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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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Shennon I, Wilson BC, Behling AH, Portlock T, Haque R, Forrester T, Nelson CA, O'Sullivan JM. The infant gut microbiome and cognitive development in malnutrition. Clin Nutr 2024; 43:1181-1189. [PMID: 38608404 DOI: 10.1016/j.clnu.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 03/11/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
Malnutrition affects 195 million children under the age of five worldwide with long term effects that include impaired cognitive development. Brain development occurs rapidly over the first 36 months of life. Whilst seemingly independent, changes to the brain and gut microbiome are linked by metabolites, hormones, and neurotransmitters as part of the gut-brain axis. In the context of severe malnutrition, the composition of the gut microbiome and the repertoire of biochemicals exchanged via the gut-brain axis vary when compared to healthy individuals. These effects are primarily due to the recognized interacting determinants, macro- and micronutrient deficiencies, infection, infestations and toxins related to poor sanitation, and a dearth of psycho-social stimulation. The standard of care for the treatment of severe acute malnutrition is focused on nutritional repletion and weight restoration through the provision of macro- and micronutrients, the latter usually in excess of recommended dietary allowances (RDA). However, existing formulations and supplements have not been designed to specifically address key recovery requirements for brain and gut microbiome development. Animal model studies indicate that treatments targeting the gut microbiome could improve brain development. Despite this, research on humans targeting the gut microbiome with the aim of restoring brain functionality are scarce. We conclude that there is a need for assessment of cognition and the use of various tools that permit visualization of the brain anatomy and function (e.g., Magnetic resonance imaging (MRI), functional near-infrared spectroscopy (fNIRS), electroencephalogram (EEG)) to understand how interventions targeting the gut microbiome impact brain development.
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Affiliation(s)
- Inoli Shennon
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Brooke C Wilson
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Anna H Behling
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Theo Portlock
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Rashidul Haque
- Infectious Disease Division, International Centre for Diarrheal Disease Research, Bangladesh
| | - Terrence Forrester
- UWI Solutions for Developing Countries, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Charles A Nelson
- Department of Pediatrics, Division of Developmental Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Harvard Graduate School of Education, Cambridge, MA, USA
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Auckland 1010, New Zealand; MRC Lifecourse Epidemiology Unit, University of Southampton, University Road, Southampton SO17 1BJ, UK; Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore.
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Surono IS, Popov I, Verbruggen S, Verhoeven J, Kusumo PD, Venema K. Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia. PLoS One 2024; 19:e0299349. [PMID: 38551926 PMCID: PMC10980242 DOI: 10.1371/journal.pone.0299349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/06/2024] [Indexed: 04/01/2024] Open
Abstract
The role of the gut microbiota in energy metabolism of the host has been established, both in overweight/obesity, as well as in undernutrition/stunting. Dysbiosis of the gut microbiota may predispose to stunting. The aim of this study was to compare the gut microbiota composition of stunted Indonesian children and non-stunted children between 36 and 45 months from two sites on the East Nusa Tenggara (ENT) islands. Fecal samples were collected from 100 stunted children and 100 non-stunted children in Kupang and North Kodi. The gut microbiota composition was determined by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Moreover, fecal SCFA concentrations were analyzed. The microbiota composition was correlated to anthropometric parameters and fecal metabolites. The phyla Bacteroidetes (Bacteroidota; q = 0.014) and Cyanobacteria (q = 0.049) were significantly higher in stunted children. Three taxa at genus levels were consistently significantly higher in stunted children at both sampling sites, namely Lachnoclostridium, Faecalibacterium and Veillonella (q < 7 * 10-4). These and 9 other taxa positively correlated to the z-score length-for-age (zlen), while 11 taxa negatively correlated with zlen. Several taxa also correlated with sanitary parameters, some of which were also significantly different between the two groups. All three fecal SCFA concentrations (acetate, propionate and butyrate) and their total were lower in stunted children compared to non-stunted children, although not significant for butyrate, indicating lower energy-extraction by the gut microbiota. Also, since SCFA have been shown to be involved in gut barrier function, barrier integrity may be affected in the stunted children. It remains to be seen if the three taxa are involved in stunting, or are changed due to e.g. differences in diet, hygiene status, or other factors. The observed differences in this study do not agree with our previous observations in children on Java, Indonesia. There are differences in infrastructure facilities such as clean water and sanitation on ENT and Java, which may contribute to the differences observed. The role of the gut microbiota in stunting therefore requires more in depth studies. Trial registration: the trial was registered at ClinicalTrials.gov with identifier number NCT05119218.
