Vitucci
- Department of Medicine, Movement Sciences and Wellness, University Parthenope, Naples, Italy
- CEINGE-Biotecnologie Avanzate “Franco Salvatore”, Napoli, Italy
| | | | - Corrado Lupo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Mario Capasso
- CEINGE-Biotecnologie Avanzate “Franco Salvatore”, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Stefania Orrù
- Department of Medicine, Movement Sciences and Wellness, University Parthenope, Naples, Italy
- CEINGE-Biotecnologie Avanzate “Franco Salvatore”, Napoli, Italy
| | - Alberto Rainoldi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Federico Schena
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Pasqualina Buono
- Department of Medicine, Movement Sciences and Wellness, University Parthenope, Naples, Italy
- CEINGE-Biotecnologie Avanzate “Franco Salvatore”, Napoli, Italy
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18
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Ioachimescu OC. State of the art: Alternative overlap syndrome-asthma and obstructive sleep apnea. J Investig Med 2024; 72:589-619. [PMID: 38715213 DOI: 10.1177/10815589241249993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In the general population, Bronchial Asthma (BA) and Obstructive Sleep Apnea (OSA) are among the most prevalent chronic respiratory disorders. Significant epidemiologic connections and complex pathogenetic pathways link these disorders via complex interactions at genetic, epigenetic, and environmental levels. The coexistence of BA and OSA in an individual likely represents a distinct syndrome, that is, a collection of clinical manifestations attributable to several mechanisms and pathobiological signatures. To avoid terminological confusion, this association has been named alternative overlap syndrome (vs overlap syndrome represented by the chronic obstructive pulmonary disease-OSA association). This comprehensive review summarizes the complex, often bidirectional links between the constituents of the alternative overlap syndrome. Cross-sectional, population, or clinic-based studies are unlikely to elucidate causality or directionality in these relationships. Even longitudinal epidemiological evaluations in BA cohorts developing over time OSA, or OSA cohorts developing BA during follow-up cannot exclude time factors or causal influence of other known or unknown mediators. As such, a lot of pathophysiological interactions described here have suggestive evidence, biological plausibility, potential or actual directionality. By showcasing existing evidence and current knowledge gaps, the hope is that deliberate, focused, and collaborative efforts in the near-future will be geared toward opportunities to shine light on the unknowns and accelerate discovery in this field of health, clinical care, education, research, and scholarly endeavors.
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19
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Ha J, Kim J, Kim S, Lee KJ, Shin H. Garlic-Induced Enhancement of Bifidobacterium: Enterotype-Specific Modulation of Gut Microbiota and Probiotic Populations. Microorganisms 2024; 12:1971. [PMID: 39458280 PMCID: PMC11509698 DOI: 10.3390/microorganisms12101971] [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: 09/09/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/28/2024] Open
Abstract
The gut microbiome is a dynamic ecosystem crucial for maintaining its host's health by regulating various immune and metabolic functions. Since diet plays a fundamental role in shaping the gut microbiome, understanding the relationship between food consumption and microbiome structure is essential. Although medicinal plants are widely recognized for their broad health benefits, their specific impact on the gut microbiome remains unclear. In this study, we investigated the effects of garlic (Allium sativum) on the gut microbiome using an in vitro human fecal incubation model. Our findings revealed that the impact of garlic on gut microbial structure varied depending on the dominant gut microbiome components (enterotypes). The Bacteroides-dominant enterotype exhibited significant changes in overall microbial diversity in response to garlic, while the Prevotella-dominant enterotype remained unaffected. Additionally, the garlic treatment led to specific alterations in microbiota composition, such as an increase in beneficial probiotics like Bifidobacterium. We validated garlic's prebiotic potential by promoting the growth of Bifidobacterium adolescentis under in vitro culture conditions. Our study highlights the importance of understanding enterotype-specific responses to diet and suggests that garlic may serve as a dietary supplement for modulating gut microbiota and promoting the growth of beneficial probiotics.
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Affiliation(s)
- Jina Ha
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Jinwoo Kim
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
- Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Seongok Kim
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
- Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Kwang Jun Lee
- Division of Zoonotic and Vector Borne Diseases Research, Center for Infectious Diseases Research, National Institute of Health, Cheongju 28159, Republic of Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
- Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
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20
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Li W, Tang H, Xue K, Ying T, Wu M, Qu Z, Dong C, Jin T, Brunius C, Hallmans G, Åman P, Johansson A, Landberg R, Liu Y, He G. Personalized Microbial Fingerprint Associated with Differential Glycemic Effects of a Whole Grain Rye Intervention on Chinese Adults. Mol Nutr Food Res 2024; 68:e2400274. [PMID: 39091068 DOI: 10.1002/mnfr.202400274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/13/2024] [Indexed: 08/04/2024]
Abstract
SCOPE This study aims to identify the gut enterotypes that explain differential responses to intervention with whole grain rye by proposing an "enterotype - metabolic" model. METHODS AND RESULTS A 12-week randomized controlled trial is conducted in Chinese adults, with 79 subjects consuming whole grain products with fermented rye bran (FRB) and 77 consuming refined wheat products in this exploratory post-hoc analysis. Responders or non-responders are identified according to whether blood glucose decreased by more than 10% after rye intervention. Compared to non-responders, responders in FRB have higher baseline Bacteroides (p < 0.001), associated with reduced blood glucose (p < 0.001), increased Faecalibacterium (p = 0.020) and Erysipelotrichaceae_UCG.003 (p = 0.022), as well as deceased 7β-hydroxysteroid dehydrogenase (p = 0.033) after intervention. The differentiated gut microbiota and metabolites between responders and non-responders after intervention are enriched in aminoacyl-tRNA biosynthesis. CONCLUSION The work confirms the previously suggested importance of microbial enterotypes in differential responses to whole grain interventions and supports taking enterotypes into consideration for improved efficacy of whole grain intervention for preventing type 2 diabetes. Altered short-chain fatty acids and bile acid metabolism might be a potential mediator for the beneficial effects of whole grain rye on glucose metabolism.
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Affiliation(s)
- Wenyun Li
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Laboratory of Metabonomics and Systems Biology, Human Phenome Institute, Fudan University, Shanghai, 200032, China
| | - Kun Xue
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Tao Ying
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Min Wu
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Zheng Qu
- Department of Gastroenterology, Zhongye Hospital, Shanghai, 200003, China
| | - Chenglin Dong
- Department of Clinical Laboratory, Zhongye Hospital, Shanghai, 200003, China
| | - Taiyi Jin
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Carl Brunius
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, 901 87, Sweden
| | - Per Åman
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Anders Johansson
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, 901 87, Sweden
- Department of Odontology, Section of Molecular Periodontology, Umeå University, Umeå, 901 87, Sweden
| | - Rikard Landberg
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Yuwei Liu
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Gengsheng He
- School of Public Health, Fudan University/Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
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Li Y, Liu M, Kong B, Zhang G, Zhang Q. The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet. Front Microbiol 2024; 15:1439652. [PMID: 39144222 PMCID: PMC11322145 DOI: 10.3389/fmicb.2024.1439652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Objective This study aimed to investigate the effect of selenium on gut microbiota in mice with breast cancer under a high-fat diet. Methods A total of 12 female BALB/c mice were randomly divided into two groups: 4 T1 + selenium+ high-fat diet group and 4 T1 + high-fat diet group. Mice were injected with 4 T1 cells on the right 4th mammary fat pad and kept on a high-fat diet. Fecal samples were collected, and DNA was extracted for metagenomic sequencing and bioinformatics analysis. Relevant target genes and pathways were annotated and metabolically analyzed to explore the intervention effect of selenium on breast cancer in the high-fat diet state. Results Selenium supplementation in the high-fat diet altered the composition and diversity of gut microbiota in mice with breast cancer. The gut microbial composition was significantly different in the selenium intervention group, with an increased abundance of Proteobacteria, Actinobacteria, and Verrucomicrobia phyla and species such as Helicobacter ganmani, Helicobacter japonicus, and Akkermansia muciniphila, while phyla, such as Bacteroidetes, Firmicutes, Deferribacteres, and Spirochaetes, and species, such as Prevotella sp. MGM2, Muribaculum intestinale, Lactobacillus murinus, and Prevotella sp. MGM1, were decreased. Functional analysis revealed differential expression of genes related to carbohydrate-active enzymes, pathogen-host interactions, cell communication, cell auto-induction, membrane transporters, and virulence factors. Furthermore, 37 COGs and 48 metabolites with rising metabolic potential in the selenium intervention group were predicted. Conclusion Selenium alters the homeostasis of gut microbiota in mice with breast cancer on a high-fat diet, affecting their composition, abundance, and associated metabolism. These findings suggest that the mechanism involves interfering with gut microbiota homeostasis, leading to altered synthesis of tumor-associated proteins and fatty acids and inducing tumor cell apoptosis and pyroptosis.
