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Zhu X, Chen W, Xue J, Dai W, Maimaitituerxun R, Liu Y, Xu H, Zhou Q, Zhou Q, Chen C, Wang Z, Xie H. Dietary Live Microbes Intake Associated With Biological Aging and Mortality. J Gerontol A Biol Sci Med Sci 2024; 79:glae202. [PMID: 39158955 DOI: 10.1093/gerona/glae202] [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: 02/26/2024] [Indexed: 08/20/2024] Open
Abstract
This observational study aimed to investigate associations between dietary live microbe intake and mortality, as well as biological aging. Adults from the 1999-2018 National Health and Nutrition Examination Survey were categorized into low, medium, and high dietary live microbe groups. Foods with medium and high live microbe content were aggregated into a medium-high consumption category. The outcomes included all-cause, cardiovascular, and cancer mortality, along with biological age (BA) acceleration assessed by the Klemera-Doubal method (KDM) and PhenoAge. Multiple regression analyses and mediation analyses were conducted to assess associations, adjusting for potential confounders. A total of 34 133 adults were included in our analyses. Over an average follow-up period of 9.92 years, 5 462 deaths occurred. In multivariate adjusted models, every 100 g of medium-high group foods consumed was associated with reduced all-cause mortality (hazard ratio [HR] 0.94, 95% confidence interval [CI] 0.91 to 0.97, p < .001) and cardiovascular mortality (HR 0.91, 95% CI 0.86 to 0.96, p < .001), but not with cancer mortality (HR 1.01, 95% CI 0.95 to 1.07, p = .768). Every 100 g medium-high group foods consumption was associated with decreased KDM-BA acceleration (fully adjusted regression coefficient -0.09, 95% CI -0.15 to -0.04, p = .001) and PhenoAge acceleration (fully adjusted regression coefficient -0.07, 95% CI -0.11 to -0.03, p < .001). Mediation analysis showed that BA acceleration partially mediated live microbes-mortality associations. Our results suggest that higher dietary live microbe intake is associated with lower mortality risk and slower biological aging. However, further research is needed to verify these findings.
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Affiliation(s)
- Xu Zhu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Epidemiology and Health Statistics, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Wenhang Chen
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Xue
- Department of Scientific Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenjie Dai
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | | | - Yamin Liu
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiaoling Zhou
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Quan Zhou
- Department of Science and Education, The First People's Hospital of Changde City, Changde, Hunan, China
| | - Chunyuan Chen
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, China
| | - Zhenxing Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, China
| | - Hui Xie
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, China
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Anisman H, Doubad D, Asokumar A, Matheson K. Psychosocial and neurobiological aspects of the worldwide refugee crisis: From vulnerability to resilience. Neurosci Biobehav Rev 2024; 165:105859. [PMID: 39159733 DOI: 10.1016/j.neubiorev.2024.105859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 08/06/2024] [Accepted: 08/15/2024] [Indexed: 08/21/2024]
Abstract
Anisman, H., Doubad, D., Asokumar, A. & Matheson, K. Psychosocial and neurobiological aspects of the worldwide refugee crisis: From vulnerability to resilience. NEUROSCI BIOBEHAV REV, XXXX. Immigration occurs between countries either to obtain employment, for family reunification or to escape violence and other life-threatening conditions. Refugees and asylum seekers are often obligated to overcome a uniquely challenging set of circumstances prior to and during migration. Settlement following immigration may pose yet another set of stressors related to acculturation to the host country, as well as financial insecurity, discrimination, language barriers, and social isolation. Here we discuss the multiple consequences of immigration experiences, focusing on the health disturbances that frequently develop in adults and children. Aside from the psychosocial influences, immigration-related challenges may cause hormonal, inflammatory immune, and microbiota changes that favor psychological and physical illnesses. Some biological alterations are subject to modification by epigenetic changes, which have implications for intergenerational trauma transmission, as might disruptions in parenting behaviors and family dysfunction. Despite the hardships experienced, many immigrants and their families exhibit positive psychological adjustment after resettlement. We provide information to diminish the impacts associated with immigration and offer strength-based approaches that may foster resilience.
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Affiliation(s)
- H Anisman
- Carleton University, Department of Neuroscience, Ottawa, Ontario K1S 5B6, Canada.
| | - D Doubad
- Carleton University, Department of Neuroscience, Ottawa, Ontario K1S 5B6, Canada
| | - A Asokumar
- Carleton University, Department of Neuroscience, Ottawa, Ontario K1S 5B6, Canada
| | - K Matheson
- Carleton University, Department of Neuroscience, Ottawa, Ontario K1S 5B6, Canada
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Liang Z, Sun X, Shi J, Tian Y, Wang Y, Cheng Y, Liu Y. Association of the live microbe intake from foods with all-cause and cardiovascular disease-specific mortality: a prospective cohort study. Eur J Nutr 2024; 63:2327-2337. [PMID: 38775828 DOI: 10.1007/s00394-024-03409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/21/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Live dietary microbes have been hypothesized to promoting human health. However, there has been lacking perceptions to crystallize nexus between consumption of foods with live microbes and mortality. OBJECTIVE To investigate the association of consumption of foods with medium to high amounts of live microbes with all-cause, cancer-specific, and cardiovascular disease (CVD)-specific mortality. METHODS The data were obtained from the National Health and Nutrition Examination Survey 1999-2018 at baseline linked to the 2019 National Death Index records. Based on consumption of foods that were categorized as either having medium or high microbial content (MedHi foods), participants were classified into three groups. Kaplan-Meier survival curves and multivariable Cox regression models were used to estimate the association of consumption of MedHi foods with mortality. Population-attributable fractions (PAFs) of consumption of MedHi foods in relation to mortality risk were also estimated. RESULTS A total of 35,299 adults aged ≥ 20 years were included in this study. During a median follow-up of 9.67 years, compared with adults in G1, those in G3 had 16% (hazard ratio [HR], 0.84; 95% confidence interval [CI], 0.77-0.90) reduced risk of all-cause mortality, and 23% (HR, 0.77; 95% CI, 0.67-0.89) reduced risk of CVD-specific mortality. The PAF of high (G3) vs. intermediate or low consumption of MedHi foods (G1 + G2) with all-cause and CVD-specific mortality was 3.4% and 4.3%, respectively. CONCLUSIONS Consumption of foods with higher microbial concentrations is associated with a reduced risk of all-cause and CVD-specific mortality in US adults.
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Affiliation(s)
- Zhuoshuai Liang
- Department of Epidemiology and Biostatistics, School of Public Health of Jilin University, Changchun, 130021, China
| | - Xiaoyue Sun
- Department of Epidemiology and Biostatistics, School of Public Health of Jilin University, Changchun, 130021, China
| | - Jikang Shi
- Department of Clinical Nutrition, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Yuyang Tian
- Department of Epidemiology and Biostatistics, School of Public Health of Jilin University, Changchun, 130021, China
| | - Yujian Wang
- Department of Epidemiology and Biostatistics, School of Public Health of Jilin University, Changchun, 130021, China
| | - Yi Cheng
- The Cardiovascular Center, the First Hospital of Jilin University, Changchun, 130021, China.
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health of Jilin University, Changchun, 130021, China.
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, School of Public Health, Jilin University, Changchun, 130062, China.
