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Pheeha SM, Tamuzi JL, Chale-Matsau B, Manda S, Nyasulu PS. A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa. Microorganisms 2023; 11:2118. [PMID: 37630678 PMCID: PMC10458939 DOI: 10.3390/microorganisms11082118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.
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Affiliation(s)
- Sara M. Pheeha
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Department of Chemical Pathology, Faculty of Medicine and Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- National Health Laboratory Service, Dr George Mukhari Academic Hospital, Pretoria 0208, South Africa
| | - Jacques L. Tamuzi
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
| | - Bettina Chale-Matsau
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- National Health Laboratory Service, Steve Biko Academic Hospital, Pretoria 0002, South Africa
| | - Samuel Manda
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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Balaji V, Dinh DM, Kane AV, Soofi S, Ahmed I, Rizvi A, Chatterjee M, Babji S, Duara J, Moy J, Naumova EN, Wanke CA, Ward HD, Bhutta ZA. Longitudinal Analysis of the Intestinal Microbiota among a Cohort of Children in Rural and Urban Areas of Pakistan. Nutrients 2023; 15:1213. [PMID: 36904212 PMCID: PMC10005232 DOI: 10.3390/nu15051213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
The profile of the intestinal microbiota is known to be altered in malnourished young children in low- and middle-income countries. However, there are limited studies longitudinally evaluating the intestinal microbiota in malnourished young children in resource-limited settings over the first two years of life. In this longitudinal pilot study, we determined the effect of age, residential location, and intervention on the composition, relative abundance, and diversity of the intestinal microbiota in a representative sample of children under 24 months of age with no diarrhea in the preceding 72 h in the urban and rural areas of Sindh, Pakistan nested within a cluster-randomized trial evaluating the effect of zinc and micronutrients on growth and morbidity (ClinicalTrials.gov Identifier: NCT00705445). The major findings were age-related with significant changes in alpha and beta diversity with increasing age. There was a significant increase in the relative abundance of the Firmicutes and Bacteroidetes phyla and a significant decrease in that of the Actinobacteria and Proteobacteria phyla (p < 0.0001). There were significant increases in the relative abundances of the major genera Bifidobacterium, Escherichia/Shigella and Streptococcus (p < 0.0001), and no significant change in the relative abundance of Lactobacillus. Using the LEfSE algorithm, differentially abundant taxa were identified between children in the first and second years of age, between those residing in rural and urban areas, and those who received different interventions at different ages from 3 to 24 months. The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them. Further longitudinal studies with larger numbers of well-nourished and malnourished children are required to fully characterize the intestinal microbiota of children in this region.
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Affiliation(s)
- Veeraraghavan Balaji
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Microbiology, Christian Medical College, Vellore 632004, India
| | - Duy M. Dinh
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Anne V. Kane
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Sajid Soofi
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Imran Ahmed
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Arjumand Rizvi
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Meera Chatterjee
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Sudhir Babji
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Microbiology, Christian Medical College, Vellore 632004, India
| | - Joanne Duara
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Joy Moy
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Elena N. Naumova
- Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Christine A. Wanke
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Honorine D. Ward
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Zulfiqar A. Bhutta
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 3E2, Canada
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Kazemifard N, Dehkohneh A, Baradaran Ghavami S. Probiotics and probiotic-based vaccines: A novel approach for improving vaccine efficacy. Front Med (Lausanne) 2022; 9:940454. [PMID: 36313997 PMCID: PMC9606607 DOI: 10.3389/fmed.2022.940454] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Vaccination is defined as the stimulation and development of the adaptive immune system by administering specific antigens. Vaccines' efficacy, in inducing immunity, varies in different societies due to economic, social, and biological conditions. One of the influential biological factors is gut microbiota. Cross-talks between gut bacteria and the host immune system are initiated at birth during microbial colonization and directly control the immune responses and protection against pathogen colonization. Imbalances in the gut microbiota composition, termed dysbiosis, can trigger several immune disorders through the activity of the adaptive immune system and impair the adequate response to the vaccination. The bacteria used in probiotics are often members of the gut microbiota, which have health benefits for the host. Probiotics are generally consumed as a component of fermented foods, affect both innate and acquired immune systems, and decrease infections. This review aimed to discuss the gut microbiota's role in regulating immune responses to vaccination and how probiotics can help induce immune responses against pathogens. Finally, probiotic-based oral vaccines and their efficacy have been discussed.