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Affiliation(s)
- Yinan Li
- Beijing University of Chinese Medicine, Beijing, China
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Min Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Bingtan Kong
- Beijing University of Chinese Medicine, Beijing, China
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ganlin Zhang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Qing Zhang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
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Güven Gülhan Ü, Nikerel E, Çakır T, Erdoğan Sevilgen F, Durmuş S. Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma. Mol Omics 2024; 20:397-416. [PMID: 38780313 DOI: 10.1039/d4mo00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer. Here, an enterotype-based meta-analysis of fecal shotgun metagenomic studies was performed, including 1579 samples of healthy controls (CTR), colorectal adenoma (ADN) and colorectal cancer (CRC) in total. Gut microbiota of healthy people were clustered into three enterotypes (Ruminococcus-, Bacteroides- and Prevotella-dominated enterotypes). Reference-based enterotype assignments were performed for CRC and ADN samples, using the supervised machine learning algorithm, K-nearest neighbors. Differential abundance analyses and random forest classification were conducted on each enterotype between healthy controls and CRC-ADN groups, revealing novel enterotype-specific microbial markers for non-invasive CRC screening strategies. Furthermore, we identified microbial species unique to each enterotype that play a role in the production of secondary bile acids and short-chain fatty acids, unveiling the correlation between cancer-associated gut microbes and dietary patterns. The enterotype-based approach in this study is promising in elucidating the mechanisms of differential gut microbiome profiles, thereby improving the efficacy of personalized microbiota-based solutions.
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Affiliation(s)
- Ünzile Güven Gülhan
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, TR 34755, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Fatih Erdoğan Sevilgen
- The Institute for Data Science & Artificial Intelligence, Boğaziçi University, Istanbul, TR 34342, Turkey
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Saliha Durmuş
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
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23
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Fan Q, Xu Y, Xiao Y, Yang C, Lyu W, Yang H. Linking growth performance and carcass traits with enterotypes in Muscovy ducks. Anim Biosci 2024; 37:1213-1224. [PMID: 38665077 PMCID: PMC11222842 DOI: 10.5713/ab.23.0482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 07/05/2024] Open
Abstract
OBJECTIVE Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks. METHODS A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis. RESULTS Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield. CONCLUSION Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks.
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Affiliation(s)
- Qian Fan
- College of Animal Sciences & Technology, Zhejiang A & F University, Hangzhou, 311300,
China
- State Key Laboratory of Hazard Factors and Risk Prevention and Control of Agricultural Product Quality and Safety, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Science, Hangzhou, 310021,
China
| | - Yini Xu
- College of Animal Sciences & Technology, Zhejiang A & F University, Hangzhou, 311300,
China
- State Key Laboratory of Hazard Factors and Risk Prevention and Control of Agricultural Product Quality and Safety, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Science, Hangzhou, 310021,
China
| | - Yingping Xiao
- State Key Laboratory of Hazard Factors and Risk Prevention and Control of Agricultural Product Quality and Safety, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Science, Hangzhou, 310021,
China
| | - Caimei Yang
- College of Animal Sciences & Technology, Zhejiang A & F University, Hangzhou, 311300,
China
| | - Wentao Lyu
- State Key Laboratory of Hazard Factors and Risk Prevention and Control of Agricultural Product Quality and Safety, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Science, Hangzhou, 310021,
China
| | - Hua Yang
- State Key Laboratory of Hazard Factors and Risk Prevention and Control of Agricultural Product Quality and Safety, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Science, Hangzhou, 310021,
China
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24
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Soares Dias Portela A, Saxena V, Rosenn E, Wang SH, Masieri S, Palmieri J, Pasinetti GM. Role of Artificial Intelligence in Multinomial Decisions and Preventative Nutrition in Alzheimer's Disease. Mol Nutr Food Res 2024; 68:e2300605. [PMID: 38175857 DOI: 10.1002/mnfr.202300605] [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: 08/23/2023] [Revised: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Alzheimer's disease (AD) affects 50 million people worldwide, an increase of 35 million since 2015, and it is known for memory loss and cognitive decline. Considering the morbidity associated with AD, it is important to explore lifestyle elements influencing the chances of developing AD, with special emphasis on nutritional aspects. This review will first discuss how dietary factors have an impact in AD development and the possible role of Artificial Intelligence (AI) and Machine Learning (ML) in preventative care of AD patients through nutrition. The Mediterranean-DASH diets provide individuals with many nutrient benefits which assists the prevention of neurodegeneration by having neuroprotective roles. Lack of micronutrients, protein-energy, and polyunsaturated fatty acids increase the chance of cognitive decline, loss of memory, and synaptic dysfunction among others. ML software has the ability to design models of algorithms from data introduced to present practical solutions that are accessible and easy to use. It can give predictions for a precise medicine approach to evaluate individuals as a whole. There is no doubt the future of nutritional science lies on customizing diets for individuals to reduce dementia risk factors, maintain overall health and brain function.
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Affiliation(s)
| | - Vrinda Saxena
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Eric Rosenn
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Shu-Han Wang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Sibilla Masieri
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Joshua Palmieri
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Giulio Maria Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
- Geriatrics Research, Education and Clinical Center, JJ Peters VA Medical Center, Bronx, NY, 10468, USA
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25
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Roth‐Walter F, Adcock IM, Benito‐Villalvilla C, Bianchini R, Bjermer L, Caramori G, Cari L, Chung KF, Diamant Z, Eguiluz‐Gracia I, Knol EF, Jesenak M, Levi‐Schaffer F, Nocentini G, O'Mahony L, Palomares O, Redegeld F, Sokolowska M, Van Esch BCAM, Stellato C. Metabolic pathways in immune senescence and inflammaging: Novel therapeutic strategy for chronic inflammatory lung diseases. An EAACI position paper from the Task Force for Immunopharmacology. Allergy 2024; 79:1089-1122. [PMID: 38108546 PMCID: PMC11497319 DOI: 10.1111/all.15977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The accumulation of senescent cells drives inflammaging and increases morbidity of chronic inflammatory lung diseases. Immune responses are built upon dynamic changes in cell metabolism that supply energy and substrates for cell proliferation, differentiation, and activation. Metabolic changes imposed by environmental stress and inflammation on immune cells and tissue microenvironment are thus chiefly involved in the pathophysiology of allergic and other immune-driven diseases. Altered cell metabolism is also a hallmark of cell senescence, a condition characterized by loss of proliferative activity in cells that remain metabolically active. Accelerated senescence can be triggered by acute or chronic stress and inflammatory responses. In contrast, replicative senescence occurs as part of the physiological aging process and has protective roles in cancer surveillance and wound healing. Importantly, cell senescence can also change or hamper response to diverse therapeutic treatments. Understanding the metabolic pathways of senescence in immune and structural cells is therefore critical to detect, prevent, or revert detrimental aspects of senescence-related immunopathology, by developing specific diagnostics and targeted therapies. In this paper, we review the main changes and metabolic alterations occurring in senescent immune cells (macrophages, B cells, T cells). Subsequently, we present the metabolic footprints described in translational studies in patients with chronic asthma and chronic obstructive pulmonary disease (COPD), and review the ongoing preclinical studies and clinical trials of therapeutic approaches aiming at targeting metabolic pathways to antagonize pathological senescence. Because this is a recently emerging field in allergy and clinical immunology, a better understanding of the metabolic profile of the complex landscape of cell senescence is needed. The progress achieved so far is already providing opportunities for new therapies, as well as for strategies aimed at disease prevention and supporting healthy aging.
