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De Filippo C, Chioccioli S, Meriggi N, Troise AD, Vitali F, Mejia Monroy M, Özsezen S, Tortora K, Balvay A, Maudet C, Naud N, Fouché E, Buisson C, Dupuy J, Bézirard V, Chevolleau S, Tondereau V, Theodorou V, Maslo C, Aubry P, Etienne C, Giovannelli L, Longo V, Scaloni A, Cavalieri D, Bouwman J, Pierre F, Gérard P, Guéraud F, Caderni G. Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets. MICROBIOME 2024; 12:180. [PMID: 39334498 PMCID: PMC11438057 DOI: 10.1186/s40168-024-01900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 08/05/2024] [Indexed: 09/30/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) risk is strongly affected by dietary habits with red and processed meat increasing risk, and foods rich in dietary fibres considered protective. Dietary habits also shape gut microbiota, but the role of the combination between diet, the gut microbiota, and the metabolite profile on CRC risk is still missing an unequivocal characterisation. METHODS To investigate how gut microbiota affects diet-associated CRC risk, we fed Apc-mutated PIRC rats and azoxymethane (AOM)-induced rats the following diets: a high-risk red/processed meat-based diet (MBD), a normalised risk diet (MBD with α-tocopherol, MBDT), a low-risk pesco-vegetarian diet (PVD), and control diet. We then conducted faecal microbiota transplantation (FMT) from PIRC rats to germ-free rats treated with AOM and fed a standard diet for 3 months. We analysed multiple tumour markers and assessed the variations in the faecal microbiota using 16S rRNA gene sequencing together with targeted- and untargeted-metabolomics analyses. RESULTS In both animal models, the PVD group exhibited significantly lower colon tumorigenesis than the MBD ones, consistent with various CRC biomarkers. Faecal microbiota and its metabolites also revealed significant diet-dependent profiles. Intriguingly, when faeces from PIRC rats fed these diets were transplanted into germ-free rats, those transplanted with MBD faeces developed a higher number of preneoplastic lesions together with distinctive diet-related bacterial and metabolic profiles. PVD determines a selection of nine taxonomic markers mainly belonging to Lachnospiraceae and Prevotellaceae families exclusively associated with at least two different animal models, and within these, four taxonomic markers were shared across all the three animal models. An inverse correlation between nonconjugated bile acids and bacterial genera mainly belonging to the Lachnospiraceae and Prevotellaceae families (representative of the PVD group) was present, suggesting a potential mechanism of action for the protective effect of these genera against CRC. CONCLUSIONS These results highlight the protective effects of PVD while reaffirming the carcinogenic properties of MBD diets. In germ-free rats, FMT induced changes reminiscent of dietary effects, including heightened preneoplastic lesions in MBD rats and the transmission of specific diet-related bacterial and metabolic profiles. Importantly, to the best of our knowledge, this is the first study showing that diet-associated cancer risk can be transferred with faeces, establishing gut microbiota as a determinant of diet-associated CRC risk. Therefore, this study marks the pioneering demonstration of faecal transfer as a means of conveying diet-related cancer risk, firmly establishing the gut microbiota as a pivotal factor in diet-associated CRC susceptibility. Video Abstract.
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Grants
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- JTC-2017-7 Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"
- Expression of interest # 895 HDHL INTIMIC-Knowledge Platform on food, diet, intestinal microbiomics and human health
- Expression of interest # 895 HDHL INTIMIC-Knowledge Platform on food, diet, intestinal microbiomics and human health
- PE00000003 National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - NextGenerationEU; Project title "ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security - Working ON Foods"
- PE00000003 National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - NextGenerationEU; Project title "ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security - Working ON Foods"
- PE00000003 National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - NextGenerationEU; Project title "ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security - Working ON Foods"
- ECS00000017 European Union - NextGenerationEU - National Recovery and Resilience Plan, Mission 4 Component 2 - Investment 1.5 - THE - Tuscany Health Ecosystem
- ECS00000017 European Union - NextGenerationEU - National Recovery and Resilience Plan, Mission 4 Component 2 - Investment 1.5 - THE - Tuscany Health Ecosystem
- G. Caderni University of Florence (Fondo ex-60%), Italy
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Affiliation(s)
- Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy.
| | - Sofia Chioccioli
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy
| | - Antonio Dario Troise
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy
| | - Mariela Mejia Monroy
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Serdar Özsezen
- Netherlands Organisation for Applied Scientific Research, Zeist, Netherlands
| | - Katia Tortora
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Aurélie Balvay
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Maudet
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nathalie Naud
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Edwin Fouché
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Charline Buisson
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Jacques Dupuy
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Valérie Bézirard
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Sylvie Chevolleau
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - Valérie Tondereau
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Vassilia Theodorou
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Claire Maslo
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Perrine Aubry
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Camille Etienne
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Lisa Giovannelli
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Vincenzo Longo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy
| | - Andrea Scaloni
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy
| | | | - Jildau Bouwman
- Netherlands Organisation for Applied Scientific Research, Zeist, Netherlands
| | - Fabrice Pierre
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Philippe Gérard
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Françoise Guéraud
- Toxalim, INRAE, ENVT, INP-Purpan, UPS, Toulouse University, Toulouse, 31027, France
| | - Giovanna Caderni
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, Italy.
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Florence, Italy.
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2
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Vinogradova E, Mukhanbetzhanov N, Nurgaziyev M, Jarmukhanov Z, Aipova R, Sailybayeva A, Bekbossynova M, Kozhakhmetov S, Kushugulova A. Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts. mSystems 2024:e0058524. [PMID: 39287374 DOI: 10.1128/msystems.00585-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines. IMPORTANCE The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.
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Affiliation(s)
- Elizaveta Vinogradova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Madiyar Nurgaziyev
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Zharkyn Jarmukhanov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Rakhilya Aipova
- Kazakh Research Institute of Soil Science and Agricultural Chemistry named after U.Uspanov, Almaty, Kazakhstan
| | | | | | - Samat Kozhakhmetov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Almagul Kushugulova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- JSC "National Research Cardiac Surgery Center", Astana, Kazakhstan
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Berni Canani R, Carucci L, Coppola S, D'Auria E, O'Mahony L, Roth-Walter F, Vassilopolou E, Agostoni C, Agache I, Akdis C, De Giovanni Di Santa Severina F, Faketea G, Greenhawt M, Hoffman K, Hufnagel K, Meyer R, Milani GP, Nowak-Wegrzyn A, Nwaru B, Padua I, Paparo L, Diego P, Reese I, Roduit C, Smith PK, Santos A, Untersmayr E, Vlieg-Boerstra B, Venter C. Ultra-processed foods, allergy outcomes and underlying mechanisms in children: An EAACI task force report. Pediatr Allergy Immunol 2024; 35:e14231. [PMID: 39254357 DOI: 10.1111/pai.14231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Consumption of ultra-processed foods [UPFs] may be associated with negative health outcomes. Limited data exist regarding the potential role of UPFs in the occurrence of allergic diseases. The underlying mechanisms underpinning any such associations are also poorly elucidated. METHODS We performed a systematic review and narrative evidence synthesis of the available literature to assess associations between UPF consumption and pediatric allergy outcomes (n = 26 papers), including data on the association seen with the gut microbiome (n = 16 papers) or immune system (n = 3 papers) structure and function following PRISMA guidelines. RESULTS Dietary exposure to fructose, carbonated soft drinks, and sugar intake was associated with an increased risk of asthma, allergic rhinitis, and food allergies in children. Commercial baby food intake was associated with childhood food allergy. Childhood intake of fructose, fruit juices, sugar-sweetened beverages, high carbohydrate UPFs, monosodium glutamate, UPFs, and advanced glycated end-products (AGEs) was associated with the occurrence of allergic diseases. Exposure to UPFs and common ingredients in UPFs seem to be associated with increased occurrence of allergic diseases such as asthma, wheezing, food allergies, atopic dermatitis, and allergic rhinitis, in many, but not all studies. CONCLUSION More preclinical and clinical studies are required to better define the link between UPF consumption and the risk of allergies and asthma. These observational studies ideally require supporting data with clearly defined UPF consumption, validated dietary measures, and mechanistic assessments to definitively link UPFs with the risk of allergies and asthma.
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Affiliation(s)
- Roberto Berni Canani
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- ImmunoNutritionLab at the CEINGE Advanced Biotechnologies Research Center, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies University of Naples Federico II, Naples, Italy
- European Laboratory for the Investigation of Food-Induced Diseases, University of Naples Federico II, Naples, Italy
| | - Laura Carucci
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- ImmunoNutritionLab at the CEINGE Advanced Biotechnologies Research Center, University of Naples Federico II, Naples, Italy
| | - Serena Coppola
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- ImmunoNutritionLab at the CEINGE Advanced Biotechnologies Research Center, University of Naples Federico II, Naples, Italy
| | - Enza D'Auria
- Allergy Unit-Buzzi Children's Hospital-University of Milan, Milan, Italy
| | - Liam O'Mahony
- Department of Medicine, School of Microbiology, APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Franziska Roth-Walter
- Department of Interdisciplinary Life Sciences, Messerli Research Institute, University of Veterinary Medicine, Medical University and University of Vienna, Vienna, Austria
- Center of Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Emilia Vassilopolou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, Thessaloniki, Greece
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Carlo Agostoni
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Iaona Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania
| | - Cezmi Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Fiorenza De Giovanni Di Santa Severina
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- ImmunoNutritionLab at the CEINGE Advanced Biotechnologies Research Center, University of Naples Federico II, Naples, Italy
| | - Gaby Faketea
- Department of Pediatrics, "Karamandaneio" Children's Hospital of Patra, Patras, Greece
- Department of Pharmacology, "luliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Matt Greenhawt
- Section of Pediatric Allergy and Immunology, University of Colorado, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Karin Hoffman
- Center of Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Karin Hufnagel
- Department of Interdisciplinary Life Sciences, Messerli Research Institute, University of Veterinary Medicine, Medical University and University of Vienna, Vienna, Austria
- Center of Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Rosan Meyer
- Department of Nutrition and Dietetics, Winchester University, Winchester, UK
- Department of Medicine, KU Leuven, Leuven, Belgium
| | - Gregorio Paolo Milani
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Anna Nowak-Wegrzyn
- Department of Pediatrics, Hassenfeld Children's Hospital, NYU Grossman School of Medicine, New York, New York, USA
- Department of Pediatrics, Gastroenterology and Nutrition, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Bright Nwaru
- Krefting Research Centre, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Ines Padua
- Department of Sciences, University Institute of Health Sciences, Gandra, Portugal
- i4HB/UCIBIO - Translational Toxicology Research Laboratory, Gandra, Portugal
- CUF Porto Trindade Hospital, Porto, Portugal
| | - Lorella Paparo
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- ImmunoNutritionLab at the CEINGE Advanced Biotechnologies Research Center, University of Naples Federico II, Naples, Italy
| | - Peroni Diego
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Imke Reese
- Practice for Dietary Advice & Nutrition Therapy in Adverse Food Reactions, Munich, Germany
| | - Caroline Roduit
- Division of Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
- CK-CARE, Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Peter K Smith
- Griffith University, Southport, Queensland, Australia
| | - Alexandra Santos
- Department of Women and Children's Health (Pediatric Allergy), Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London, UK
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
- Children's Allergy Service, Evelina London Children's Hospital, Guy's and St Thomas' Hospital, London, UK
| | - Eva Untersmayr
- Center for Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Berber Vlieg-Boerstra
- Department of Paediatrics, OLVG Hospital, Amsterdam, The Netherlands
- Rijnstate Allergy Centre, Rijnstate Hospital, Arnhem, The Netherlands
| | - Carina Venter
- Section of Pediatric Allergy and Immunology, University of Colorado, Children's Hospital Colorado, Aurora, Colorado, USA
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Maukonen M, Koponen KK, Havulinna AS, Kaartinen NE, Niiranen T, Méric G, Pajari AM, Knight R, Salomaa V, Männistö S. Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults. Eur J Nutr 2024; 63:2247-2260. [PMID: 38753173 PMCID: PMC11377619 DOI: 10.1007/s00394-024-03406-x] [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: 04/16/2024] [Indexed: 09/06/2024]
Abstract
PURPOSE Population-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cereals), red and processed meat (RPM) or dairy (fermented milk, cheese, other dairy products) are related to gut microbiome in Finnish adults. METHODS We utilized data from the National FINRISK/FINDIET 2002 Study (n = 1273, aged 25-64 years, 55% women). Diet was assessed with 48-hour dietary recalls. Gut microbiome was analyzed using shallow shotgun sequencing. We applied multivariate analyses with linear models and permutational ANOVAs adjusted for relevant confounders. RESULTS Fruit consumption was positively (beta = 0.03, SE = 0.01, P = 0.04), while a dairy subgroup including milk, cream and ice-creams was inversely associated (beta=-0.03, SE 0.01, P = 0.02) with intra-individual gut microbiome diversity (alpha-diversity). Plant-based foods (R2 = 0.001, P = 0.03) and dairy (R2 = 0.002, P = 0.01) but not RPM (R2 = 0.001, P = 0.38) contributed to the compositional differences in gut microbiome (beta-diversity). Plant-based foods were associated with several butyrate producers/cellulolytic species including Roseburia hominis. RPM associations included an inverse association with R. hominis. Dairy was positively associated with several lactic producing/probiotic species including Lactobacillus delbrueckii and potentially opportunistic pathogens including Citrobacter freundii. Dairy, fermented milk, vegetables, and cereals were associated with specific microbial functions. CONCLUSION Our results suggest a potential association between plant-based foods and dairy or their subgroups with microbial diversity measures. Furthermore, our findings indicated that all the food groups were associated with distinct overall microbial community compositions. Plant-based food consumption particularly was associated with a larger number of putative beneficial species.