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Affiliation(s)
- Nesa Kazemifard
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abolfazl Dehkohneh
- Department for Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany,Department of Biology Chemistry Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Shaghayegh Baradaran Ghavami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran,*Correspondence: Shaghayegh Baradaran Ghavami
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Liu Z, Fan YM, Ashorn P, Chingwanda C, Maleta K, Hallamaa L, Hyöty H, Chaima D, Ashorn U. Lack of Associations between Environmental Exposures and Environmental Enteric Dysfunction among 18-Month-Old Children in Rural Malawi. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10891. [PMID: 36078607 PMCID: PMC9517768 DOI: 10.3390/ijerph191710891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Environmental enteric dysfunction (EED) is common and contributes to linear growth faltering (stunting) and mortality among children in low-resource settings. A few studies on the environmental causes of EED have been conducted but the exact exposures that cause or predispose children to EED are context-specific and not clear. This study aimed to assess associations between selected environmental exposures and EED markers among 620 18-month-old children. This was a secondary analysis of data from Malawian children who participated in a randomized controlled trial (iLiNS-DYAD, registered at clinicaltrials.gov as NCT01239693) from birth to 18 months of age. Data on environmental exposures, including drinking water source, sanitation, exposure to animals, housing materials, season, residential area, and food insecurity were collected at enrolment. Biomarkers of EED included concentrations of calprotectin, regenerating 1B protein (REG1B), and alpha-1-antitrypsin from stool samples to assess intestinal inflammation, repair, and permeability, respectively. We performed bivariate and multivariable analyses to assess associations between environmental exposures and EED biomarkers. Adjusting for possible confounders, we did not find associations between the selected environmental exposures and the three biomarkers. These results do not provide support for our hypothesis that the studied adverse environmental exposures are associated with increased concentrations of children's EED markers in rural Malawi.
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Affiliation(s)
- Zhifei Liu
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
- Department of Paediatrics, Tampere University Hospital, 33521 Tampere, Finland
| | - Chilungamo Chingwanda
- School of Public Health & Family Medicine, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Kenneth Maleta
- School of Public Health & Family Medicine, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Lotta Hallamaa
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Heikki Hyöty
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, 33521 Tampere, Finland
| | - David Chaima
- School of Public Health & Family Medicine, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
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Puga AM, Samaniego-Vaesken MDL, Montero-Bravo A, Ruperto M, Partearroyo T, Varela-Moreiras G. Iron Supplementation at the Crossroads of Nutrition and Gut Microbiota: The State of the Art. Nutrients 2022; 14:nu14091926. [PMID: 35565894 PMCID: PMC9102039 DOI: 10.3390/nu14091926] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022] Open
Abstract
Gut microbiota has received significant attention owing to its decisive role in human health and disease. Diet exerts a significant influence on the variety and number of bacteria residing in the intestinal epithelium. On the other hand, as iron is a key micronutrient for blood formation and oxygen supply, its deficiency is highly prevalent worldwide. In fact, it is the most common cause of anemia and thus, iron supplementation is widespread. However, there is concern due to some potential risks linked to iron supplementation. Therefore, we have reviewed the available evidence of the effects that iron supplementation exerts on the gut microbiota as well as its potential benefits and risks. The compiled information suggests that iron supplementation is potentially harmful for gut microbiota. Therefore, it should be performed with caution, and by principle, recommended only to individuals with proven iron deficiency or iron-deficiency anemia to avoid potential adverse effects. In any case, large and long-term population studies are urgently needed to confirm or refute these results, mainly focused on vulnerable populations.