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Affiliation(s)
- F. Roth‐Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine ViennaMedical University Vienna and University ViennaViennaAustria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
| | - I. M. Adcock
- Molecular Cell Biology Group, National Heart & Lung InstituteImperial College LondonLondonUK
| | - C. Benito‐Villalvilla
- Department of Biochemistry and Molecular Biology, School of ChemistryComplutense University of MadridMadridSpain
| | - R. Bianchini
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine ViennaMedical University Vienna and University ViennaViennaAustria
| | - L. Bjermer
- Department of Respiratory Medicine and Allergology, Lung and Allergy research, Allergy, Asthma and COPD Competence CenterLund UniversityLundSweden
| | - G. Caramori
- Department of Medicine and SurgeryUniversity of ParmaPneumologiaItaly
| | - L. Cari
- Department of Medicine, Section of PharmacologyUniversity of PerugiaPerugiaItaly
| | - K. F. Chung
- Experimental Studies Medicine at National Heart & Lung InstituteImperial College London & Royal Brompton & Harefield HospitalLondonUK
| | - Z. Diamant
- Department of Respiratory Medicine and Allergology, Institute for Clinical ScienceSkane University HospitalLundSweden
- Department of Respiratory Medicine, First Faculty of MedicineCharles University and Thomayer HospitalPragueCzech Republic
- Department of Clinical Pharmacy & PharmacologyUniversity Groningen, University Medical Center Groningen and QPS‐NLGroningenThe Netherlands
| | - I. Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de Málaga‐Instituto de Investigación Biomédica de Málaga (IBIMA)‐ARADyALMálagaSpain
| | - E. F. Knol
- Departments of Center of Translational Immunology and Dermatology/AllergologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - M. Jesenak
- Department of Paediatrics, Department of Pulmonology and Phthisiology, Comenius University in Bratislava, Jessenius Faculty of Medicine in MartinUniversity Teaching HospitalMartinSlovakia
| | - F. Levi‐Schaffer
- Institute for Drug Research, Pharmacology Unit, Faculty of MedicineThe Hebrew University of JerusalemJerusalemIsrael
| | - G. Nocentini
- Department of Medicine, Section of PharmacologyUniversity of PerugiaPerugiaItaly
| | - L. O'Mahony
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of MedicineUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
| | - O. Palomares
- Department of Biochemistry and Molecular Biology, School of ChemistryComplutense University of MadridMadridSpain
| | - F. Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | - M. Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZürichDavosSwitzerland
- Christine Kühne – Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - B. C. A. M. Van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of ScienceUtrecht UniversityUtrechtThe Netherlands
| | - C. Stellato
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”University of SalernoSalernoItaly
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Park G, Kim S, Lee W, Kim G, Shin H. Deciphering the Impact of Defecation Frequency on Gut Microbiome Composition and Diversity. Int J Mol Sci 2024; 25:4657. [PMID: 38731876 PMCID: PMC11083994 DOI: 10.3390/ijms25094657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.
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Affiliation(s)
- Gwoncheol Park
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
- Department of Health, Nutrition & Food Sciences, College of Education, Health & Human Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Seongok Kim
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - WonJune Lee
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Gyungcheon Kim
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Hakdong Shin
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
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Li X, Tan JS, Xu J, Zhao Z, Zhao Q, Zhang Y, Duan A, Huang Z, Zhang S, Gao L, Yang YJ, Yang T, Jin Q, Luo Q, Yang Y, Liu Z. Causal impact of gut microbiota and associated metabolites on pulmonary arterial hypertension: a bidirectional Mendelian randomization study. BMC Pulm Med 2024; 24:185. [PMID: 38632547 PMCID: PMC11025270 DOI: 10.1186/s12890-024-03008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Patients with pulmonary arterial hypertension (PAH) exhibit a distinct gut microbiota profile; however, the causal association between gut microbiota, associated metabolites, and PAH remains elusive. We aimed to investigate this causal association and to explore whether dietary patterns play a role in its regulation. METHODS Summary statistics of gut microbiota, associated metabolites, diet, and PAH were obtained from genome-wide association studies. The inverse variance weighted method was primarily used to measure the causal effect, with sensitivity analyses using the weighted median, weighted mode, simple mode, MR pleiotropy residual sum and outlier (MR-PRESSO), and MR-Egger methods. A reverse Mendelian randomisation analysis was also performed. RESULTS Alistipes (odds ratio [OR] = 2.269, 95% confidence interval [CI] 1.100-4.679, P = 0.027) and Victivallis (OR = 1.558, 95% CI 1.019-2.380, P = 0.040) were associated with an increased risk of PAH, while Coprobacter (OR = 0.585, 95% CI 0.358-0.956, P = 0.032), Erysipelotrichaceae (UCG003) (OR = 0.494, 95% CI 0.245-0.996, P = 0.049), Lachnospiraceae (UCG008) (OR = 0.596, 95% CI 0.367-0.968, P = 0.036), and Ruminococcaceae (UCG005) (OR = 0.472, 95% CI 0.231-0.962, P = 0.039) protected against PAH. No associations were observed between PAH and gut microbiota-derived metabolites (trimethylamine N-oxide [TMAO] and its precursors betaine, carnitine, and choline), short-chain fatty acids (SCFAs), or diet. Although inverse variance-weighted analysis demonstrated that elevated choline levels were correlated with an increased risk of PAH, the results were not consistent with the sensitivity analysis. Therefore, the association was considered insignificant. Reverse Mendelian randomisation analysis demonstrated that PAH had no causal impact on gut microbiota-derived metabolites but could contribute to increased the levels of Butyricicoccus and Holdemania, while decreasing the levels of Clostridium innocuum, Defluviitaleaceae UCG011, Eisenbergiella, and Ruminiclostridium 5. CONCLUSIONS Gut microbiota were discovered suggestive evidence of the impacts of genetically predicted abundancy of certain microbial genera on PAH. Results of our study point that the production of SCFAs or TMAO does not mediate this association, which remains to be explained mechanistically.
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Affiliation(s)
- Xin Li
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Jiang-Shan Tan
- Emergency and Critical Care Center, Fuwai Hospital, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Xu
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zhihui Zhao
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Qing Zhao
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Yi Zhang
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
- Department of ICU, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- University of Electronic Science and Technology of China, Chengdu, China
| | - Anqi Duan
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Zhihua Huang
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Sicheng Zhang
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Luyang Gao
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Yue Jin Yang
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Yang
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
| | - Qi Jin
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Qin Luo
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China.
| | - Yanmin Yang
- Emergency and Critical Care Center, Fuwai Hospital, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhihong Liu
- Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No.167 Beilishi Rd, Xicheng District, Beijing, 10003, China.
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van de Wouw M, Wang Y, Workentine ML, Vaghef-Mehrabani E, Barth D, Mercer EM, Dewey D, Arrieta MC, Reimer RA, Tomfohr-Madsen L, Giesbrecht GF. Cluster-specific associations between the gut microbiota and behavioral outcomes in preschool-aged children. MICROBIOME 2024; 12:60. [PMID: 38515179 PMCID: PMC10956200 DOI: 10.1186/s40168-024-01773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND The gut microbiota is recognized as a regulator of brain development and behavioral outcomes during childhood. Nonetheless, associations between the gut microbiota and behavior are often inconsistent among studies in humans, perhaps because many host-microbe relationships vary widely between individuals. This study aims to stratify children based on their gut microbiota composition (i.e., clusters) and to identify novel gut microbiome cluster-specific associations between the stool metabolomic pathways and child behavioral outcomes. METHODS Stool samples were collected from a community sample of 248 typically developing children (3-5 years). The gut microbiota was analyzed using 16S sequencing while LC-MS/MS was used for untargeted metabolomics. Parent-reported behavioral outcomes (i.e., Adaptive Skills, Internalizing, Externalizing, Behavioral Symptoms, Developmental Social Disorders) were assessed using the Behavior Assessment System for Children (BASC-2). Children were grouped based on their gut microbiota composition using the Dirichlet multinomial method, after which differences in the metabolome and behavioral outcomes were investigated. RESULTS Four different gut microbiota clusters were identified, where the cluster enriched in both Bacteroides and Bifidobacterium (Ba2) had the most distinct stool metabolome. The cluster characterized by high Bifidobacterium abundance (Bif), as well as cluster Ba2, were associated with lower Adaptive Skill scores and its subcomponent Social Skills. Cluster Ba2 also had significantly lower stool histidine to urocanate turnover, which in turn was associated with lower Social Skill scores in a cluster-dependent manner. Finally, cluster Ba2 had increased levels of compounds involved in Galactose metabolism (i.e., stachyose, raffinose, alpha-D-glucose), where alpha-D-glucose was associated with the Adaptive Skill subcomponent Daily Living scores (i.e., ability to perform basic everyday tasks) in a cluster-dependent manner. CONCLUSIONS These data show novel associations between the gut microbiota, its metabolites, and behavioral outcomes in typically developing preschool-aged children. Our results support the concept that cluster-based groupings could be used to develop more personalized interventions to support child behavioral outcomes. Video Abstract.
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Affiliation(s)
- Marcel van de Wouw
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Yanan Wang
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Microbiomes for One Systems Health, Health & Biosecurity, CSIRO, Adelaide, SA, Australia
| | - Matthew L Workentine
- Faculty of Veterinary Medicine, UCVM Bioinformatics, University of Calgary, Calgary, Alberta, Canada
| | - Elnaz Vaghef-Mehrabani
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta, Canada
| | - Delaney Barth
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Emily M Mercer
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, University of Calgary, Calgary, Alberta, Canada
| | - Deborah Dewey
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute (HBI), University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, University of Calgary, Calgary, Alberta, Canada
| | - Raylene A Reimer
- Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta, Canada
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Lianne Tomfohr-Madsen
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta, Canada
- Faculty of Education, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada.