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Affiliation(s)
- Mirkka Maukonen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.
| | - Kari K Koponen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | | | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Guillaume Méric
- Baker Heart and Diabetes Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Monash University, Melbourne, Australia
- La Trobe University, Melbourne, Australia
| | | | - Rob Knight
- University of California San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Satu Männistö
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
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Schneider E, O'Riordan KJ, Clarke G, Cryan JF. Feeding gut microbes to nourish the brain: unravelling the diet-microbiota-gut-brain axis. Nat Metab 2024; 6:1454-1478. [PMID: 39174768 DOI: 10.1038/s42255-024-01108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
The prevalence of brain disorders, including stress-related neuropsychiatric disorders and conditions with cognitive dysfunction, is rising. Poor dietary habits contribute substantially to this accelerating trend. Conversely, healthy dietary intake supports mood and cognitive performance. Recently, the communication between the microorganisms within the gastrointestinal tract and the brain along the gut-brain axis has gained prominence as a potential tractable target to modulate brain health. The composition and function of the gut microbiota is robustly influenced by dietary factors to alter gut-brain signalling. To reflect this interconnection between diet, gut microbiota and brain functioning, we propose that a diet-microbiota-gut-brain axis exists that underpins health and well-being. In this Review, we provide a comprehensive overview of the interplay between diet and gut microbiota composition and function and the implications for cognition and emotional functioning. Important diet-induced effects on the gut microbiota for the development, prevention and maintenance of neuropsychiatric disorders are described. The diet-microbiota-gut-brain axis represents an uncharted frontier for brain health diagnostics and therapeutics across the lifespan.
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Affiliation(s)
| | | | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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Brichacek AL, Florkowski M, Abiona E, Frank KM. Ultra-Processed Foods: A Narrative Review of the Impact on the Human Gut Microbiome and Variations in Classification Methods. Nutrients 2024; 16:1738. [PMID: 38892671 PMCID: PMC11174918 DOI: 10.3390/nu16111738] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Ultra-processed foods (UPFs) are foods that are industrially processed and are often pre-packaged, convenient, energy-dense, and nutrient-poor. UPFs are widespread in the current Western diet and their proposed contribution to non-communicable diseases such as obesity and cardiovascular disease is supported by numerous studies. UPFs are hypothesized to affect the body in multiple ways, including by inducing changes in the gut microbiome. This review summarizes the available research on the effect of UPFs on the gut microbiome. We also review current usage of the NOVA food classification system in randomized controlled trials and observational studies and how its implementation effects UPF research. Despite some differences in methodology between studies, results often associate UPF consumption with a number of negative health consequences. There are attempts to standardize a UPF classification system; however, reaching and implementing a consensus is difficult. Future studies focusing on the mechanisms by which UPFs effect the body, including through the microbiome and metabolome, will be essential to refine our understanding of the effects of UPFs on human health.
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Affiliation(s)
| | | | | | - Karen M. Frank
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Building 10, 10 Center Drive MSC 1508, Bethesda, MD 20892, USA; (A.L.B.); (M.F.); (E.A.)
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7
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Zhao J, Kuang L, Hu A, Zhang Q, Yang D, Wang C. OGNNMDA: a computational model for microbe-drug association prediction based on ordered message-passing graph neural networks. Front Genet 2024; 15:1370013. [PMID: 38689654 PMCID: PMC11058190 DOI: 10.3389/fgene.2024.1370013] [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: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
In recent years, many excellent computational models have emerged in microbe-drug association prediction, but their performance still has room for improvement. This paper proposed the OGNNMDA framework, which applied an ordered message-passing mechanism to distinguish the different neighbor information in each message propagation layer, and it achieved a better embedding ability through deeper network layers. Firstly, the method calculates four similarity matrices based on microbe functional similarity, drug chemical structure similarity, and their respective Gaussian interaction profile kernel similarity. After integrating these similarity matrices, it concatenates the integrated similarity matrix with the known association matrix to obtain the microbe-drug heterogeneous matrix. Secondly, it uses a multi-layer ordered message-passing graph neural network encoder to encode the heterogeneous network and the known association information adjacency matrix, thereby obtaining the final embedding features of the microbe-drugs. Finally, it inputs the embedding features into the bilinear decoder to get the final prediction results. The OGNNMDA method performed comparative experiments, ablation experiments, and case studies on the aBiofilm, MDAD and DrugVirus datasets using 5-fold cross-validation. The experimental results showed that OGNNMDA showed the strongest prediction performance on aBiofilm and MDAD and obtained sub-optimal results on DrugVirus. In addition, the case studies on well-known drugs and microbes also support the effectiveness of the OGNNMDA method. Source codes and data are available at: https://github.com/yyzg/OGNNMDA.
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Affiliation(s)
- Jiabao Zhao
- School of Computer Science and School of Cyberspace Science, Xiangtan University, Xiangtan, China
| | - Linai Kuang
- School of Computer Science and School of Cyberspace Science, Xiangtan University, Xiangtan, China
| | - An Hu
- School of Computer Science and School of Cyberspace Science, Xiangtan University, Xiangtan, China
| | - Qi Zhang
- School of Computer Science and School of Cyberspace Science, Xiangtan University, Xiangtan, China
| | - Dinghai Yang
- School of Computer Science and School of Cyberspace Science, Xiangtan University, Xiangtan, China
| | - Chunxiang Wang
- Hunan Institute of Engineering College of textile and clothing, Xiangtan, China
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8
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Delavy M, Sertour N, Patin E, Le Chatelier E, Cole N, Dubois F, Xie Z, Saint-André V, Manichanh C, Walker AW, Quintana-Murci L, Duffy D, d’Enfert C, Bougnoux ME, Consortium MI. Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response. Gut Microbes 2023; 15:2287618. [PMID: 38017705 PMCID: PMC10732203 DOI: 10.1080/19490976.2023.2287618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.
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Affiliation(s)
- Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Natacha Sertour
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | | | - Nathaniel Cole
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Florian Dubois
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Zixuan Xie
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Violaine Saint-André
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Chaysavanh Manichanh
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Alan W. Walker
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
| | - Milieu Intérieur Consortium
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
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9
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Song S, Shon J, Yang WR, Kang HB, Kim KH, Park JY, Lee S, Baik SY, Lee KR, Park YJ. Short-Term Effects of Weight-Loss Meal Replacement Programs with Various Macronutrient Distributions on Gut Microbiome and Metabolic Parameters: A Pilot Study. Nutrients 2023; 15:4744. [PMID: 38004139 PMCID: PMC10675061 DOI: 10.3390/nu15224744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
It has emerged the gut microbiome is crucially linked to metabolic health and obesity. Macronutrient distribution has been discussed as a key parameter in weight-loss programs, but little is known about its impact on the gut microbiome. We investigated the effects of weight-loss meal replacement programs with different macronutrient ratios on the gut microbiota and metabolic parameters in subjects with overweight and obesity. Three low-calorie meal replacement programs with different ratios of carbohydrates, proteins, and lipids were designed: a balanced diet (Group B, 60:15:30), a high-lipid-low-carbohydrate diet (Group F, 35:20:55), and a protein-enriched diet (Group P, 40:25:35). Sixty overweight or obese participants were provided with the meals twice daily for 3 weeks. In all groups, diet intervention resulted in reduced body weight and BMI. The relative abundance of Bacteroidetes and Firmicutes phyla decreased and increased, respectively, which increased the Firmicutes/Bacteroidetes (F/B) ratio in all subjects, particularly in Groups B and P. Alpha- and beta-diversity were augmented at the phylum level in Group P. In conclusion, short-term interventions with weight-loss meal replacement programs increased butyrate-producing bacteria and the F/B ratio. Moreover, the protein-enriched diet significantly increased alpha- and beta-diversity compared to the balanced diet and the high-lipid-low-carbohydrate diet.
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Affiliation(s)
- Seungmin Song
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jinyoung Shon
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Woo-ri Yang
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Han-Bit Kang
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Keun-Ha Kim
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Ju-Yeon Park
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Sanghoo Lee
- SCL Healthcare Inc., Yongin-si 16954, Republic of Korea
| | - Sae Yun Baik
- Hanaro Medical Foundation, Seoul 03159, Republic of Korea
| | - Kyoung-Ryul Lee
- SCL Healthcare Inc., Yongin-si 16954, Republic of Korea
- Hanaro Medical Foundation, Seoul 03159, Republic of Korea
| | - Yoon Jung Park
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
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10
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Asuncion P, Liu C, Castro R, Yon V, Rosas M, Hooshmand S, Kern M, Hong MY. The effects of fresh mango consumption on gut health and microbiome - Randomized controlled trial. Food Sci Nutr 2023; 11:2069-2078. [PMID: 37051355 PMCID: PMC10084975 DOI: 10.1002/fsn3.3243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/19/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Some individual fruits have been widely researched for their effects on overall health and correlations with chronic diseases. The beneficial effects of mango supplementation on metabolic diseases have been detected. However, research into mango consumption on gut health, including the microbiome, is limited to processed mango preparations or peels. Our goal was to examine the effects of fresh mango consumption on the gut microbiome, gut permeability proteins, and bowel movement habits in overweight/obese individuals. In a 12-week crossover design study, 27 participants consumed 100 kcal/day of either mangos or low-fat cookies with a washout period of 4 weeks. The mango intervention showed higher Shannon-Wiener and Simpson alpha diversity indices of the microbiome than the low-fat cookie intervention in week 4. Significant differences in beta diversity of the microbiome were found between diet interventions at week 12. Mango consumption increased the abundance of Prevotella maculosa, Corynebacterium pyruviciproducens, and Mogibacterium timidum while it decreased Prevotella copri. Low-fat cookie intake increased Cyanobacterium aponinum and Desulfovibrio butyratiphilus and reduced Alloscardovia omnicolens. There were no significant differences in circulating gut permeability protein (ZO-1, claudin-2, and occludin) levels. There was a slight increase in the amount of bowel movement with mango consumption, but no significant findings for frequency, consistency, strain, pain, and constipation in bowel movement between trials. Given these results, it can be concluded that consumption of mango may have positive effects on the gut health, which may yield possible health benefits for chronic disease that deserve further study.
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Affiliation(s)
- Pia Asuncion
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Changqi Liu
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Robert Castro
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Viviana Yon
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Martin Rosas
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Shirin Hooshmand
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Mark Kern
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Mee Young Hong
- School of Exercise and Nutritional SciencesSan Diego State UniversitySan DiegoCaliforniaUSA
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11
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Tristan Asensi M, Napoletano A, Sofi F, Dinu M. Low-Grade Inflammation and Ultra-Processed Foods Consumption: A Review. Nutrients 2023; 15:1546. [PMID: 36986276 PMCID: PMC10058108 DOI: 10.3390/nu15061546] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Low-grade inflammation alters the homeostasis of the organism and favors the onset of many chronic diseases. The global growth in the prevalence of noncommunicable diseases in recent years has been accompanied by an increase in the consumption of ultra-processed foods (UPF). Known to be hyperpalatable, economic and ready-to-eat, increased consumption of UPF has already been recognized as a risk factor for several chronic diseases. Different research groups have tried to investigate whether UPF consumption could promote low-grade inflammation and thus favor the development of noncommunicable diseases. Current evidence highlights the adverse health effects of UPF characteristics, not only due to the nutrients provided by a diet rich in UPF, but also due to the non-nutritive components present in UPF and the effect they may have on gut health. This review aims to summarize the available evidence on the possible relationship between excessive UPF consumption and modulation of low-grade inflammation, as potential promoters of chronic disease.