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Bragazzi NL, Del Rio D, Mayer EA, Mena P. We Are What, When, And How We Eat: The Evolutionary Impact of Dietary Shifts on Physical and Cognitive Development, Health, and Disease. Adv Nutr 2024; 15:100280. [PMID: 39067763 PMCID: PMC11367649 DOI: 10.1016/j.advnut.2024.100280] [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: 05/24/2024] [Revised: 07/07/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
"We are what, when, and how we eat": the evolution of human dietary habits mirrors the evolution of humans themselves. Key developments in human history, such as the advent of stone tool technology, the shift to a meat-based diet, control of fire, advancements in cooking and fermentation techniques, and the domestication of plants and animals, have significantly influenced human anatomical, physiological, social, cognitive, and behavioral changes. Advancements in scientific methods, such as the analysis of microfossils like starch granules, plant-derived phytoliths, and coprolites, have yielded unprecedented insights into past diets. Nonetheless, the isolation of ancient food matrices remains analytically challenging. Future technological breakthroughs and a more comprehensive integration of paleogenomics, paleoproteomics, paleoglycomics, and paleometabolomics will enable a more nuanced understanding of early human ancestors' diets, which holds the potential to guide contemporary dietary recommendations and tackle modern health challenges, with far-reaching implications for human well-being, and ecological impact on the planet.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy
| | - Daniele Del Rio
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy.
| | - Emeran A Mayer
- Goodman-Luskin Microbiome Center, David Geffen School of Medicine, University of California, Los Angeles, CA, United States; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | - Pedro Mena
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy
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Light SH, Nagler CR. Regulation of immune responses to food by commensal microbes. Immunol Rev 2024; 326:203-218. [PMID: 39285525 DOI: 10.1111/imr.13396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
The increasing prevalence of immune-mediated non-communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co-evolved host-microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome-based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.
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Affiliation(s)
- Samuel H Light
- Biological Sciences Division, Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Cathryn R Nagler
- Biological Sciences Division, Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
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Demangel C, Surace L. Host-pathogen interactions from a metabolic perspective: methods of investigation. Microbes Infect 2024; 26:105267. [PMID: 38007087 DOI: 10.1016/j.micinf.2023.105267] [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: 05/17/2023] [Revised: 10/21/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
Metabolism shapes immune homeostasis in health and disease. This review presents the range of methods that are currently available to investigate the dialog between metabolism and immunity at the systemic, tissue and cellular levels, particularly during infection.
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Affiliation(s)
- Caroline Demangel
- Institut Pasteur, Université Paris Cité, Inserm U1224, Immunobiology and Therapy Unit, Paris, France
| | - Laura Surace
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany.
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Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell 2024; 187:4554-4570.e18. [PMID: 38981480 DOI: 10.1016/j.cell.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.
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Affiliation(s)
- Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alberto Arrè
- Department CIBIO, University of Trento, Trento, Italy; Zoe Ltd, London, UK
| | - Kate M Bermingham
- Zoe Ltd, London, UK; Department of Nutritional Sciences, King's College London, London, UK
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | | | - Emily R Leeming
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Monia Lobina
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tim D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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Li X, Lu C, Mao X, Fan J, Yao J, Jiang J, Wu L, Ren J, Shen J. Bibliometric analysis of research on gut microbiota and bile acids: publication trends and research frontiers. Front Microbiol 2024; 15:1433910. [PMID: 39234549 PMCID: PMC11371755 DOI: 10.3389/fmicb.2024.1433910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/07/2024] [Indexed: 09/06/2024] Open
Abstract
The gut microbiota is widely regarded as a "metabolic organ" that could generate myriad metabolites to regulate human metabolism. As the microbiota metabolites, bile acids (BAs) have recently been identified as the critical endocrine molecules that mediate the cross-talk between the host and intestinal microbiota. This study provided a comprehensive insight into the gut microbiota and BA research through bibliometric analysis from 2003 to 2022. The publications on this subject showed a dramatic upward trend. Although the USA and China have produced the most publications, the USA plays a dominant role in this expanding field. Specifically, the University of Copenhagen was the most productive institution. Key research hotspots are the gut-liver axis, short-chain fatty acids (SCFAs), cardiovascular disease (CVD), colorectal cancer (CRC), and the farnesoid x receptor (FXR). The molecular mechanisms and potential applications of the gut microbiota and BAs in cardiometabolic disorders and gastrointestinal cancers have significant potential for further research.
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Affiliation(s)
- Xin Li
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Department of General Practice, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Can Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xue Mao
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiahong Fan
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianting Yao
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jingjie Jiang
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lele Wu
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingjing Ren
- Department of General Practice, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Shen
- Department of General Medicine and Geriatrics, Linping Campus, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
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Anzuay MS, Chiatti MH, Intelangelo AB, Ludueña LM, Viso NP, Angelini JG, Taurian T. Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants. Curr Genet 2024; 70:12. [PMID: 39093429 DOI: 10.1007/s00294-024-01296-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/02/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.
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Affiliation(s)
- María Soledad Anzuay
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina
| | - Mario Hernán Chiatti
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina
| | | | | | - Natalia Pin Viso
- Instituto de Microbiología y Zoología Agrícola, IMyZA, IABiMo, INTA, Hurlingham, Buenos Aires, Argentina
| | | | - Tania Taurian
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto, Argentina.
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, Río Cuarto, Córdoba, 5800, Argentina.
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de Jonge PA, van den Born BJH, Zwinderman AH, Nieuwdorp M, Dutilh BE, Herrema H. Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage. Nat Commun 2024; 15:6346. [PMID: 39068184 PMCID: PMC11283538 DOI: 10.1038/s41467-024-50777-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.
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Affiliation(s)
- Patrick A de Jonge
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Bert-Jan H van den Born
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology; Biostatistics and Bioinformatics; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics; Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity; Faculty of Biological Sciences; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Hilde Herrema
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands.
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11
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Grondin JA, Jamal A, Mowna S, Seto T, Khan WI. Interaction between Intestinal Parasites and the Gut Microbiota: Implications for the Intestinal Immune Response and Host Defence. Pathogens 2024; 13:608. [PMID: 39204209 PMCID: PMC11356857 DOI: 10.3390/pathogens13080608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Intestinal parasites, including helminths and protozoa, account for a significant portion of the global health burden. The gastrointestinal (GI) tract not only serves as the stage for these parasitic infections but also as the residence for millions of microbes. As the intricacies of the GI microbial milieu continue to unfold, it is becoming increasingly apparent that the interactions between host, parasite, and resident microbes help dictate parasite survival and, ultimately, disease outcomes. Across both clinical and experimental models, intestinal parasites have been shown to impact microbial composition and diversity. Reciprocally, microbes can directly influence parasitic survival, colonization and expulsion. The gut microbiota can also indirectly impact parasites through the influence and manipulation of the host. Studying this host-parasite-microbiota axis may help bring about novel therapeutic strategies for intestinal parasitic infection as well as conditions such as inflammatory bowel disease (IBD). In this review, we explore the relationship between intestinal parasites, with a particular focus on common protozoa and helminths, and the gut microbiota, and how these interactions can influence the host defence and intestinal immune response. We will also explore the impact of this tripartite relationship in a clinical setting and its broader implications for human health.
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Affiliation(s)
- Jensine A. Grondin
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.A.G.); (A.J.); (S.M.); (T.S.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Asif Jamal
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.A.G.); (A.J.); (S.M.); (T.S.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sadrina Mowna
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.A.G.); (A.J.); (S.M.); (T.S.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Tyler Seto
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.A.G.); (A.J.); (S.M.); (T.S.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Waliul I. Khan
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada; (J.A.G.); (A.J.); (S.M.); (T.S.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
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12
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Li Y, Peters BA, Yu B, Perreira KM, Daviglus M, Chan Q, Knight R, Boerwinkle E, Isasi CR, Burk R, Kaplan R, Wang T, Qi Q. Blood metabolomic shift links diet and gut microbiota to multiple health outcomes among Hispanic/Latino immigrants in the U.S. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.19.24310722. [PMID: 39072018 PMCID: PMC11275661 DOI: 10.1101/2024.07.19.24310722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Immigrants from less industrialized countries who are living in the U.S. often bear an elevated risk of multiple disease due to the adoption of a U.S. lifestyle. Blood metabolome holds valuable information on environmental exposure and the pathogenesis of chronic diseases, offering insights into the link between environmental factors and disease burden. Analyzing 634 serum metabolites from 7,114 Hispanics (1,141 U.S.-born, 5,973 foreign-born) in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), we identified profound blood metabolic shift during acculturation. Machine learning highlighted the prominent role of non-genetic factors, especially food and gut microbiota, in these changes. Immigration-related metabolites correlated with plant-based foods and beneficial gut bacteria for foreign-born Hispanics, and with meat-based or processed food and unfavorable gut bacteria for U.S.-born Hispanics. Cardiometabolic traits, liver, and kidney function exhibited a link with immigration-related metabolic changes, which were also linked to increased risk of diabetes, severe obesity, chronic kidney disease, and asthma. Graphical abstract Highlights A substantial proportion of identified blood metabolites differ between U.S.-born and foreign-born Hispanics/Latinos in the U.S.Food and gut microbiota are the major modifiable contributors to blood metabolomic difference between U.S.-born and foreign-born Hispanics/Latinos.U.S. nativity related metabolites collectively correlate with a spectrum of clinical traits and chronic diseases.
