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Houngbédji M, Jespersen JS, Wilfrid Padonou S, Jespersen L. Cereal-based fermented foods as microbiota-directed products for improved child nutrition and health in sub-Saharan Africa. Crit Rev Food Sci Nutr 2024:1-22. [PMID: 38973125 DOI: 10.1080/10408398.2024.2365342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Several strategies, programs and policies have long been developed and implemented to alleviate child malnutrition in sub-Saharan African countries. However, stunting and wasting still persist at an alarming rate, suggesting that alternative strategies are needed to induce faster progress toward the 2030 SDGs targets of reducing malnutrition. Gut microbiota-directed intervention is now being recognized as an unconventional powerful approach to mitigate malnutrition and improve overall child health. In an African setting, manufactured probiotic and synbiotic foods or supplements may not be successful owing to the non-affordability and high attachment of African populations to their food tradition. This review analyses the potential of indigenous fermented cereal-based products including porridges, doughs, beverages, bread- and yoghurt-like products, to be used as microbiota-directed foods for over 6 months children. The discussion includes relevant strategies to effectively enhance the beneficial effects of these products on gut microbiota composition for improved child health and nutrition in sub-Saharan Africa. Characterization of probiotic features and general safety of food processing in sub-Saharan Africa as well as randomized clinical studies are still lacking to fully ascertain the health effects and suitability of these fermented foods in preventing and treating child malnutrition and diarrhea.
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Affiliation(s)
- Marcel Houngbédji
- Laboratoire de Sciences et Technologies des Aliments, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Jéricho, Cotonou, Benin
- Laboratoire de Sciences et Technologie des Aliments, des Bioressources et de Nutrition Humaine, Université Nationale d'Agriculture, Sakété, Bénin
| | | | - Sègla Wilfrid Padonou
- Laboratoire de Sciences et Technologies des Aliments, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Jéricho, Cotonou, Benin
- Laboratoire de Sciences et Technologie des Aliments, des Bioressources et de Nutrition Humaine, Université Nationale d'Agriculture, Sakété, Bénin
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, Copenhagen, Frederiksberg C, Denmark
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Seyoum Y, Greffeuille V, Kouadio DKD, Kuong K, Turpin W, M'Rabt R, Chochois V, Fortin S, Perignon M, Fiorentino M, Berger J, Burja K, Ponce MC, Chamnan C, Wieringa FT, Humblot C. Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice. Nat Commun 2024; 15:5204. [PMID: 38890302 PMCID: PMC11189458 DOI: 10.1038/s41467-024-49093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Faecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. Here, in a double-blinded cluster-randomized controlled trial on 380 Cambodian schoolchildren, we characterize the impact of six months consumption of two types of rice fortified with different levels of vitamins and minerals on pre-specified outcomes. We investigate the association between the faecal microbiota (16SrRNA sequencing) and age, sex, nutritional status (underweight, stunting), micronutrient status (iron, zinc and vitamin A deficiencies, anaemia, iron deficient anaemia, hemoglobinopathy), inflammation (systemic, gut), and parasitic infection. We show that the faecal microbiota is characterised by a surprisingly high proportion of Lactobacillaceae. We discover that deficiencies in specific micronutrients, such as iron and vitamin A, correlate with particular microbiota profiles, whereas zinc deficiency shows no such association. The nutritional intervention with the two rice treatments impacts both the composition and functions predicted from compositional analysis in different ways. (ClinicalTrials.gov (Identifier: NCT01706419)).
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Affiliation(s)
- Yohannes Seyoum
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Valérie Greffeuille
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Dorgeles Kouakou Dje Kouadio
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Khov Kuong
- Department of Fisheries Post-Harvest Technologies and Quality Control, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Williams Turpin
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
- Division of Gastroenterology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Rachida M'Rabt
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Vincent Chochois
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Sonia Fortin
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Marlène Perignon
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- MoISA, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Marion Fiorentino
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- SESSTIM, INSERM, IRD, Aix Marseille Univ, Marseille, France
| | - Jacques Berger
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Kurt Burja
- United Nations World Food Programme, Phnom Penh, Cambodia
| | - Maiza Campos Ponce
- Section Infectious Diseases, department of Health Sciences, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Chhoun Chamnan
- Department of Fisheries Post-Harvest Technologies and Quality Control, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Frank T Wieringa
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Christèle Humblot
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France.
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3
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Chibuye M, Mende DR, Spijker R, Simuyandi M, Luchen CC, Bosomprah S, Chilengi R, Schultsz C, Harris VC. Systematic review of associations between gut microbiome composition and stunting in under-five children. NPJ Biofilms Microbiomes 2024; 10:46. [PMID: 38782939 PMCID: PMC11116508 DOI: 10.1038/s41522-024-00517-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.
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Affiliation(s)
- Mwelwa Chibuye
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel R Mende
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rene Spijker
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michelo Simuyandi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Chaluma C Luchen
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Samuel Bosomprah
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biostatistics, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - Roma Chilengi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- The Zambia National Public Health Institute (ZNPHI), Lusaka, Zambia
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Vanessa C Harris
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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Olteanu G, Ciucă-Pană MA, Busnatu ȘS, Lupuliasa D, Neacșu SM, Mititelu M, Musuc AM, Ioniță-Mîndrican CB, Boroghină SC. Unraveling the Microbiome-Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications. Int J Mol Sci 2024; 25:5561. [PMID: 38791599 PMCID: PMC11122276 DOI: 10.3390/ijms25105561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host-microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions.
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Affiliation(s)
- Gabriel Olteanu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Maria-Alexandra Ciucă-Pană
- Department of Cardiology, Carol Davila University of Medicine and Pharmacy, Bagdasar-Arseni Emergency Hospital, 050474 Bucharest, Romania;
| | - Ștefan Sebastian Busnatu
- Department of Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Dumitru Lupuliasa
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Sorinel Marius Neacșu
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Magdalena Mititelu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Adina Magdalena Musuc
- Institute of Physical Chemistry—Ilie Murgulescu, Romanian Academy, 060021 Bucharest, Romania
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Toxicology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania;
| | - Steluța Constanța Boroghină
- Department of Complementary Sciences, History of Medicine and Medical Culture, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
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Shama T, O’Sullivan JM, Rahman N, Kakon SH, Tofail F, Hossain MI, Zeilani M, Haque R, Gluckman P, Forrester T, Nelson CA. Multidimensional evaluation of the early emergence of executive function and development in Bangladeshi children using nutritional and psychosocial intervention: A randomized controlled trial protocol. PLoS One 2024; 19:e0296529. [PMID: 38489293 PMCID: PMC10942035 DOI: 10.1371/journal.pone.0296529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
INTRODUCTION Reversing malnutrition-induced impairment of cognition and emotional regulation is a critical global gap. We hypothesize that brain-targeted micronutrient supplemented nutritional rehabilitation in children with moderate acute malnutrition, followed by 2 years micronutrient supplementation will impact on the cognition and emotion regulation of these children. METHODS The primary outcome of this prospective, randomized controlled trial is to study the development of executive functions (EFs) and emotion regulation (ER) in this cohort. Moderate acute malnourished (MAM; WLZ/WHZ <-2 and ≥-3 z-score, and/or 11.5 cm ≤ MUAC < 12.5cm; n = 140)children aged around one year (11m-13m) in Mirpur, Dhaka, Bangladesh will be randomized (1:1) to receive either locally produced Ready to Use Supplementary Food (RUSF) or Enhanced Ready to Use Supplementary Food (E-RUSF) until anthropometric recovery (WLZ/WHZ > -1SD), or for 3 months after enrollment (whichever is earlier). The randomized MAMs groups will be given either Small Quantity Lipid Based Nutrient Supplement (SQLNS) or Enhanced Small Quantity Lipid Based Nutrient Supplement (E-SQLNS), respectively until the end of the 2-year follow up period. Standard psychosocial stimulation will be provided to the MAMs intervention groups. Biological samples will be collected, anthropometric and neurocognitive assessments will be performed at 2 (22m-26m) and 3 (34m-38m) years of age. Two control groups will be recruited: 1), non-malnourished one-year (11m-13m) old children (WLZ/WHZ score>-1SD; n = 70); and 2) three-year (34m-38m) old children (n = 70) with untreated MAM (WHZ <-2 and ≥-3 z-score, and/or 11.5≤MUAC<12.5 cm). The 3-year-old MAM reference group will be assessed once and provided with 2 months of nutritional rehabilitation support (RUSF Nutriset's Plumpy'Sup™).
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Affiliation(s)
- Talat Shama
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Justin M. O’Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Navin Rahman
- Laboratories of Cognitive Neuroscience, Department of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Shahria H. Kakon
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Fahmida Tofail
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Md Iqbal Hossain
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Mamane Zeilani
- Department of External Research and Nutrition Strategy, Nutriset SAS, Malaunay, France
| | - Rashidul Haque
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Peter Gluckman
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Terrence Forrester
- Faculty of Medical Sciences, UWI Solutions for Developing Countries, The University of the West Indies (UWI), Kingston, Jamaica
| | - Charles A. Nelson
- Laboratories of Cognitive Neuroscience, Department of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Graduate School of Education, Cambridge, Massachusetts, United States of America
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Mehta NH, Huey SL, Kuriyan R, Peña-Rosas JP, Finkelstein JL, Kashyap S, Mehta S. Potential Mechanisms of Precision Nutrition-Based Interventions for Managing Obesity. Adv Nutr 2024; 15:100186. [PMID: 38316343 PMCID: PMC10914563 DOI: 10.1016/j.advnut.2024.100186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
Precision nutrition (PN) considers multiple individual-level and environmental characteristics or variables to better inform dietary strategies and interventions for optimizing health, including managing obesity and metabolic disorders. Here, we review the evidence on potential mechanisms-including ones to identify individuals most likely to respond-that can be leveraged in the development of PN interventions addressing obesity. We conducted a review of the literature and included laboratory, animal, and human studies evaluating biochemical and genetic data, completed and ongoing clinical trials, and public programs in this review. Our analysis describes the potential mechanisms related to 6 domains including genetic predisposition, circadian rhythms, physical activity and sedentary behavior, metabolomics, the gut microbiome, and behavioral and socioeconomic characteristics, i.e., the factors that can be leveraged to design PN-based interventions to prevent and treat obesity-related outcomes such as weight loss or metabolic health as laid out by the NIH 2030 Strategic Plan for Nutrition Research. For example, single nucleotide polymorphisms can modify responses to certain dietary interventions, and epigenetic modulation of obesity risk via physical activity patterns and macronutrient intake have also been demonstrated. Additionally, we identified limitations including questions of equitable implementation across a limited number of clinical trials. These include the limited ability of current PN interventions to address systemic influences such as supply chains and food distribution, healthcare systems, racial or cultural inequities, and economic disparities, particularly when designing and implementing PN interventions in low- and middle-income communities. PN has the potential to help manage obesity by addressing intra- and inter-individual variation as well as context, as opposed to "one-size fits all" approaches though there is limited clinical trial evidence to date.
