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Iqbal NT, Chen RY, Griffin NW, Hibberd MC, Khalid A, Sadiq K, Jamil Z, Ahmed K, Iqbal J, Hotwani A, Kabir F, Rahman N, Rizvi A, Idress R, Ahmed Z, Ahmed S, Umrani F, Syed S, Moore SR, Ali A, Barratt MJ, Gordon JI. A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction. mSphere 2024; 9:e0019624. [PMID: 38742887 DOI: 10.1128/msphere.00196-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Environmental enteric dysfunction (EED) is a subclinical syndrome of altered small intestinal function postulated to be an important contributor to childhood undernutrition. The role of small intestinal bacterial communities in the pathophysiology of EED is poorly defined due to a paucity of studies where there has been a direct collection of small intestinal samples from undernourished children. Sixty-three members of a Pakistani cohort identified as being acutely malnourished between 3 and 6 months of age and whose wasting (weight-for-length Z-score [WLZ]) failed to improve after a 2-month nutritional intervention underwent esophagogastroduodenoscopy (EGD). Paired duodenal luminal aspirates and duodenal mucosal biopsies were obtained from 43 children. Duodenal microbiota composition was characterized by sequencing bacterial 16S rRNA gene amplicons. Levels of bacterial taxa (amplicon sequence variants [ASVs]) were referenced to anthropometric indices, histopathologic severity in biopsies, expression of selected genes in the duodenal mucosa, and fecal levels of an immunoinflammatory biomarker (lipocalin-2). A "core" group of eight bacterial ASVs was present in the duodenal samples of 69% of participants. Streptococcus anginosus was the most prevalent, followed by Streptococcus sp., Gemella haemolysans, Streptococcus australis, Granulicatella elegans, Granulicatella adiacens, and Abiotrophia defectiva. At the time of EGD, none of the core taxa were significantly correlated with WLZ. Statistically significant correlations were documented between the abundances of Granulicatella elegans and Granulicatella adiacens and the expression of duodenal mucosal genes involved in immune responses (dual oxidase maturation factor 2, serum amyloid A, and granzyme H). These results suggest that a potential role for members of the oral microbiota in pathogenesis, notably Streptococcus, Gemella, and Granulicatella species, warrants further investigation.IMPORTANCEUndernutrition among women and children is a pressing global health problem. Environmental enteric dysfunction (EED) is a disease of the small intestine (SI) associated with impaired gut mucosal barrier function and reduced capacity for nutrient absorption. The cause of EED is ill-defined. One emerging hypothesis is that alterations in the SI microbiota contribute to EED. We performed a culture-independent analysis of the SI microbiota of a cohort of Pakistani children with undernutrition who had failed a standard nutritional intervention, underwent upper gastrointestinal tract endoscopy, and had histologic evidence of EED in their duodenal mucosal biopsies. The results revealed a shared group of bacterial taxa in their duodenums whose absolute abundances were correlated with levels of the expression of genes in the duodenal mucosa that are involved in inflammatory responses. A number of these bacterial taxa are more typically found in the oral microbiota, a finding that has potential physiologic and therapeutic implications.
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Affiliation(s)
- Najeeha T Iqbal
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Robert Y Chen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas W Griffin
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew C Hibberd
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aqsa Khalid
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Zehra Jamil
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Najeeb Rahman
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Arjumand Rizvi
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Zubair Ahmed
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Sana Syed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Sean R Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Michael J Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
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Serrano Matos YA, Cano J, Shafiq H, Williams C, Sunny J, Cowardin CA. Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition. MICROBIOME 2024; 12:71. [PMID: 38589975 PMCID: PMC11003143 DOI: 10.1186/s40168-024-01783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Childhood undernutrition is a major global health challenge with devastating lifelong consequences. Linear growth stunting due to undernutrition has been linked to poor health outcomes, and mothers who experience growth stunting in childhood are more likely to give birth to stunted children later in life. Based on these findings, we hypothesized that intergenerational colonization of mice with microbiota from human donors with undernutrition may recapitulate certain immune and growth changes observed in this disorder. RESULTS To test this hypothesis, we developed a gnotobiotic murine model of undernutrition using microbiota from human infants with healthy or stunted growth trajectories. Intergenerational colonization with microbiota derived from children with growth stunting lead to less linear growth and the development of immune features of undernutrition and enteropathy, including intestinal villus blunting, lower liver IGF-1 and accumulation of intraepithelial lymphocytes and plasma cells in the small intestine. In contrast, colonization after weaning lead to fewer host phenotypic changes between these distinct microbial communities. CONCLUSIONS These results are broadly consistent with previous findings demonstrating that exposure of the immune system to microbial products during the weaning phase is a critical determinant of later life immune function. Overall, our results suggest intergenerational colonization with human microbiota samples is a useful approach with which to investigate microbiota-dependent changes in growth and immunity in early life. Murine models that capture the intergenerational and multifactorial nature of undernutrition are critical to understanding the underlying biology of this disorder. Video Abstract.