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta, Canada.
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.
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Dural AŞ, Ergün C, Urhan M. Investigation of the Relationship Between Serum Low-Density Lipoprotein Cholesterol Levels with Genetic Polymorphisms, Gut Microbiota, and Nutrition. Metab Syndr Relat Disord 2024; 22:133-140. [PMID: 37971853 DOI: 10.1089/met.2023.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Background: To prevent cardiovascular disease (CVD), it is important to determine the factors that are associated with its development. High serum low-density lipoprotein (LDL) cholesterol (LDL-C) levels are a modifiable prevention and treatment target known to contribute to the development of CVD, but the factors affecting blood cholesterol levels, including LDL-C, remain controversial. Objective: In this study, the factors (genetic, nutritional, and gut microbiota) thought to be effective on serum LDL-C levels were discussed from a holistic perspective, and the effects of the relationship between these factors on LDL-C levels were examined. Methods: The study was carried out with 609 adults (48% male) who applied to a private health institution between 2016 and 2022. Results: It was observed that serum LDL-C levels were positively correlated with body mass index (BMI) (P = 0.000) and different ApoE alleles had significant effects on LDL-C levels. It was observed that the highest LDL-C levels were in the ɛ4+ group, followed by ɛ3+ and ɛ2+ groups, respectively (P = 0.000). Results showed that dietary cholesterol and fiber consumption did not significantly affect serum LDL-C levels (P = 0.705 and P = 0.722, respectively). It was also observed that enterotypes and the butyrate synthesis potential of intestinal microbiota did not cause significant changes in serum LDL-C levels (P = 0.369 and P = 975, respectively). Conclusion: Serum LDL-C levels are affected by modifiable factors such as BMI and nonmodifiable factors such as APOE genotype. By identifying these factors and conducting further studies on them, new ways to improve serum LDL-C levels, which is an important factor in the development of CVD, can be identified. In addition, no significant effect of gene-nutrient or microbiota-nutrient interactions on serum LDL-C levels was detected. Further research is needed, especially on the relationship between intestinal microbiota and serum LDL levels.
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Affiliation(s)
- Asu Şevval Dural
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Bahçeşehir University, İstanbul, Turkey
| | - Can Ergün
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Bahçeşehir University, İstanbul, Turkey
| | - Murat Urhan
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Ege University, Karşıyaka, Turkey
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30
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Lee HK, Kim NE, Shin CM, Oh TJ, Yoon H, Park YS, Kim N, Won S, Lee DH. Gut microbiome signature of metabolically healthy obese individuals according to anthropometric, metabolic and inflammatory parameters. Sci Rep 2024; 14:3449. [PMID: 38342934 PMCID: PMC10859373 DOI: 10.1038/s41598-024-53837-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 02/06/2024] [Indexed: 02/13/2024] Open
Abstract
In this study, we investigated the characteristics of gut microbiome in the metabolically healthy obese (MHO) patients, and how they correlate with metabolic and inflammatory profiles. A total of 120 obese people without metabolic comorbidities were recruited, and their clinical phenotypes, metabolic and inflammatory parameters were analysed. The faecal microbial markers originating from bacterial cell and extracellular vesicle (EV) were profiled using 16S rDNA sequencing. The total study population could be classified into two distinct enterotypes (enterotype I: Prevotellaceae-predominant, enterotype II: Akkermansia/Bacteroides-predominant), based on their stool EV-derived microbiome profile. When comparing the metabolic and inflammatory profiles, subjects in enterotype I had higher levels of serum IL-1β [false discovery rate (FDR) q = 0.050] and had a lower level of microbial diversity than enterotype II (Wilcoxon rank-sum test p < 0.01). Subjects in enterotype I had relatively higher abundance of Bacteroidetes, Prevotellaceae and Prevotella-derived EVs, and lower abundance of Actinobacteria, Firmicutes, Proteobacteria, Akkermansia and Bacteroides-derived EVs (FDR q < 0.05). In conclusion, HMO patients can be categorised into two distinct enterotypes by the faecal EV-derived microbiome profile. The enterotyping may be associated with different metabolic and inflammatory profiles. Further studies are warranted to elucidate the long-term prognostic impact of EV-derived microbiome in the obese population.
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Affiliation(s)
- Ho-Kyoung Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Nam-Eun Kim
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea.
| | - Tae Jung Oh
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Hyuk Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Young Soo Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173, Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, South Korea.
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31
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Luan F, Zhou Y, Ma X, Li Y, Peng Y, Jia X, Li N, Wang X, Luo Y, Man M, Zhang Q, Wang C, Yu K, Zhao M, Wang C. Gut microbiota composition and changes in patients with sepsis: potential markers for predicting survival. BMC Microbiol 2024; 24:45. [PMID: 38302899 PMCID: PMC10832068 DOI: 10.1186/s12866-024-03188-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Sepsis can cause immune dysregulation and multiple organ failure in patients and eventually lead to death. The gut microbiota has demonstrated its precise therapeutic potential in the treatment of various diseases. This study aimed to discuss the structural changes of the gut microbiota in patients with sepsis and to analyze the differences in the gut microbiota of patients with different prognoses. METHODS We conducted a multicenter study in which rectal swab specimens were collected on the first and third days of sepsis diagnosis. A total of 70 specimens were collected, and gut microbiota information was obtained by 16S rRNA analysis. RESULTS The relative abundance of Enterococcus decreased in rectal swab specimens during the first three days of diagnosis in patients with sepsis, while the relative abundance of inflammation-associated Bacillus species such as Escherichia coli, Enterobacteriaceae, and Bacteroidetes increased. By comparing the differences in the flora of the survival group and the death group, we found that the abundance of Veillonella and Ruminococcus in the death group showed an increasing trend (p < 0.05), while the abundance of Prevotella_6 and Prevotella_sp_S4_BM14 was increased in surviving patients (p < 0.05). CONCLUSIONS The Firmicutes/Bacteroidetes ratio, reflecting overall gut microbial composition, was significantly lower on day three of sepsis diagnosis. Changes in the abundance of specific gut microbiota may serve as prognostic markers in patients with sepsis.
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Affiliation(s)
- Feiyu Luan
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yang Zhou
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Xiaohui Ma
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yue Li
- Departments of Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yahui Peng
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Xiaonan Jia
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Nana Li
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Xibo Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yinghao Luo
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Mingyin Man
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Qianqian Zhang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Chunying Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Kaijiang Yu
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China.
| | - Mingyan Zhao
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China.
| | - Changsong Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, 150001, Heilongjiang, China.
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Jiang S, Si J, Mo J, Zhang S, Chen K, Gao J, Xu D, Bai L, Lan G, Liang J. Integrated Microbiome and Serum Metabolome Analysis Reveals Molecular Regulatory Mechanisms of the Average Daily Weight Gain of Yorkshire Pigs. Animals (Basel) 2024; 14:278. [PMID: 38254447 PMCID: PMC10812420 DOI: 10.3390/ani14020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The average daily weight gain (ADG) is considered a crucial indicator for assessing growth rates in the swine industry. Therefore, investigating the gastrointestinal microbiota and serum metabolites influencing the ADG in pigs is pivotal for swine breed selection. This study involved the inclusion of 350 purebred Yorkshire pigs (age: 90 ± 2 days; body weight: 41.20 ± 4.60 kg). Concurrently, serum and fecal samples were collected during initial measurements of blood and serum indices. The pigs were categorized based on their ADG, with 27 male pigs divided into high-ADG (HADG) and low-ADG (LADG) groups based on their phenotype values. There were 12 pigs in LADG and 15 pigs in HADG. Feces and serum samples were collected on the 90th day. Microbiome and non-targeted metabolomics analyses were conducted using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS). Pearson correlation, with Benjamini-Hochberg (BH) adjustment, was employed to assess the associations between these variables. The abundance of Lactobacillus and Prevotella in LADG was significantly higher than in HADG, while Erysipelothrix, Streptomyces, Dubosiella, Parolsenella, and Adlercreutzia in LADG were significantly lower than in HADG. The concentration of glutamine, etiocholanolone glucuronide, and retinoyl beta-glucuronide in LADG was significantly higher than in HADG, while arachidonic acid, allocholic acid, oleic acid, phenylalanine, and methyltestosterone in LADG were significantly lower than in HADG. The Lactobacillus-Streptomyces networks (Lactobacillus, Streptomyces, methyltestosterone, phenylalanine, oleic acid, arachidonic acid, glutamine, 3-ketosphingosine, L-octanoylcarnitine, camylofin, 4-guanidinobutyrate 3-methylcyclopentadecanone) were identified as the most influential at regulating swine weight gain. These findings suggest that the gastrointestinal tract regulates the daily weight gain of pigs through the network of Lactobacillus and Streptomyces. However, this study was limited to fecal and serum samples from growing and fattening boars. A comprehensive consideration of factors affecting the daily weight gain in pig production, including gender, parity, season, and breed, is warranted.