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13
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Sandys O, Stokkers PCF, Te Velde AA. DAMP-ing IBD: Extinguish the Fire and Prevent Smoldering. Dig Dis Sci 2024:10.1007/s10620-024-08523-5. [PMID: 38963463 DOI: 10.1007/s10620-024-08523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
In inflammatory bowel diseases (IBD), the most promising therapies targeting cytokines or immune cell trafficking demonstrate around 40% efficacy. As IBD is a multifactorial inflammation of the intestinal tract, a single-target approach is unlikely to solve this problem, necessitating an alternative strategy that addresses its variability. One approach often overlooked by the pharmaceutically driven therapeutic options is to address the impact of environmental factors. This is somewhat surprising considering that IBD is increasingly viewed as a condition heavily influenced by such factors, including diet, stress, and environmental pollution-often referred to as the "Western lifestyle". In IBD, intestinal responses result from a complex interplay among the genetic background of the patient, molecules, cells, and the local inflammatory microenvironment where danger- and microbe-associated molecular patterns (D/MAMPs) provide an adjuvant-rich environment. Through activating DAMP receptors, this array of pro-inflammatory factors can stimulate, for example, the NLRP3 inflammasome-a major amplifier of the inflammatory response in IBD, and various immune cells via non-specific bystander activation of myeloid cells (e.g., macrophages) and lymphocytes (e.g., tissue-resident memory T cells). Current single-target biological treatment approaches can dampen the immune response, but without reducing exposure to environmental factors of IBD, e.g., by changing diet (reducing ultra-processed foods), the adjuvant-rich landscape is never resolved and continues to drive intestinal mucosal dysregulation. Thus, such treatment approaches are not enough to put out the inflammatory fire. The resultant smoldering, low-grade inflammation diminishes physiological resilience of the intestinal (micro)environment, perpetuating the state of chronic disease. Therefore, our hypothesis posits that successful interventions for IBD must address the complexity of the disease by simultaneously targeting all modifiable aspects: innate immunity cytokines and microbiota, adaptive immunity cells and cytokines, and factors that relate to the (micro)environment. Thus the disease can be comprehensively treated across the nano-, meso-, and microscales, rather than with a focus on single targets. A broader perspective on IBD treatment that also includes options to adapt the DAMPing (micro)environment is warranted.
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Affiliation(s)
- Oliver Sandys
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands
| | - Pieter C F Stokkers
- Department of Gastroenterology and Hepatology, OLVG West, Amsterdam, The Netherlands
| | - Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands.
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14
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Wang L, Ren B, Wu S, Song H, Xiong L, Wang F, Shen X. Current research progress, opportunities, and challenges of Limosillactobacillus reuteri-based probiotic dietary strategies. Crit Rev Food Sci Nutr 2024:1-21. [PMID: 38920093 DOI: 10.1080/10408398.2024.2369946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Limosillactobacillus reuteri (L. reuteri), a type of Lactobacillus spp., stands out as the most extensively researched probiotic. Its remarkable intestinal adhesion has led to widespread applications in both the food and medical sectors. Notably, recent research highlights the probiotic efficacy of L. reuteri sourced from breast milk, particularly in influencing social behavior and mitigating atopic dermatitis. In this review, our emphasis is on surveying recent literature regarding the promotion of host's health by L. reuteri. We aim to provide a concise summary of the latest regulatory effects and potential mechanisms attributed to L. reuteri in the realms of metabolism, brain- and immune-related functions. The mechanism through which L. reuteri promotes host health by modulating the intestinal microenvironment primarily involves promoting intestinal epithelial renewal, bolstering intestinal barrier function, regulating gut microbiota and its metabolites, and suppressing inflammation and immune responses. Additionally, this review delves into new technologies, identifies shortcomings, and addresses challenges in current L. reuteri research. Finally, the application prospects of L. reuteri are provided. Therefore, a better understanding of the role and mechanisms of L. reuteri will contribute significantly to the development of new probiotic functional foods and enable precise, targeted interventions for various diseases.
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Affiliation(s)
- Luanfeng Wang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Bo Ren
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Shufeng Wu
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Haizhao Song
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Ling Xiong
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Fang Wang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Xinchun Shen
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
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15
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Xu J, Duar RM, Quah B, Gong M, Tin F, Chan P, Sim CK, Tan KH, Chong YS, Gluckman PD, Frese SA, Kyle D, Karnani N. Delayed colonization of Bifidobacterium spp. and low prevalence of B. infantis among infants of Asian ancestry born in Singapore: insights from the GUSTO cohort study. Front Pediatr 2024; 12:1421051. [PMID: 38915873 PMCID: PMC11194334 DOI: 10.3389/fped.2024.1421051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024] Open
Abstract
Background The loss of ancestral microbes, or the "disappearing microbiota hypothesis" has been proposed to play a critical role in the rise of inflammatory and immune diseases in developed nations. The effect of this loss is most consequential during early-life, as initial colonizers of the newborn gut contribute significantly to the development of the immune system. Methods In this longitudinal study (day 3, week 3, and month 3 post-birth) of infants of Asian ancestry born in Singapore, we studied how generational immigration status and common perinatal factors affect bifidobacteria and Bifidobacterium longum subsp. infantis (B. infantis) colonization. Cohort registry identifier: NCT01174875. Results Our findings show that first-generation migratory status, perinatal antibiotics usage, and cesarean section birth, significantly influenced the abundance and acquisition of bifidobacteria in the infant gut. Most importantly, 95.6% of the infants surveyed in this study had undetectable B. infantis, an early and beneficial colonizer of infant gut due to its ability to metabolize the wide variety of human milk oligosaccharides present in breastmilk and its ability to shape the development of a healthy immune system. A comparative analysis of B. infantis in 12 countries by their GDP per capita showed a remarkably low prevalence of this microbe in advanced economies, especially Singapore. Conclusion This study provides new insights into infant gut microbiota colonization, showing the impact of generational immigration on early-life gut microbiota acquisition. It also warrants the need to closely monitor the declining prevalence of beneficial microbes such as B. infantis in developed nations and its potential link to increasing autoimmune and allergic diseases.
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Affiliation(s)
- Jia Xu
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
| | | | - Baoling Quah
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
| | - Min Gong
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
| | - Felicia Tin
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
| | - Penny Chan
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
- Department of Clinical Data Engagement, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Choon Kiat Sim
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
| | - Kok Hian Tan
- SingHealth Duke-NUS Institute for Patient Safety and Quality, Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore, Singapore
- Department of Maternal Fetal Medicine, KK Women’s and Children’s Hospital, Singapore, Singapore
| | - Yap Seng Chong
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynecology and Human Potential Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter D. Gluckman
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
- Centre for SPDS Centre for Informed Futures, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Steven A. Frese
- Department of Nutrition, University of Nevada, Reno, NV, United States
| | - David Kyle
- Infinant Health, Inc., Davis, CA, United States
| | - Neerja Karnani
- Department of Human Development, Singapore Institute for Clinical Sciences, Agency for Science (SICS), Technology and Research, Singapore (A*STAR), Singapore, Singapore
- Department of Clinical Data Engagement, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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16
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Rook GAW. Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES). Neurosci Biobehav Rev 2024; 161:105653. [PMID: 38582194 DOI: 10.1016/j.neubiorev.2024.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.
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Affiliation(s)
- Graham A W Rook
- Centre for Clinical Microbiology, Department of infection, UCL (University College London), London, UK.