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Affiliation(s)
- Yadeliz A Serrano Matos
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jasmine Cano
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hamna Shafiq
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Claire Williams
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Julee Sunny
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Carrie A Cowardin
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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Mostafa I, Sthity RA, Lamiya UH, Tariqujjaman M, Mahfuz M, Hasan SMT, Ahmed T. Effect of Gut Microbiota-Directed Complementary Food Supplementation on Fecal and Plasma Biomarkers of Gut Health and Environmental Enteric Dysfunction in Slum-Dwelling Children with Moderate Acute Malnutrition. CHILDREN (BASEL, SWITZERLAND) 2024; 11:69. [PMID: 38255381 PMCID: PMC10814735 DOI: 10.3390/children11010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
Dietary supplementation with a gut microbiota-directed complementary food (MDCF-2) significantly improved weight gain and repaired gut microbiota, as reported in a recent randomized controlled trial on Bangladeshi children with moderate acute malnutrition (MAM). Environmental enteric dysfunction (EED) is a small bowel disorder, and recent evidence shows that it is linked to growth failure in children. Therefore, we intended to investigate whether supplementation with MDCF-2 has any role in modifying gut health by changing the levels of biomarkers of EED and gut inflammation in children with MAM. We randomly assigned 124 children aged 12-18 months to one of two intervention diets, either MDCF-2 or ready-to-use supplementary food (RUSF). Approximately 50 g of the diet was administered in two feeding sessions daily for 12 weeks. Stool and plasma biomarkers were assessed to evaluate intestinal health. Results showed that the average change in citrulline concentration (µmol/L) significantly increased among children who consumed MDCF-2 compared to those who consumed RUSF (mean difference-in-differences: 123.10; 95% CI: 3.60, 242.61; p = 0.044). The research findings demonstrated that MDCF-2 might have a beneficial effect on improving the gastrointestinal health of malnourished children.
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Affiliation(s)
- Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - Rahvia Alam Sthity
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
| | - Umme Habiba Lamiya
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
| | - Md. Tariqujjaman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - S. M. Tafsir Hasan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; (R.A.S.); (U.H.L.); (M.T.); (M.M.); (S.M.T.H.); (T.A.)
- Department of Public Health Nutrition, James P Grant School of Public Health, BRAC University, Dhaka 1212, Bangladesh
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Serrano Matos YA, Cano J, Shafiq H, Williams C, Sunny J, Cowardin CA. Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.547849. [PMID: 37461523 PMCID: PMC10350093 DOI: 10.1101/2023.07.07.547849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Childhood undernutrition is a major global health challenge with devastating lifelong consequences. Linear growth stunting due to undernutrition has been linked to poor outcomes, and mothers who experience stunting are more likely to give birth to stunted children. Murine models that capture the intergenerational and multifactorial nature of undernutrition are critical to understanding the underlying biology of this disorder. Here we report a gnotobiotic mouse model of undernutrition using microbiota from human infants with healthy or stunted growth trajectories. Intergenerational transmission of microbiota from parents to offspring leads to the development of growth and immune features of undernutrition and enteropathy, including reduced linear growth, intestinal villus blunting and accumulation of intraepithelial lymphocytes. In contrast, colonization after weaning reduces sensitivity to detect changes driven by distinct microbial communities. Overall, these results suggest intergenerational colonization is a useful approach with which to investigate microbiota-dependent growth and immunity in early life.
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Affiliation(s)
- Yadeliz A. Serrano Matos
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- These authors contributed equally
| | - Jasmine Cano
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- These authors contributed equally
| | - Hamna Shafiq
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Claire Williams
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Julee Sunny
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Carrie A. Cowardin
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Senior author
- Lead contact
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