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Affiliation(s)
- Neel H Mehta
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Samantha L Huey
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Center for Precision Nutrition and Health, Cornell University, Ithaca, NY, United States
| | - Rebecca Kuriyan
- Division of Nutrition, St. John's Research Institute, Bengaluru, Karnataka, India
| | - Juan Pablo Peña-Rosas
- Global Initiatives, The Department of Nutrition and Food Safety, World Health Organization, Geneva, Switzerland
| | - Julia L Finkelstein
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Center for Precision Nutrition and Health, Cornell University, Ithaca, NY, United States; Division of Nutrition, St. John's Research Institute, Bengaluru, Karnataka, India
| | - Sangeeta Kashyap
- Division of Endocrinology, Diabetes and Metabolism, Weill Cornell Medicine New York Presbyterian, New York, NY, United States
| | - Saurabh Mehta
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Center for Precision Nutrition and Health, Cornell University, Ithaca, NY, United States; Division of Medical Informatics, St. John's Research Institute, Bengaluru, Karnataka, India.
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Vresk L, Flanagan M, Daniel AI, Potani I, Bourdon C, Spiegel-Feld C, Thind MK, Farooqui A, Ling C, Miraglia E, Hu G, Wen B, Zlotkin S, James P, McGrath M, Bandsma RHJ. Micronutrient status in children aged 6-59 months with severe wasting and/or nutritional edema: implications for nutritional rehabilitation formulations. Nutr Rev 2024:nuad165. [PMID: 38350491 DOI: 10.1093/nutrit/nuad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Undernutrition remains a global struggle and is associated with almost 45% of deaths in children younger than 5 years. Despite advances in management of severe wasting (though less so for nutritional edema), full and sustained recovery remains elusive. Children with severe wasting and/or nutritional edema (also commonly referred to as severe acute malnutrition and part of the umbrella term "severe malnutrition") continue to have a high mortality rate. This suggests a likely multifactorial etiology that may include micronutrient deficiency. Micronutrients are currently provided in therapeutic foods at levels based on expert opinion, with few supportive studies of high quality having been conducted. This narrative review looks at the knowledge base on micronutrient deficiencies in children aged 6-59 months who have severe wasting and/or nutritional edema, in addition to highlighting areas where further research is warranted (See "Future Directions" section).
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Affiliation(s)
- Laura Vresk
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mary Flanagan
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Allison I Daniel
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Isabel Potani
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Celine Bourdon
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carolyn Spiegel-Feld
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehakpreet K Thind
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amber Farooqui
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Catriona Ling
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emiliano Miraglia
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Guanlan Hu
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bijun Wen
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stanley Zlotkin
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Philip James
- Emergency Nutrition Network, Oxford, United Kingdom
| | | | - Robert H J Bandsma
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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8
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Ye Q, Sun S, Deng J, Chen X, Zhang J, Lin S, Du H, Gao J, Zou X, Lin X, Cai Y, Lu Z. Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder. Sci Rep 2023; 13:20253. [PMID: 37985845 PMCID: PMC10661725 DOI: 10.1038/s41598-023-47760-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3-6 and 7-12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759.
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Affiliation(s)
- Qina Ye
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Shaodan Sun
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Jian Deng
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Xiaogang Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Jing Zhang
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Suihua Lin
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Hongxuan Du
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Jinxiong Gao
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Xiaoyin Zou
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Xiaoling Lin
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Yawen Cai
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Zhuoming Lu
- Department of Traditional Chinese Medicine, Guangzhou Women and Children Medical Center, No. 9 Jinsui Road, Guangzhou, 510623, China.
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9
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Wan X, Li J, Ao M, McLaughlin RW, Fan F, Wang D, Zheng J. The intestinal microbiota of a Risso's dolphin (Grampus griseus): possible relationships with starvation raised by macro-plastic ingestion. Int Microbiol 2023; 26:1001-1007. [PMID: 37059916 PMCID: PMC10104690 DOI: 10.1007/s10123-023-00355-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Ingesting marine plastics is increasingly common in cetaceans, but little is known about their potential effects. Here, by utilizing 16S rRNA gene sequencing, we profiled the intestinal bacterial communities of a stranded Risso's dolphin (Grampus griseus) which died because of the ingestion of rubber gloves. In this study, we explored the potential relationships between starvation raised by plastic ingestion with the dolphin gut microbiota. Our results showed significant differences in bacterial diversity and composition among the different anatomical areas along the intestinal tract, which may be related to the intestinal emptying process under starvation. In addition, the intestinal bacterial composition of the Risso's dolphin showed both similarity and divergence to that of other toothed whales, suggesting potential roles of both host phylogeny and habitat shaping of the cetacean intestinal microbiome. Perhaps, the microbiota is reflecting a potentially disordered intestinal microbial profile caused by the ingestion of macro-plastics which led to starvation. Moreover, two operational taxonomic units (0.17% of the total reads) affiliated with Actinobacillus and Acinetobacter lwoffii were detected along the intestinal tract. These bacterial species may cause infections in immunocompromised dolphins which are malnourished. This preliminary study profiles the intestinal microbiota of a Risso's dolphin, and provides an additional understanding of the potential relationships between starvation raised by ingesting macro-plastics with cetacean gut microbiota.
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Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jia Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Mengxue Ao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | | | - Fei Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- National Aquatic Biological Resource Center, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Huang Y, Tang J, Cai Z, Qi Y, Jiang S, Ma T, Yue Y, Huang F, Yang H, Ma Y. Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection. Heliyon 2023; 9:e22124. [PMID: 38045157 PMCID: PMC10692819 DOI: 10.1016/j.heliyon.2023.e22124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 10/24/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023] Open
Abstract
Objectives To study the characteristics of intestinal microbiota at different stages of Mycobacterium tuberculosis infection. Methods Fecal samples of 19 active tuberculosis (ATB) patients, 21 latent tuberculosis infection (LTBI) individuals, and 20 healthy controls (HC) were collected. Gut microbiota of all the participants were analyzed by 16S rDNA sequencing. Clinical information of ATB patients was also collected and analyzed. Results Both ATB and LTBI groups showed significant decreases in microbial diversity and decline of Clostridia. For ATB patients, bacteria within phylum Proteobacteria increased. While for LTBI individuals, genera Prevotella and Rosburia enriched. The abundance of Faecalibacterium, Clostridia and Gammaproteobacteria has the potential to diagnose ATB, with the area under the curve (AUC) of 0.808, 0.784 and 0.717. And Prevotella and Rosburia has the potential to diagnose LTBI, with the AUC of 0.689 and 0.689. Notably, in ATB patients, the relative abundance of Blautia was negatively correlated with the proportions of peripheral T cells and CD8+T cells. And serum direct bilirubin was positively correlated with Bacteroidales, while negatively correlated with Clostridiales in ATB patients. Conclusions The specifically changed bacteria are promising markers for ATB and LTBI diagnosis. Some gut bacteria contribute to anti-MTB immunity through interactions with T cells and bilirubin.
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Affiliation(s)
- Yuan Huang
- Department of Clinical Laboratory, Air Force Medical Center, Beijing, 100142, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Jinhua Tang
- Department of Clinical Laboratory, Air Force Medical Center, Beijing, 100142, China
| | - Zheng Cai
- Department of Clinical Laboratory, Air Force Medical Center, Beijing, 100142, China
| | - Yun Qi
- Department of Gynecology & Pediatrics, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Shen Jiang
- Department of Gynecology & Pediatrics, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Tingting Ma
- Department of Gynecology & Pediatrics, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Ying Yue
- Department of Gynecology & Pediatrics, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Fang Huang
- Department of Clinical Laboratory, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Han Yang
- Department of Clinical Laboratory, Xi'an Chest Hospital, Xi'an, Shaanxi Province, 710100, China
| | - Yueyun Ma
- Department of Clinical Laboratory, Air Force Medical Center, Beijing, 100142, China
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11
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Wen B, Farooqui A, Bourdon C, Tarafdar N, Ngari M, Chimwezi E, Thitiri J, Mwalekwa L, Walson JL, Voskuijl W, Berkley JA, Bandsma RHJ. Intestinal disturbances associated with mortality of children with complicated severe malnutrition. COMMUNICATIONS MEDICINE 2023; 3:128. [PMID: 37773543 PMCID: PMC10541881 DOI: 10.1038/s43856-023-00355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Children admitted to hospital with complicated severe malnutrition (CSM) have high mortality despite compliance with standard WHO management guidelines. Limited data suggests a relationship between intestinal dysfunction and poor prognosis in CSM, but this has not been explicitly studied. This study aimed to evaluate the role of intestinal disturbances in CSM mortality. METHODS A case-control study nested within a randomized control trial was conducted among children hospitalized with CSM in Kenya and Malawi. Children who died (cases, n = 68) were compared with those who were discharged, propensity matched to the cases on age, HIV and nutritional status (controls, n = 68) on fecal metabolomics that targeted about 70 commonly measured metabolites, and enteropathy markers: fecal myeloperoxidase (MPO), fecal calprotectin, and circulating intestinal fatty acid binding protein (I-FABP). RESULTS The fecal metabolomes of cases show specific reductions in amino acids, monosaccharides, and microbial fermentation products, when compared to controls. SCFA levels did not differ between groups. The overall fecal metabolomics signature moderately differentiates cases from controls (AUC = 0.72). Enteropathy markers do not differ between groups overall, although serum I-FABP is elevated in cases in a sensitivity analysis among non-edematous children. Integrative analysis with systemic data suggests an indirect role of intestinal inflammation in the causal path of mortality. CONCLUSIONS Intestinal disturbances appear to have an indirect association with acute mortality. Findings of the study improve our understanding of pathophysiological pathways underlying mortality of children with CSM.