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17
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Sargsian S, Mondragón-Palomino O, Lejeune A, Ercelen D, Jin WB, Varghese A, Lim YAL, Guo CJ, Loke P, Cadwell K. Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. MICROBIOME 2024; 12:86. [PMID: 38730492 PMCID: PMC11084060 DOI: 10.1186/s40168-024-01793-1] [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: 06/05/2023] [Accepted: 03/10/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria. RESULTS Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. CONCLUSION We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.
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Affiliation(s)
- Shushan Sargsian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Defne Ercelen
- Department of Medicine, Division of Gastroenterology and Hepatology, New York University Langone Health, New York, NY, 10016, USA
| | - Wen-Bing Jin
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - Alan Varghese
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yvonne A L Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Chun-Jun Guo
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Ken Cadwell
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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18
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de Noronha SISR, de Moraes LAG, Hassell JE, Stamper CE, Arnold MR, Heinze JD, Foxx CL, Lieb MM, Cler KE, Karns BL, Jaekel S, Loupy KM, Silva FCS, Chianca-Jr DA, Lowry CA, de Menezes RC. High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats. Biol Res 2024; 57:23. [PMID: 38705984 PMCID: PMC11071217 DOI: 10.1186/s40659-024-00505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
Obesity, associated with the intake of a high-fat diet (HFD), and anxiety are common among those living in modern urban societies. Recent studies suggest a role of microbiome-gut-brain axis signaling, including a role for brain serotonergic systems in the relationship between HFD and anxiety. Evidence suggests the gut microbiome and the serotonergic brain system together may play an important role in this response. Here we conducted a nine-week HFD protocol in male rats, followed by an analysis of the gut microbiome diversity and community composition, brainstem serotonergic gene expression (tph2, htr1a, and slc6a4), and anxiety-related defensive behavioral responses. We show that HFD intake decreased alpha diversity and altered the community composition of the gut microbiome in association with obesity, increased brainstem tph2, htr1a and slc6a4 mRNA expression, including in the caudal part of the dorsomedial dorsal raphe nucleus (cDRD), a subregion previously associated with stress- and anxiety-related behavioral responses, and, finally, increased anxiety-related defensive behavioral responses. The HFD increased the Firmicutes/Bacteroidetes ratio relative to control diet, as well as higher relative abundances of Blautia, and decreases in Prevotella. We found that tph2, htr1a and slc6a4 mRNA expression were increased in subregions of the dorsal raphe nucleus in the HFD, relative to control diet. Specific bacterial taxa were associated with increased serotonergic gene expression in the cDRD. Thus, we propose that HFD-induced obesity is associated with altered microbiome-gut-serotonergic brain axis signaling, leading to increased anxiety-related defensive behavioral responses in rats.
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Affiliation(s)
- Sylvana I S Rendeiro de Noronha
- Department of Biological Sciences, Laboratory of Cardiovascular Physiology, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Lauro Angelo Gonçalves de Moraes
- Department of Biological Sciences, Laboratory of Cardiovascular Physiology, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Computing Department, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - James E Hassell
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Christopher E Stamper
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Mathew R Arnold
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Jared D Heinze
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Christine L Foxx
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Margaret M Lieb
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Kristin E Cler
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Bree L Karns
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Sophia Jaekel
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Kelsey M Loupy
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Fernanda C S Silva
- Department of Biological Sciences, Laboratory of Cardiovascular Physiology, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Deoclécio Alves Chianca-Jr
- Department of Biological Sciences, Laboratory of Cardiovascular Physiology, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Rodrigo Cunha de Menezes
- Department of Biological Science Laboratory of Cardiovascular Physiology, Campus Morro do Cruzeiro s/n, Ouro Preto, 35400-000, MG, Brazil.
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19
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O'Toole PW. Ageing, microbes and health. Microb Biotechnol 2024; 17:e14477. [PMID: 38801344 PMCID: PMC11129672 DOI: 10.1111/1751-7915.14477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
The human gut microbiome is a modifier of the risk for many non-communicable diseases throughout the lifespan. In ageing, the effect of the microbiome appears to be more pronounced because of the lower physiological reserve. Microbial metabolites and other bioactive products act upon some of the key physiological processes involved in the Hallmarks of Ageing. Dietary interventions that delay age-related change in the microbiome have also led to delayed onset of ageing-related health loss, and improved levels of cognitive function, inflammatory status and frailty. Cross-sectional analysis of thousands of gut microbiome datasets from around the world has identified key taxa that are depleted during accelerated health loss, and other taxa that become more abundant, but these signatures differ in some geographical regions. The key challenges for research in this area are to experimentally prove that particular species or strains directly contribute to health-related ageing outcomes, and to develop practical ways of retaining or re-administering them on a population basis. The promotion of a health-associated gut microbiome in ageing mirrors the challenge of maintaining planetary microbial ecosystems in the face of anthropogenic effects and climate change. Lessons learned from acting at the individual level can inform microbiome-targeting strategies for achieving Sustainable Development Goals at a global level.
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Affiliation(s)
- Paul W. O'Toole
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
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20
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O’Dwyer DN, Kim JS, Ma SF, Ranjan P, Das P, Lipinski JH, Metcalf JD, Falkowski NR, Yow E, Anstrom K, Dickson RP, Huang Y, Gilbert JA, Martinez FJ, Noth I. Commensal Oral Microbiota, Disease Severity, and Mortality in Fibrotic Lung Disease. Am J Respir Crit Care Med 2024; 209:1101-1110. [PMID: 38051927 PMCID: PMC11092942 DOI: 10.1164/rccm.202308-1357oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis (IPF). Methods: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with IPF in the multicenter CleanUP-IPF (Study of Clinical Efficacy of Antimicrobial Therapy Strategy Using Pragmatic Design in IPF) trial. Buccal swabs were collected from usual care and antimicrobial cohorts. Microbiome data were correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan-Meier analysis, and Cox proportional hazards models. Measurements and Main Results: Greater buccal microbial diversity associated with lower FVC at baseline (mean difference, -3.60; 95% confidence interval [CI], -5.92 to -1.29% predicted FVC per 1-unit increment). The buccal proportion of Streptococcus correlated positively with FVC (mean difference, 0.80; 95% CI, 0.16 to 1.43% predicted per 10% increase) (n = 490). Greater microbial diversity was associated with an increased risk of death (hazard ratio, 1.73; 95% CI, 1.03-2.90), whereas a greater proportion of Streptococcus was associated with a reduced risk of death (HR, 0.85; 95% CI, 0.73 to 0.99). The Streptococcus genus was mainly composed of Streptococcus mitis species. Conclusions: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal S. mitis spp associates with preserved lung function and improved survival.
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Affiliation(s)
- David N. O’Dwyer
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - John S. Kim
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Piyush Ranjan
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Jay H. Lipinski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joseph D. Metcalf
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Nicole R. Falkowski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Eric Yow
- Department of Biostatistics, Duke University, Durham, North Carolina
| | - Kevin Anstrom
- Department of Biostatistics, University of North Carolina–Chapel Hill Gillings School of Global Public Health, Chapel Hill, North Carolina
| | - Robert P. Dickson
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, Michigan; and
| | - Yong Huang
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California
| | | | - Imre Noth
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
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21
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Liu Y, Ma L, Riqing D, Qu J, Chen J, Zhandu D, Li B, Jiang M. Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood. Animals (Basel) 2024; 14:1365. [PMID: 38731369 PMCID: PMC11083404 DOI: 10.3390/ani14091365] [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: 04/05/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen's survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages.
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Affiliation(s)
- Yili Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (Y.L.); (D.R.); (B.L.)
| | - Liangliang Ma
- College of Grassland Resources, Southwest Minzu University, Chengdu 610041, China;
| | - Daojie Riqing
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (Y.L.); (D.R.); (B.L.)
| | - Jiu Qu
- Agriculture and Rural Affairs Bureau of Naqu City, Naqu 852000, China; (J.Q.); (D.Z.)
| | - Jiyong Chen
- Yushu Prefecture Animal Disease Prevention and Control Center, Yushu 815000, China;
| | - Danzeng Zhandu
- Agriculture and Rural Affairs Bureau of Naqu City, Naqu 852000, China; (J.Q.); (D.Z.)
| | - Biao Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (Y.L.); (D.R.); (B.L.)
| | - Mingfeng Jiang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (Y.L.); (D.R.); (B.L.)