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Affiliation(s)
- Marta Tristan Asensi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Antonia Napoletano
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Francesco Sofi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Unit of Clinical Nutrition, Careggi University Hospital, 50134 Florence, Italy
| | - Monica Dinu
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
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12
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Shi L, Xu Y, Feng M. Role of Gut Microbiome in Immune Regulation and Immune Checkpoint Therapy of Colorectal Cancer. Dig Dis Sci 2023; 68:370-379. [PMID: 36575326 DOI: 10.1007/s10620-022-07689-0] [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: 04/26/2022] [Accepted: 09/01/2022] [Indexed: 12/29/2022]
Abstract
Colorectal cancer (CRC) is one of the most frequent gastrointestinal malignant tumors worldwide. Immune checkpoint therapies (ICTs) have been proven to be a reliable treatment for some subtypes of CRC. Gut microbiome is closely involved in intestinal carcinogenesis through the regulation of local immune and inflammation of colonic mucosa. Numerous studies have demonstrated that the immunotherapeutic efficacy of CRC and other kinds of cancer is influenced by the immunosuppressive microenvironment constituted by intestinal microbiome and their metabolites. This Review will discuss the recent advances in how gut microbiome can modify the immune microenvironment and its potential role in ICTs of CRC.
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Affiliation(s)
- Linsen Shi
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Yumei Xu
- Department of Radiation Oncology Center, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Min Feng
- Department of Gastrointestinal Surgery, The Affiliated Drum Tower Hospital of NanJing Medical University, 321 Zhongshan Road, Nanjing, 210002, People's Republic of China.
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13
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Xia Y, Lee G, Takei N, Takahashi H, Kuda T. Detection of typical indigenous gut bacteria related to turmeric (Curcuma longa) powder in mouse caecum and human faecal cultures. Mol Biol Rep 2023; 50:2963-2974. [PMID: 36648695 DOI: 10.1007/s11033-022-08237-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/22/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Turmeric (Curcuma longa; TM) is widely used as a spice and possesses anti-inflammatory, antioxidant, and antibacterial properties. The relationship between TM functions and gut microbiota is still unclear. METHODS AND RESULTS To investigate the effect of TM on gut microbiota and to identify indigenous gut bacteria that are responsive to TM, we fed Institute of Cancer Research mice a diet containing either no fibre (NF, n = 6) or 5% (w/w) TM (n = 6) for 14 days. Moreover, we obtained human stool samples from four healthy volunteers and incubated the samples without (control) or with 2% (w/v) TM at 37 °C for 24 h. Subsequently, microbiota analysis in murine caecal samples and human faecal cultures was performed using 16S rRNA (V4) amplicon sequencing. Higher faecal weights (p < 0.01) and lower plasma triacylglycerol levels (p < 0.05) were measured in the TM-fed mice than in the NF-fed mice. Furthermore, TM feeding increased the abundance of butyrate-producing and other short-chain fatty acid (SCFA)-producing bacteria in mice as well as in human faecal cultures, and Roseburia bacteria were detected as TM-responsive indigenous gut bacteria (TM-RIB) both in mice and in human faecal cultures. Lastly, in the case of human faecal cultures, SCFA contents and antioxidant properties were higher in TM cultures than in control cultures (p < 0.05). CONCLUSION TM appears to hold the potential to positively affect the host by altering the gut microbiota. Further studies are required to clarify the synergistic effects of TM and TM-RIB.
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Affiliation(s)
- Yumeng Xia
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.
| | - Gayang Lee
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Natsumi Takei
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
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14
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McKay I, van Dorst J, Katz T, Doumit M, Prentice B, Owens L, Belessis Y, Chuang S, Jaffe A, Thomas T, Coffey M, Ooi CY. Diet and the gut-lung axis in cystic fibrosis - direct & indirect links. Gut Microbes 2023; 15:2156254. [PMID: 36573804 PMCID: PMC9809969 DOI: 10.1080/19490976.2022.2156254] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) is a multisystem, autosomal, recessive disease primarily affecting the lungs, pancreas, gastrointestinal tract, and liver. Whilst there is increasing evidence of a microbial 'gut-lung axis' in chronic respiratory conditions, there has been limited analysis of such a concept in CF. We performed a comprehensive dietary and microbiota analysis to explore the interactions between diet, gastrointestinal microbiota, respiratory microbiota, and clinical outcomes in children with CF. Our results demonstrate significant alterations in intestinal inflammation and respiratory and gastrointestinal microbiota when compared to age and gender matched children without CF. We identified correlations between the gastrointestinal and respiratory microbiota, lung function, CF pulmonary exacerbations and anthropometrics, supporting the concept of an altered gut-lung axis in children with CF. We also identified significant differences in dietary quality with CF children consuming greater relative proportions of total, saturated and trans fats, and less relative proportions of carbohydrates, wholegrains, fiber, insoluble fiber, starch, and resistant starch. Our findings position the CF diet as a potential modulator in gastrointestinal inflammation and the proposed gut-lung axial relationship in CF. The dietary intake of wholegrains, fiber and resistant starch may be protective against intestinal inflammation and should be explored as potential therapeutic adjuvants for children with CF.
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Affiliation(s)
- Isabelle McKay
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Josie van Dorst
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Tamarah Katz
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Nutrition and Dietetics, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Michael Doumit
- Department of Physiotherapy, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Bernadette Prentice
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Louisa Owens
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Yvonne Belessis
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Sandra Chuang
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Torsten Thomas
- Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, Australia
- University of New South Wales, Centre for Marine Science and Innovation, Randwick, Australia
| | - Michael Coffey
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
| | - Chee Y. Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
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15
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Douglas GL, DeKerlegand D, Dlouhy H, Dumont-Leblond N, Fields E, Heer M, Krieger S, Mehta S, Rooney BV, Torralba MG, Whiting SE, Crucian B, Lorenzi H, Smith SM, Young M, Zwart SR. Impact of diet on human nutrition, immune response, gut microbiome, and cognition in an isolated and confined mission environment. Sci Rep 2022; 12:20847. [PMID: 36522361 PMCID: PMC9755260 DOI: 10.1038/s41598-022-21927-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/06/2022] [Indexed: 12/23/2022] Open
Abstract
Long-duration spaceflight impacts human physiology, including well documented immune system dysregulation. The space food system has the potential to serve as a countermeasure to maladaptive physiological changes during spaceflight. However, the relationship between dietary requirements, the food system, and spaceflight adaptation requires further investigation to adequately define countermeasures and prioritize resources on future spaceflight missions. We evaluated the impact of an enhanced spaceflight diet, with increased quantity and variety of fruits, vegetables, fish, and other foods rich in flavonoids and omega-3 fatty acids, compared to a standard spaceflight diet on multiple health and performance outcomes in 16 subjects over four 45-day closed chamber missions in the NASA Human Exploration Research Analog (HERA). Subjects consuming the enhanced spaceflight diet had lower cholesterol levels, lower stress (i.e. cortisol levels), better cognitive speed, accuracy, and attention, and a more stable microbiome and metatranscriptome than subjects consuming the standard diet. Although no substantial changes were observed in the immune response, there were also no immune challenges, such as illness or infection, so the full benefits of the diet may not have been apparent in these analog missions. These results indicate that a spaceflight diet rich in fruits, vegetables, and omega-3 fatty acids produces significant health and performance benefits even over short durations. Further investigation is required to fully develop dietary countermeasures to physiological decrements observed during spaceflight. These results will have implications for food resource prioritization on spaceflight missions.
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Affiliation(s)
- Grace L. Douglas
- grid.419085.10000 0004 0613 2864Human Health and Performance Directorate (SF4), NASA Johnson Space Center, 2101 NASA Parkway, Houston, TX 77058 USA
| | | | - Holly Dlouhy
- grid.481680.30000 0004 0634 8729KBR, Houston, TX USA
| | - Nathan Dumont-Leblond
- grid.421142.00000 0000 8521 1798Centre de Recherche de L’Institut Universitaire de Cardiologie Et de Pneumologie de Québec, Quebec City, QC Canada
| | | | - Martina Heer
- grid.10388.320000 0001 2240 3300IU International University of Applied Sciences and University of Bonn, Bonn, Germany
| | | | | | | | | | | | - Brian Crucian
- grid.419085.10000 0004 0613 2864Human Health and Performance Directorate (SF4), NASA Johnson Space Center, 2101 NASA Parkway, Houston, TX 77058 USA
| | - Hernan Lorenzi
- grid.469946.0J Craig Venter Institute, Rockville, MD USA
| | - Scott M. Smith
- grid.419085.10000 0004 0613 2864Human Health and Performance Directorate (SF4), NASA Johnson Space Center, 2101 NASA Parkway, Houston, TX 77058 USA
| | - Millennia Young
- grid.419085.10000 0004 0613 2864Human Health and Performance Directorate (SF4), NASA Johnson Space Center, 2101 NASA Parkway, Houston, TX 77058 USA
| | - Sara R. Zwart
- grid.176731.50000 0001 1547 9964University of Texas Medical Branch, Galveston, TX USA
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16
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Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges. NPJ Biofilms Microbiomes 2022; 8:81. [PMID: 36253412 PMCID: PMC9576740 DOI: 10.1038/s41522-022-00338-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
As one of the promising next-generation probiotics (NGPs), Akkermansia muciniphila, a well-known mucin-degrading bacterium, has been proven to be closely related to the metabolic diseases of its human host. However, the role of A. muciniphila in the host’s intestinal health remains ambiguous. Here, we comprehensively summarize and discuss the characteristics, the distribution, and the colonization of A. muciniphila in the human gastrointestinal tract (GIT). We propose that the application of A. muciniphila as a biomarker for longevity, for diagnostics and prognostics of intestinal diseases, or for intestinal health should be cautiously considered. Precise dietary regulation can mediate the treatment of intestinal diseases by altering the abundance of A. muciniphila. Although the beneficial role of A. muciniphila and its component in intestinal inflammation has been discovered, in gnotobiotic mice with specific gut microbiota, certain genotype, and colorectal cancer, or in animal models infected with a specific pathogen, A. muciniphila may be related to the occurrence and development of intestinal diseases. Genomic analysis, emphasizing the strain-level phylogenetic differences of A. muciniphila, indicates that a clear description and discussion of each strain is critical before its practical application. Our review provides much needed insight for the precise application of A. muciniphila.
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17
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Atzeni A, Martínez MÁ, Babio N, Konstanti P, Tinahones FJ, Vioque J, Corella D, Fitó M, Vidal J, Moreno-Indias I, Pertusa-Martinez S, Álvarez-Sala A, Castañer O, Goday A, Damas-Fuentes M, Belzer C, Martínez-Gonzalez MÁ, Hu FB, Salas-Salvadó J. Association between ultra-processed food consumption and gut microbiota in senior subjects with overweight/obesity and metabolic syndrome. Front Nutr 2022; 9:976547. [PMID: 36299993 PMCID: PMC9589409 DOI: 10.3389/fnut.2022.976547] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022] Open
Abstract
The production and consumption of ultra-processed foods (UPF) has increased considerably during the last years worldwide. Collective evidence shows the association between UPF consumption and adverse health outcomes, including inflammatory gastro-intestinal disorders and obesity. The gut microbiota has been suggested as potential mediator of the effects of UPF consumption on metabolism and health. However, few studies have been conducted in order to elucidate these aspects. Therefore, the aim of the present study was to assess the cross-sectional associations between UPF consumption and gut microbiota in a population of senior subjects (n = 645) within the frame of the PREDIMED-Plus trial. Eligible participants were men and women (aged 55-75 years), without documented history of cardiovascular disease at enrollment, with overweight/obesity (body mass index ≤ 27 and <40 kg/m2) and metabolic syndrome. Using the information of food frequency questionnaires, the consumption of UPF, expressed as a percentage of total dietary energy intake in kcal/day, was calculated considering those food items classified in group 4 of NOVA system. Population was categorized according to tertiles of UPF consumption. Taxonomic fecal microbiota information, along with blood biochemical parameters, anthropometric measurements and clinical data were obtained. Bioinformatics analysis was performed to study the association between fecal microbiota composition and UPF consumption. We observed that subjects allocated in the highest tertile of UPF consumption (21.4 ± 5.0 % kcal/day) presented lower adherence to MedDiet (p < 0.001) and higher total energy intake (p < 0.001). The taxonomic analysis of the fecal microbiota revealed a significant (Benjamini-Hochberg adjusted p < 0.2) positive association between specific taxa and tertiles (T) of UPF consumption: Alloprevotella (p = 0.041 vs. T2; p = 0.065 vs. T3), Negativibacillus (p = 0.096 vs. T3), Prevotella (p = 0.116 vs. T3), and Sutterella (p = 0.116 vs. T2). UPF consumption was positively associated with lower adherence to MedDiet and higher total energy intake in senior subjects with overweight obesity and metabolic syndrome. In addition, positive association with specific fecal microbiota taxa related to inflammatory gastro-intestinal diseases and low consumption of fruits and vegetables, was observed.