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Kortekangas E, Fan YM, Chaima D, Lehto KM, Malamba-Banda C, Matchado A, Chingwanda C, Liu Z, Ashorn U, Cheung YB, Dewey KG, Maleta K, Ashorn P. Associations between Gut Microbiota and Intestinal Inflammation, Permeability and Damage in Young Malawian Children. J Trop Pediatr 2022; 68:6527323. [PMID: 35149871 PMCID: PMC8846364 DOI: 10.1093/tropej/fmac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Environmental enteric dysfunction (EED) is common in low- and middle-income countries and associated with childhood undernutrition. The composition of gut microbiota has been implicated in the pathogenesis of EED. Our aim was to assess the associations between gut microbiota and EED biomarkers in rural Malawian children. We hypothesized that there would be an inverse association between microbiota maturity and diversity and fecal concentrations of EED biomarkers. METHODS We used data from fecal samples collected at 6, 18 and 30 months from 611 children who were followed up during a nutrition intervention trial. The primary time point for analysis was 18 months. Microbiota data were obtained through 16S rRNA sequencing and variables included microbiota maturity and diversity, phylogenetic dissimilarity and relative abundances of individual taxa. EED biomarkers included calprotectin (marker of inflammation), alpha-1 antitrypsin (intestinal permeability) and REG1B (intestinal damage). RESULTS There was an inverse association between microbiota maturity and diversity and fecal concentrations of all 3 EED biomarkers at 18 months (p≤0.001). The results were similar at 30 months, while at 6 months inverse associations were found only with calprotectin and alpha-1 antitrypsin concentrations. At 18 months, EED biomarkers were not associated with phylogenetic dissimilarity, but at 6 and 30 months several associations were observed. Individual taxa predicting EED biomarker concentrations at 18 months included several Bifidobacterium and Enterobacteriaceae taxa as well as potentially displaced oral taxa. CONCLUSIONS Our findings support the hypothesis of an inverse association between microbiota maturity and diversity and EED in rural Malawian children.
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Affiliation(s)
- Emma Kortekangas
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland,Correspondence: Emma Kortekangas, Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Global Health, Tampere University, Arvo Ylpön katu 34, Arvo building, Tampere 33014, Finland. Tel: +358-3-355-111. Fax +358-3-213-4473. E-mail <>
| | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - David Chaima
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Kirsi-Maarit Lehto
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Chikondi Malamba-Banda
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Andrew Matchado
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi,Department of Nutrition and Institute for Global Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Chilungamo Chingwanda
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Zhifei Liu
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Yin Bun Cheung
- Program in Health Services & Systems Research and Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kathryn G Dewey
- Department of Nutrition and Institute for Global Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Kenneth Maleta
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland,Department of Pediatrics, Tampere University Hospital, Tampere 33520, Finland
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de Goffau MC, Jallow AT, Sanyang C, Prentice AM, Meagher N, Price DJ, Revill PA, Parkhill J, Pereira DIA, Wagner J. Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network. Nat Microbiol 2022; 7:132-144. [PMID: 34972822 PMCID: PMC8727306 DOI: 10.1038/s41564-021-01023-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P. stercorea or F. prausnitzii and were found to develop steadily with age, whereas P. copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.
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Affiliation(s)
- Marcus C de Goffau
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Chilel Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - David J Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - Peter A Revill
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Dora I A Pereira
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Josef Wagner
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia.