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22
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McCumber AW, Kim YJ, Granek J, Tighe RM, Gunsch CK. Soil exposure modulates the immune response to an influenza challenge in a mouse model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:170865. [PMID: 38340827 DOI: 10.1016/j.scitotenv.2024.170865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
There is increasing evidence that early life microbial exposure aids in immune system maturation, more recently known as the "old friends" hypothesis. To test this hypothesis, 4-week-old mice were exposed to soils of increasing microbial diversity for four weeks followed by an intranasal challenge with either live or heat inactivated influenza A virus and monitored for 7 additional days. Perturbations of the gut and lung microbiomes were explored through 16S rRNA amplicon sequencing. RNA-sequencing was used to examine the host response in the lung tissue through differential gene expression. We determined that compared to the gut microbiome, the lung microbiome is more susceptible to changes in beta diversity following soil exposure with Lachnospiraceae ASVs accounting for most of the differences between groups. While several immune system genes were found to be significantly differentially expressed in lung tissue due to soil exposures, there were no differences in viral load or weight loss. This study shows that exposure to diverse microbial communities through soil exposure alters the gut and lung microbiomes resulting in differential expression of specific immune system related genes within the lung following an influenza challenge.
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Affiliation(s)
- Alexander W McCumber
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Yeon Ji Kim
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA
| | - Joshua Granek
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Robert M Tighe
- Department of Medicine, Duke University, Durham, NC, USA
| | - Claudia K Gunsch
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA.
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23
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Sliwa K, Viljoen CA, Stewart S, Miller MR, Prabhakaran D, Kumar RK, Thienemann F, Piniero D, Prabhakaran P, Narula J, Pinto F. Cardiovascular disease in low- and middle-income countries associated with environmental factors. Eur J Prev Cardiol 2024; 31:688-697. [PMID: 38175939 DOI: 10.1093/eurjpc/zwad388] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024]
Abstract
There is a growing recognition that the profound environmental changes that have occurred over the past century pose threats to human health. Many of these environmental factors, including air pollution, noise pollution, as well as exposure to metals such as arsenic, cadmium, lead, and other metals, are particularly detrimental to the cardiovascular health of people living in low-to-middle income countries (LMICs). Low-to-middle income countries are likely to be disproportionally burdened by cardiovascular diseases provoked by environmental factors. Moreover, they have the least capacity to address the core drivers and consequences of this phenomenon. This review summarizes the impact of environmental factors such as climate change, air pollution, and metal exposure on the cardiovascular system, and how these specifically affect people living in LMICs. It also outlines how behaviour changes and interventions that reduce environmental pollution would have significant effects on the cardiovascular health of those from LMICs, and globally.
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Affiliation(s)
- Karen Sliwa
- Cape Heart Institute, Chris Barnard Building, University of Cape Town, Faculty of Health Sciences, Cnr Anzio Road and Falmouth Road, 7925, Observatory, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Main Road, 7925, Observatory, Cape Town, South Africa
| | - Charle André Viljoen
- Cape Heart Institute, Chris Barnard Building, University of Cape Town, Faculty of Health Sciences, Cnr Anzio Road and Falmouth Road, 7925, Observatory, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Main Road, 7925, Observatory, Cape Town, South Africa
| | - Simon Stewart
- Institute for Health Research, University of Notre Dame Australia, 32 Mouat St, Fremantle, Western Australia, 6160, Australia
- Eduardo Mondlane University, 3435 Avenida Julius Nyerere, Maputo, Mozambique
| | - Mark R Miller
- Centre for Cardiovascular Science, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh, EH4 3RL, UK
| | - Dorairaj Prabhakaran
- Centre for Chronic Disease Control, C1/52, Safdarjung Development Area, New Delhi, 110016, India
| | - Raman Krishna Kumar
- Department of Pediatric Cardiology, Amrita Institute of Medical Sciences and Research Centre, Ponekkara PO, Cochin 682041, Kerala, India
| | - Friedrich Thienemann
- Cape Heart Institute, Chris Barnard Building, University of Cape Town, Faculty of Health Sciences, Cnr Anzio Road and Falmouth Road, 7925, Observatory, Cape Town, South Africa
- Department of Internal Medicine, University Hospital Zurich, University of Zurich, 100 Rämistrasse, 8091 Zurich, Switzerland
| | - Daniel Piniero
- Facultad de Medicina, Universidad de Buenos Aires, Arenales 2463, Buenos Aires, C1124AAN, Argentina
| | - Poornima Prabhakaran
- Centre for Chronic Disease Control, C1/52, Safdarjung Development Area, New Delhi, 110016, India
| | - Jagat Narula
- Department of Cardiology, McGovern Medical School, University of Texas Health, 7000 Fannin St, Houston, TX 77030, USA
| | - Fausto Pinto
- Department of Cardiology, Faculty of Medicine, University of Lisbon, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
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24
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Ding M, Li B, Chen H, Ross RP, Stanton C, Zhao J, Chen W, Yang B. Bifidobacterium longum Subsp. infantis Promotes IgA Level of Growing Mice in a Strain-Specific and Intestinal Niche-Dependent Manner. Nutrients 2024; 16:1148. [PMID: 38674840 PMCID: PMC11054607 DOI: 10.3390/nu16081148] [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: 03/04/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Throughout infancy, IgA is crucial for maintaining gut mucosal immunity. This study aims to determine whether supplementing newborn mice with eight different strains of Bifidobacterium longum subsp. infantis might regulate their IgA levels. The strains were gavaged to BALB/C female (n = 8) and male (n = 8) dams at 1-3 weeks old. Eight strains of B. longum subsp. infantis had strain-specific effects in the regulation of intestinal mucosal barriers. B6MNI, I4MI, and I10TI can increase the colonic IgA level in females and males. I8TI can increase the colonic IgA level in males. B6MNI was also able to significantly increase the colonic sIgA level in females. B6MNI, I4MI, I8TI, and I10TI regulated colonic and Peyer's patch IgA synthesis genes but had no significant effect on IgA synthesis pathway genes in the jejunum and ileum. Moreover, the variety of sIgA-coated bacteria in male mice was changed by I4MI, I5TI, I8TI, and B6MNI. These strains also can decrease the relative abundance of Escherichia coli. These results indicate that B. longum subsp. infantis can promote IgA levels but show strain specificity. Different dietary habits with different strains of Bifidobacterium may have varying effects on IgA levels when supplemented in early infancy.
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Affiliation(s)
- Mengfan Ding
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Bowen Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Reynolds Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China; (R.P.R.); (C.S.)
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
| | - Catherine Stanton
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China; (R.P.R.); (C.S.)
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (M.D.); (B.L.); (H.C.); (J.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China; (R.P.R.); (C.S.)
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25
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Caffrey EB, Sonnenburg JL, Devkota S. Our extended microbiome: The human-relevant metabolites and biology of fermented foods. Cell Metab 2024; 36:684-701. [PMID: 38569469 DOI: 10.1016/j.cmet.2024.03.007] [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: 10/20/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.
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Affiliation(s)
- Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA.