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Affiliation(s)
- Shan Jiang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jinglei Si
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
- Guangxi State Farms Yongxin Animal Husbandary Group Co., Ltd., Nanning 530022, China
| | - Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Shuai Zhang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Kuirong Chen
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Jiuyu Gao
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Di Xu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
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Ruiz-Valdepeñas Montiel V, Vargas E, Ben Hassine A, Simon I, Duvvuri A, Chang AY, Nandhakumar P, Bulbarello A, Düsterloh A, Mak T, Wang J. Decentralized ORP Measurements for Gut Redox Status Monitoring: Toward Personalized Gut Microbiota Balance. Anal Chem 2024; 96:480-487. [PMID: 38150379 DOI: 10.1021/acs.analchem.3c04570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Gut microbiome targeting has emerged as a new generation of personalized medicine and a potential wellness and disease driver. Specifically, the gut redox balance plays a key role in shaping the gut microbiota and its link with the host, immune system, and disease evolution. In this sense, precise and personalized nutrition has proven synergy and capability to modulate the gut microbiome environment through the formulation of dietary interventions, such as vitamin support. Accordingly, there are urgent demands for simple and effective analytical platforms for understanding the relationship between the tailored vitamin administration and the gut microbiota balance by rapid noninvasive on-the-spot oxidation/reduction potential monitoring for frequent and close surveillance of the gut redox status and targeting by personalized nutrition interventions. Herein, we present a disposable potentiometric sensor chip and a homemade multiwell potentiometric array to address the interplay of vitamin levels with the oxidation/reduction potential in human feces and saliva. The potentiometric ORP sensing platforms have been successfully validated and scaled up for the setup of a multiapplication prototype for cross-talk-free simple screening of many specimens. The interpersonal variability of the gut microbiota environment illustrates the potential of feces and saliva samples for noninvasive, frequent, and decentralized monitoring of the gut redox status to support timely human microbiota surveillance and guide precise dietary intervention toward restoring and promoting personalized gut redox balance.
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Affiliation(s)
- Víctor Ruiz-Valdepeñas Montiel
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
- Department of Analytical Chemistry, Chemistry Faculty, University Complutense of Madrid, E-28040 Madrid, Spain
| | - Eva Vargas
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Amira Ben Hassine
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Ignasi Simon
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Andres Duvvuri
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - An-Yi Chang
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Ponnusamy Nandhakumar
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | | | | | - Tim Mak
- DSM-Firmenich AG, Kaiseraugst 4303, Switzerland
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
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Milhem F, Skates E, Wilson M, Komarnytsky S. Obesity-Resistant Mice on a High-Fat Diet Display a Distinct Phenotype Linked to Enhanced Lipid Metabolism. Nutrients 2024; 16:171. [PMID: 38202000 PMCID: PMC10780630 DOI: 10.3390/nu16010171] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Individually, metabolic variations can significantly influence predisposition to obesity in the form of the obesity-prone (super-responders) and obesity-resistant (non-responders) phenotypes in response to modern calorie-dense diets. In this study, C57BL/6J mice (n = 76) were randomly assigned to either a low-fat diet (LFD) or a high-fat diet (HFD) for 6 weeks, followed by selection of the normally obese (HFD), non-responders (NR), super-responders (SR), or super-responders switched back to the low-fat diet (SR-LFD) for an additional 8 weeks. SR mice showed the highest gains in body weight, lean and fat body mass, and total and free water, in part due to increased feed efficiency, despite having a respiratory exchange ratio (RER) similar to that of NR mice. A switch to the LFD was sufficient to revert most of the observed physiological changes in the SR-LFD mice; however, voluntary physical activity and exercise capacity did not return to the basal level. NR mice showed the highest food intake, lowest feed efficiency, increased oxygen consumption during the light (rest) cycle, increased physical activity during the dark (active) cycle, and increased heat production during both cycles. These variations were observed in the absence of changes in food intake and fecal parameters; however, NR fecal lipid content was lower, and the NR fecal microbiome profile was characterized by reduced abundance of Actinobacteria. Taken together, our findings suggest that NR mice showed an increased ability to metabolize excessive dietary fats in skeletal muscle at the expense of reduced exercise capacity that persisted for the duration of the study. These findings underscore the need for further comprehensive investigations into the mechanisms of obesity resistance, as they hold potential implications for weight-loss strategies in human subjects.
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Affiliation(s)
- Fadia Milhem
- Plants for Human Health Institute, NC State University, 600 Laureate Way, Kannapolis, NC 28081, USA; (F.M.); (E.S.); (M.W.)
- Department of Food, Bioprocessing, and Nutrition Sciences, NC State University, 400 Dan Allen Drive, Raleigh, NC 27695, USA
- Department of Nutrition, University of Petra, 317 Airport Road, Amman 11196, Jordan
| | - Emily Skates
- Plants for Human Health Institute, NC State University, 600 Laureate Way, Kannapolis, NC 28081, USA; (F.M.); (E.S.); (M.W.)
| | - Mickey Wilson
- Plants for Human Health Institute, NC State University, 600 Laureate Way, Kannapolis, NC 28081, USA; (F.M.); (E.S.); (M.W.)
| | - Slavko Komarnytsky
- Plants for Human Health Institute, NC State University, 600 Laureate Way, Kannapolis, NC 28081, USA; (F.M.); (E.S.); (M.W.)
- Department of Food, Bioprocessing, and Nutrition Sciences, NC State University, 400 Dan Allen Drive, Raleigh, NC 27695, USA
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Bartsch M, Hahn A, Berkemeyer S. Bridging the Gap from Enterotypes to Personalized Dietary Recommendations: A Metabolomics Perspective on Microbiome Research. Metabolites 2023; 13:1182. [PMID: 38132864 PMCID: PMC10744656 DOI: 10.3390/metabo13121182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Advances in high-throughput DNA sequencing have propelled research into the human microbiome and its link to metabolic health. We explore microbiome analysis methods, specifically emphasizing metabolomics, how dietary choices impact the production of microbial metabolites, providing an overview of studies examining the connection between enterotypes and diet, and thus, improvement of personalized dietary recommendations. Acetate, propionate, and butyrate constitute more than 95% of the collective pool of short-chain fatty acids. Conflicting data on acetate's effects may result from its dynamic signaling, which can vary depending on physiological conditions and metabolic phenotypes. Human studies suggest that propionate has overall anti-obesity effects due to its well-documented chemistry, cellular signaling mechanisms, and various clinical benefits. Butyrate, similar to propionate, has the ability to reduce obesity by stimulating the release of appetite-suppressing hormones and promoting the synthesis of leptin. Tryptophan affects systemic hormone secretion, with indole stimulating the release of GLP-1, which impacts insulin secretion, appetite suppression, and gastric emptying. Bile acids, synthesized from cholesterol in the liver and subsequently modified by gut bacteria, play an essential role in the digestion and absorption of dietary fats and fat-soluble vitamins, but they also interact directly with intestinal microbiota and their metabolites. One study using statistical methods identified primarily two groupings of enterotypes Bacteroides and Ruminococcus. The Prevotella-dominated enterotype, P-type, in humans correlates with vegetarians, high-fiber and carbohydrate-rich diets, and traditional diets. Conversely, individuals who consume diets rich in animal fats and proteins, typical in Western-style diets, often exhibit the Bacteroides-dominated, B-type, enterotype. The P-type showcases efficient hydrolytic enzymes for plant fiber degradation but has limited lipid and protein fermentation capacity. Conversely, the B-type features specialized enzymes tailored for the degradation of animal-derived carbohydrates and proteins, showcasing an enhanced saccharolytic and proteolytic potential. Generally, models excel at predictions but often struggle to fully elucidate why certain substances yield varied responses. These studies provide valuable insights into the potential for personalized dietary recommendations based on enterotypes.