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Affiliation(s)
- Bijun Wen
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada
- Department of Translational medicine, Hospital for Sick Children, Toronto, Canada
| | - Amber Farooqui
- Department of Translational medicine, Hospital for Sick Children, Toronto, Canada
| | - Celine Bourdon
- Department of Translational medicine, Hospital for Sick Children, Toronto, Canada
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
| | - Nawar Tarafdar
- Department of Translational medicine, Hospital for Sick Children, Toronto, Canada
| | - Moses Ngari
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Johnstone Thitiri
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Laura Mwalekwa
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Paediatrics, Coast General Hospital, Mombasa, Kenya
| | - Judd L Walson
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
- Departments of Global Health, Medicine, Pediatrics and Epidemiology, University of Washington, Seattle, WA, USA
| | - Wieger Voskuijl
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
- Amsterdam Institute for Global Health and Development, Department of Global Health, Amsterdam University Medical Centres, Amsterdam, The Netherlands
- Department of Paediatrics and Child Health, Kamuzu University of Health Sciences (formerly College of Medicine), Blantyre, Malawi
| | - James A Berkley
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Robert H J Bandsma
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada.
- Department of Translational medicine, Hospital for Sick Children, Toronto, Canada.
- The Childhood Acute Illness & Nutrition Network, Nairobi, Kenya.
- Department of Biomedical Sciences, Kamuzu University of Health Sciences (formerly College of Medicine), Blantyre, Malawi.
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12
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Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
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Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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13
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Dje Kouadio DK, Wieringa F, Greffeuille V, Humblot C. Bacteria from the gut influence the host micronutrient status. Crit Rev Food Sci Nutr 2023:1-16. [PMID: 37366286 DOI: 10.1080/10408398.2023.2227888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Micronutrient deficiencies or "hidden hunger" remains a serious public health problem in most low- and middle-income countries, with severe consequences for child development. Traditional methods of treatment and prevention, such as supplementation and fortification, have not always proven to be effective and may have undesirable side-effects (i.e., digestive troubles with iron supplementation). Commensal bacteria in the gut may increase bioavailability of specific micronutrients (i.e., minerals), notably by removing anti-nutritional compounds, such as phytates and polyphenols, or by the synthesis of vitamins. Together with the gastrointestinal mucosa, gut microbiota is also the first line of protection against pathogens. It contributes to the reinforcement of the integrity of the intestinal epithelium and to a better absorption of micronutrients. However, its role in micronutrient malnutrition is still poorly understood. Moreover, the bacterial metabolism is also dependent of micronutrients acquired from the gut environment and resident bacteria may compete or collaborate to maintain micronutrient homeostasis. Gut microbiota composition can therefore be modulated by micronutrient availability. This review brings together current knowledge on this two-way relationship between micronutrients and gut microbiota bacteria, with a focus on iron, zinc, vitamin A and folate (vitamin B9), as these deficiencies are public health concerns in a global context.
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Affiliation(s)
- Dorgeles Kouakou Dje Kouadio
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Frank Wieringa
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Valérie Greffeuille
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
| | - Christèle Humblot
- QualiSud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- French National Research Institute for Sustainable Development (IRD), Montpellier, France, France
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14
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Kambale RM, Ntagazibwa JN, Kasengi JB, Zigashane AB, Francisca IN, Mashukano BN, Amani Ngaboyeka G, Bahizire E, Zech F, Bindels LB, Van der Linden D. Probiotics for children with uncomplicated severe acute malnutrition (PruSAM study): A randomized controlled trial in the Democratic Republic of Congo. Am J Clin Nutr 2023; 117:976-984. [PMID: 37137616 DOI: 10.1016/j.ajcnut.2023.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Severe acute malnutrition (SAM) contributes to nearly 1 million deaths annually worldwide, with diarrhea and pneumonia being the common morbidity associated with mortality. OBJECTIVES To assess the effect of probiotics on diarrhea, pneumonia, and nutritional recovery in children with uncomplicated SAM. METHODS A randomized, double-blind, placebo-controlled study was conducted involving 400 children with uncomplicated SAM randomly assigned to ready-to-use therapeutic food (RUTF) either with (n = 200) or without (n = 200) probiotics. Patients received 1 mL daily dose of a blend of Lacticasebacillus rhamnosus GG and Limosilactobacillus reuteri DSM 17938 (dosage, 2 billion colony-forming units; 50:50) or placebo during 1 mo. They were simultaneously fed with the RUTF for 6 to 12 wk, depending on patients' recovery rates. The primary outcome was the duration of diarrhea. Secondary outcomes included diarrheal and pneumonic incidence, nutritional recovery, and transfer to inpatient care rate. RESULTS For children with diarrhea, the number of days of disease was lower in the probiotic group (4.11; 95% CI: 3.37, 4.51) than that in the placebo group (6.68; 95% CI: 6.26, 7.13; P < 0.001). For children aged 16 mo or older, the risk of diarrhea was lower in the probiotic group (75.6%; 95% CI: 66.2, 82.9) than that in the placebo group (95.0%; 95% CI: 88.2, 97.9; P < 0.001), but no significant difference of the risk for the youngest. In the probiotic group, nutritional recovery happened earlier: at the 6th wk, 40.6% of the infants were waiting for nutritional recovery, contrasting with 68.7% of infants in the placebo group; but the nutritional recovery rate at the 12th wk was similar between the groups. Probiotics had no effect on pneumonic incidence and transfer to inpatient care. CONCLUSIONS This trial supports using probiotics for the treatment of children with uncomplicated SAM. Its effect on diarrhea could positively affect nutritional programs in resource-limited settings. This trial was registered https://pactr.samrc.ac.za as PACTR202108842939734.
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Affiliation(s)
- Richard Mbusa Kambale
- Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium; Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo; Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo; Center for Tropical Diseases and Global Health, Université catholique de Bukavu, Bukavu, Democratic Republic of the Congo.
| | - Joseph Ntagerwa Ntagazibwa
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo
| | - Joe Bwija Kasengi
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo
| | - Adrien Burume Zigashane
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo
| | - Isia Nancy Francisca
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo
| | - Benjamin Ntaligeza Mashukano
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; General Pediatrics, Pediatric Department, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of Congo
| | - Gaylord Amani Ngaboyeka
- Ecole Régionale de Santé Publique, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Esto Bahizire
- Faculty of Medicine, Université catholique de Bukavu, Bukavu, Democratic Republic of Congo; Center for Tropical Diseases and Global Health, Université catholique de Bukavu, Bukavu, Democratic Republic of the Congo; Center for Research in Natural Sciences of Lwiro, Bukavu, Democratic Republic of the Congo; Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Francis Zech
- Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Dimitri Van der Linden
- Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium; Pediatric Infectious Diseases, Specialized Pediatrics Service, Pediatric Department, Cliniques universitaires Saint Luc, Brussels, Belgium
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15
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Magdy Wasfy R, Zoaiter M, Bilen M, Tidjani Alou M, Lo CI, Bellali S, Caputo A, Alibar S, Andrieu C, Raoult D, Fournier PE, Million M. Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis. Antonie Van Leeuwenhoek 2023; 116:541-555. [PMID: 37029880 DOI: 10.1007/s10482-023-01824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
The novel bacterial strain Marseille-P4005T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.
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Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Malak Zoaiter
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Melhem Bilen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Sara Bellali
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Aurelia Caputo
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Stéphane Alibar
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Pierre Edouard Fournier
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France.
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France.
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France.
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Piazzesi A, Putignani L. Impact of helminth-microbiome interactions on childhood health and development-A clinical perspective. Parasite Immunol 2023; 45:e12949. [PMID: 36063358 DOI: 10.1111/pim.12949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/01/2022]
Abstract
Humans have co-existed with parasites for virtually the entirety of our existence as a species. Today, nearly one third of the human population is infected with at least one helminthic species, most of which reside in the intestinal tract, where they have co-evolved alongside the human gut microbiota (GM). Appreciation for the interconnected relationship between helminths and GM has increased in recent years. Here, we review the evidence of how helminths and GM can influence various aspects of childhood development and the onset of paediatric diseases. We discuss the emerging evidence of how many of the changes that parasitic worms inflict on their host is enacted through gut microbes. In this light, we argue that helminth-induced microbiota modifications are of great importance in both facing the global challenge of overcoming parasitic infections, and in replicating helminthic protective effects against inflammatory diseases. We propose that deepening our knowledge of helminth-microbiota interactions will uncover novel, safer and more effective therapeutic strategies in combatting an array of childhood disorders.
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Affiliation(s)
- Antonia Piazzesi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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17
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Inflammation and malnutrition in inflammatory bowel disease. Lancet Gastroenterol Hepatol 2023; 8:579-590. [PMID: 36933563 DOI: 10.1016/s2468-1253(23)00011-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 03/17/2023]
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis, has become increasingly prevalent worldwide in the past decade. The nutritional status of patients with IBD is often impaired, with malnutrition presenting as imbalanced energy or nutrient intake, including protein-energy malnutrition, disease-related malnutrition, sarcopenia, and micronutrient deficiency. Additionally, malnutrition can manifest as overweight, obesity, and sarcopenic obesity. Malnutrition can lead to disturbances in gut microbiome composition that might alter homoeostasis and cause a dysbiotic state, potentially triggering inflammatory responses. Despite the clear link between IBD and malnutrition, little is known about the pathophysiological mechanisms beyond protein-energy malnutrition and micronutrient deficiencies that could promote inflammation through malnutrition, and vice versa. This Review focuses on potential mechanisms that trigger a vicious cycle between malnutrition and inflammation, and their clinical and therapeutic implications.