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel Diseases Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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26
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Tian Z, Zhang X, Yao G, Jin J, Zhang T, Sun C, Wang Z, Zhang Q. Intestinal flora and pregnancy complications: Current insights and future prospects. IMETA 2024; 3:e167. [PMID: 38882493 PMCID: PMC11170975 DOI: 10.1002/imt2.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 06/18/2024]
Abstract
Numerous studies have demonstrated the pivotal roles of intestinal microbiota in many physiopathological processes through complex interactions with the host. As a unique period in a woman's lifespan, pregnancy is characterized by changes in hormones, immunity, and metabolism. The gut microbiota also changes during this period and plays a crucial role in maintaining a healthy pregnancy. Consequently, anomalies in the composition and function of the gut microbiota, namely, gut microbiota dysbiosis, can predispose individuals to various pregnancy complications, posing substantial risks to both maternal and neonatal health. However, there are still many controversies in this field, such as "sterile womb" versus "in utero colonization." Therefore, a thorough understanding of the roles and mechanisms of gut microbiota in pregnancy and its complications is essential to safeguard the health of both mother and child. This review provides a comprehensive overview of the changes in gut microbiota during pregnancy, its abnormalities in common pregnancy complications, and potential etiological implications. It also explores the potential of gut microbiota in diagnosing and treating pregnancy complications and examines the possibility of gut-derived bacteria residing in the uterus/placenta. Our aim is to expand knowledge in maternal and infant health from the gut microbiota perspective, aiding in developing new preventive and therapeutic strategies for pregnancy complications based on intestinal microecology.
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Affiliation(s)
- Zhenyu Tian
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Xinjie Zhang
- Department of Biology University College London London UK
| | - Guixiang Yao
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Jiajia Jin
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Tongxue Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Chunhua Sun
- Department of Health Management Center, Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan China
| | - Zhe Wang
- Department of Geriatrics Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan China
| | - Qunye Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
- Cardiovascular Disease Research Center of Shandong First Medical University Central Hospital Affiliated to Shandong First Medical University Jinan China
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27
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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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28
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Rampelli S, Gallois S, D’Amico F, Turroni S, Fabbrini M, Scicchitano D, Candela M, Henry A. The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. iScience 2024; 27:109211. [PMID: 38433907 PMCID: PMC10904984 DOI: 10.1016/j.isci.2024.109211] [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: 10/23/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Sandrine Gallois
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
- Institute of Environmental Science and Technology, ST, 08193 Bellaterra, Spain
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Amanda Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
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29
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Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
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Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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Carter MM, Spencer SP. Resisting weight gain with prebiotic fibre. Nat Metab 2024; 6:389-391. [PMID: 38409603 DOI: 10.1038/s42255-024-00998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.
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Valentino V, Magliulo R, Farsi D, Cotter PD, O'Sullivan O, Ercolini D, De Filippis F. Fermented foods, their microbiome and its potential in boosting human health. Microb Biotechnol 2024; 17:e14428. [PMID: 38393607 PMCID: PMC10886436 DOI: 10.1111/1751-7915.14428] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.
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Affiliation(s)
- Vincenzo Valentino
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Raffaele Magliulo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
| | - Dominic Farsi
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
| | - Paul D. Cotter
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Orla O'Sullivan
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Danilo Ercolini
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
| | - Francesca De Filippis
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
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Filippou C, Themistocleous SC, Marangos G, Panayiotou Y, Fyrilla M, Kousparou CA, Pana ZD, Tsioutis C, Johnson EO, Yiallouris A. Microbial Therapy and Breast Cancer Management: Exploring Mechanisms, Clinical Efficacy, and Integration within the One Health Approach. Int J Mol Sci 2024; 25:1110. [PMID: 38256183 PMCID: PMC10816061 DOI: 10.3390/ijms25021110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
This comprehensive review elucidates the profound relationship between the human microbiome and breast cancer management. Recent findings highlight the significance of microbial alterations in tissue, such as the gut and the breast, and their role in influencing the breast cancer risk, development, progression, and treatment outcomes. We delve into how the gut microbiome can modulate systemic inflammatory responses and estrogen levels, thereby impacting cancer initiation and therapeutic drug efficacy. Furthermore, we explore the unique microbial diversity within breast tissue, indicating potential imbalances brought about by cancer and highlighting specific microbes as promising therapeutic targets. Emphasizing a holistic One Health approach, this review underscores the importance of integrating insights from human, animal, and environmental health to gain a deeper understanding of the complex microbe-cancer interplay. As the field advances, the strategic manipulation of the microbiome and its metabolites presents innovative prospects for the enhancement of cancer diagnostics and therapeutics. However, rigorous clinical trials remain essential to confirm the potential of microbiota-based interventions in breast cancer management.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Andreas Yiallouris
- School of Medicine, European University Cyprus, 6 Diogenis Str., 2404 Engomi, P.O. Box 22006, Nicosia 1516, Cyprus
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Onwusereaka CO, Jalaludin J, Oluchi SE, Poh Choo VC. New generation sequencing: molecular approaches for the detection and monitoring of bioaerosols in an indoor environment: a systematic review. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2023-0004. [PMID: 38214730 DOI: 10.1515/reveh-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
INTRODUCTION The exposure of occupants to indoor air pollutants has increased in recent decades. The aim of this review is to discuss an overview of new approaches that are used to study fungal aerosols. Thus, this motivation was to compensate the gaps caused by the use of only traditional approaches in the study of fungal exposure. CONTENT The search involved various databases such as; Science Direct, PubMed, SAGE, Springer Link, EBCOHOST, MEDLINE, CINAHL, Cochrane library, Web of Science and Wiley Online Library. It was limited to full text research articles that reported the use of non-viable method in assessing bioaerosol, written in English Language, full text publications and published from year 2015-2022. SUMMARY AND OUTLOOK A total of 15 articles met the inclusion criteria and was included in this review. The use of next-generation sequencing, which is more commonly referred to as high-throughput sequencing (HTS) or molecular methods in microbial studies is based on the detection of genetic material of organisms present in a given sample. Applying these methods to different environments permitted the identification of the microorganisms present, and a better comprehension of the environmental impacts and ecological roles of microbial communities. Based on the reviewed articles, there is evidence that dust samples harbour a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples using 18S metagenomics approach.
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Affiliation(s)
- Cynthia Oluchi Onwusereaka
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Selangor, Malaysia
| | - Juliana Jalaludin
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Selangor, Malaysia
| | - Sampson Emilia Oluchi
- Department of Community Health, Faculty of Medicine and Health Science, Universiti Putra Malaysia Serdang, Selangor, Malaysia
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Rühlemann MC, Bang C, Gogarten JF, Hermes BM, Groussin M, Waschina S, Poyet M, Ulrich M, Akoua-Koffi C, Deschner T, Muyembe-Tamfum JJ, Robbins MM, Surbeck M, Wittig RM, Zuberbühler K, Baines JF, Leendertz FH, Franke A. Functional host-specific adaptation of the intestinal microbiome in hominids. Nat Commun 2024; 15:326. [PMID: 38182626 PMCID: PMC10770139 DOI: 10.1038/s41467-023-44636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024] Open
Abstract
Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.
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Affiliation(s)
- M C Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
| | - C Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - J F Gogarten
- Applied Zoology and Nature Conservation, University of Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - B M Hermes
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - M Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - S Waschina
- Nutriinformatics Research Group, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - M Poyet
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - M Ulrich
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - C Akoua-Koffi
- Training and Research Unit for in Medical Sciences, Alassane Ouattara University / University Teaching Hospital of Bouaké, Bouaké, Côte d'Ivoire
| | - T Deschner
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - J J Muyembe-Tamfum
- National Institute for Biomedical Research, National Laboratory of Public Health, Kinshasa, Democratic Republic of the Congo
| | - M M Robbins
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - M Surbeck
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R M Wittig
- Institute of Cognitive Sciences, CNRS UMR5229 University Lyon 1, Bron Cedex, France
- Taï Chimpanzee Project, CSRS, Abidjan, Côte d'Ivoire
| | - K Zuberbühler
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
- School of Psychology & Neuroscience, University of St Andrews, St Andrews, Scotland, UK
| | - J F Baines
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - F H Leendertz
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - A Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
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Deehan EC, Zhang Z, Nguyen NK, Perez-Muñoz ME, Cole J, Riva A, Berry D, Prado CM, Walter J. Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum. Gut Microbes 2024; 16:2363021. [PMID: 38860973 PMCID: PMC11174067 DOI: 10.1080/19490976.2024.2363021] [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: 12/18/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Dietary fiber supplements are a strategy to close the 'fiber gap' and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa involved in AX fermentation were identified by bioorthogonal non-canonical amino acid tagging. Associations between GI symptoms, fecal microbiota features, and diet history were systematically investigated. AX supplementation increased symptoms during the first three weeks relative to MCC (p < 0.05, Mann-Whitney tests), but subjects 'adapted' with symptoms reverting to baseline levels toward the end of treatment. Symptom adaptations were individualized and correlated with the relative abundance of Bifidobacterium longum at baseline (rs = 0.74, p = 0.002), within the bacterial community that utilized AX (rs = 0.69, p = 0.006), and AX-induced shifts in acetate (rs = 0.54, p = 0.039). Lower baseline consumption of animal-based foods and higher whole grains associated with less severity and better adaptation. These findings suggest that humans do 'adapt' to tolerate efficacious fiber doses, and this process is linked to their microbiome and dietary factors known to interact with gut microbes, providing a basis for the development of strategies for improved tolerance of dietary fibers.