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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He J, Zheng W, Tao C, Guo H, Xue Y, Zhao R, Yao W. Heat stress during late gestation disrupts maternal microbial transmission with altered offspring's gut microbial colonization and serum metabolites in a pig model. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115111. [PMID: 32663631 DOI: 10.1016/j.envpol.2020.115111] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Heat stress (HS) during gestation has been associated with negative outcomes, such as preterm birth or postnatal metabolic syndromes. The intestinal microbiota is a unique ecosystem playing an essential role in mediating the metabolism and health of mammals. Here we hypothesize late gestational HS alters maternal microbial transmission and structures offspring's intestinal microbiota and serum metabolic profiles. Our results show maternal HS alters bacterial β-diversity and composition in sows and their piglets. In the maternal intestine, genera Ruminococcaceae UCG-005, [Eubacterium] coprostanoligenes group and Halomonas are higher by HS (q < 0.05), whereas the populations of Streptococcus, Bacteroidales RF16 group_norank and Roseburia are decreased (q < 0.05). In the maternal vagina, HS mainly elevates the proportions of phylum Bacteroidetes and Fusobacteria (q < 0.05), whereas reduces the population of Clostridiales Family XI (q < 0.05). In the neonatal intestine, maternal HS promotes the population of Proteobacteria but reduces the relative abundance of Firmicutes (q < 0.05). Moreover, the core Operational taxonomic units (OTU) analysis indicates the proportions of Clostridium sensu stricto 1, Romboutsia and Turicibacter are decreased by maternal HS in the intestinal and vaginal co-transmission, whereas that of phylum Proteobacteria and Epsilonbacteraeota, such as Escherichia-Shigella, Klebsiella, Acinetobacter, and Comamonas are increased in both the intestinal and vaginal co-transmission and the vagina. Additionally, Aeromonas is the only genus that is transmitted from environmental sources. Lastly, we evaluate the importance of neonatal differential OTU for the differential serum metabolites. The results indicate Acinetobacter significantly contributes to the differences in the adrenocorticotropic hormone (ACTH) and glucose levels due to HS (P < 0.05). Further, Stenotrophomonas is the most important variable for Cholesterol, low-density lipoprotein (LDL), diamine oxidase (DAO), blood urea nitrogen (BUN) and 5-hydroxytryptamine (5-HT) (P < 0.10). Overall, our data provides evidence for the maternal HS in establishing the neonatal microbiota via affecting maternal transmission, which in turn affects the maintenance of metabolic health.
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Affiliation(s)
- Jianwen He
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Weijiang Zheng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China; National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Huiduo Guo
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yongqiang Xue
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ruqian Zhao
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wen Yao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China; National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China; Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China.
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10
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Hughes RL, Arnold CD, Young RR, Ashorn P, Maleta K, Fan YM, Ashorn U, Chaima D, Malamba-Banda C, Kable ME, Dewey KG. Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi. Sci Rep 2020; 10:14861. [PMID: 32908192 PMCID: PMC7481312 DOI: 10.1038/s41598-020-71922-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
An unhealthy gut microbial community may act as a barrier to improvement in growth and health outcomes in response to nutritional interventions. The objective of this analysis was to determine whether the infant microbiota modified the effects of a randomized controlled trial of lipid-based nutrient supplements (LNS) in Malawi on growth and inflammation at 12 and 18 months, respectively. We characterized baseline microbiota composition of fecal samples at 6 months of age (n = 506, prior to infant supplementation, which extended to 18 months) using 16S rRNA gene sequencing of the V4 region. Features of the gut microbiota previously identified as being involved in fatty acid or micronutrient metabolism or in outcomes relating to growth and inflammation, especially in children, were investigated. Prior to correction for multiple hypothesis testing, the effects of LNS on growth appeared to be modified by Clostridium (p-for-interaction = 0.02), Ruminococcus (p-for-interaction = 0.007), and Firmicutes (p-for-interaction = 0.04) and effects on inflammation appeared to be modified by Faecalibacterium (p-for-interaction = 0.03) and Streptococcus (p-for-interaction = 0.004). However, after correction for multiple hypothesis testing these findings were not statistically significant, suggesting that the gut microbiota did not alter the effect of LNS on infant growth and inflammation in this cohort.