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Uwaezuoke SN, Odimegwu CL, Mbanefo NR, Eneh CI, Arodiwe IO, Muoneke UV, Ogbuka FN, Ndiokwelu CO, Akwue AT. Vitamin D 3 supplementation as an adjunct in the management of childhood infectious diarrhea: a systematic review. BMC Infect Dis 2023; 23:159. [PMID: 36918811 PMCID: PMC10015675 DOI: 10.1186/s12879-023-08077-3] [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: 10/10/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Some studies have reported the possible role of vitamin D3 in ameliorating disease outcomes in childhood infectious diarrhea. However, findings about its effectiveness and the association of serum vitamin D levels with diarrhea risk appear inconsistent. We aimed to determine the efficacy of oral vitamin D3 as an adjunct in managing childhood infectious diarrhea and the relationship between vitamin D status and the disease. METHODS We searched the PubMed and Google Scholar electronic databases for relevant articles without limiting their year of publication. We selected primary studies that met the review's inclusion criteria, screened their titles and abstracts, and removed duplicates. We extracted data items from selected studies using a structured data-extraction form. We conducted a quality assessment of randomized controlled trials (RCTs) and non-randomized studies with the Cochrane collaboration tool and the Newcastle Ottawa Scale, respectively. We assessed the strength of the relationship between serum vitamin D levels and diarrhea using the correlation model. We estimated the I2 and tau2 values to assess between-study heterogeneity. RESULTS Nine full-text articles were selected, consisting of one RCT, three cross-sectional studies, two cohort studies, two longitudinal/prospective studies, and one case-control study. A total of 5,545 participants were evaluated in the nine studies. Six non-randomized studies provided weak evidence of the relationship between vitamin D levels and diarrhea risk as there was no correlation between the two variables. The only RCT failed to demonstrate any beneficial role of vitamin D3 in reducing the risk of recurrent diarrhea. The calculated I2 and tau2 values of 86.5% and 0.03, respectively suggested a high between-study heterogeneity which precluded a meta-analysis of study results. CONCLUSION Oral vitamin D3 may not be an effective adjunct in managing childhood infectious diarrhea. Additionally, the relationship between vitamin D status and infectious diarrhea appears weak. We recommend more adequately-powered RCTs to determine the effectiveness of vitamin D3 as an adjunct therapy in infectious diarrhea.
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Affiliation(s)
- Samuel N Uwaezuoke
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria.
| | - Chioma L Odimegwu
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria
| | - Ngozi R Mbanefo
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria
| | - Chizoma I Eneh
- Department of Pediatrics, Enugu State University Teaching Hospital, Enugu, Nigeria
| | - Ijeoma O Arodiwe
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria
| | - Uzoamaka V Muoneke
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria
| | - Francis N Ogbuka
- Department of Pediatrics, Enugu State University Teaching Hospital, Enugu, Nigeria
| | - Chibuzo O Ndiokwelu
- Department of Pediatrics, The University of Nigeria Teaching Hospital Ituku-Ozalla Enugu, Enugu, Nigeria
| | - Anthony T Akwue
- Emergency Department, ASEER field Hospital, Mecca, Kingdom of Saudi Arabia
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19
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Naseri K, Dabiri H, Olfatifar M, Shahrbaf MA, Yadegar A, Soheilian-Khorzoghi M, Sadeghi A, Saadati S, Rostami-Nejad M, Verma AK, Zali MR. Evaluation of gut microbiota of iranian patients with celiac disease, non-celiac wheat sensitivity, and irritable bowel syndrome: are there any similarities? BMC Gastroenterol 2023; 23:15. [PMID: 36647022 PMCID: PMC9841652 DOI: 10.1186/s12876-023-02649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIMS Individuals with celiac disease (CD), non-celiac wheat sensitivity (NCWS), and irritable bowel syndrome (IBS), show overlapping clinical symptoms and experience gut dysbiosis. A limited number of studies so far compared the gut microbiota among these intestinal conditions. This study aimed to investigate the similarities in the gut microbiota among patients with CD, NCWS, and IBS in comparison to healthy controls (HC). MATERIALS AND METHODS In this prospective study, in total 72 adult subjects, including CD (n = 15), NCWS (n = 12), IBS (n = 30), and HC (n = 15) were recruited. Fecal samples were collected from each individual. A quantitative real-time PCR (qPCR) test using 16S ribosomal RNA was conducted on stool samples to assess the relative abundance of Firmicutes, Bacteroidetes, Bifidobacterium spp., and Lactobacillus spp. RESULTS In all groups, Firmicutes and Lactobacillus spp. had the highest and lowest relative abundance respectively. The phylum Firmicutes had a higher relative abundance in CD patients than other groups. On the other hand, the phylum Bacteroidetes had the highest relative abundance among healthy subjects but the lowest in patients with NCWS. The relative abundance of Bifidobacterium spp. was lower in subjects with CD (P = 0.035) and IBS (P = 0.001) compared to the HCs. Also, the alteration of Firmicutes to Bacteroidetes ratio (F/B ratio) was statistically significant in NCWS and CD patients compared to the HCs (P = 0.05). CONCLUSION The principal coordinate analysis (PCoA), as a powerful multivariate analysis, suggested that the investigated gut microbial profile of patients with IBS and NCWS share more similarities to the HCs. In contrast, patients with CD had the most dissimilarity compared to the other groups in the context of the studied gut microbiota.
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Affiliation(s)
- Kaveh Naseri
- grid.1017.70000 0001 2163 3550School of Health and Biomedical Sciences, RMIT University, Melbourne, VIC Australia
| | - Hossein Dabiri
- grid.411600.2Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- grid.444830.f0000 0004 0384 871XGastroenterology and Hepatology Diseases Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Mohammad Amin Shahrbaf
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- grid.411600.2Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mona Soheilian-Khorzoghi
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeede Saadati
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anil K. Verma
- grid.7010.60000 0001 1017 3210Celiac Disease Research Laboratory, Department of Pediatrics, Università Politecnica Delle Marche, 60123 Ancona, Italy
| | - Mohammad Reza Zali
- grid.411600.2Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhao J, Lu W, Huang S, Le Maho Y, Habold C, Zhang Z. Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring. Microbiol Spectr 2022; 10:e0015722. [PMID: 36318010 PMCID: PMC9784777 DOI: 10.1128/spectrum.00157-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
Food resources are vital for animals to survive, and gut microbiota play an essential role in transferring nutritional materials into functional metabolites for hosts. Although the fact that diet affects host microbiota is well known, its impacts on offspring remain unclear. In this study, we assessed the effects of low-protein and niacin-deficient diets on reproduction performance, body growth, and gut microbiota of greater long-tailed hamsters (Tscherskia triton) under laboratory conditions. We found that maternal low-protein diet (not niacin deficiency) had a significant negative effect on reproduction performance of female hamsters (longer mating latency with males and smaller litter size) and body growth (lower body weight) of both female hamsters and their offspring. Both protein- and niacin-deficient diets showed significant maternal effects on the microbial community in the offspring. A maternal low-protein diet (not niacin deficiency) significantly reduced the abundance of major bacterial taxa producing short-chain fatty acids, increased the abundance of probiotic taxa, and altered microbial function in the offspring. The negative effects of maternal nutritional deficiency on gut microbiota are more pronounced in the protein group than the niacin group and in offspring more than in female hamsters. Our results suggest that a low-protein diet could alter gut microbiota in animals, which may result in negative impacts on their fitness. It is necessary to conduct further analysis to reveal the roles of nutrition, as well as its interaction with gut microbes, in affecting fitness of greater long-tailed hamsters under field conditions. IMPORTANCE Gut microbes are known to be essential for hosts to digest food and absorb nutrients. Currently, it is still unclear how maternal nutrient deficiency affects the fitness of animals by its effect on gut microbes. Here, we evaluated the effects of protein- and niacin-deficient diets on mating behavior, reproduction, body growth, and gut microbiota of both mothers and offspring of the greater long-tailed hamster (Tscherskia triton) under laboratory conditions. We found that a low-protein diet significantly reduced maternal reproduction performance and body growth of both mothers and their offspring. Both protein and niacin deficiencies showed significant maternal effects on the microbial community of the offspring. Our results hint that nutritional deficiency may be a potential factor in causing the observed sustained population decline of the greater long-tailed hamsters due to intensified monoculture in the North China Plain, and this needs further field investigation.
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Affiliation(s)
- Jidong Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi'an, People’s Republic of China
| | - Wei Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Shuli Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yvon Le Maho
- University of Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
- Scientific Centre of Monaco, Monaco Principality, Monaco
| | - Caroline Habold
- University of Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
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Eow SY, Gan WY, Jiang T, Loh SP, Lee LJ, Chin YS, Than LTL, How KN, Thong PL, Liu Y, Zhao J, Chen L. MYBIOTA: A birth cohort on maternal and infant microbiota and its impact on infant health in Malaysia. Front Nutr 2022; 9:994607. [PMID: 36238465 PMCID: PMC9552002 DOI: 10.3389/fnut.2022.994607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/15/2022] Open
Abstract
Background The microbiota plays a key role in early immunity maturation that affects infant health and is associated with the development of non-communicable diseases and allergies in later life. Objective The MYBIOTA is a prospective mother-infant cohort study in Malaysia aiming to determine the association between gut microbiota with infant health (temperament, gastrointestinal disorders, eczema, asthma, and developmental delays) in Selangor, Malaysia. Methods Pregnant mothers will be enrolled in their first trimester of pregnancy, and follow-ups will be done for infants during their first year of life. Maternal-infant biological samples (blood, feces, saliva, urine, and breast milk), anthropometric, dietary, and clinical information will be collected at different time points from early pregnancy to 12 months postpartum. Discussion This study could provide a better understanding of the colonization and development of the gut microbiome during early life and its impact on infant health. Clinical trial registration https://clinicaltrials.gov/, identifier NCT04919265.
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Affiliation(s)
- Shiang Yen Eow
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wan Ying Gan
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Tiemin Jiang
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, China
| | - Su Peng Loh
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Ling Jun Lee
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yit Siew Chin
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Research Center of Excellence, Nutrition and Non-communicable Diseases, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kang Nien How
- Unit of Dermatology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pui Ling Thong
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yanpin Liu
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
| | - Junying Zhao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
| | - Lijun Chen
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
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22
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Pinho RM, Garas LC, Huang BC, Weimer BC, Maga EA. Malnourishment affects gene expression along the length of the small intestine. Front Nutr 2022; 9:894640. [PMID: 36118759 PMCID: PMC9478944 DOI: 10.3389/fnut.2022.894640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Malnourishment is a risk factor for childhood mortality, jeopardizing the health of children by aggravating pneumonia/acute respiratory infections and diarrheal diseases. Malnourishment causes morphophysiological changes resulting in stunting and wasting that have long-lasting consequences such as cognitive deficit and metabolic dysfunction. Using a pig model of malnutrition, the interplay between the phenotypic data displayed by the malnourished animals, the gene expression pattern along the intestinal tract, microbiota composition of the intestinal contents, and hepatic metabolite concentrations from the same animals were correlated using a multi-omics approach. Samples from the duodenum, jejunum, and ileum of malnourished (protein and calorie-restricted diet) and full-fed (no dietary restrictions) piglets were subjected to RNA-seq. Gene co-expression analysis and phenotypic correlations were made with WGCNA, while the integration of transcriptome with microbiota composition and the hepatic metabolite profile was done using mixOmics. Malnourishment caused changes in tissue gene expression that influenced energetic balance, cell proliferation, nutrient absorption, and response to stress. Repression of antioxidant genes, including glutathione peroxidase, in coordination with induction of metal ion transporters corresponded to the hepatic metabolite changes. These data indicate oxidative stress in the intestine of malnourished animals. Furthermore, several of the phenotypes displayed by these animals could be explained by changes in gene expression.