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Affiliation(s)
- Alessandro Atzeni
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - María Ágeles Martínez
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Nancy Babio
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Francisco J Tinahones
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | - Jesús Vioque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria y Biomédica de Alicante, Universidad Miguel Hernández (ISABIAL-UMH), Alicante, Spain
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Montserrat Fitó
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Josep Vidal
- CIBER Diabetes y Enfermedades Metabólicas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Department of Endocrinology, Institut d'Investigacions Biomédiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Isabel Moreno-Indias
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | | | - Andrea Álvarez-Sala
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Olga Castañer
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Albert Goday
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain.,IMIM, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Miguel Damas-Fuentes
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Miguel Á Martínez-Gonzalez
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Frank B Hu
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States.,Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Jordi Salas-Salvadó
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
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18
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Mokhtari EB, Ridenhour BJ. Filtering ASVs/OTUs via mutual information-based microbiome network analysis. BMC Bioinformatics 2022; 23:380. [PMID: 36114453 PMCID: PMC9482178 DOI: 10.1186/s12859-022-04919-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Microbial communities are widely studied using high-throughput sequencing techniques, such as 16S rRNA gene sequencing. These techniques have attracted biologists as they offer powerful tools to explore microbial communities and investigate their patterns of diversity in biological and biomedical samples at remarkable resolution. However, the accuracy of these methods can negatively affected by the presence of contamination. Several studies have recognized that contamination is a common problem in microbial studies and have offered promising computational and laboratory-based approaches to assess and remove contaminants. Here we propose a novel strategy, MI-based (mutual information based) filtering method, which uses information theoretic functionals and graph theory to identify and remove contaminants. We applied MI-based filtering method to a mock community data set and evaluated the amount of information loss due to filtering taxa. We also compared our method to commonly practice traditional filtering methods. In a mock community data set, MI-based filtering approach maintained the true bacteria in the community without significant loss of information. Our results indicate that MI-based filtering method effectively identifies and removes contaminants in microbial communities and hence it can be beneficial as a filtering method to microbiome studies. We believe our filtering method has two advantages over traditional filtering methods. First, it does not required an arbitrary choice of threshold and second, it is able to detect true taxa with low abundance.
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Affiliation(s)
- Elham Bayat Mokhtari
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
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19
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Detection of indigenous gut bacteria related to red chilli pepper (Capsicum annuum) in murine caecum and human faecal cultures. Mol Biol Rep 2022; 49:10239-10250. [PMID: 36068389 DOI: 10.1007/s11033-022-07875-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Red chilli pepper (Capsicum annuum; RP) is a popular spice containing the active compound capsaicin. Indigenous gut bacteria and metabolism can affect host health. The functions of capsaicin, including the regulation of metabolic health and anti-oxidant properties, may be correlated with the gut microbiota. METHODS To identify indigenous gut bacteria that are responsive to RP, Institute of Cancer Research mice fed a diet with no fibre or with 5% (w/w) RP for 14 days. Additionally, human stool samples collected from four healthy volunteers were incubated without (control) or with 2% (w/v) RP at 37 °C for 24 h. Microbiota in murine caecal samples and human faecal cultures were analysed using 16S rRNA (V4) amplicon sequencing. RESULTS Compared with the microbiota in mice fed no-fibre diets, Lachnospiraceae spp.-, Muribaculaceae spp.-, and Phacaeicola vulgatus-like bacteria were defined as murine RP-responsive indigenous gut bacteria (RP-RIB). In the human faecal cultures, acetate and propionate levels were higher in RP cultures than in the control cultures. Subdoligranulum spp.-, Blautia spp.-, Faecalibacterium prausnitzii-, P. vulgatus-, and Prevotella copri-like bacteria were defined as human RP-RIB. Compared with control culture Fe-reducing power was increased in the culture with RP. CONCLUSION RP increases the amount of short-chain fatty acid-producing bacteria and beneficial gut bacteria in mouse and human faecal cultures. Overall, RP could have a positive effect on the host by altering the gut microbiota.
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20
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Turpin W, Dong M, Sasson G, Raygoza Garay JA, Espin-Garcia O, Lee SH, Neustaeter A, Smith MI, Leibovitzh H, Guttman DS, Goethel A, Griffiths AM, Huynh HQ, Dieleman LA, Panaccione R, Steinhart AH, Silverberg MS, Aumais G, Jacobson K, Mack D, Murthy SK, Marshall JK, Bernstein CN, Abreu MT, Moayyedi P, Paterson AD, Xu W, Croitoru K. Mediterranean-Like Dietary Pattern Associations With Gut Microbiome Composition and Subclinical Gastrointestinal Inflammation. Gastroenterology 2022; 163:685-698. [PMID: 35643175 DOI: 10.1053/j.gastro.2022.05.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Case-control studies have shown that patients with Crohn's disease (CD) have a microbial composition different from healthy individuals. Although the causes of CD are unknown, epidemiologic studies suggest that diet is an important contributor to CD risk, potentially via modulation of bacterial composition and gut inflammation. We hypothesized that long-term dietary clusters (DCs) are associated with gut microbiome compositions and gut inflammation. Our objectives were to identify dietary patterns and assess whether they are associated with alterations in specific gut microbial compositions and subclinical levels of gut inflammation in a cohort of healthy first-degree relatives (FDRs) of patients with CD. METHODS As part of the Genetic, Environmental, Microbial (GEM) Project, we recruited a cohort of 2289 healthy FDRs of patients with CD. Individuals provided stool samples and answered a validated food frequency questionnaire reflecting their habitual diet during the year before sample collection. Unsupervised analysis identified 3 dietary and 3 microbial composition clusters. RESULTS DC3, resembling the Mediterranean diet, was strongly associated with a defined microbial composition, with an increased abundance of fiber-degrading bacteria, such as Ruminococcus, as well as taxa such as Faecalibacterium. The DC3 diet was also significantly associated with lower levels of subclinical gut inflammation, defined by fecal calprotectin, compared with other dietary patterns. No significant associations were found between individual food items and fecal calprotectin, suggesting that long-term dietary patterns rather than individual food items contribute to subclinical gut inflammation. Additionally, mediation analysis demonstrated that DC3 had a direct effect on subclinical inflammation that was partially mediated by the microbiota. CONCLUSIONS Overall, these results indicated that Mediterranean-like dietary patterns are associated with microbiome and lower intestinal inflammation. This study will help guide future dietary strategies that affect microbial composition and host gut inflammation to prevent diseases.
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Affiliation(s)
- Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mei Dong
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Gila Sasson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Juan Antonio Raygoza Garay
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, and Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anna Neustaeter
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Haim Leibovitzh
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Ashleigh Goethel
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hien Q Huynh
- Division of Gastroenterology and Nutrition, Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Levinus A Dieleman
- Division of Gastroenterology and the Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Remo Panaccione
- Inflammatory Bowel Disease Clinic, Division of Gastroenterology and Hepatology, University of Calgary, Calgary, Alberta, Canada
| | - A Hillary Steinhart
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, and Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Guy Aumais
- Department of Medicine, Hôpital Maisonneuve-Rosemont, Montreal University, Montreal, Quebec, Canada
| | - Kevan Jacobson
- Canadian Gastro-Intestinal Epidemiology Consortium (CanGIEC); British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Sanjay K Murthy
- The Ottawa Hospital Inflammatory Bowel Disease Centre, Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - John K Marshall
- Department of Medicine, McMaster University, Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
| | - Charles N Bernstein
- Inflammatory Bowel Disease Clinical and Research Centre, and Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maria T Abreu
- Department of Medicine, Crohn's and Colitis Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Paul Moayyedi
- Department of Medicine, McMaster University, Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
| | - Andrew D Paterson
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada; Genetics and Genome Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Wei Xu
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, and Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada.
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21
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Dong C, Chan SSM, Jantchou P, Racine A, Oldenburg B, Weiderpass E, Heath AK, Tong TYN, Tjønneland A, Kyrø C, Bueno de Mesquita B, Kaaks R, Katzke VA, Bergman MM, Boeing H, Palli D, Masala G, Tumino R, Sacerdote C, Colorado-Yohar SM, Sánchez MJ, Grip O, Lindgren S, Luben R, Huybrechts I, Gunter MJ, Mahamat-Saleh Y, Boutron-Ruault MC, Carbonnel F. Meat Intake Is Associated with a Higher Risk of Ulcerative Colitis in a Large European Prospective Cohort Studyø. J Crohns Colitis 2022; 16:1187-1196. [PMID: 35396592 PMCID: PMC10020974 DOI: 10.1093/ecco-jcc/jjac054] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS We aimed to investigate the association between protein intake and risk of inflammatory bowel disease [IBD] in the European Prospective Investigation into Cancer and Nutrition. METHODS A total of 413 593 participants from eight European countries were included. Dietary data were collected at baseline from validated food frequency questionnaires. Dietary data were calibrated to correct errors in measures related to each country-specific questionnaire. Associations between proteins [total, animal, and vegetable] or food sources of animal proteins, and IBD risk were estimated by Cox proportional hazard models. RESULTS After a mean follow-up of 16 years, 177 patients with Crohn's disease [CD] and 418 with ulcerative colitis [UC], were identified. There was no association between total protein, animal protein, or vegetable protein intakes and CD or UC risks. Total meat and red meat intakes were associated with UC risk (hazard ratio [HR] for the 4th vs 1st quartile = 1.40, 95% confidence interval [CI] = 0.99-1.98, p-trend = 0.01; and 1.61, 95% CI = 1.10-2.36, p-trend = 0.007, respectively]. There was no association between other food sources of animal protein [processed meat, fish, shellfish, eggs, poultry] and UC. We found no association between food sources of animal proteins and CD risk. CONCLUSIONS Meat and red meat consumptions are associated with higher risks of UC. These results support dietary counselling of low meat intake in people at high-risk of IBD.
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Affiliation(s)
- Catherine Dong
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
- Department of Gastroenterology, University Hospital of Bicêtre, Assistance Publique-Hôpitaux de Paris and Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Simon S M Chan
- Norwich Medical School, Department of Medicine, University of East Anglia, Norwich, UK
- Department of Gastroenterology, Norfolk and Norwich University Hospital NHS Trust, Norwich, UK
| | - Prevost Jantchou
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
- Sainte Justine University Hospital, Montréal, QC, Canada
| | - Antoine Racine
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
- Department of Gastroenterology, University Hospital of Bicêtre, Assistance Publique-Hôpitaux de Paris and Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Tammy Y N Tong
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Kyrø
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bas Bueno de Mesquita
- National Institute for Public Health and the Environment [RIVM], Bilthoven, The Netherlands
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research
Center, Heidelberg, Germany
| | - Verena A Katzke
- Division of Cancer Epidemiology, German Cancer Research
Center, Heidelberg, Germany
| | - Manuela M Bergman
- Department of Epidemiology, German Institute of Human Nutrition, Potsdam, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition, Potsdam, Germany
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute, Florence, Italy
| | - Giovanna Masala
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute, Florence, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, Azienda Sanitaria Provinciale, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital, Turin, Italy
| | - Sandra M Colorado-Yohar
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
- CIBER Epidemiologia y Salud Pública [CIBERESP], Madrid, Spain
- National School of Public Health, Research Group on Demography and Health, University of Antioquia, Medellín, Colombia
| | - Maria-Jose Sánchez
- CIBER Epidemiologia y Salud Pública [CIBERESP], Madrid, Spain
- Escuela Andaluza de Salud Pública [EASP], Granada, Spain
- Instituto de Investigación Biosanitaria, Granada, Spain
- Department of Preventive Medicine and Public Health, University of Granada, Granada, Spain
| | - Olof Grip
- Department of Gastroenterology and Hepatology, University Hospital Malmö, Malmö, Sweden
| | - Stefan Lindgren
- Department of Gastroenterology and Hepatology, University Hospital Malmö, Malmö, Sweden
| | - Robert Luben
- Strangeways Research Laboratory, Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Inge Huybrechts
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marc J Gunter
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Yahya Mahamat-Saleh
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Marie-Christine Boutron-Ruault
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Franck Carbonnel
- INSERM, Centre for Research in Epidemiology and Population Health, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France
- Department of Gastroenterology, University Hospital of Bicêtre, Assistance Publique-Hôpitaux de Paris and Université Paris-Saclay, Le Kremlin Bicêtre, France
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22
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Alteration in Gut Microbiota Associated with Zinc Deficiency in School-Age Children. Nutrients 2022; 14:nu14142895. [PMID: 35889856 PMCID: PMC9319427 DOI: 10.3390/nu14142895] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/10/2022] Open
Abstract
Zinc deficiency could lead to a dynamic variation in gut microbial composition and function in animals. However, how zinc deficiency affects the gut microbiome in school-age children remains unclear. The purpose of this study was to profile the dynamic shifts in the gut microbiome of school-age children with zinc deficiency, and to determine whether such shifts are associated with dietary intake. A dietary survey, anthropometric measurements, and serum tests were performed on 177 school-age children, and 67 children were selected to explore the gut microbial community using amplicon sequencing. School-age children suffered from poor dietary diversity and insufficient food and nutrient intake, and 32% of them were zinc deficient. The inflammatory cytokines significantly increased in the zinc deficiency (ZD) group compared to that in the control (CK) group (p < 0.05). There was no difference in beta diversity, while the Shannon index was much higher in the ZD group (p < 0.05). At the genus level, Coprobacter, Acetivibrio, Paraprevotella, and Clostridium_XI were more abundant in the ZD group (p < 0.05). A functional predictive analysis showed that the metabolism of xenobiotics by cytochrome P450 was significantly depleted in the ZD group (p < 0.05). In conclusion, gut microbial diversity was affected by zinc deficiency with some specific bacteria highlighted in the ZD group, which may be used as biomarkers for further clinical diagnosis of zinc deficiency.