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Affiliation(s)
- Edward C. Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, Canada
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Nguyen K. Nguyen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), WEL Research Institute, Wavre, Belgium
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Janis Cole
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Alessandra Riva
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Carla M. Prado
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork – National University of Ireland, Cork, Ireland
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Wang X, Wang H, Yu Q, Fu S, Yang Z, Ye Q, Lin F, Cai G. "High dietary live microbe intake is correlated with reduced risk of depressive symptoms: A cross-sectional study of NHANES 2007-2016". J Affect Disord 2024; 344:198-206. [PMID: 37827261 DOI: 10.1016/j.jad.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/31/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Recent research indicated that levels of dietary live microorganisms were inconsistently associated with the prevalence of depressive symptoms. This study aimed to investigate the correlation between consumption of live microorganisms and symptoms of depression. METHODS Data on 21,653 study participants were obtained from the National Health and Nutrition Examination Survey (NHANES). Dietary information was assessed using a self-report questionnaire. Depressive status was assessed using the Patient Health Questionnaire (PHQ-9). Generalized linear model, restricted cubic spline (RCS), and subgroup analyses were performed in this study. RESULTS After full adjustment for confounders, participants in the moderate-dietary microbe intake group had a lower prevalence of depressive symptoms than those in the lowest intake group [odds ratio (OR): 0.813, 95 % confidence interval (CI): 0.678-0.974, P = 0.026, and pseudo R2 = 0.12]. Participants in the highest-dietary microbe intake group had a lower prevalence of depressive symptoms than those in the lowest intake group (OR: 0.714, 95 % CI: 0.586-0.870, P = 0.001, and pseudo R2 = 0.12). An L-shaped dose-response relationship was observed in the RCS (the P value for nonlinear relationship = 0.007). In subgroup analyses, participants with male identity, normal weight, and high physical activity (PA) level showed a substantial correlation between dietary live microbe consumption and depressive symptoms (all P values for interaction <0.050). LIMITATIONS This study was limited by its cross-sectional study design, and self-reported dietary live microbe consumption and depressive symptoms. CONCLUSIONS A high dietary live microbe intake was nonlinearly correlated with a lower prevalence of depressive symptoms.
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Affiliation(s)
- Xuefei Wang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 35001, China; Fujian Medical University, Fuzhou 35001, China
| | | | - Qianwen Yu
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 35001, China
| | - Shibo Fu
- Fujian Medical University, Fuzhou 35001, China
| | | | - Qinyong Ye
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 35001, China.
| | - Fabin Lin
- Department of Neurosurgery, Fujian Medical University Union Hospital, Fuzhou 35001, China.
| | - Guoen Cai
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 35001, China.
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Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
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Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Capeding MRZ, Phee LCM, Ming C, Noti M, Vidal K, Le Carrou G, Frézal A, Moll JM, Vogt JK, Myers PN, Nielsen BH, Boulangé CL, Samuel TM, Berger B, Cercamondi CI. Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines. Front Nutr 2023; 10:1319873. [PMID: 38162520 PMCID: PMC10755859 DOI: 10.3389/fnut.2023.1319873] [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: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation. Methods This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21 days old) randomized for 8 weeks to a control group (CG; n = 77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*108 CFU/day; n = 75) or high dose (Hi-EG; 1.8*1010 CFU/day; n = 76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids. Results Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups. Discussion B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.
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Affiliation(s)
| | | | - Chang Ming
- Biostatistics & Data, Nestlé Research, Lausanne, Switzerland
| | - Mario Noti
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Karine Vidal
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Gilles Le Carrou
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - A. Frézal
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | | | | | | | - Claire L. Boulangé
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Tinu Mary Samuel
- Nestlé Product Technology Center – Nutrition, Société des Produits Nestlé S.A., Vevey, Switzerland
| | - Bernard Berger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Colin Ivano Cercamondi
- Nestlé Product Technology Center – Nutrition, Société des Produits Nestlé S.A., Vevey, Switzerland
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39
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Han SJ, Stacy A, Corral D, Link VM, De Siqueira MK, Chi L, Teijeiro A, Yong DS, Perez-Chaparro PJ, Bouladoux N, Lim AI, Enamorado M, Belkaid Y, Collins N. Microbiota configuration determines nutritional immune optimization. Proc Natl Acad Sci U S A 2023; 120:e2304905120. [PMID: 38011570 PMCID: PMC10710091 DOI: 10.1073/pnas.2304905120] [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: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/29/2023] Open
Abstract
Mild or transient dietary restriction (DR) improves many aspects of health and aging. Emerging evidence from us and others has demonstrated that DR also optimizes the development and quality of immune responses. However, the factors and mechanisms involved remain to be elucidated. Here, we propose that DR-induced optimization of immunological memory requires a complex cascade of events involving memory T cells, the intestinal microbiota, and myeloid cells. Our findings suggest that DR enhances the ability of memory T cells to recruit and activate myeloid cells in the context of a secondary infection. Concomitantly, DR promotes the expansion of commensal Bifidobacteria within the large intestine, which produce the short-chain fatty acid acetate. Acetate conditioning of the myeloid compartment during DR enhances the capacity of these cells to kill pathogens. Enhanced host protection during DR is compromised when Bifidobacteria expansion is prevented, indicating that microbiota configuration and function play an important role in determining immune responsiveness to this dietary intervention. Altogether, our study supports the idea that DR induces both memory T cells and the gut microbiota to produce distinct factors that converge on myeloid cells to promote optimal pathogen control. These findings suggest that nutritional cues can promote adaptation and co-operation between multiple immune cells and the gut microbiota, which synergize to optimize immunity and protect the collective metaorganism.
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Affiliation(s)
- Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Dan Corral
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Verena M. Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | | | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ana Teijeiro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Daniel S. Yong
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - P. Juliana Perez-Chaparro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
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40
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Gancz AS, Farrer AG, Nixon MP, Wright S, Arriola L, Adler C, Davenport ER, Gully N, Cooper A, Britton K, Dobney K, Silverman JD, Weyrich LS. Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain. Nat Microbiol 2023; 8:2315-2325. [PMID: 38030898 PMCID: PMC11323141 DOI: 10.1038/s41564-023-01527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Andrew G Farrer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle P Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
| | - Sterling Wright
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Luis Arriola
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christina Adler
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Emily R Davenport
- Department of Biology, The Pennsylvania State University, State College, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
| | - Neville Gully
- School of Dentistry, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Alan Cooper
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Gulbali Institute, Charles Sturt University, Albury, New South Wales, Australia
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Faculty of Arts and Social Sciences, University of Sydney, Sydney, New South Wales, Australia
- Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK
- Department of Archaeology, Faculty of Environment, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin D Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Statistics, The Pennsylvania State University, State College, PA, USA
- Department of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA.
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA.
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41
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Pan L, Cai B. Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects. Microorganisms 2023; 11:2904. [PMID: 38138048 PMCID: PMC10745930 DOI: 10.3390/microorganisms11122904] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.
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Affiliation(s)
- Lin Pan
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China;
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao 066102, China
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42
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Yersin S, Garneau JR, Schneeberger PHH, Osman KA, Cercamondi CI, Muhummed AM, Tschopp R, Zinsstag J, Vonaesch P. Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits. Sci Rep 2023; 13:21342. [PMID: 38049420 PMCID: PMC10696028 DOI: 10.1038/s41598-023-47748-8] [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: 09/01/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2-5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, D-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.