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Affiliation(s)
- Madeline Bartsch
- NutritionLab, Faculty of Agricultural Sciences and Landscape Architecture, Osnabrueck University of Applied Sciences, Am Kruempel 31, 49090 Osnabrueck, Germany;
- Institute of Food Science and Human Nutrition, Leibniz University Hannover, 30167 Hannover, Germany;
| | - Andreas Hahn
- Institute of Food Science and Human Nutrition, Leibniz University Hannover, 30167 Hannover, Germany;
| | - Shoma Berkemeyer
- NutritionLab, Faculty of Agricultural Sciences and Landscape Architecture, Osnabrueck University of Applied Sciences, Am Kruempel 31, 49090 Osnabrueck, Germany;
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Wang D, Tang G, Wang Y, Yu J, Chen L, Chen J, Wu Y, Zhang Y, Cao Y, Yao J. Rumen bacterial cluster identification and its influence on rumen metabolites and growth performance of young goats. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 15:34-44. [PMID: 37771855 PMCID: PMC10522951 DOI: 10.1016/j.aninu.2023.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/07/2023] [Accepted: 05/15/2023] [Indexed: 09/30/2023]
Abstract
Enterotypes, which are defined as bacterial clusters in the gut microbiome, have been found to have a close relationship to host metabolism and health. However, this concept has never been used in the rumen, and little is known about the complex biological relationships between ruminants and their rumen bacterial clusters. In this study, we used young goats (n = 99) as a model, fed them the same diet, and analyzed their rumen microbiome and corresponding bacterial clusters. The relationships between the bacterial clusters and rumen fermentation and growth performance in the goats were further investigated. Two bacterial clusters were identified in all goats: the P-cluster (dominated by genus Prevotella, n = 38) and R-cluster (dominated by Ruminococcus, n = 61). Compared with P-cluster goats, R-cluster goats had greater growth rates, concentrations of propionate, butyrate, and 18 free amino acids¸ and proportion of unsaturated fatty acids, but lower acetate molar percentage, acetate to propionate ratio, and several odd and branched chain and saturated fatty acids in rumen fluid (P < 0.05). Several members of Firmicutes, including Ruminococcus, Oscillospiraceae NK4A214 group, and Christensenellaceae R-7 group were significantly higher in the R-cluster, whereas Prevotellaceae members, such as Prevotella and Prevotellaceae UCG-003, were significantly higher in P-cluster (P < 0.01). Co-occurrence networks showed that R-cluster enriched bacteria had significant negative correlations with P-cluster enriched bacteria (P < 0.05). Moreover, we found the concentrations of propionate, butyrate and free amino acids, and the proportions of unsaturated fatty acids were positively correlated with R-cluster enriched bacteria (P < 0.05). The concentrations of acetate, acetate to propionate ratio, and the proportion of odd and branched chain and saturated fatty acids were positively correlated with P-cluster enriched bacteria (P < 0.05). Overall, our results indicated that rumen bacterial clusters can influence rumen fermentation and growth performance of young goats, which may shed light on modulating the rumen microbiome in early life to improve the growth performance of ruminant animals.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yannan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Junjian Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanbo Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuanjie Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Li X, Hu S, Yin J, Peng X, King L, Li L, Xu Z, Zhou L, Peng Z, Ze X, Zhang X, Hou Q, Shan Z, Liu L. Effect of synbiotic supplementation on immune parameters and gut microbiota in healthy adults: a double-blind randomized controlled trial. Gut Microbes 2023; 15:2247025. [PMID: 37614109 PMCID: PMC10453972 DOI: 10.1080/19490976.2023.2247025] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
Synbiotics are increasingly used by the general population to boost immunity. However, there is limited evidence concerning the immunomodulatory effects of synbiotics in healthy individuals. Therefore, we conducted a double-blind, randomized, placebo-controlled study in 106 healthy adults. Participants were randomly assigned to receive either synbiotics (containing Bifidobacterium lactis HN019 1.5 × 108 CFU/d, Lactobacillus rhamnosus HN001 7.5 × 107 CFU/d, and fructooligosaccharide 500 mg/d) or placebo for 8 weeks. Immune parameters and gut microbiota composition were measured at baseline, mid, and end of the study. Compared to the placebo group, participants receiving synbiotic supplementation exhibited greater reductions in plasma C-reactive protein (P = 0.088) and interferon-gamma (P = 0.008), along with larger increases in plasma interleukin (IL)-10 (P = 0.008) and stool secretory IgA (sIgA) (P = 0.014). Additionally, synbiotic supplementation led to an enrichment of beneficial bacteria (Clostridium_sensu_stricto_1, Lactobacillus, Bifidobacterium, and Collinsella) and several functional pathways related to amino acids and short-chain fatty acids biosynthesis, whereas reduced potential pro-inflammatory Parabacteroides compared to baseline. Importantly, alternations in anti-inflammatory markers (IL-10 and sIgA) were significantly correlated with microbial variations triggered by synbiotic supplementation. Stratification of participants into two enterotypes based on pre-treatment Prevotella-to-Bacteroides (P/B) ratio revealed a more favorable effect of synbiotic supplements in individuals with a higher P/B ratio. In conclusion, this study suggested the beneficial effects of synbiotic supplementation on immune parameters, which were correlated with synbiotics-induced microbial changes and modified by microbial enterotypes. These findings provided direct evidence supporting the personalized supplementation of synbiotics for immunomodulation.
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Affiliation(s)
- Xiaoqin Li
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Hu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiawei Yin
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaobo Peng
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei King
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linyan Li
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zihui Xu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhou
- Academy of Nutrition and Health, Hubei Province Key Laboratory of Occupational, Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, China
| | - Zhao Peng
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaolei Ze
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition & Health, Guangzhou, China
| | - Xuguang Zhang
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition & Health, Guangzhou, China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei province, China
| | - Zhilei Shan
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liegang Liu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Mohr AE, Ahern MM, Sears DD, Bruening M, Whisner CM. Gut microbiome diversity, variability, and latent community types compared with shifts in body weight during the freshman year of college in dormitory-housed adolescents. Gut Microbes 2023; 15:2250482. [PMID: 37642346 PMCID: PMC10467528 DOI: 10.1080/19490976.2023.2250482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/26/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Significant human gut microbiome changes during adolescence suggest that microbial community evolution occurs throughout important developmental periods including the transition to college, a typical life phase of weight gain. In this observational longitudinal study of 139 college freshmen living in on-campus dormitories, we tracked changes in the gut microbiome via 16S amplicon sequencing and body weight across a single academic year. Participants were grouped by weight change categories of gain (WG), loss (WL), and maintenance (WM). Upon assessment of the community structure, unweighted and weighted UniFrac metrics revealed significant shifts with substantial variation explained by individual effects within weight change categories. Genera that positively contributed to these associations with weight change included Bacteroides, Blautia, and Bifidobacterium in WG participants and Prevotella and Faecalibacterium in WL and WM participants. Moreover, the Prevotella/Bacteroides ratio was significantly different by weight change category, with WL participants displaying an increased ratio. Importantly, these genera did not display co-dominance nor ease of transition between Prevotella- and Bacteroides-dominated states. We further assessed the overall taxonomic variation, noting the increased stability of the WL compared to the WG microbiome. Finally, we found 30 latent community structures within the microbiome with significant associations with waist circumference, sleep, and dietary factors, with alcohol consumption chief among them. Our findings highlight the high level of individual variation and the importance of initial gut microbiome community structure in college students during a period of major lifestyle changes. Further work is needed to confirm these findings and explore mechanistic relationships between gut microbes and weight change in free-living individuals.
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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
| | - Mary M. Ahern
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Dorothy D. Sears
- 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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Lai B, Jiang H, Gao Y, Zhou X. Causal effects of gut microbiota on scoliosis: A bidirectional two-sample mendelian randomization study. Heliyon 2023; 9:e21654. [PMID: 37964843 PMCID: PMC10641244 DOI: 10.1016/j.heliyon.2023.e21654] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Background Recent studies have shown altered gut microbiome composition in patients with scoliosis. However, the causal effect of gut microbiota on scoliosis remains unknown. Methods A Mendelian randomization (MR) study was conducted to quantify the impact of 191 gut microbiome taxa's instrumental variables from the MibioGen Genome-wide association study (GWAS) on scoliosis risk using data from the FinnGen GWAS (1168 cases and 16,4682 controls). Inverse variance weighted (IVW) was the main method, and MR results were verified by sensitive analysis. Results Bilophila, Eubacterium (eligens group), Prevotella9, and Ruminococcus2 were discovered to have a protective effect on the risk of scoliosis. Ruminococcaceae UCG009, Catenibacterium, Coprococcus2, Eubacterium (ventriosum group), Lachnospiraceae (FCS020 group), Ruminiclostridium6, and Mollicutes RF9 may increase the occurrence of scoliosis. Heterogeneity (P > 0.05) and pleiotropy (P > 0.05) analysis confirmed the robustness of the MR results. Conclusion Our study identified four protective bacteria taxa on scoliosis and seven microbiota that may increase scoliosis occurrence. Further MR analysis is required to corroborate our findings, using a more sophisticated technique to obtain estimates with less bias and greater precision or GWAS summary data with more gut microbiome and scoliosis patients.