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Affiliation(s)
- Raquel M. Pinho
- Department of Animal Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Raquel M. Pinho
| | - Lydia C. Garas
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - B. Carol Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth A. Maga
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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23
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Ma F, Huo Y, Li H, Yang F, Liao J, Han Q, Li Y, Pan J, Hu L, Guo J, Tang Z. New insights into the interaction between duodenal toxicity and microbiota disorder under copper exposure in chicken: Involving in endoplasmic reticulum stress and mitochondrial toxicity. Chem Biol Interact 2022; 366:110132. [PMID: 36030842 DOI: 10.1016/j.cbi.2022.110132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 12/17/2022]
Abstract
Copper (Cu) has been widely used in industrial agricultural production, but excess use can lead to toxic effect on host physiology, which poses a threaten to public hygiene. However, the relationship between gut microbiota and Cu-induced intestinal toxicity is unclear. Here, we identified that intestinal flora disturbance was related to duodenal toxicity under Cu exposure. We found that excess Cu disturbed gut microbiota homeostasis, resulting in Cu accumulation and intestinal damage. In addition, Cu considerably increased intestinal permeability by reducing expression of tight junction proteins (Claudlin-1, Occludin, and ZO-1). Meanwhile, Cu could induce endoplasmic reticulum stress, mitophagy, and mitochondria-mediated apoptosis in the duodenum, with the evidence by the elevated levels of GRP78, GRP94, LC3Ⅱ/LC3Ⅰ and Caspase-3 protein expression. Correlation analysis showed that Melainabacteria was closely related to tight junction proteins and endoplasmic reticulum stress of duodenum, indicating that disturbance of intestinal flora may aggravate the toxic effect of Cu. Therefore, our results suggest that the destruction of intestinal flora induced by excessive Cu may further lead to intestinal barrier damage, ultimately leading to endoplasmic reticulum stress, mitophagy and apoptosis. This research provides a new insight into interpretation of the interrelationship between microbiota disorder and duodenal toxicity under Cu exposure.
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Affiliation(s)
- Feiyang Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Yihui Huo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Huayu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Fan Yang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jianzhao Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Qingyue Han
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiaqiang Pan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Lianmei Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Dahiya D, Nigam PS. Clinical Potential of Microbial Strains, Used in Fermentation for Probiotic Food, Beverages and in Synbiotic Supplements, as Psychobiotics for Cognitive Treatment through Gut–Brain Signaling. Microorganisms 2022; 10:microorganisms10091687. [PMID: 36144289 PMCID: PMC9505539 DOI: 10.3390/microorganisms10091687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/14/2022] Open
Abstract
Pure and viable strains of microorganisms identified and characterized as probiotic strains are used in the fermentation process to prepare probiotic food and beverages. These products are sources of nutrition and help in the maintenance of gut microflora. The intake of food products prepared with the use of probiotic microorganisms and containing their metabolites and whole microbial cells can be considered as a natural formulation of synbiotic products with prebiotic substrates and culture. Other than through the intake of fermented food and beverages, probiotic microorganisms can be taken through a supplement, which is a complementary form prepared by combining separate sources of prebiotic substrates and specific probiotic cultures. Whether a fermented solid food or beverage, both the components in the product are in a synergistic relationship and contribute to several health benefits at a lower cost. The aim of this article is to review the relevant literature and present the outcomes of recent studies which have been conducted to explore the clinical potential of probiotic strains and their effect on psychological conditions. Studies have shown the relationship between gut microbiota and the brain, and their interaction through signaling. The studies have concluded that the gut–brain axis can be manipulated with the intake of probiotic foods or synbiotic supplements containing specific probiotic strains accompanied with their complementary prebiotics for the enhanced sustainability of healthy GIT microflora.
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Affiliation(s)
| | - Poonam Singh Nigam
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, UK
- Correspondence:
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25
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Matar G, Bilen M. Culturomics, a potential approach paving the way toward bacteriotherapy. Curr Opin Microbiol 2022; 69:102194. [PMID: 35994842 DOI: 10.1016/j.mib.2022.102194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022]
Abstract
The human microbiota has been extensively studied over the past decade to describe its role in health and diseases. Numerous studies showed the presence of bacterial imbalance in a variety of human health conditions, suggesting great potential for the development of bacteriotherapies. Identifying mechanisms involving the human microbiota has been very challenging due to the complex data generated by molecular approaches and the limited number of organisms isolated by culture and described. This review summarizes the efforts done to describe the human microbiota through culturomics and the advancements in culturing the organisms residing at different body sites.
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Affiliation(s)
- Ghassan Matar
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Melhem Bilen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA.
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26
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Probiotics, Prebiotics, Synbiotics, and Fermented Foods as Potential Biotics in Nutrition Improving Health via Microbiome-Gut-Brain Axis. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8070303] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biological, social, and psychological practices greatly affect the dietary intake of people; as a result, health-related complexities occur. Functional food and supplements have become popular due to their nutraceutical benefits, which make different choices of fermented food and beverages available to people. This review describes the characteristics of probiotics, prebiotics, post- and paraprobiotics, and their role in nutrition and in the sustainability of health. Currently, several synbiotic supplements have attracted consumers in the nutraceutical market to offer a number of health benefits, which are complementary mixtures of selected characterized probiotic cultures and prebiotic substrates. Traditional fermented foods consumed in different cultures are different than probiotics and symbiotic preparations, though these could be considered potential biotics in nutrition. Fermented foods are part of a staple diet in several countries and are cost-effective due to their preparation using seasonal raw materials available from local agriculture practices. Intake of all biotics discussed in this article is intended to improve the population of beneficial microbiota in the gut, which has proved important for the microbiome–gut–brain axis, influencing the activity of vagus nerve.
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Patterson GT, Osorio EY, Peniche A, Dann SM, Cordova E, Preidis GA, Suh JH, Ito I, Saldarriaga OA, Loeffelholz M, Ajami NJ, Travi BL, Melby PC. Pathologic Inflammation in Malnutrition Is Driven by Proinflammatory Intestinal Microbiota, Large Intestine Barrier Dysfunction, and Translocation of Bacterial Lipopolysaccharide. Front Immunol 2022; 13:846155. [PMID: 35720380 PMCID: PMC9204284 DOI: 10.3389/fimmu.2022.846155] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Acute malnutrition, or wasting, is implicated in over half of all deaths in children under five and increases risk of infectious disease. Studies in humans and preclinical models have demonstrated that malnutrition is linked to an immature intestinal microbiota characterized by increased prevalence of Enterobacteriaceae. Observational studies in children with moderate acute malnutrition (MAM) have also observed heightened systemic inflammation and increased circulating bacterial lipopolysaccharides (LPS; endotoxin). However, the mechanisms that underpin the systemic inflammatory state and endotoxemia, and their pathophysiological consequences, remain uncertain. Understanding these pathophysiological mechanisms is necessary to design targeted treatments that will improve the unacceptable rate of failure or relapse that plague current approaches. Here we use a mouse model of MAM to investigate the mechanisms that promote inflammation in the malnourished host. We found that mice with MAM exhibited increased systemic inflammation at baseline, increased translocation of bacteria and bacterial LPS, and an exaggerated response to inflammatory stimuli. An exaggerated response to bacterial LPS was associated with increased acute weight loss. Remarkably, intestinal inflammation and barrier dysfunction was found in the cecum and colon. The cecum showed a dysbiotic microbiota with expansion of Gammaproteobacteria and some Firmicutes, and contraction of Bacteroidetes. These changes were paralleled by an increase in fecal LPS bioactivity. The inflammatory phenotype and weight loss was modulated by oral administration of non-absorbable antibiotics that altered the proportion of cecal Gammaproteobacteria. We propose that the heightened inflammation of acute malnutrition is the result of changes in the intestinal microbiota, intestinal barrier dysfunction in the cecum and colon, and increased systemic exposure to LPS.
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Affiliation(s)
- Grace T Patterson
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Elvia Y Osorio
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Alex Peniche
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Sara M Dann
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
| | - Erika Cordova
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, United States
| | - Ji Ho Suh
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, United States
| | - Ichiaki Ito
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Omar A Saldarriaga
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Michael Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Nadim J Ajami
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Bruno L Travi
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
| | - Peter C Melby
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
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Association of human milk oligosaccharides and nutritional status of young infants among Bangladeshi mother-infant dyads. Sci Rep 2022; 12:9456. [PMID: 35676397 PMCID: PMC9177541 DOI: 10.1038/s41598-022-13296-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Human milk oligosaccharides (HMOs) support the development of a healthy gut microbiome and the growth of infants. We aimed to determine the association of different HMOs with severe acute malnutrition (SAM) among Bangladeshi young infants. This study was nested within a single-blind, randomized, pilot clinical trial (NCT0366657). A total of 45 breastmilk samples from mothers of < 6 months old infants who had SAM (n = 26) or were non-malnourished (n = 19) and were analyzed for constituent HMOs. Of the infants with SAM, 14 (53.85%) had secretor mothers, and 11 (57.89%) of the non-malnourished infants had secretor mothers. A one-unit increase in the relative abundance of sialylated HMOs was associated with higher odds of SAM in age and sex adjusted model (aOR = 2.00, 90% CI 1.30, 3.06), in age, sex, and secretor status adjusted model (aOR = 1.96, 90% CI 1.29, 2.98), and also in age and sex adjusted model among non-secretor mothers (aOR = 2.86, 90% CI 1.07, 7.62). In adjusted models, there was no evidence of a statistically significant association between SAM and fucosylated or undecorated HMOs. Our study demonstrates that a higher relative abundance of sialylated HMOs in mothers’ breastmilk may have a negative impact on young infants’ nutritional status.