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Xu AA, Kennedy LK, Hoffman K, White DL, Kanwal F, El-Serag HB, Petrosino JF, Jiao L. Dietary Fatty Acid Intake and the Colonic Gut Microbiota in Humans. Nutrients 2022; 14:2722. [PMID: 35807903 PMCID: PMC9268849 DOI: 10.3390/nu14132722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
A high-fat diet has been associated with systemic diseases in humans and alterations in gut microbiota in animal studies. However, the influence of dietary fatty acid intake on gut microbiota in humans has not been well studied. In this cross-sectional study, we examined the association between intake of total fatty acids (TFAs), saturated fatty acids (SFAs), trans fatty acids (TrFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), n3-FAs, and n6-FAs, and the community composition and structure of the adherent colonic gut microbiota. We obtained 97 colonic biopsies from 34 participants with endoscopically normal colons. Microbial DNA was used to sequence the 16S rRNA V4 region. The DADA2 and SILVA database were used for amplicon sequence variant assignment. Dietary data were collected using the Block food frequency questionnaire. The biodiversity and the relative abundance of the bacterial taxa by higher vs. lower fat intake were compared using the Mann−Whitney test followed by multivariable negative binomial regression model. False discovery rate−adjusted p-values (q value) < 0.05 indicated statistical significance. The beta diversity of gut bacteria differed significantly by intake of all types of fatty acids. The relative abundance of Sutterella was significantly higher with higher intake of TFAs, MUFAs, PUFAs, and n6-FAs. The relative abundance of Tyzzerella and Fusobacterium was significantly higher with higher intake of SFAs. Tyzzerella was also higher with higher intake of TrFA. These observations were confirmed by multivariate analyses. Dietary fat intake was associated with bacterial composition and structure. Sutterella, Fusobacterium, and Tyzzerella were associated with fatty acid intake.
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Affiliation(s)
- Anthony A. Xu
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
| | - Luke K. Kennedy
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (K.H.); (J.F.P.)
| | - Donna L. White
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
| | - Fasiha Kanwal
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Hashem B. El-Serag
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Joseph F. Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (K.H.); (J.F.P.)
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; (A.A.X.); (L.K.K.); (D.L.W.); (F.K.); (H.B.E.-S.)
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Zhang Y, Chen H, Lu M, Cai J, Lu B, Luo C, Dai M. Habitual Diet Pattern Associations with Gut Microbiome Diversity and Composition: Results from a Chinese Adult Cohort. Nutrients 2022; 14:nu14132639. [PMID: 35807820 PMCID: PMC9268000 DOI: 10.3390/nu14132639] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
The influence of long-term diet on gut microbiota is an active area of investigation. The present work aimed to explore the associations between habitual diet patterns and gut microbiota in a large sample of asymptomatic Chinese adults. The gut microbiome was profiled through the sequencing of the 16S rRNA gene in stool samples from 702 Chinese adults aged 50–75 years who underwent colonoscopies and were diagnosed to be free of colorectal neoplasm. Long-term dietary consumption was assessed through a food-frequency questionnaire. The microbial associations with specific food groups and the posteriori dietary pattern were tested using the Kruskal–Wallis H test, permutational ANOVAs, and multivariate analyses with linear models. The Shannon indexes generally shared similar levels across different food intake frequency groups. Whole grain and vegetable intakes totally explained 1.46% of the microbiota compositional variance. Using the data-driven posteriori approach, a general dietary pattern characterized by lower intakes of refined grains was highlighted to be associated with higher abundances of the genus Anaerostipes and a species of it. We also observed 17 associations between various food group intakes and specific genera and species. For instance, the relative abundances of the genus Weissella and an uncultured species of it were negatively associated with red meat intake. The results of this study support the idea that the usual dietary consumption measured by certain food items or summary indexes is associated with gut microbial features. These results deepen the understanding of complex relationships of diet and gut microbiota, as well as their implications for gut microbiome studies of human chronic diseases.
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Affiliation(s)
- Yuhan Zhang
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
| | - Hongda Chen
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
- Correspondence: (H.C.); (M.D.); Tel.: +86-10-6915-4660 (H.C.); +86-10-6915-4651 (M.D.)
| | - Ming Lu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
| | - Jie Cai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China;
| | - Bin Lu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
| | - Chenyu Luo
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
| | - Min Dai
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.Z.); (M.L.); (B.L.); (C.L.)
- Correspondence: (H.C.); (M.D.); Tel.: +86-10-6915-4660 (H.C.); +86-10-6915-4651 (M.D.)
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Gaundal L, Myhrstad MCW, Rud I, Gjøvaag T, Byfuglien MG, Retterstøl K, Holven KB, Ulven SM, Telle-Hansen VH. Gut microbiota is associated with dietary intake and metabolic markers in healthy individuals. Food Nutr Res 2022; 66:8580. [PMID: 35844956 PMCID: PMC9250133 DOI: 10.29219/fnr.v66.8580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/18/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Background Metabolic diseases have been related to gut microbiota, and new knowledge indicates that diet impacts host metabolism through the gut microbiota. Identifying specific gut bacteria associated with both diet and metabolic risk markers may be a potential strategy for future dietary disease prevention. However, studies investigating the association between the gut microbiota, diet, and metabolic markers in healthy individuals are scarce. Objective We explored the relationship between a panel of gut bacteria, dietary intake, and metabolic and anthropometric markers in healthy adults. Design Forty-nine volunteers were included in this cross-sectional study. Measures of glucose, serum triglyceride, total cholesterol, hemoglobin A1c (HbA1c), blood pressure (BP), and body mass index (BMI) were collected after an overnight fast, in addition to fecal samples for gut microbiota analyzes using a targeted approach with a panel of 48 bacterial DNA probes and assessment of dietary intake by a Food Frequency Questionnaire (FFQ). Correlations between gut bacteria, dietary intake, and metabolic and anthropometric markers were assessed by Pearson’s correlation. Gut bacteria varying according to dietary intake and metabolic markers were assessed by a linear regression model and adjusted for age, sex, and BMI. Results Of the 48 gut bacteria measured, 24 and 16 bacteria correlated significantly with dietary intake and metabolic and/or anthropometric markers, respectively. Gut bacteria including Alistipes, Lactobacillus spp., and Bacteroides stercoris differed according to the intake of the food components, fiber, sodium, saturated fatty acids, and dietary indices, and metabolic markers (BP and total cholesterol) after adjustments. Notably, Bacteroides stercoris correlated positively with the intake of fiber, grain products, and vegetables, and higher Bacteroides stercoris abundance was associated with higher adherence to Healthy Nordic Food Index (HNFI) and lower diastolic BP after adjustment. Conclusion Our findings highlight the relationship between the gut microbiota, diet, and metabolic markers in healthy individuals. Further investigations are needed to address whether these findings are causally linked and whether targeting these gut bacteria can prevent metabolic diseases.
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Affiliation(s)
- Line Gaundal
- Department of Nursing and Health Promotion, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Mari C. W. Myhrstad
- Department of Nursing and Health Promotion, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Ida Rud
- Nofima AS (Norwegian Institute of Food, Fisheries and Aquaculture Research), Ås, Norway
| | - Terje Gjøvaag
- Department of Occupational Therapy, Prosthetics and Orthotics, Oslo Metropolitan University, Oslo, Norway
| | | | - Kjetil Retterstøl
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, Oslo, Norway
- The Norwegian National Advisory Unit on Familial Hypercholesterolemia, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kirsten B. Holven
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, Oslo, Norway
- The Norwegian National Advisory Unit on Familial Hypercholesterolemia, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Stine M. Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, Oslo, Norway
| | - Vibeke H. Telle-Hansen
- Department of Nursing and Health Promotion, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
- Vibeke H. Telle-Hansen, Faculty of Health Sciences, Oslo Metropolitan University, Post box 4, St. Olavsplass, 0130 Oslo, Norway.
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26
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Selvakumar D, Evans D, Coyte KZ, McLaughlin J, Brass A, Hancock L, Cruickshank S. Understanding the development and function of the gut microbiota in health and inflammation. Frontline Gastroenterol 2022; 13:e13-e21. [PMID: 35812026 PMCID: PMC9234741 DOI: 10.1136/flgastro-2022-102119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota is known to play an important role in maintaining gut health through a symbiotic relationship with the host. Altered gut microbiota is a common feature of several diseases of the gastrointestinal tract; however, the causal relationship between microbiota and disease pathogenesis is poorly understood. Necrotising enterocolitis (NEC) and inflammatory bowel disease (IBD) are both severe inflammatory diseases affecting the gastrointestinal tract. Although they affect very different patient populations, with NEC primarily being a disease of prematurity and IBD predominantly affecting adults although children can be affected, they both demonstrate common features of gut microbial dysbiosis and a dysregulated host immune response. By comparing and contrasting the changes in gut microbiota, host immune response and function, we aim to highlight common features in diseases that may seem clinically unrelated. Key areas of interest are the role of pattern recognition receptors in altered recognition and responses to the gut microbiota by the host immune system and the associated dysfunctional gut epithelial barrier. The challenge of identifying causal relationships between microbiota and disease is ever-present; however, considering a disease-agnostic approach may help to identify mechanistic pathways shared across several clinical diseases.
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Affiliation(s)
- Deepak Selvakumar
- Department of Colorectal Surgery, Manchester University NHS Foundation Trust, Manchester, UK,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Dolan Evans
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Katharine Z Coyte
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - John McLaughlin
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK,Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andy Brass
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Laura Hancock
- Department of Colorectal Surgery, Manchester University NHS Foundation Trust, Manchester, UK,Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Sheena Cruickshank
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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Choi Y, Hoops SL, Thoma CJ, Johnson AJ. A Guide to Dietary Pattern-Microbiome Data Integration. J Nutr 2022; 152:1187-1199. [PMID: 35348723 PMCID: PMC9071309 DOI: 10.1093/jn/nxac033] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
The human gut microbiome is linked to metabolic and cardiovascular disease risk. Dietary modulation of the human gut microbiome offers an attractive pathway to manipulate the microbiome to prevent microbiome-related disease. However, this promise has not been realized. The complex system of diet and microbiome interactions is poorly understood. Integrating observational human diet and microbiome data can help researchers and clinicians untangle the complex systems of interactions that predict how the microbiome will change in response to foods. The use of dietary patterns to assess diet-microbiome relations holds promise to identify interesting associations and result in findings that can directly translate into actionable dietary intake recommendations and eating plans. In this article, we first highlight the complexity inherent in both dietary and microbiome data and introduce the approaches generally used to explore diet and microbiome simultaneously in observational studies. Second, we review the food group and dietary pattern-microbiome literature focusing on dietary complexity-moving beyond nutrients. Our review identified a substantial and growing body of literature that explores links between the microbiome and dietary patterns. However, there was very little standardization of dietary collection and assessment methods across studies. The 54 studies identified in this review used ≥7 different methods to assess diet. Coupled with the variation in final dietary parameters calculated from dietary data (e.g., dietary indices, dietary patterns, food groups, etc.), few studies with shared methods and assessment techniques were available for comparison. Third, we highlight the similarities between dietary and microbiome data structures and present the possibility that multivariate and compositional methods, developed initially for microbiome data, could have utility when applied to dietary data. Finally, we summarize the current state of the art for diet-microbiome data integration and highlight ways dietary data could be paired with microbiome data in future studies to improve the detection of diet-microbiome signals.