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Affiliation(s)
- Bowen Lai
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Heng Jiang
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yuan Gao
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xuhui Zhou
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
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40
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Guan Y, Zheng L, Liang G. The Viral Version of Enterotypes. J Crohns Colitis 2023; 17:1371-1372. [PMID: 37384636 DOI: 10.1093/ecco-jcc/jjad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Affiliation(s)
- Yongjuan Guan
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Lei Zheng
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100048, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100048, China
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100048, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100048, China
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41
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Shannon CE, Ní Chathail MB, Mullin SM, Meehan A, McGillicuddy FC, Roche HM. Precision nutrition for targeting pathophysiology of cardiometabolic phenotypes. Rev Endocr Metab Disord 2023; 24:921-936. [PMID: 37402955 PMCID: PMC10492734 DOI: 10.1007/s11154-023-09821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Obesity is a heterogenous disease accompanied by a broad spectrum of cardiometabolic risk profiles. Traditional paradigms for dietary weight management do not address biological heterogeneity between individuals and have catastrophically failed to combat the global pandemic of obesity-related diseases. Nutritional strategies that extend beyond basic weight management to instead target patient-specific pathophysiology are warranted. In this narrative review, we provide an overview of the tissue-level pathophysiological processes that drive patient heterogeneity to shape distinct cardiometabolic phenotypes in obesity. Specifically, we discuss how divergent physiology and postprandial phenotypes can reveal key metabolic defects within adipose, liver, or skeletal muscle, as well as the integrative involvement of the gut microbiome and the innate immune system. Finally, we highlight potential precision nutritional approaches to target these pathways and discuss recent translational evidence concerning the efficacy of such tailored dietary interventions for different obesity phenotypes, to optimise cardiometabolic benefits.
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Affiliation(s)
- Christopher E Shannon
- Nutrigenomics Research Group, UCD Conway Institute, and Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Republic of Ireland
- School of Medicine, University College Dublin, Dublin, Republic of Ireland
- Division of Diabetes, Department of Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Méabh B Ní Chathail
- Nutrigenomics Research Group, UCD Conway Institute, and Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Republic of Ireland
| | - Sinéad M Mullin
- Nutrigenomics Research Group, UCD Conway Institute, and Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Republic of Ireland
| | - Andrew Meehan
- School of Medicine, University College Dublin, Dublin, Republic of Ireland
| | | | - Helen M Roche
- Nutrigenomics Research Group, UCD Conway Institute, and Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Republic of Ireland.
- Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland.
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Li L, Yan S, Liu S, Wang P, Li W, Yi Y, Qin S. In-depth insight into correlations between gut microbiota and dietary fiber elucidates a dietary causal relationship with host health. Food Res Int 2023; 172:113133. [PMID: 37689844 DOI: 10.1016/j.foodres.2023.113133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023]
Abstract
Dietary fiber exerts a wide range of biological benefits on host health, which not only provides a powerful source of nutrition for gut microbiota but also supplies key microbial metabolites that directly affect host health. This review mainly focuses on the decomposition and metabolism of dietary fiber and the essential genera Bacteroides and Bifidobacterium in dietary fiber fermentation. Dietary fiber plays an essential role in host health by impacting outcomes related to obesity, enteritis, immune health, cancer and neurodegenerative diseases. Additionally, the gut microbiota-independent pathway of dietary fiber affecting host health is also discussed. Personalized dietary fiber intake combined with microbiome, genetics, epigenetics, lifestyle and other factors has been highlighted for development in the future. A higher level of evidence is needed to demonstrate which microbial phenotype benefits from which kind of dietary fiber. In-depth insights into the correlation between gut microbiota and dietary fiber provide strong theoretical support for the precise application of dietary fiber, which elucidates a dietary causal relationship with host health.
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Affiliation(s)
- Lili Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Shuling Yan
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangjiang Liu
- Shandong University, Qingdao 266237, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Yuetao Yi
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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Brennan L, de Roos B. Role of metabolomics in the delivery of precision nutrition. Redox Biol 2023; 65:102808. [PMID: 37423161 PMCID: PMC10461186 DOI: 10.1016/j.redox.2023.102808] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/14/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
Precision nutrition aims to deliver personalised dietary advice to individuals based on their personal genetics, metabolism and dietary/environmental exposures. Recent advances have demonstrated promise for the use of omic technologies for furthering the field of precision nutrition. Metabolomics in particular is highly attractive as measurement of metabolites can capture information on food intake, levels of bioactive compounds and the impact of diets on endogenous metabolism. These aspects contain useful information for precision nutrition. Furthermore using metabolomic profiles to identify subgroups or metabotypes is attractive for the delivery of personalised dietary advice. Combining metabolomic derived metabolites with other parameters in prediction models is also an exciting avenue for understanding and predicting response to dietary interventions. Examples include but not limited to role of one carbon metabolism and associated co-factors in blood pressure response. Overall, while evidence exists for potential in this field there are also many unanswered questions. Addressing these and clearly demonstrating that precision nutrition approaches enable adherence to healthier diets and improvements in health will be key in the near future.
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Affiliation(s)
- Lorraine Brennan
- Institute of Food and Health and Conway Institute, UCD School of Agriculture and Food Science, UCD, Belfield, Dublin 4, Ireland.
| | - Baukje de Roos
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
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Agamennone V, van den Broek TJ, de Kat Angelino-Bart A, Hoevenaars FPM, van der Kamp JW, Schuren FHJ. Individual and Group-Based Effects of In Vitro Fiber Interventions on the Fecal Microbiota. Microorganisms 2023; 11:2001. [PMID: 37630561 PMCID: PMC10459671 DOI: 10.3390/microorganisms11082001] [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: 07/11/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
The development of microbiome-targeted strategies is limited by individual differences in gut microbiome composition and metabolic responses to interventions. In vitro models that can replicate this variation allow us to conduct pre-clinical studies and assess efficacy. This study describes the exposure of 16 individual fecal microbiota samples to 5 different fibers using an in vitro system for the anaerobic cultivation of bacteria. The individual microbiota differed in composition and metabolite profiles (short-chain fatty acids and branched-chain fatty acids) after incubation with the fibers. Furthermore, microbiota composition after fiber incubation was significantly different between subjects with good intestinal health and subjects with Inflammatory Bowel Disease (IBD). α-diversity was differently affected by dietary fibers; for example, exposure to psyllium resulted in increased diversity in the healthy group and in decreased diversity in the IBD group. Instead, the functional metabolic profile did not differ between the two groups. Finally, the combination of all fibers, tested on the microbiota from IBD subjects, resulted in stronger overall effects on both microbiota composition and metabolite production compared to the single fibers. These results confirm that incubation with dietary fiber results in different compositional and functional effects on individual microbiota and that in vitro models represent successful tools for studying individual fiber effects.
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Affiliation(s)
| | | | | | | | | | - Frank H. J. Schuren
- Microbiology and Systems Biology Group, TNO, 2333 BE Leiden, The Netherlands
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45
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Pigsborg K, Stentoft-Larsen V, Demharter S, Aldubayan MA, Trimigno A, Khakimov B, Engelsen SB, Astrup A, Hjorth MF, Dragsted LO, Magkos F. Predicting weight loss success on a new Nordic diet: an untargeted multi-platform metabolomics and machine learning approach. Front Nutr 2023; 10:1191944. [PMID: 37599689 PMCID: PMC10434509 DOI: 10.3389/fnut.2023.1191944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Background and aim Results from randomized controlled trials indicate that no single diet performs better than other for all people living with obesity. Regardless of the diet plan, there is always large inter-individual variability in weight changes, with some individuals losing weight and some not losing or even gaining weight. This raises the possibility that, for different individuals, the optimal diet for successful weight loss may differ. The current study utilized machine learning to build a predictive model for successful weight loss in subjects with overweight or obesity on a New Nordic Diet (NND). Methods Ninety-one subjects consumed an NND ad libitum for 26 weeks. Based on their weight loss, individuals were classified as responders (weight loss ≥5%, n = 46) or non-responders (weight loss <2%, n = 24). We used clinical baseline data combined with baseline urine and plasma untargeted metabolomics data from two different analytical platforms, resulting in a data set including 2,766 features, and employed symbolic regression (QLattice) to develop a predictive model for weight loss success. Results There were no differences in clinical parameters at baseline between responders and non-responders, except age (47 ± 13 vs. 39 ± 11 years, respectively, p = 0.009). The final predictive model for weight loss contained adipic acid and argininic acid from urine (both metabolites were found at lower levels in responders) and generalized from the training (AUC 0.88) to the test set (AUC 0.81). Responders were also able to maintain a weight loss of 4.3% in a 12 month follow-up period. Conclusion We identified a model containing two metabolites that were able to predict the likelihood of achieving a clinically significant weight loss on an ad libitum NND. This work demonstrates that models based on an untargeted multi-platform metabolomics approach can be used to optimize precision dietary treatment for obesity.