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Affiliation(s)
- Riley L Hughes
- Department of Nutrition, University of California, Davis, CA, USA
| | - Charles D Arnold
- Department of Nutrition, University of California, Davis, CA, USA
| | - Rebecca R Young
- Department of Nutrition, University of California, Davis, CA, USA
| | - Per Ashorn
- Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Ken Maleta
- College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Yue-Mei Fan
- Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ulla Ashorn
- Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - David Chaima
- School of Public Health and Family Medicine, University of Malawi College of Medicine, Blantyre, Malawi
| | - Chikondi Malamba-Banda
- School of Public Health and Family Medicine, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mary E Kable
- Immunity and Disease Prevention, Western Human Nutrition Research Center, Agricultural Research Service, USDA, Davis, CA, USA
| | - Kathryn G Dewey
- Department of Nutrition, University of California, Davis, CA, USA.
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11
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Kortekangas E, Kamng'ona AW, Fan Y, Cheung YB, Ashorn U, Matchado A, Poelman B, Maleta K, Dewey KG, Ashorn P. Environmental exposures and child and maternal gut microbiota in rural Malawi. Paediatr Perinat Epidemiol 2020; 34:161-170. [PMID: 32011017 PMCID: PMC7154550 DOI: 10.1111/ppe.12623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/24/2019] [Accepted: 11/17/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Gut microbiota composition is associated with child health, but the effect of the environment on microbiota composition is not well understood. Few studies have been conducted in low-income settings where childhood malnutrition is common and possibly related to microbiota composition. OBJECTIVES To investigate whether gut microbiota composition in young children and their mothers is associated with different environmental exposures in rural Malawi. We hypothesized that more adverse environmental exposures would be associated with lower levels of microbiota maturity and diversity. METHODS Faecal samples from up to 631 children and mothers participating in a nutrition intervention trial were collected at 1, 6, 12, 18, and 30 months (children) and at 1 month (mothers) after birth and analysed for microbiota composition with 16S rRNA sequencing. Bacterial OTU and genus abundances, measures of microbiota maturity and diversity, and UniFrac distances were compared between participants with different environmental exposures. The exposure variables included socio-economic status, water source, sanitary facility, domestic animals, maternal characteristics, season, antibiotic use, and delivery mode. RESULTS Measures of microbiota maturity and diversity in children were inversely associated with maternal education at 6, 18, and 30 months and did not otherwise differ consistently between participants with different environmental exposures. Phylogenetic distance was related to season of stool sample collection at all time points. At the level of individual OTUs and genera, season of stool sample collection, type of water source, and maternal education showed most associations with child gut microbiota, while HIV status was the most important predictor of relative OTU and genus abundances in mothers. CONCLUSION The results do not support the hypothesis that adverse environmental exposures are broadly associated with lower microbiota maturity and diversity but suggest that environmental exposures influence the abundance of several bacterial OTUs and genera and that low maternal education is associated with higher microbiota maturity and diversity.
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Affiliation(s)
- Emma Kortekangas
- Center for Child Health ResearchFaculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Arox W. Kamng'ona
- Department of Biomedical SciencesCollege of MedicineUniversity of MalawiBlantyreMalawi,Program in International and Community NutritionUniversity of California DavisDavisCAUSA
| | - Yue‐Mei Fan
- Center for Child Health ResearchFaculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Yin Bun Cheung
- Program in Health Services & Systems Research and Centre for Quantitative MedicineDuke‐NUS Medical SchoolSingaporeSingapore
| | - Ulla Ashorn
- Center for Child Health ResearchFaculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Andrew Matchado
- Program in International and Community NutritionUniversity of California DavisDavisCAUSA,School of Public Health and Family MedicineUniversity of Malawi College of MedicineBlantyreMalawi
| | - Basho Poelman
- Center for Child Health ResearchFaculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Kenneth Maleta
- School of Public Health and Family MedicineUniversity of Malawi College of MedicineBlantyreMalawi
| | | | - Per Ashorn
- Center for Child Health ResearchFaculty of Medicine and Health TechnologyTampere UniversityTampereFinland,Department of PaediatricsTampere University HospitalTampereFinland
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