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Affiliation(s)
- Yuni Choi
- Division of Epidemiology and Community Health, University of Minnesota, School of Public Health, Minneapolis, MN
| | - Susan L Hoops
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, MN
| | - Calvin J Thoma
- BioTechnology Institute, University of Minnesota, Saint Paul, MN
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, University of Minnesota, School of Public Health, Minneapolis, MN
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28
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Idowu S, Bertrand PP, Walduck AK. Homeostasis and Cancer Initiation: Organoids as Models to Study the Initiation of Gastric Cancer. Int J Mol Sci 2022; 23:2790. [PMID: 35269931 PMCID: PMC8911327 DOI: 10.3390/ijms23052790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer represents a significant disease burden worldwide. The factors that initiate cancer are not well understood. Chronic inflammation such as that triggered by H. pylori infection is the most significant cause of gastric cancer. In recent years, organoid cultures developed from human and animal adult stem cells have facilitated great advances in our understanding of gastric homeostasis. Organoid models are now being exploited to investigate the role of host genetics and bacterial factors on proliferation and DNA damage in gastric stem cells. The impact of a chronic inflammatory state on gastric stem cells and the stroma has been less well addressed. This review discusses what we have learned from the use of organoid models to investigate cancer initiation, and highlights questions on the contribution of the microbiota, chronic inflammatory milieu, and stromal cells that can now be addressed by more complex coculture models.
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Affiliation(s)
| | | | - Anna K. Walduck
- STEM College, RMIT University, Melbourne, VIC 3000, Australia; (S.I.); (P.P.B.)
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29
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Rahman SU, Gong H, Mi R, Huang Y, Han X, Chen Z. Chitosan Protects Immunosuppressed Mice Against Cryptosporidium parvum Infection Through TLR4/STAT1 Signaling Pathways and Gut Microbiota Modulation. Front Immunol 2022; 12:784683. [PMID: 35095858 PMCID: PMC8795679 DOI: 10.3389/fimmu.2021.784683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 01/03/2023] Open
Abstract
Cryptosporidium parvum infection is very common in infants, immunocompromised patients, or in young ruminants, and chitosan supplementation exhibits beneficial effects against the infection caused by C. parvum. This study investigated whether chitosan supplementation modulates the gut microbiota and mediates the TLR4/STAT1 signaling pathways and related cytokines to attenuate C. parvum infection in immunosuppressed mice. Immunosuppressed C57BL/6 mice were divided into five treatment groups. The unchallenged mice received a basal diet (control), and three groups of mice challenged with 1 × 106 C. parvum received a basal diet, a diet supplemented with 50 mg/kg/day paromomycin, and 1 mg/kg/day chitosan, and unchallenged mice treated with 1 mg/kg/day chitosan. Chitosan supplementation regulated serum biochemical indices and significantly (p < 0.01) reduced C. parvum oocyst excretion in infected mice treated with chitosan compared with the infected mice that received no treatment. Chitosan-fed infected mice showed significantly (p < 0.01) decreased mRNA expression levels of interferon-gamma (IFN-γ) and tumor necrosis factor-α (TNF-α) compared to infected mice that received no treatment. Chitosan significantly inhibited TLR4 and upregulated STAT1 protein expression (p < 0.01) in C. parvum-infected mice. 16S rRNA sequencing analysis revealed that chitosan supplementation increased the relative abundance of Bacteroidetes/Bacteroides, while that of Proteobacteria, Tenericutes, Defferribacteres, and Firmicutes decreased (p < 0.05). Overall, the findings revealed that chitosan supplementation can ameliorate C. parvum infection by remodeling the composition of the gut microbiota of mice, leading to mediated STAT1/TLR4 up- and downregulation and decreased production of IFN-γ and TNF-α, and these changes resulted in better resolution and control of C. parvum infection.
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Affiliation(s)
- Sajid Ur Rahman
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Haiyan Gong
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Rongsheng Mi
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yan Huang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xiangan Han
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhaoguo Chen
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China. Microbiol Spectr 2022; 10:e0144221. [PMID: 35044201 PMCID: PMC8768838 DOI: 10.1128/spectrum.01442-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacterium longum predominates in the human gut throughout the life span, from birth to old age, and could alter the intestinal microbial population and immune function in the elderly. We investigated the intestinal bacterial diversity in the elderly, and further evaluated the genetic diversity and population structure of B. longum. The results revealed a distinct difference in gut bacterial populations between the elderly from Xiangyang and its neighboring region, Enshi city. A total of 62 bifidobacterial strains were isolated, 30 of which were found to be B. longum. The multilocus sequence typing (MLST) analysis also revealed that 437 B. longum isolates from diverse regions worldwide, including the 30 isolated in this study, could be classified into 341 sequence types (STs). They could be further clustered into 10 clonal complexes and 127 singleton STs, indicating a highly genetic diversity among B. longum isolates. Two putative clone complexes (CCs) containing the isolates from Xiangyang were found to be geographically specific, and a 213-bp recombination fragment was detected. Phylogenetic trees divided these 437 isolates into three lineages, corresponding to the three subspecies of B. longum. It is noteworthy that two isolates from the elderly were identified to be B. longum subsp. suis, while the others were B. longum subsp. longum. Together, our study characterized the intestinal bacterial diversity and evolution of B. longum in the elderly, and it could contribute to further studies on the genotyping and discrimination of B. longum. IMPORTANCEBifidobacterium longum are common inhabitants of the human gut throughout the life span, and have been associated with health-promoting effects, yet little is known about the genotype profile and evolution of these isolates. Our study showed that there was significant difference in gut bacterial community and abundance of B. longum between the elderly from two neighboring cities. Furthermore, the possible geographically specific STs, CCs, and intraspecies recombination fragment were found among the B. longum isolates from elderly.
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Parker J, O'Brien C, Hawrelak J. A narrative review of the role of gastrointestinal dysbiosis in the pathogenesis of polycystic ovary syndrome. Obstet Gynecol Sci 2022; 65:14-28. [PMID: 34958733 PMCID: PMC8784943 DOI: 10.5468/ogs.21185] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Diet-induced gastrointestinal dysbiosis has been hypothesized to play a significant role in stimulating an increase in gastrointestinal permeability and activating systemic inflammation in women with polycystic ovary syndrome (PCOS). We reviewed the current proof-of-concept studies on the proposed mechanism of dysbiosis in the pathogenesis of PCOS. A literature search was performed to identify articles on changes in the intestinal microbiome (dysbiosis) and increased intestinal mucosal permeability involving lipopolysaccharide (LPS), LPS-binding protein (LPS-BP), and zonulin. We also searched for systematic reviews and meta-analyses that synthesized the results of studies on the therapeutic effects of prebiotics, probiotics, or synbiotics in women with PCOS. Our search was confined to human studies between 2012 and 2021 using the PubMed, Scopus, and Cochrane databases. Thirty-one studies met the inclusion criteria (14 microbiota, 1 LPS, 1 LPS-BP, 1 LPS and LPS-BP, 5 zonulin, 9 systematic reviews). Our analysis revealed that most studies reported reduced alpha diversity and dysbiosis in women with PCOS. Preliminary studies suggest that LPS, LPS-BP, and zonulin may be involved in the pathophysiology of increased intestinal permeability. Treatment of PCOS with prebiotics, probiotics, and synbiotics appears to have a range of beneficial effects on metabolic and biochemical profiles. This review highlights the need for continued research into the pathophysiological mechanisms of dysbiosis and the clinical efficacy of prebiotics, probiotics, and synbiotics in women with PCOS.
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Affiliation(s)
- Jim Parker
- School of Medicine, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia
| | - Claire O'Brien
- Faculty of Science and Technology, University of Canberra, Canberra, Australia
| | - Jason Hawrelak
- College of Health and Medicine, University of Tasmania, Tasmania, Australia
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Adeva-Andany MM, Fernández-Fernández C, Carneiro-Freire N, Vila-Altesor M, Ameneiros-Rodríguez E. The differential effect of animal versus vegetable dietary protein on the clinical manifestations of diabetic kidney disease in humans. Clin Nutr ESPEN 2022; 48:21-35. [DOI: 10.1016/j.clnesp.2022.01.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
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Kommentar. DIABETOL STOFFWECHS 2021. [DOI: 10.1055/a-1687-3383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Huang A, Sun L, Lin F, Guo J, Jiang J, Shen B, Chen J. Medical Image Recognition Technology in the Effect of Substituting Soybean Meal for Fish Meal on the Diversity of Intestinal Microflora in Channa argus. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5269169. [PMID: 34868520 PMCID: PMC8639257 DOI: 10.1155/2021/5269169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/22/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Purpose To study the application of medical image recognition technology based on backpropagation neural network (BPNN) in the effect of soybean meal replacing fish meal on intestinal microbial diversity of Channa argus and to evaluate the application value of this intelligent algorithm, Channa argus was fed with different contents of soybean meal instead of fish meal. Methods After intestinal samples were collected and bacteria were isolated, microscopic imaging was performed, and the images were classified and identified. BPNN was constructed to perform denoising, smoothing, and segmentation. Results After BPNN processing, the bacteria were completely separated from the original image background, and the bacteria was in the closed state, which was beneficial to feature extraction and species recognition. If there were 2 hidden layer nodes, the segmentation accuracy of bacterial microscopic images was the highest, up to 97.3%. With the replacement ratio of fish meal increased, the species of intestinal microbiome gradually enriched, and the relative abundance of intestinal microbiome was higher after fish meal was completely replaced by soybean meal (replacement). The intestinal microbial enzyme activities were affected by different fish meal and soybean meal contents in the diet. The glutamate transaminase and adenosine deaminase activities were increased after the replacement and were higher than those before the replacement, with statistically significant differences (P < 0.05). Conclusion Replacement of fish meal with soybean meal has a significant effect on the intestinal flora diversity of Channa argus, and there is a close relationship between them. The image recognition technology based on BPNN has high recognition rate and segmentation accuracy for microbiological microscopic images.
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Affiliation(s)
- Aixia Huang
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Lihui Sun
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Feng Lin
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Jianlin Guo
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Jianhu Jiang
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Binqian Shen
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
| | - Jianming Chen
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China
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Zhang JY, Lo HC, Yang FL, Liu YF, Wu WM, Chou CC. Plant-Based, Antioxidant-Rich Snacks Elevate Plasma Antioxidant Ability and Alter Gut Bacterial Composition in Older Adults. Nutrients 2021; 13:nu13113872. [PMID: 34836127 PMCID: PMC8624639 DOI: 10.3390/nu13113872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Plant-rich diets alleviate oxidative stress and gut dysbiosis and are negatively linked to age-associated chronic disorders. This study examined the effects of consuming plant-based, antioxidant-rich smoothies and sesame seed snacks (PBASS) on antioxidant ability and gut microbial composition in older adults. Healthy and sub-healthy older adults (n = 42, 79.7 ± 8.6 years old) in two senior living facilities were given PBASS for 4 months. Blood and fecal samples were collected from these individuals at the baseline and after 2 and 4 months of PBASS consumption. After 2 months, serum levels of albumin and high-density lipoprotein-cholesterol and the ratio of reduced to oxidized glutathione (GSH/GSSG) had increased significantly and erythrocytic glutathione, GSH/GSSG and superoxide dismutase activity had decreased significantly compared with baseline levels (p < 0.05). After 4 months, red blood cells, hematocrit, serum blood urea nitrogen and erythrocyte glutathione peroxidase activity had decreased significantly, whereas plasma and erythrocyte protein-bound sulfhydryl groups had increased significantly. Furthermore, plasma glutathione and total antioxidant capacity were significantly greater after 2 months and increased further after 4 months of PBASS consumption. The results of next generation sequencing showed that PBASS consumption prompted significant decreases in observed bacterial species, their richness, and the abundance of Actinobacteria and Patescibacteria and increases in Bacteroidetes in feces. Our results suggest that texture-modified, plant-based snacks are useful nutrition support to benefit healthy ageing via the elevation of antioxidant ability and alteration of gut microbiota.
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Affiliation(s)
- Jing-Yao Zhang
- Department of Nutritional Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan; (J.-Y.Z.); (F.L.Y.); (Y.-F.L.); (W.-M.W.)
| | - Hui-Chen Lo
- Department of Nutritional Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan; (J.-Y.Z.); (F.L.Y.); (Y.-F.L.); (W.-M.W.)
- Ph.D. Program in Nutrition and Food Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan
- Correspondence: ; Tel.: +886-2-29052510
| | - Feili Lo Yang
- Department of Nutritional Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan; (J.-Y.Z.); (F.L.Y.); (Y.-F.L.); (W.-M.W.)