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Affiliation(s)
- Kristina Pigsborg
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Mona Adnan Aldubayan
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
- King Saud bin Abdulaziz University for Health Sciences, College of Applied Medical Sciences, Riyadh, Saudi Arabia
| | - Alessia Trimigno
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Arne Astrup
- Obesity and Nutritional Sciences, Novo Nordisk Foundation, Hellerup, Denmark
| | - Mads Fiil Hjorth
- Obesity and Nutritional Sciences, Novo Nordisk Foundation, Hellerup, Denmark
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Faidon Magkos
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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Stefura T, Rusinek J, Zając M, Zapała B, Gosiewski T, Sroka-Oleksiak A, Salamon D, Pędziwiatr M, Major P. Duodenal microbiota and weight-loss following sleeve gastrectomy and Roux-en-Y gastric bypass - a pilot study. BMC Surg 2023; 23:173. [PMID: 37365522 PMCID: PMC10291748 DOI: 10.1186/s12893-023-02076-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Bariatric surgery is the most effective method of morbid obesity treatment. Microbiota has many functions in human body and many of them remain to be unknown. The aim of this study was to establish if the composition of duodenal microbiota influences success rate of bariatric surgery. METHODS It was a prospective cohort study. The data concerning demographics and comorbidities was collected perioperatively. The duodenal biopsies were collected prior to surgery with the gastroscope. Then DNA analysis was conducted. The data connected to the operation outcomes was gathered after 6 and 12 months after surgery. RESULTS Overall, 32 patients were included and divided into two groups (successful - group 1 and unsuccessful - group 0) based on percentage excess weight loss after 6 months were created. The Total Actual Abundance was higher in group 0. In group 0 there was a significantly higher amount of Roseburia and Arthrobacter (p = 0.024, p = 0.027, respectively). Genus LDA effect size analysis showed Prevotella, Megasphaera and Pseudorhodobacter in group 1 to be significant. Whereas abundance of Roseburia and Arthrobacter were significant in group 0. CONCLUSIONS Duodenal microbiota composition may be a prognostic factor for the success of the bariatric surgery but further research on the larger group is needed.
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Affiliation(s)
- Tomasz Stefura
- Department of Medical Education, Jagiellonian University Medical College, Krakow, Poland
| | - Jakub Rusinek
- Students' Scientific Group at 2nd Department of General Surgery, Jagiellonian University, Medical College, Krakow, Poland
| | - Maciej Zając
- Students' Scientific Group at 2nd Department of General Surgery, Jagiellonian University, Medical College, Krakow, Poland
| | - Barbara Zapała
- Department of Clinical Biochemistry, Jagiellonian University Medical College, Krakow, Poland
| | - Tomasz Gosiewski
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | | | - Dominika Salamon
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Pędziwiatr
- 2nd Department of General Surgery, Jagiellonian University Medical College, Kopernika 21 St, 31-501, Kraków, Poland
| | - Piotr Major
- 2nd Department of General Surgery, Jagiellonian University Medical College, Kopernika 21 St, 31-501, Kraków, Poland.
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Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun 2023; 14:3310. [PMID: 37339957 DOI: 10.1038/s41467-023-38558-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/04/2023] [Indexed: 06/22/2023] Open
Abstract
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | | | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Patrick Veiga
- Danone Nutricia Research, Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Muriel Derrien
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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Lv M, Zhang J, Deng J, Hu J, Zhong Q, Su M, Lin D, Xu T, Bai X, Li J, Guo X. Analysis of the relationship between the gut microbiota enterotypes and colorectal adenoma. Front Microbiol 2023; 14:1097892. [PMID: 37082183 PMCID: PMC10110881 DOI: 10.3389/fmicb.2023.1097892] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
IntroductionThe essence of enterotypes is to stratify the entire human gut microbiota, and dysregulation of gut microbiota is closely related to the development of colorectal adenoma. Enterotypes may therefore be a useful target for the prevention of colorectal adenoma. However, the relationship between gut microbiota and colorectal adenoma has not been fully elucidated. In this study, we aimed to analyze the differences in gut microbiome composition between adenoma and control populations.MethodsWe recruited 31 patients with colorectal adenoma and 71 non-adenoma controls. Patient demographics, risk factors, fecal samples from each subject were collected and metagenomic sequencing was performed. LEfSe analysis was used to reveal differences in intestinal microbiome composition. Multiple logistic regression analysis was used to determine the association between enterotypes and colorectal adenoma.ResultsThe results showed that Prevotella enterotype (enterotype 4) is only present in adenoma group. Logistic regression analysis showed that Prevotella enterotype was an independent risk factor for colorectal adenoma.DiscussionThe Prevotella enterotype may increase the occurrence of colorectal adenoma through inflammatory association and interference with glucose and lipid metabolism in human body. In conclusion, the differences we observed between different enterotypes add a new potential factor to the development of colorectal adenoma.
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Affiliation(s)
- Miwei Lv
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Jiawei Zhang
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaxin Deng
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiancong Hu
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinghua Zhong
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingli Su
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dezheng Lin
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tian Xu
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Xuhao Bai
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Juan Li
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Juan Li,
| | - Xuefeng Guo
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Xuefeng Guo,
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Luo S, Hou Y, Xie L, Zhang H, Liu C, Chen T. Effects of microwave on the potential microbiota modulating effects of agro-industrial by-product fibers among different individuals. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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50
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Polo A, Albiac MA, Da Ros A, Ardèvol VN, Nikoloudaki O, Verté F, Di Cagno R, Gobbetti M. The Effect of Hydrolyzed and Fermented Arabinoxylan-Oligo Saccharides (AXOS) Intake on the Middle-Term Gut Microbiome Modulation and Its Metabolic Answer. Nutrients 2023; 15:nu15030590. [PMID: 36771297 PMCID: PMC9920721 DOI: 10.3390/nu15030590] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Although fermentation and hydrolyzation are well-known processes to improve the bioavailability of nutrients and enable the fortification with dietary fibers, the effect of such pre-treatments on the prebiotic features of arabinoxylan-oligosaccharides (AXOS) had not been explored. The middle-term in vitro simulation through the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) demonstrated that the feeding with different formulations (namely oat bran, rye bran and wheat bran) containing hydrolyzed AXOS fermented by lactic acid bacteria significantly increased the synthesis of short-chain fatty acids (SCFA) by colon microbiota, with hydrolyzed and fermented rye bran displaying the highest effect. After two weeks from the interruption of intake, SCFA concentrations significantly decreased but remained still significantly higher compared to the original condition. The microbiome was also affected, with a significant abundance increase in Lactobacillaceae taxon after feeding with all fermented and hydrolyzed formulates. Hydrolyzed and fermented rye bran showed the highest changes. The fungal community, even if it had a lower variety compared to bacteria, was also modulated after feeding with AXOS formulations, with an increase in Candida relative abundance and a decrease in Issatchenkia. On the contrary, the intake of non-hydrolyzed and non-fermented wheat bran did not produce relevant changes of relative abundances. After two weeks from intake interruption (wash out period) such changes were mitigated, and the gut microbiome modulated again to a final structure that was more like the original condition. This finding suggests that hydrolyzed AXOS fermented by lactic acid bacteria could have a more powerful prebiotic effect compared to non-hydrolyzed and non-fermented wheat bran, shaping the colon microbiome and its metabolic answer. However, the intake should be continuous to assure persistent effects. Opening a window into the ecological evolutions and plausible underlying mechanisms, the findings reinforce the perspective to explore more in depth the use of hydrolyzed and fermented AXOS as additional ingredient for bread fortification.
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Affiliation(s)
- Andrea Polo
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
- Correspondence:
| | - Marta Acin Albiac
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
| | - Alessio Da Ros
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
| | | | - Olga Nikoloudaki
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
| | | | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Universitá di Bolzano, 39100 Bozen, Italy
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