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Shahzad M, Andrews SC, Ul-Haq Z. Exploring the role of Microbiome in Susceptibility, Treatment Response and Outcome among Tuberculosis Patients from Pakistan: study protocol for a prospective cohort study (Micro-STOP). BMJ Open 2022; 12:e058463. [PMID: 35672071 PMCID: PMC9174774 DOI: 10.1136/bmjopen-2021-058463] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis is a common infectious disease associated with significant morbidity and mortality, especially in low-income and middle-income countries. Successful treatment of the disease requires prolonged intake (6-8 months) of multiple antibiotics with potentially detrimental consequences on the composition and functional potential of the human microbiome. The protocol described in the current study aims to identify microbiome (oral and gut) signatures associated with TB pathogenesis, treatment response and outcome in humans. METHODS AND ANALYSIS Four hundred and fifty, newly diagnosed patients with TB from three district levels (Peshawar, Mardan and Swat) TB diagnosis and treatment centres, will be recruited in this non-interventional, prospective cohort study and will be followed and monitored until treatment completion. Demographic and dietary intake data, anthropometric measurement and blood, stool and salivary rinse samples will be collected at baseline, day 15, month-2 and end of the treatment. Additionally, we will recruit age (±3 years) and sex-matched healthy controls (n=30). Blood sampling will allow monitoring of the immune response during the treatment, while salivary rinse and faecal samples will allow monitoring of dynamic changes in oral and gut microbiome diversity. Within this prospective cohort study, a nested case-control study design will be conducted to assess perturbations in oral and gut microbiome diversity (microbial dysbiosis) and immune response and compare between the patients groups (treatment success vs failure). ETHICS AND DISSEMINATION The study has received ethics approval from the Ethic Board of Khyber Medical University Peshawar, and administrative approval from Provincial TB Control Programme of Khyber Pakhtunkhwa, Pakistan. The study results will be presented in national and international conferences and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT04985994.
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Affiliation(s)
- Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- School of Biological Sciences, University of Reading, Reading, UK
| | - Simon C Andrews
- School of Biological Sciences, University of Reading, Reading, UK
| | - Zia Ul-Haq
- Institute of Public Health & Social Sciences, Khyber Medical University, Peshawar, Pakistan
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Otiti MI, Kariuki S, Wang D, Hall LJ, Ter Kuile FO, Allen S. PRObiotics and SYNbiotics to improve gut health and growth in infants in western Kenya (PROSYNK Trial): study protocol for a 4-arm, open-label, randomised, controlled trial. Trials 2022; 23:284. [PMID: 35410317 PMCID: PMC8996226 DOI: 10.1186/s13063-022-06211-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Malnutrition amongst under-fives remains common in resource-poor countries and is resistant to current interventions. New opportunities have emerged to target “environmental enteric dysfunction” (EED) that refers to the abnormal gut structure and function that results from colonisation of the gut with pathogenic microbes and compromises nutrition and growth in early life. Although the gut microbiome may provide a defence against ingested gut pathogens through colonisation resistance, its development is adversely affected by multiple environmental factors. Dietary supplements of pro- or synbiotics may build the resilience of the gut microbiome against these environmental factors and boost colonisation resistance. We aim to assess whether dietary supplementation of newborns in rural Kenya with pro/synbiotics prevents or ameliorates EED and improves growth. Methods Six hundred newborns less than 4 days old will be recruited from Homa Bay County Teaching and Referral Hospital, western Kenya. Newborns will be randomly allocated, stratified by HIV exposure, in a 1:1:1:1 ratio to one of 4 study arms to receive either of two synbiotics, a probiotic or no supplement. Supplements will be given daily for 10 days and then weekly until 6 months of age. Participants will be followed until the age of 2 years. The primary outcome is systemic inflammation at 6 months assessed by plasma alpha-1-acid glycoprotein. Secondary outcomes include biomarkers of gut health and growth, anthropometric indices, morbidity and mortality. Discussion As dietary supplements with pro- or synbiotics may improve gut health and can be administered in early life, our findings may inform the package of interventions to prevent malnutrition and improve growth in Africa and similar low-resource settings. Trial registration Pan African Clinical Trials Registry, Trial number: PACTR202003893276712. Date: 02/03/2020 https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=9798 Supplementary Information The online version contains supplementary material available at 10.1186/s13063-022-06211-1.
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Zhang X, Li C, Shahzad K, Han M, Guo Y, Huang X, Wu T, Wang L, Zhang Y, Tang H, Zhang Q, Wang M, Zhou P, Zhong F. Seasonal Differences in Fecal Microbial Community Structure and Metabolism of House-Feeding Chinese Merino Fine-Wool Sheep. Front Vet Sci 2022; 9:875729. [PMID: 35400091 PMCID: PMC8989412 DOI: 10.3389/fvets.2022.875729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
The digestive tract microorganisms play a very important role in the host's nutrient intake, environmental suitability, and affect the host's physiological mechanism. Previous studies showed that in different seasons, mammalian gut microbes would be different. However, most of them are concentrated in wild animals. It remains unclear how seasonal change affects the gut microbes of Chinese merino fine-wool Sheep. Therefore, in this experiment, we continuously collected blood and feces samples of 50 Chinese merino fine-wool sheep in different seasons, measured the physiological indicators of blood, and passed 16S rRNA amplicon sequencing, determined the microbial community structure of fecal microorganisms and predicted flora function by PICRUSt. The results of blood physiological indicators showed that WBC, Neu and Bas in spring were significantly higher than those of other seasons. Fecal microbial sequencing revealed seasonal changes in gut microbial diversity and richness. Among them, Chinese merino fine-wool sheep had the highest gut microbes in summer. Firmicutes and Bacteroidetes were the dominant phyla, and they were unaffected by seasonal fluctuations. LEfSE analysis was used to analyze representative microorganisms in different seasons. The Lachnospiraceae and its genera (Lachnospiraceae_NK4A136_group, Lachnospiraceae_AC2044_group, g_unclassified_f_ Lachnospiraceae) were representative microorganisms in the three seasons of spring, summer and winter with harsh environmental conditions; while in autumn with better environmental conditions, the Ruminococcaceae and its genus (Ruminococcaceae_UCG-009 and Ruminococcaceae_UCG-005) were the representative microorganism. In autumn, the ABC transporter and the pyruvate metabolic pathway were significantly higher than other seasons. Correlation analysis results showed that Lachnospiraceae participated in the ABC transporters metabolic pathway, which caused changes in the blood physiological indicators. Overall, our results showed that, in response to seasonal changes, Chinese merino fine-wool sheep under house-feeding have adjusted their own gut microbial community structure, causing changes in the metabolism, and thus changing the physiological conditions of the blood. In the cold season, producers should focus on regulating the nutritional level of feed, enhancing the level of butyric acid in young animals to increase the ABC transporter, resist the external harsh environment, and improve the survival rate.
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Affiliation(s)
- Xingxing Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mengli Han
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yanhua Guo
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xin Huang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tongzhong Wu
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Limin Wang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yiyuan Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hong Tang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Qian Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- *Correspondence: Mengzhi Wang
| | - Ping Zhou
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Ping Zhou
| | - Fagang Zhong
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Fagang Zhong
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Dahiya D, Nigam PS. The Gut Microbiota Influenced by the Intake of Probiotics and Functional Foods with Prebiotics Can Sustain Wellness and Alleviate Certain Ailments like Gut-inflammation and Colon-Cancer. Microorganisms 2022; 10:microorganisms10030665. [PMID: 35336240 PMCID: PMC8954736 DOI: 10.3390/microorganisms10030665] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/12/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota is composed of several microbial strains, with diverse and variable combinations in healthy and sick persons, changing at different stages of life. A healthy balance between host and gut microorganisms must be maintained in order to perform the normal physiological, metabolic, and immune functions and prevent disease development. Disturbances in the balance of the gut microbiota by diverse reasons initiate several health issues and promote the progression of certain diseases. This review is based on published research and reports that describe the role of probiotic microorganisms in the sustainability of health and the alleviation of certain diseases. Information is presented on the GRAS strains that are used as probiotics in the food industry for the production of fermented milk, yogurt, fermented food, functional foods, and probiotic drinks. To maintain a healthy microbiota, probiotic supplements in the form of freeze-dried live cells of probiotic strains are also available in different forms to consumers. The health benefits of lactic acid bacteria and other microorganisms and their role in the control of certain diseases such as gut inflammation, diabetes, and bowel cancer and in the safeguarding of the gut epithelial permeability from the invasion of pathogens are discussed.
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Affiliation(s)
- Divakar Dahiya
- Wexham Park Hospital, Wexham Street, Slough SL2 4HL, Berkshire, UK;
| | - Poonam Singh Nigam
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
- Correspondence:
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Song S, Guo Y, Yang Y, Fu D. Advances in pathogenesis and therapeutic strategies for osteoporosis. Pharmacol Ther 2022; 237:108168. [PMID: 35283172 DOI: 10.1016/j.pharmthera.2022.108168] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023]
Abstract
Osteoporosis, is the most common bone disorder worldwide characterized by low bone mineral density, leaving affected bones vulnerable to fracture. Bone homeostasis depends on the precise balance between bone resorption by osteoclasts and bone matrix formation by mesenchymal lineage osteoblasts, and involves a series of complex and highly regulated steps. Bone homeostasis will be disrupted when the speed of bone resorption is faster than bone formation. Based on various regulatory mechanisms of bone homeostasis, a series of drugs targeting osteoporosis have emerged in clinical practice, including bisphosphonates, selective estrogen receptor modulators, calcitonin, molecular-targeted drugs and so on. However, many drugs have major adverse effects or are unsuitable for long-term use. Therefore, it is very urgent to find more effective therapeutic drugs based on the new pathogenesis of osteoporosis. In this review, we summarize novel mechanisms involved in the pathological process of osteoporosis, including the roles of gut microbiome, autophagy, iron balance and cellular senescence. Based on the above pathological mechanism, we found promising drugs for osteoporosis treatment, such as: probiotics, alpha-ketoglutarate, senolytics and hydrogen sulfide. This new finding may provide an important basis for elucidating the complex pathological mechanisms of osteoporosis and provide promising drugs for clinical osteoporosis treatment.