- Ph.D. Program in Nutrition and Food Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan
| | - Yi-Fang Liu
- Department of Nutritional Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan; (J.-Y.Z.); (F.L.Y.); (Y.-F.L.); (W.-M.W.)
| | - Wen-Mein Wu
- Department of Nutritional Science, Fu Jen Catholic University, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205, Taiwan; (J.-Y.Z.); (F.L.Y.); (Y.-F.L.); (W.-M.W.)
| | - Chi-Chun Chou
- Department of Otolaryngology, Yonghe Cardinal Tien Hospital, Zhongxing St., Yonghe Dist., New Taipei City 23445, Taiwan;
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Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr 2021; 115:432-443. [PMID: 34617562 PMCID: PMC8827078 DOI: 10.1093/ajcn/nqab332] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Individual diet components and specific dietary regimens have been shown to impact the gut microbiome. OBJECTIVES Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort. METHODS Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants. RESULTS Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P ≤ 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P ≤ 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P ≤ 1.2 × 10-7), which was better explained by diet than health status. CONCLUSIONS We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.
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Affiliation(s)
| | | | - Nicole S Litwin
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | - Diana Gutierrez Lopez
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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Gao J, Guo X, Wei W, Li R, Hu K, Liu X, Jiang W, Liu S, Wang W, Sun H, Wu H, Zhang Y, Gu W, Li Y, Sun C, Han T. The Association of Fried Meat Consumption With the Gut Microbiota and Fecal Metabolites and Its Impact on Glucose Homoeostasis, Intestinal Endotoxin Levels, and Systemic Inflammation: A Randomized Controlled-Feeding Trial. Diabetes Care 2021; 44:1970-1979. [PMID: 34253560 DOI: 10.2337/dc21-0099] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE This randomized controlled-feeding trial aimed to determine the impact of fried meat intake on the gut microbiota and fecal cometabolites and whether such impacts influenced host glucose homoeostasis, intestinal endotoxin levels, and systemic inflammation. RESEARCH DESIGN AND METHODS A total of 117 overweight adults were randomized into two groups. Fifty-nine participants were provided fried meat four times per week, and 58 participants were restricted from fried meat intake, while holding food group and nutrient compositions constant, for 4 weeks. The gut microbiota was analyzed by 16S rRNA sequencing. Glucose and insulin concentrations at 0, 30, 60, and 120 min of an oral glucose tolerance test, fecal microbiota-host cometabolite levels, and intestinal endotoxin and inflammation serum biomarker levels were measured. The area under the curve (AUC) for insulin, insulinogenic index (IGI), and muscle insulin resistance index (MIRI) were calculated. RESULTS The participants who consumed fried meat had lower IGI values than the control subjects, but they had higher MIRI and AUC values of insulin and lipopolysaccharide (LPS), TNF-α, IL-10, and IL-1β levels (P < 0.05). Fried meat intake lowered microbial community richness and decreased Lachnospiraceae and Flavonifractor abundances while increasing Dialister, Dorea, and Veillonella abundances (P FDR <0.05), provoking a significant shift in the fecal cometabolite profile, with lower 3-indolepropionic acid, valeric acid, and butyric acid concentrations and higher carnitine and methylglutaric acid concentrations (P FDR <0.05). Changes in these cometabolite levels were significantly associated with changes in IGI and MIRI values and LPS, FGF21, TNF-α, IL-1β, and IL-10 levels (P < 0.05). CONCLUSIONS Fried meat intake impaired glucose homoeostasis and increased intestinal endotoxin and systemic inflammation levels by influencing the gut microbiota and microbial-host cometabolites.
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Affiliation(s)
- Jian Gao
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xiaoyu Guo
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Wei Wei
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ran Li
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China.,Harbin Center for Disease Control and Prevention, Harbin, China
| | - Ke Hu
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xin Liu
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Wenbo Jiang
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Siyao Liu
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN.,Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
| | - Weiqi Wang
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Hu Sun
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Huanyu Wu
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Yuntao Zhang
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Wenbo Gu
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ying Li
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Harbin Medical University, Ministry of Education, Harbin, China.,NHC Key Laboratory of Cell Translation, Harbin Medical University, Harbin, China
| | - Changhao Sun
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Tianshu Han
- Department of Nutrition and Food Hygiene, National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China .,Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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38
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Qi L. Fried Foods, Gut Microbiota, and Glucose Metabolism. Diabetes Care 2021; 44:1907-1909. [PMID: 34417280 PMCID: PMC8740929 DOI: 10.2337/dci21-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, and Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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Byrd AL, Liu M, Fujimura KE, Lyalina S, Nagarkar DR, Charbit B, Bergstedt J, Patin E, Harrison OJ, Quintana-Murci L, Mellman I, Duffy D, Albert ML. Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. J Exp Med 2021; 218:211527. [PMID: 33175106 PMCID: PMC7664509 DOI: 10.1084/jem.20200606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/20/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022] Open
Abstract
As microbial therapeutics are increasingly being tested in diverse patient populations, it is essential to understand the host and environmental factors influencing the microbiome. Through analysis of 1,359 gut microbiome samples from 946 healthy donors of the Milieu Intérieur cohort, we detail how microbiome composition is associated with host factors, lifestyle parameters, and disease states. Using a genome-based taxonomy, we found biological sex was the strongest driver of community composition. Additionally, bacterial populations shift across decades of life (age 20-69), with Bacteroidota species consistently increased with age while Actinobacteriota species, including Bifidobacterium, decreased. Longitudinal sampling revealed that short-term stability exceeds interindividual differences. By accounting for these factors, we defined global shifts in the microbiomes of patients with non-gastrointestinal tumors compared with healthy donors. Together, these results demonstrated that the microbiome displays predictable variations as a function of sex, age, and disease state. These variations must be considered when designing microbiome-targeted therapies or interpreting differences thought to be linked to pathophysiology or therapeutic response.
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Affiliation(s)
- Allyson L Byrd
- Department of Cancer Immunology, Genentech Inc., San Francisco, CA
| | - Menghan Liu
- Department of Cancer Immunology, Genentech Inc., San Francisco, CA.,Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY
| | - Kei E Fujimura
- Department of Cancer Immunology, Genentech Inc., San Francisco, CA
| | | | | | - Bruno Charbit
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Paris, France
| | - Jacob Bergstedt
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique, Paris, France
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique, Paris, France.,Collège de France, Paris, France
| | - Ira Mellman
- Department of Cancer Immunology, Genentech Inc., San Francisco, CA
| | - Darragh Duffy
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Paris, France.,Translational Immunology Lab, Institut Pasteur, Paris, France
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The role of a Mediterranean diet and physical activity in decreasing age-related inflammation through modulation of the gut microbiota composition. Br J Nutr 2021; 128:1299-1314. [PMID: 34423757 DOI: 10.1017/s0007114521003251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chronic inflammation is known to be a predominant factor in the development of many age-related conditions including CVD, type II diabetes and neurodegenerative diseases. Previous studies have demonstrated that during the ageing process there is an increase in inflammatory biomarkers, which may be partially brought about by detrimental changes in the gut microbiota. The Mediterranean diet (MedDiet) and physical activity (PA) are protective against inflammation and chronic disease, and emerging evidence has shown that these effects may be partially mediated through favourable changes in the gut microbiota. In this review, we have evaluated the published literature on the effect of a MedDiet and PA on the gut microbiota. We also discuss the relationship between the gut microbiota and inflammation with a focus on healthy ageing. While inconsistent study designs make forming definitive conclusions challenging, the current evidence suggests that both a MedDiet and PA are capable of modifying the gut microbiota in a way that is beneficial to host health. For example, the increases in the relative abundance of SCFA producing bacteria that are considered to possess anti-inflammatory properties. Modification of the gut microbiota through a MedDiet and PA presents as a potential method to attenuate age-related increases in inflammation, and additional studies utilising older individuals are needed to fill the knowledge gaps existing in current literature.
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41
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Roselli M, Natella F, Zinno P, Guantario B, Canali R, Schifano E, De Angelis M, Nikoloudaki O, Gobbetti M, Perozzi G, Devirgiliis C. Colonization Ability and Impact on Human Gut Microbiota of Foodborne Microbes From Traditional or Probiotic-Added Fermented Foods: A Systematic Review. Front Nutr 2021; 8:689084. [PMID: 34395494 PMCID: PMC8360115 DOI: 10.3389/fnut.2021.689084] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022] Open
Abstract
A large subset of fermented foods act as vehicles of live environmental microbes, which often contribute food quality assets to the overall diet, such as health-associated microbial metabolites. Foodborne microorganisms also carry the potential to interact with the human gut microbiome via the food chain. However, scientific results describing the microbial flow connecting such different microbiomes as well as their impact on human health, are still fragmented. The aim of this systematic review is to provide a knowledge-base about the scientific literature addressing the connection between foodborne and gut microbiomes, as well as to identify gaps where more research is needed to clarify and map gut microorganisms originating from fermented foods, either traditional or added with probiotics, their possible impact on human gut microbiota composition and to which extent foodborne microbes might be able to colonize the gut environment. An additional aim was also to highlight experimental approaches and study designs which could be better standardized to improve comparative analysis of published datasets. Overall, the results presented in this systematic review suggest that a complex interplay between food and gut microbiota is indeed occurring, although the possible mechanisms for this interaction, as well as how it can impact human health, still remain a puzzling picture. Further research employing standardized and trans-disciplinary approaches aimed at understanding how fermented foods can be tailored to positively influence human gut microbiota and, in turn, host health, are therefore of pivotal importance.
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Affiliation(s)
- Marianna Roselli
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Fausta Natella
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Paola Zinno
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Barbara Guantario
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Raffaella Canali
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Emily Schifano
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Olga Nikoloudaki
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Giuditta Perozzi
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
| | - Chiara Devirgiliis
- Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics), Rome, Italy
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Differences in Gut Microbiome Composition and Antibiotic Resistance Gene Distribution between Chinese and Pakistani University Students from a Common Peer Group. Microorganisms 2021; 9:microorganisms9061152. [PMID: 34072124 PMCID: PMC8229524 DOI: 10.3390/microorganisms9061152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiomes play important functional roles in human health and are also affected by many factors. However, few studies concentrate on gut microbiomes under exercise intervention. Additionally, antibiotic resistance genes (ARGs) carried by gut microbiomes may constantly pose a threat to human health. Here, ARGs and microbiomes of Chinese and Pakistanis participants were investigated using 16S rRNA gene sequencing and high-throughput quantitative PCR techniques. The exercise had no impact on gut microbiomes in the 12 individuals investigated during the observation period, while the different distribution of gut microbiomes was found in distinct nationalities. Overall, the dominant microbial phyla in the participants’ gut were Bacteroidota, Firmicutes and Proteobacteria. Some genera such as Prevotella and Dialister were more abundant in Pakistani participants and some other genera such as Bacteroides and Faecalibacterium were more abundant in Chinese participants. The microbial diversity in Chinese was higher than that in Pakistanis. Furthermore, microbial community structures were also different between Chinese and Pakistanis. For ARGs, the distribution of all detected ARGs is not distinct at each time point. Among these ARGs, floR was distributed differently in Chinese and Pakistani participants, and some ARGs such as tetQ and sul2 are positively correlated with several dominant microbiomes, particularly Bacteroidota and Firmicutes bacteria that did not fluctuate over time.
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43
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Low DY, Hejndorf S, Tharmabalan RT, Poppema S, Pettersson S. Regional Diets Targeting Gut Microbial Dynamics to Support Prolonged Healthspan. Front Microbiol 2021; 12:659465. [PMID: 33995322 PMCID: PMC8116520 DOI: 10.3389/fmicb.2021.659465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/29/2021] [Indexed: 01/16/2023] Open
Abstract
In the last 150 years, we have seen a significant increase in average life expectancy, associated with a shift from infectious to non-communicable diseases. The rising incidence of these diseases, for which age is often the largest risk factor, highlights the need for contemporary societies to improve healthy ageing for their growing silver generations. As ageing is an inevitable, non-reversing and highly individualised process, we need to better understand how non-genetic factors like diet choices and commensal gut microbes can modulate the biology of ageing. In this review, we discuss how geographical and ethnic variations influence habitual dietary patterns, nutrient structure, and gut microbial profiles with potential impact on the human healthspan. Several gut microbial genera have been associated with healthy elderly populations but are highly variable across populations. It seems unlikely that a universal pro-longevity gut microbiome exists. Rather, the optimal microbiome appears to be conditional on the microbial functionality acting on regional- and ethnicity-specific trends driven by cultural food context. We also highlight dietary and microbial factors that have been observed to elicit individual and clustered biological responses. Finally, we identify next generation avenues to modify otherwise fixed host functions and the individual ageing trajectory by manipulating the malleable gut microbiome with regionally adapted, personalised food intervention regimens targeted at prolonging human healthspan.