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Affiliation(s)
- Ingrid S. Surono
- Faculty of Engineering, Food Technology Department, Bina Nusantara University, Jakarta, Indonesia
| | - Ilia Popov
- Faculty of Engineering, Food Technology Department, Bina Nusantara University, Jakarta, Indonesia
| | - Sanne Verbruggen
- Centre for Healthy Eating & Food Innovation, Maastricht University—Campus Venlo, Venlo, The Netherlands
| | - Jessica Verhoeven
- Centre for Healthy Eating & Food Innovation, Maastricht University—Campus Venlo, Venlo, The Netherlands
| | - Pratiwi D. Kusumo
- Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation, Maastricht University—Campus Venlo, Venlo, The Netherlands
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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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Jones HJ, Bourke CD, Swann JR, Robertson RC. Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition. Annu Rev Nutr 2023; 43:327-353. [PMID: 37207356 DOI: 10.1146/annurev-nutr-061121-091234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Childhood undernutrition is a major global health burden that is only partially resolved by nutritional interventions. Both chronic and acute forms of child undernutrition are characterized by derangements in multiple biological systems including metabolism, immunity, and endocrine systems. A growing body of evidence supports a role of the gut microbiome in mediating these pathways influencing early life growth. Observational studies report alterations in the gut microbiome of undernourished children, while preclinical studies suggest that this can trigger intestinal enteropathy, alter host metabolism, and disrupt immune-mediated resistance against enteropathogens, each of which contribute to poor early life growth. Here, we compile evidence from preclinical and clinical studies and describe the emerging pathophysiological pathways by which the early life gut microbiome influences host metabolism, immunity, intestinal function, endocrine regulation, and other pathways contributing to child undernutrition. We discuss emerging microbiome-directed therapies and consider future research directions to identify and target microbiome-sensitive pathways in child undernutrition.
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Affiliation(s)
- Helen J Jones
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Claire D Bourke
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ruairi C Robertson
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
- Microenvironment and Immunity Unit, INSERM U1224, Institut Pasteur, Université Paris Cité, Paris, France
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Veeraraghavan B, Kesavelu D, Yadav B. Gut Microbiota Composition in Indian and Western Infants (0–24 Months): A Systematic Review. NUTRITION AND DIETARY SUPPLEMENTS 2023. [DOI: 10.2147/nds.s402256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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Shivakumar N, Thomas T, Devi S, Jahoor F, Kurpad AV. Free living total energy expenditure in young South Indian children at risk of environmental enteric dysfunction and its relation to faltered linear growth. Eur J Clin Nutr 2023; 77:532-537. [PMID: 36720933 DOI: 10.1038/s41430-023-01268-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/01/2023]
Abstract
BACKGROUND/OBJECTIVES Chronic immune activation in Environmental Enteric Dysfunction (EED) could lead to increased fed-state metabolic rate (MR) or total energy expenditure (TEE) and limit the energy available for optimal linear growth. In a secondary analysis, MR and TEE were compared in young Indian children from urban slums, with and without stunting or EED. SUBJECTS/METHODS Children (18-24 months, n = 69) were classified into non-stunted (LAZ ≥ -2) and stunted (LAZ < -2), and no-EED (lactulose rhamnose ratio, LRR < 0.068) and EED (LRR ≥ 0.068) groups. Associations between MR and TEE (kcal per kg bodyweight [BW] or fat free mass [FFM]) with stunting and EED were examined using logistic regression. RESULTS Median TEE was significantly higher in the stunted compared to non-stunted group (76.8 versus 92.0 kcal/kg BW/day, p = <0.01). The adjusted (for sex, FFM, EED) odds ratio (AOR) for stunting with TEE (kcal/day) was 1.01 (95% CI: 1.00, 1.01), but importantly, there was no interaction between EED and TEE. The median TEE was also significantly higher in the EED compared to the no-EED group (89.1 vs 76.8 kcal/kg BW/day, p = 0.02), and the AOR (adjusted for sex and TEE) for stunting with EED was 3.56 (95% CI:1.09, 11.63). MR (per kg BW or FFM) was not associated with stunting or EED. CONCLUSION Higher TEE and presence of EED were independently and positively associated with stunting. Children with EED also had higher TEE but not MR. Energetically, the higher TEE in stunted children may not specifically be linked to the presence of EED, although the latter independently had higher odds of stunting.
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Affiliation(s)
- Nirupama Shivakumar
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Tinku Thomas
- Department of Biostatistics, St. John's Medical College, St. John's National Academy of Health Sciences, Bangalore, India
| | - Sarita Devi
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Farook Jahoor
- USDA/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Anura V Kurpad
- Department of Physiology, St. John's Medical College, St. John's National Academy of Health Sciences, Bangalore, India.
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Coker MO, Lebeaux RM, Hoen AG, Moroishi Y, Gilbert-Diamond D, Dade EF, Palys TJ, Madan JC, Karagas MR. Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood. Sci Rep 2022; 12:13075. [PMID: 35906254 PMCID: PMC9338228 DOI: 10.1038/s41598-022-14668-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/10/2022] [Indexed: 12/15/2022] Open
Abstract
Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. We aimed to evaluate if there is an association between child growth and the saliva microbiome. We hypothesized that associations between growth and the saliva microbiome would be moderate, similarly to the association between growth and the gut microbiome. For 236 toddlers participating in the New Hampshire Birth Cohort Study, we characterized the association between multiple longitudinal anthropometric measures of body height, body weight and body mass. Body Mass Index (BMI) z-scores were calculated, and dual-energy x-ray absorptiometry (DXA) was used to estimate body composition. Shotgun metagenomic sequencing of saliva samples was performed to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Although the magnitude of associations were small, some taxa were consistently associated with growth and modified by sex. Certain taxa were associated with decreased weight or growth (including Actinomyces odontolyticus and Prevotella melaninogenica) or increased growth (such as Streptococcus mitis and Corynebacterium matruchotii) across anthropometric measures. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.
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Affiliation(s)
- Modupe O Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Oral Biology, School of Dental Medicine, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA.
| | - Rebecca M Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Diane Gilbert-Diamond
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Erika F Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Thomas J Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Departments of Pediatrics and Psychiatry, Children's Hospital at Dartmouth, Lebanon, NH, 03766, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
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