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Affiliation(s)
- Shasha Song
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, PR China
| | - Yuanyuan Guo
- Department of Pharmacy, Liyuan Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei 430077, PR China
| | - Yuehua Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, PR China
| | - Dehao Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, PR China.
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Lo CI, Traore SI, Diop A, Bilen M, Azhar EI, Bibi F, Jiman-Fatani A, Yasir M, Lagier JC, Raoult D, Fenollar F, Fournier PE. Arabiibacter massiliensis gen. nov. sp. nov., New Anaerobic Bacterium Isolated from the Human Gut. Curr Microbiol 2022; 79:47. [PMID: 34982255 DOI: 10.1007/s00284-021-02739-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Using microbial culturomics, we were able to isolate strain Marseille-P3078 from a stool sample of a healthy 50-year-old Saudi Arabian woman. To this end, we used taxonogenomics that combines phenotypic, biochemical and genomic analyses, to describe this bacterium. Cells from strain Marseille-P3078 are anaerobic and Gram-negative rods that are motile and unable to sporulate. Its genome size is 3,377,914-bp-long with a 66.33 mol% G + C content. Based on its phenotypic and genomic features, including a 94.6% 16S rRNA similarity with Paraeggerthella hongkongensis strain JCM 14552, its closest phylogenetic neighbor withstanding in nomenclature, we propose that strain Marseille-P3078T (= CSUR P3078 = DSM 104007) is the representative strain of a new genus for which we propose the name Arabiibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Cheikh Ibrahima Lo
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Awa Diop
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Melhem Bilen
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif Jiman-Fatani
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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Gut microbiome dysbiosis in malnutrition. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:205-229. [DOI: 10.1016/bs.pmbts.2022.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Diarrheal disease and gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:149-177. [DOI: 10.1016/bs.pmbts.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Zhong SR, Kuang Q, Zhang F, Chen B, Zhong ZG. Functional roles of the microbiota-gut-brain axis in Alzheimer’s disease: Implications of gut microbiota-targeted therapy. Transl Neurosci 2021; 12:581-600. [PMID: 35070442 PMCID: PMC8724360 DOI: 10.1515/tnsci-2020-0206] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Increasing scientific evidence demonstrates that the gut microbiota influences normal physiological homeostasis and contributes to pathogenesis, ranging from obesity to neurodegenerative diseases, such as Alzheimer’s disease (AD). Gut microbiota can interact with the central nervous system (CNS) through the microbiota-gut-brain axis. The interaction is mediated by microbial secretions, metabolic interventions, and neural stimulation. Here, we review and summarize the regulatory pathways (immune, neural, neuroendocrine, or metabolic systems) in the microbiota-gut-brain axis in AD pathogenesis. Besides, we highlight the significant roles of the intestinal epithelial barrier and blood–brain barrier (BBB) in the microbiota-gut-brain axis. During the progression of AD, there is a gradual shift in the gut microbiota and host co-metabolic relationship, leading to gut dysbiosis, and the imbalance of microbial secretions and metabolites, such as lipopolysaccharides (LPS) and short-chain fatty acids (SCFAs). These products may affect the CNS metabolic state and immune balance through the microbiota-gut-brain axis. Further, we summarize the potential microbiota-gut-brain axis-targeted therapy including carbohydrates, probiotics, dietary measures, and propose new strategies toward the development of anti-AD drugs. Taken together, the data in this review suggest that remodeling the gut microbiota may present a tractable strategy in the management and development of new therapeutics against AD and other neurodegenerative diseases.
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Affiliation(s)
- Si-Ran Zhong
- School of Health Medicine, Guangzhou Huashang College , Guangzhou , 511300 , People’s Republic of China
| | - Qi Kuang
- School of Health Medicine, Guangzhou Huashang College , Guangzhou , 511300 , People’s Republic of China
| | - Fan Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine , Guangzhou , 510006 , People’s Republic of China
| | - Ben Chen
- Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine , Nanning City , 530200, Guangxi Zhuang Autonomous Region , People’s Republic of China
| | - Zhen-Guo Zhong
- Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine , Nanning City , 530200, Guangxi Zhuang Autonomous Region , People’s Republic of China
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Abstract
The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.
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39
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Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients. THE ISME JOURNAL 2021; 15:3207-3220. [PMID: 34002024 PMCID: PMC8528809 DOI: 10.1038/s41396-021-00998-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 02/03/2023]
Abstract
Cachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.
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Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA. Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children. EBioMedicine 2021; 73:103644. [PMID: 34695658 PMCID: PMC8550991 DOI: 10.1016/j.ebiom.2021.103644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. METHODS We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. FINDINGS Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. INTERPRETATION Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. FUNDING The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].
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Affiliation(s)
- Helen M Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Josh L Espinoza
- J. Craig Venture Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA; Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Modupeh Betts
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Rowan Bancroft
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Schadrac C Agbla
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | | | - Mariama Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Robin M Bernstein
- Growth and Development Lab, Department of Anthropology, University of Colorado, Boulder, CO, United States of America
| | | | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom.
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Li Y, Liu Y, Wu J, Chen Q, Zhou Q, Wu F, Zhang R, Fang Z, Lin Y, Xu S, Feng B, Zhuo Y, Wu D, Che L. Comparative effects of enzymatic soybean, fish meal and milk powder in diets on growth performance, immunological parameters, SCFAs production and gut microbiome of weaned piglets. J Anim Sci Biotechnol 2021; 12:106. [PMID: 34615550 PMCID: PMC8496045 DOI: 10.1186/s40104-021-00625-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/01/2021] [Indexed: 01/22/2023] Open
Abstract
Background The objective of this study was to evaluate the replacement effects of milk powder (MK) and fish meal (FM) by enzymatic soybean (ESB) in diets on growth performance, immunological parameters, SCFAs production and gut microbiome of weaned piglets. Methods A total of 128 piglets with initial body weight at 6.95 ± 0.46 kg, were randomly assigned into 4 dietary treatments with 8 replicates per treatment and 4 piglets per replicate for a period of 14 d. Piglets were offered iso-nitrogenous and iso-energetic diets as follows: CON diet with MK and FM as high quality protein sources, ESB plus FM diet with ESB replacing MK, ESB plus MK diet with ESB replacing FM, and ESB diet with ESB replacing both MK and FM. Results No significant differences were observed in growth performance among all treatments (P > 0.05). However, piglets fed ESB plus FM or ESB diet had increased diarrhea index (P<0.01), and lower digestibility of dry matter (DM), gross energy (GE) or crude protein (CP), relative to piglets fed CON diet (P < 0.01). Moreover, the inclusion of ESB in diet markedly decreased the plasma concentration of HPT and fecal concentration of butyric acid (BA) (P<0.01). The High-throughput sequencing of 16S rRNA gene V3−V4 region of gut microbiome revealed that the inclusion of ESB in diet increased the alpha diversity, and the linear discriminant analysis effect size (LEfSe) showed that piglets fed with ESB plus FM or ESB diet contained more gut pathogenic bacteria, such as g_Peptococcus, g_Veillonella and g_Helicobacter. Conclusion The inclusion of ESB in diet did not markedly affect growth performance of piglets, but the replacement of MK or both MK and FM by ESB increased diarrhea index, which could be associated with lower nutrients digestibility and more gut pathogenic bacteria. However, piglets fed diet using ESB to replace FM did not markedly affect gut health-related parameters, indicating the potential for replacing FM with ESB in weaning diet.
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Affiliation(s)
- Yingjie Li
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yang Liu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Jiangnan Wu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Qiuhong Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Qiang Zhou
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Fali Wu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Ruinan Zhang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Zhengfeng Fang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yan Lin
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Shengyu Xu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Bin Feng
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yong Zhuo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - De Wu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China
| | - Lianqiang Che
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, People's Republic of China.
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Dwivedi M, Powali S, Rastogi S, Singh A, Gupta DK. Microbial community in human gut: a therapeutic prospect and implication in health and diseases. Lett Appl Microbiol 2021; 73:553-568. [PMID: 34365651 DOI: 10.1111/lam.13549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.
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Affiliation(s)
- M Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - S Powali
- Maulana Abdul Kalam Azad University of Technology, Kolkatta, India
| | - S Rastogi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - A Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - D K Gupta
- Department of Biochemistry, University of Allahabad, Prayagraj, India
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Li A, Wang Y, He Y, Liu B, Iqbal M, Mehmood K, Jamil T, Chang YF, Hu L, Li Y, Guo J, Pan J, Tang Z, Zhang H. Environmental fluoride exposure disrupts the intestinal structure and gut microbial composition in ducks. CHEMOSPHERE 2021; 277:130222. [PMID: 33794430 DOI: 10.1016/j.chemosphere.2021.130222] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Fluorine (F) and its compounds produced from industrial production and coal combustion can cause air, water and soil contamination, which can accumulate in animals, plants and humans via food chain threatening public health. Fluoride exposure affects liver, kidney, gastrointestinal and reproductive system in humans and animals. Literature regarding fluoride influence on intestinal structure and microbiota composition in ducks is scarce. This study was designed to investigate these effects by using simple and electron microscopy and 16S rRNA sequencing techniques. Results indicated an impaired structure with reduced relative distribution of goblet cells in the fluoride exposed group. Moreover, the gut microbiota showed a significant decrease in alpha diversity. Proteobacteria, Firmicutes and Bacteroidetes were the most abundant phyla in both control and fluoride-exposed groups. Specifically, fluoride exposure resulted in a significant decrease in the relative abundance of 9 bacterial phyla and 15 bacterial genera. Among them, 4 phyla (Latescibacteria, Dependentiae, Zixibacteria and Fibrobacteres) and 4 genera (Thauera, Hydrogenophaga, Reyranella and Arenimonas) weren't even detectable in the gut microbiota of the ducks. In summary, higher fluoride exposure can significantly damage the intestinal structure and gut microbial composition in ducks.