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Affiliation(s)
- Simon Yersin
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Pierre H H Schneeberger
- Helminth Drug Development Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | | | - Colin Ivano Cercamondi
- Department of Health Sciences and Technology, ETHZ, Rämistrasse 101, 8092, Zurich, Switzerland
| | - Abdifatah Muktar Muhummed
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Jigjiga University, Jigjiga, Ethiopia
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
| | - Rea Tschopp
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- Armauer Hansen Research Institute, Jimma Road, 1005, Addis Ababa, Ethiopia
| | - Jakob Zinsstag
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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43
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Bowers RM. Gone with a trace: cataloguing the disappearing gut microbes. Nat Rev Microbiol 2023; 21:704. [PMID: 37667007 DOI: 10.1038/s41579-023-00968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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44
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Cantu-Jungles TM, Hamaker BR. Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber. J Nutr 2023; 153:3156-3163. [PMID: 37690780 DOI: 10.1016/j.tjnut.2023.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023] Open
Abstract
Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.
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Affiliation(s)
- Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States.
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States
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45
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Li H, Ma X, Li Y, Liu Q, Tian Q, Yang X, Zhou Z, Ren J, Sun B, Feng X, Zhang H, Yin X, Li H, Ding X. The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum. Sci Rep 2023; 13:18775. [PMID: 37907561 PMCID: PMC10618524 DOI: 10.1038/s41598-023-45586-2] [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: 04/03/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023] Open
Abstract
The present study investigated the composition, abundance, and diversity of gut microbes in full-term and late-preterm infants from a medical center in eastern China. A total of 144 genomes of stool samples were captured for 16S rRNA metagenomic analyses. A high abundance of commensal intestinal bacteria was detected in these samples such as Phocaeicola vulgatus, Escherichia coli, and Faecalibacterium prausnitzii, indicating a relatively consistent diversity of gut microbes in the present full-term infants aged 38-40 weeks. However, late preterm infants (n = 50) with mandatory antimicrobials feeding exhibited lower diversity but a higher composition of opportunistic pathogens such as Enterococcus species. Centralized on the situation, we explored the regulatory effect of Clostridium butyricum as probiotics on these late preterm infants. The consumption of C. butyricum did not restore the composition of gut microbes altered by antimicrobials to normal levels, although several opportunistic pathogens decreased significantly after probiotic therapy including Staphylococcus aureus, Sphingomonas echinoides, and Pseudomonas putida. We also compared the effects of day-fed versus night-fed probiotics. Intriguingly, the nighttime feeding showed a higher proportion of C. butyricum compared with probiotic day-feeding. Finally, fecal metabolome and metabolites were analyzed in late preterm infants with (n = 20) or without probiotic therapy (n = 20). The KEGG enrichment analysis demonstrated that vitamin digestion and absorption, synaptic vesicle cycle, and biotin metabolism were significantly increased in the probiotic-treated group, while MSEA indicated that a series of metabolism were significantly enriched in probiotic-treated infants including glycerolipid, biotin, and lysine, indicating the complex effects of probiotic therapy on glutathione metabolism and nutrients digestion and absorption in late preterm infants. Overall, this study provided metagenomic and metabolomic profile of the gut microbes in full-term newborns and late preterm infants in eastern China. Further studies are needed to support and elucidate the role of probiotic feeding in late preterm infants with mandatory antimicrobial treatment.
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Affiliation(s)
- Hong Li
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Xingling Ma
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Yongfu Li
- Neonatology Department, Suzhou Science and Technology Town Hospital, Suzhou, Jiangsu, China
| | - Qin Liu
- Neonatology Department, Suzhou Science and Technology Town Hospital, Suzhou, Jiangsu, China
- Pediatric Department, Suzhou New District Yangshan Community Health Service Center, Suzhou, China
| | - Qiuyan Tian
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Xiaofeng Yang
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Zhemin Zhou
- Pasteurien College, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Jing Ren
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Bin Sun
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Xing Feng
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China
| | - Hong Zhang
- Taixing People's Hospital, Taizhou, Jiangsu, China
| | - Xiaoping Yin
- Taixing People's Hospital, Taizhou, Jiangsu, China
| | - Heng Li
- Pasteurien College, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China.
| | - Xin Ding
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, #303 Jingde Road, Gusu District, Suzhou, 215003, Jiangsu, China.
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Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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47
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Aboushaala K, Wong AYL, Barajas JN, Lim P, Al-Harthi L, Chee A, Forsyth CB, Oh CD, Toro SJ, Williams FMK, An HS, Samartzis D. The Human Microbiome and Its Role in Musculoskeletal Disorders. Genes (Basel) 2023; 14:1937. [PMID: 37895286 PMCID: PMC10606932 DOI: 10.3390/genes14101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.
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Affiliation(s)
- Khaled Aboushaala
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Arnold Y. L. Wong
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Juan Nicolas Barajas
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Perry Lim
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Ana Chee
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Christopher B. Forsyth
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Chun-do Oh
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sheila J. Toro
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | | | - Howard S. An
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Dino Samartzis
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
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48
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Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.
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Affiliation(s)
- Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
| | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, USA
| | - Keolu Fox
- Department of Anthropology, Global Health Program, and Indigenous Futures Institute, University of California, San Diego, CA, USA
| | - Emma Kowal
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Melbourne, Victoria, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, USA.
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49
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Bader AC, Van Zuylen EM, Handsley-Davis M, Alegado RA, Benezra A, Pollet RM, Ehau-Taumaunu H, Weyrich LS, Anderson MZ. A relational framework for microbiome research with Indigenous communities. Nat Microbiol 2023; 8:1768-1776. [PMID: 37770743 DOI: 10.1038/s41564-023-01471-2] [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: 11/18/2022] [Accepted: 07/26/2023] [Indexed: 09/30/2023]
Abstract
Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.
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Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada.
| | - Essie M Van Zuylen
- Department of Microbiology and Immunology, University of Otago, Dunedin North, Dunedin, New Zealand
- School of Product Design, University of Canterbury, Christchurch, New Zealand
| | - Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
| | - Rosanna A Alegado
- Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, USA
| | - Amber Benezra
- Department of Science and Technology Studies, Stevens Institute of Technology, Hoboken, NJ, USA
| | | | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
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50
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Goh SG, Haller L, Ng C, Charles FR, Jitxin L, Chen H, He Y, Gin KYH. Assessing the additional health burden of antibiotic resistant Enterobacteriaceae in surface waters through an integrated QMRA and DALY approach. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132058. [PMID: 37459761 DOI: 10.1016/j.jhazmat.2023.132058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Antibiotic resistant Enterobacteriaceae pose a significant threat to public health. However, limited studies have evaluated the health risks associated with exposure to antibiotic-resistant bacteria (ARB), especially in natural environments. While quantitative microbial risk assessment (QMRA) assesses microbial risks in terms of the probability of infection, it does not account for the severity of health outcomes. In this study, a QMRA-DALY model was developed to integrate QMRA with health burden (disability-adjusted life years (DALY)) from infections caused by ARB. The model considers uncertainties in probability of infection and health burden assessment using Monte Carlo simulations. The study collected antimicrobial resistance (AMR) surveillance data from surface waters with different land uses. Results revealed water bodies with agricultural land use to be the main AMR hotspots, with the highest additional health burden observed in infections caused by meropenem-resistant E. coli (∆DALY = 0.0105 DALY/event) compared to antibiotic-susceptible E. coli. The estimated ∆DALY for antibiotic-resistant K. pneumoniae was lower than for antibiotic-resistant E. coli (highest ∆DALY = 0.00048 DALY/event). The study highlights the need for better evaluation of AMR associated health burden, and effective measures to mitigate the risks associated with antibiotic-resistant bacteria in natural environments.
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Affiliation(s)
- Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Laurence Haller
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Charmaine Ng
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Francis Rathinam Charles
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Lim Jitxin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
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