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Affiliation(s)
- Dorrain Yanwen Low
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sophia Hejndorf
- Department of Odontology, Karolinska Institutet, Solna, Sweden
| | | | - Sibrandes Poppema
- School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia
| | - Sven Pettersson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Odontology, Karolinska Institutet, Solna, Sweden
- School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia
- National Neuroscience Institute, Singapore, Singapore
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Brostow DP, Stamper CE, Stanislawski MA, Stearns-Yoder KA, Schneider A, Postolache TT, Forster JE, Hoisington AJ, Lowry CA, Brenner LA. Dietary habits and the gut microbiota in military Veterans: results from the United States-Veteran Microbiome Project (US-VMP). GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2021; 2:e1. [PMID: 39296320 PMCID: PMC11406408 DOI: 10.1017/gmb.2021.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 09/21/2024]
Abstract
Dietary patterns influence gut microbiota composition. To date, there has not been an assessment of diet and gut microbiota in Veterans, who have a history of unique environmental exposures, including military deployment, that may influence associations between diet and gut microbiota. Our aim was to characterise Veteran habitual dietary intake and quality, and to evaluate correlations between diet and gut microbiota. We administered Food Frequency Questionnaires (FFQs) and collected stool samples from 330 Veterans. FFQ data were used to generate Healthy Eating Indices (HEI) of dietary quality. Exploratory factor analysis was used to identify two dietary patterns we defined as "Western" and "Prudent." Stool samples underwent 16S rRNA gene sequencing, and the resulting data were used to evaluate associations with dietary variables/indices. Analyses included linear regression of α-diversity, constrained analysis of principal coordinates of β-diversity, and multivariate association with linear models and Analysis of Composition of Microbiomes analyses of dietary factors and phylum- and genus-level taxa. There were no significant associations between dietary patterns or factors and α- or β-diversity. At the phylum level, increasing HEI scores were inversely associated with relative abundance of Actinobacteria, and added sugar was inversely associated with abundance of Verrucomicrobia. Veterans largely consumed a Western-style diet, characterised by poor adherence to nutritional guidelines.
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Affiliation(s)
- Diana P Brostow
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
| | - Christopher E Stamper
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
| | - Maggie A Stanislawski
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
| | - Kelly A Stearns-Yoder
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
| | - Alexandra Schneider
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
| | - Teodor T Postolache
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
- Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Veterans Affairs, VISN 5 MIRECC, Baltimore, MD, USA
| | - Jeri E Forster
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
| | - Andrew J Hoisington
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
- Department of Systems Engineering & Management, Air Force Institute of Technology, Wright-Patterson AFB, OH, USA
| | - Christopher A Lowry
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, USA
- Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Brenner
- VA Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO, USA
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Tap J, Störsrud S, Le Nevé B, Cotillard A, Pons N, Doré J, Öhman L, Törnblom H, Derrien M, Simrén M. Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome. MICROBIOME 2021; 9:74. [PMID: 33771219 PMCID: PMC8004395 DOI: 10.1186/s40168-021-01018-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/02/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms. METHODS Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. RESULTS We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism. CONCLUSIONS Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms. TRIAL REGISTRATION This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010. Video abstract.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Palaiseau, France.
| | - Stine Störsrud
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Lena Öhman
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology and Microbiology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | | | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden.
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, NC, USA.
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Shuai M, Zuo LSY, Miao Z, Gou W, Xu F, Jiang Z, Ling CW, Fu Y, Xiong F, Chen YM, Zheng JS. Multi-omics analyses reveal relationships among dairy consumption, gut microbiota and cardiometabolic health. EBioMedicine 2021; 66:103284. [PMID: 33752125 PMCID: PMC7985282 DOI: 10.1016/j.ebiom.2021.103284] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Little is known about the interplay among dairy intake, gut microbiota and cardiometabolic health in human prospective cohort studies. METHODS The present study included 1780 participants from the Guangzhou Nutrition and Health Study. We examined the prospective association between habitual dairy consumption (total dairy, milk, yogurt) and gut microbial composition using linear regression after adjusting for socio-demographic, lifestyle and dietary factors. The cross-sectional association of dairy-associated microbial features with cardiometabolic risk factors was examined with a linear regression model, adjusting for potential confounders. Serum metabolomic profiles were analyzed by partial correlation analysis. FINDINGS There was a significant overall difference in gut microbial community structure (β-diversity) comparing the highest with the lowest category for each of total dairy, milk and yogurt (P < 0.05). We observed that dairy-associated microbes and α-diversity indices were inversely associated with blood triglycerides, while positively associated with high-density lipoprotein cholesterol. A follow-up metabolomics analysis revealed the association of targeted serum metabolites with dairy-microbial features and cardiometabolic traits. Specifically, 2-hydroxy-3-methylbutyric acid, 2-hydroxybutyric acid and L-alanine were inversely associated with dairy-microbial score, while positively associated with triglycerides (FDR-corrected P < 0.1). INTERPRETATION Dairy consumption is associated with the gut microbial composition and a higher α-diversity, which provides new insights into the understanding of dairy-gut microbiota interactions and their relationship with cardiometabolic health. FUNDING This work was supported by the National Natural Science Foundation of China, Zhejiang Ten-thousand Talents Program, Westlake University and the 5010 Program for Clinical Researches of the Sun Yat-sen University.
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Affiliation(s)
- Menglei Shuai
- School of Life Sciences, Fudan University, Shanghai, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Luo-Shi-Yuan Zuo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zelei Miao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wanglong Gou
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zengliang Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chu-Wen Ling
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Feng Xiong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Ming Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Ju-Sheng Zheng
- School of Life Sciences, Fudan University, Shanghai, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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47
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Han S, Lu Y, Xie J, Fei Y, Zheng G, Wang Z, Liu J, Lv L, Ling Z, Berglund B, Yao M, Li L. Probiotic Gastrointestinal Transit and Colonization After Oral Administration: A Long Journey. Front Cell Infect Microbiol 2021; 11:609722. [PMID: 33791234 PMCID: PMC8006270 DOI: 10.3389/fcimb.2021.609722] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Orally administered probiotics encounter various challenges on their journey through the mouth, stomach, intestine and colon. The health benefits of probiotics are diminished mainly due to the substantial reduction of viable probiotic bacteria under the harsh conditions in the gastrointestinal tract and the colonization resistance caused by commensal bacteria. In this review, we illustrate the factors affecting probiotic viability and their mucoadhesive properties through their journey in the gastrointestinal tract, including a discussion on various mucosadhesion-related proteins on the probiotic cell surface which facilitate colonization.
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Affiliation(s)
- Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanmeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaojiao Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqiu Fei
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziyuan Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing, China
| | - Jie Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Björn Berglund
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mingfei Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Associations between untargeted plasma metabolomic signatures and gut microbiota composition in the Milieu Intérieur population of healthy adults. Br J Nutr 2020; 126:982-992. [PMID: 33298217 DOI: 10.1017/s0007114520004870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Host-microbial co-metabolism products are being increasingly recognised to play important roles in physiological processes. However, studies undertaking a comprehensive approach to consider host-microbial metabolic relationships remain scarce. Metabolomic analysis yielding detailed information regarding metabolites found in a given biological compartment holds promise for such an approach. This work aimed to explore the associations between host plasma metabolomic signatures and gut microbiota composition in healthy adults of the Milieu Intérieur study. For 846 subjects, gut microbiota composition was profiled through sequencing of the 16S rRNA gene in stools. Metabolomic signatures were generated through proton NMR analysis of plasma. The associations between metabolomic variables and α- and β-diversity indexes and relative taxa abundances were tested using multi-adjusted partial Spearman correlations, permutational ANOVA and multivariate associations with linear models, respectively. A multiple testing correction was applied (Benjamini-Hochberg, 10 % false discovery rate). Microbial richness was negatively associated with lipid-related signals and positively associated with amino acids, choline, creatinine, glucose and citrate (-0·133 ≤ Spearman's ρ ≤ 0·126). Specific associations between metabolomic signals and abundances of taxa were detected (twenty-five at the genus level and nineteen at the species level): notably, numerous associations were observed for creatinine (positively associated with eleven species and negatively associated with Faecalibacterium prausnitzii). This large-scale population-based study highlights metabolites associated with gut microbial features and provides new insights into the understanding of complex host-gut microbiota metabolic relationships. In particular, our results support the implication of a 'gut-kidney axis'. More studies providing a detailed exploration of these complex interactions and their implications for host health are needed.
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Dietary fruit and vegetable intake, gut microbiota, and type 2 diabetes: results from two large human cohort studies. BMC Med 2020; 18:371. [PMID: 33267887 PMCID: PMC7712977 DOI: 10.1186/s12916-020-01842-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little is known about the inter-relationship among fruit and vegetable intake, gut microbiota and metabolites, and type 2 diabetes (T2D) in human prospective cohort study. The aim of the present study was to investigate the prospective association of fruit and vegetable intake with human gut microbiota and to examine the relationship between fruit and vegetable-related gut microbiota and their related metabolites with type 2 diabetes (T2D) risk. METHODS This study included 1879 middle-age elderly Chinese adults from Guangzhou Nutrition and Health Study (GNHS). Baseline dietary information was collected using a validated food frequency questionnaire (2008-2013). Fecal samples were collected at follow-up (2015-2019) and analyzed for 16S rRNA sequencing and targeted fecal metabolomics. Blood samples were collected and analyzed for glucose, insulin, and glycated hemoglobin. We used multivariable linear regression and logistic regression models to investigate the prospective associations of fruit and vegetable intake with gut microbiota and the association of the identified gut microbiota (fruit/vegetable-microbiota index) and their related fecal metabolites with T2D risk, respectively. Replications were performed in an independent cohort involving 6626 participants. RESULTS In the GNHS, dietary fruit intake, but not vegetable, was prospectively associated with gut microbiota diversity and composition. The fruit-microbiota index (FMI, created from 31 identified microbial features) was positively associated with fruit intake (p < 0.001) and inversely associated with T2D risk (odds ratio (OR) 0.83, 95%CI 0.71-0.97). The FMI-fruit association (p = 0.003) and the FMI-T2D association (OR 0.90, 95%CI 0.84-0.97) were both successfully replicated in the independent cohort. The FMI-positive associated metabolite sebacic acid was inversely associated with T2D risk (OR 0.67, 95%CI 0.51-0.86). The FMI-negative associated metabolites cholic acid (OR 1.35, 95%CI 1.13-1.62), 3-dehydrocholic acid (OR 1.30, 95%CI 1.09-1.54), oleylcarnitine (OR 1.77, 95%CI 1.45-2.20), linoleylcarnitine (OR 1.66, 95%CI 1.37-2.05), palmitoylcarnitine (OR 1.62, 95%CI 1.33-2.02), and 2-hydroglutaric acid (OR 1.47, 95%CI 1.25-1.72) were positively associated with T2D risk. CONCLUSIONS Higher fruit intake-associated gut microbiota and metabolic alteration were associated with a lower risk of T2D, supporting the public dietary recommendation of adopting high fruit intake for the T2D prevention.
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Associations between Pro- and Anti-Inflammatory Gastro-Intestinal Microbiota, Diet, and Cognitive Functioning in Dutch Healthy Older Adults: The NU-AGE Study. Nutrients 2020; 12:nu12113471. [PMID: 33198235 PMCID: PMC7697493 DOI: 10.3390/nu12113471] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022] Open
Abstract
Dietary modulation of the gastro-intestinal microbiota is a potential target in improving healthy ageing and age-related functional outcomes, including cognitive decline. We explored the association between diet, gastro-intestinal microbiota and cognition in Dutch healthy older adults of the ‘New dietary strategies addressing the specific needs of the elderly population for healthy aging in Europe’ (NU-AGE) study. The microbiota profile of 452 fecal samples from 226 subjects was determined using a 16S ribosomal RNA gene-targeted microarray. Dietary intake was assessed by 7-day food records. Cognitive functioning was measured with an extensive cognitive test battery. We observed a dietary and microbial pro- to anti-inflammatory gradient associated with diets richer in animal- or plant-based foods. Fresh fruits, nuts, seeds and peanuts, red and processed meat and grain products were most strongly associated to microbiota composition. Plant-rich diets containing fresh fruits, nuts, seeds and peanuts were positively correlated with alpha-diversity, various taxa from the Bacteroidetes phylum and anti-inflammatory species, including those related to Faecalibacterium prausnitzii and Eubacterium rectale and E. biforme. Animal product-rich diets associated with pro-inflammatory species, including those related to Ruminococcus gnavus and Collinsella spp.. Cognition was neither associated with microbiota composition nor alpha-diversity. In conclusion, diets richer in animal- and plant-based foods were related to a pro- and anti-inflammatory microbial profile, while cognition was associated with neither.
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