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Affiliation(s)
- Aoyun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yajing Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Yuanyuan He
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bingxian Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Mudassar Iqbal
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Tariq Jamil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743, Jena, Germany
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lianmei Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jianying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaqiang Pan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG. The role of the gut microbiome in the development of schizophrenia. Schizophr Res 2021; 234:4-23. [PMID: 32336581 DOI: 10.1016/j.schres.2020.02.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a heterogeneous neurodevelopmental disorder involving the convergence of a complex and dynamic bidirectional interaction of genetic expression and the accumulation of prenatal and postnatal environmental risk factors. The development of the neural circuitry underlying social, cognitive and emotional domains requires precise regulation from molecular signalling pathways, especially during critical periods or "windows", when the brain is particularly sensitive to the influence of environmental input signalling. Many of the brain regions involved, and the molecular substrates sub-serving these domains are responsive to life-long microbiota-gut-brain (MGB) axis signalling. This intricate microbial signalling system communicates with the brain via the vagus nerve, immune system, enteric nervous system, enteroendocrine signalling and production of microbial metabolites, such as short-chain fatty acids. Preclinical data has demonstrated that MGB axis signalling influences neurotransmission, neurogenesis, myelination, dendrite formation and blood brain barrier development, and modulates cognitive function and behaviour patterns, such as, social interaction, stress management and locomotor activity. Furthermore, preliminary clinical studies suggest altered gut microbiota profiles in schizophrenia. Unravelling MGB axis signalling in the context of an evolving dimensional framework in schizophrenia may provide a more complete understanding of the neurobiological architecture of this complex condition and offers the possibility of translational interventions.
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Affiliation(s)
- John R Kelly
- Department of Psychiatry, Trinity College Dublin, Ireland
| | - Chiara Minuto
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Timothy G Dinan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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Krishinchand H, Naidoo K, Mahabeer P, Archary M. Paediatric Enterobacteriaceae infections in hospitalised children in Durban, KwaZulu-Natal. S Afr J Infect Dis 2021. [DOI: 10.4102/sajid.v36i1.279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Ecklu-Mensah G, Gilbert J, Devkota S. Dietary Selection Pressures and Their Impact on the Gut Microbiome. Cell Mol Gastroenterol Hepatol 2021; 13:7-18. [PMID: 34329765 PMCID: PMC8600059 DOI: 10.1016/j.jcmgh.2021.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022]
Abstract
The human gut microbiota harbors a heterogeneous and dynamic community of microorganisms that coexist with the host to exert a marked influence on human physiology and health. Throughout the lifespan, diet can shape the composition and diversity of the members of the gut microbiota by determining the microorganisms that will colonize, persist, or become extinct. This is no more pronounced than during early-life succession of the gut microbiome when food type and source changes relatively often and food preferences are established, which is largely determined by geographic location and the customs and cultural practices of that environment. These dietary selection pressures continue throughout life, as society has become increasingly mobile and as we consume new foods to which we have had no previous exposure. Dietary selection pressures also come in the form of overall reduction or excess such as with the growing problems of food insecurity (lack of food) as well as of dietary obesity (overconsumption). These are well-documented forms of dietary selection pressures that have profound impact on the gut microbiota that ultimately may contribute to or worsen disease. However, diets and dietary components can also be used to promote healthy microbial functions in the gut, which will require tailored approaches taking into account an individual's personal history and doing away with one-size-fits-all nutrition. Herein, we summarize current knowledge on major dietary selection pressures that influence gut microbiota structure and function across and within populations, and discuss both the potential of personalized dietary solutions to health and disease and the challenges of implementation.
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Affiliation(s)
- Gertrude Ecklu-Mensah
- Department of Pediatrics, University of California San Diego, La Jolla, California,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Jack Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California,Correspondence Address Correspondence to: Suzanne Devkota, PhD, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048. fax: (310) 423-0224
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Zhou C, Zhao H, Wang T. Transformation and differential abundance analysis of microbiome data incorporating phylogeny. Bioinformatics 2021; 37:4652-4660. [PMID: 34302462 DOI: 10.1093/bioinformatics/btab543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Microbiome data have proven extremely useful for understanding microbial communities and their impacts in health and disease. Although microbiome analysis methods and standards are evolving rapidly, obtaining meaningful and interpretable results from microbiome studies still requires careful statistical treatment. In particular, many existing and emerging methods for differential abundance analysis fail to account for the fact that microbiome data are high-dimensional and sparse, compositional, negatively and positively correlated, and phylogenetically structured. To better describe microbiome data and improve the power of differential abundance testing, there is still a great need for the continued development of appropriate statistical methodology. RESULTS In this paper, we propose a model-based approach for microbiome data transformation, and a phylogenetically informed procedure for differential abundance (DA) testing based on the transformed data. First, we extend the Dirichlet-tree multinomial (DTM) to zero-inflated DTM (ZIDTM) for multivariate modeling of microbial counts, addressing data sparsity, and correlation and phylogeny among bacterial taxa. Then, within this framework and using a Bayesian formulation, we introduce posterior mean transformation to convert raw counts into nonzero relative abundances that sum to one, accounting for the compositionality nature of microbiome data. Second, using the transformed data, we propose adaptive analysis of composition of microbiomes (adaANCOM) for DA testing by constructing log-ratios adaptively on the tree for each taxon, greatly reducing the computational complexity of ANCOM in high dimensions. Finally, we present extensive simulation studies, an analysis of HMP data across 18 body sites and 2 visits, and an application to a gut microbiome and malnutrition study, to investigate the performance of posterior mean transformation and adaANCOM. Comparisons with ANCOM and other DA testing procedures show that adaANCOM controls the false discovery rate well, allows for easy interpretation of the results, and is computationally efficient for high-dimensional problems. AVAILABILITY The developed R package is available at https://github.com/ZRChao/adaANCOM. For replicability purposes, scripts for our simulations and data analysis are available at https://github.com/ZRChao/Papers_supplementary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chao Zhou
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China.,SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, Connecticut, U.S.A.,SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China.,SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China.,MoE Key Lab of Artificial Intelligence, Shanghai Jiao Tong University, Shanghai, China
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Mehta S, Huey SL, McDonald D, Knight R, Finkelstein JL. Nutritional Interventions and the Gut Microbiome in Children. Annu Rev Nutr 2021; 41:479-510. [PMID: 34283919 DOI: 10.1146/annurev-nutr-021020-025755] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: (a) Can diet modify the composition, diversity, or function of the gut microbiome, and (b) will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York 14853, USA; .,Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Samantha L Huey
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Daniel McDonald
- Center for Microbiome Innovation and Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation and Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Departments of Bioengineering and Computer Science & Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Julia L Finkelstein
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York 14853, USA; .,Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
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In Vivo Implications of Potential Probiotic Lactobacillus reuteri LR6 on the Gut and Immunological Parameters as an Adjuvant Against Protein Energy Malnutrition. Probiotics Antimicrob Proteins 2021; 12:517-534. [PMID: 31218544 DOI: 10.1007/s12602-019-09563-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The present study investigated the impact of probiotic Lactobacillus reuteri LR6 on the gut and systemic immunity using protein energy malnourished (PEM) murine model. Thirty male Swiss albino mice were divided into five groups: control (C), malnourished (M), probiotic fermented milk (PFM), skim milk (SM), and bacterial suspension (BS) with six mice per group. Group C was fed with conventional diet throughout the study while the other groups were fed with protein calorie restricted diet until the development of malnutrition. After development of malnutrition, group M was continued with the restricted diet while other groups were fed with re-nourished diet supplemented with PFM, SM, and BS for 1 week, respectively. Thereafter, mice were sacrificed and different histological, microbiological, and immunological parameters were studied. Probiotics feeding in PEM model as fermented product or bacterial suspension improved the intestinal health in terms of intact morphology of colonic crypts, normal goblet cells, and intact lamina propria with no inflammation in large intestine, absence of fibrosis, and no inflammation in spleen. The number of secretory IgA+ cells was significantly higher in group PFM and BS. Also, increase in the phagocytic percentage of the macrophages and bone marrow derived dendritic cells (DCs) were observed in the PFM and BS group in comparison to the group M. In comparison to the group M and SM, lactobacilli, bifidobacteria, and Firmicutes counts were significantly higher in the group PFM and BS. This study concludes that probiotic supplementation to re-nutrition diet could emerge as wonder therapeutics against PEM.
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Liu C, Meng X, Zhang H, Yang F, Pan X, Tang K. Early-life famine exposure and rheumatoid arthritis in Chinese adult populations: a retrospective cohort study. BMJ Open 2021; 11:e043416. [PMID: 34226211 PMCID: PMC8258564 DOI: 10.1136/bmjopen-2020-043416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE This study aimed to explore the association between famine exposure in early life and the odds of rheumatoid arthritis (RA) in adulthood. DESIGN A population-based retrospective cohort study. SETTING China. PARTICIPANTS A total of 111 706 participants (1775 with RA) born from 1956 to 1964 were selected from the baseline survey of a large cohort in China. PRIMARY AND SECONDARY OUTCOME MEASURES Four famine exposure groups were generated based on dates of birth, namely prenatal-exposed, infant-exposed, preschool-exposed and non-exposed groups. Logistic regressions were used to explore the association between famine exposure and self-reported RA in adulthood, adjusting for sex, region, monthly income, highest education, alcohol consumption, tobacco use, body mass index (BMI) and metabolic equivalent tasks. Analyses were also performed with stratification for sex (female or male), residing region (urban or rural), famine severity (severe or non-severe) and BMI (≥24 or <24). RESULTS The study included 1775 (1.59%) RA cases and 109 931 (98.41%) non-RA controls. Among them, 22 413 (20.06%) were prenatal-exposed, 14 899 (13.34%) were infant-exposed and 34 356 (30.76%) were preschool-exposed. Prenatal exposure to famine was not associated with onset of RA in adulthood. Infant-exposed group and preschool-exposed group had significantly elevated odds of getting RA compared with non-exposed group (infant-exposed: OR=1.44, 95% CI 1.24 to 1.67; preschool-exposed: OR=1.38, 95% CI 1.22 to 1.57, p<0.001), and the relationship was stronger among women, urban residents and participants with BMI ≥24. Similar results were additionally observed when an age-balanced control group was used. CONCLUSIONS Exposure to the Great Chinese Famine in early life after birth especially in infancy may be associated with a higher risk of RA in adulthood. Strengthening early-life nutrition could be an implication to prevent future RA.
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Affiliation(s)
- Chunyu Liu
- Vanke School of Public Health, Tsinghua University, Beijing, China
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing, China
| | - Xiangrui Meng
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Hao Zhang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing, China
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Fan Yang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing, China
| | - Xiaoyu Pan
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
| | - Kun Tang
- Vanke School of Public Health, Tsinghua University, Beijing, China
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