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Backhaus J, Kann S, Hahn A, Weinreich F, Blohm M, Tanida K, Feldt T, Sarfo FS, Di Cristanziano V, Loderstädt U, Ehrhardt S, Schoppen S, Tagbor H, Frickmann H, Eberhardt KA. Clustering of Gastrointestinal Microorganisms in Human Stool Samples from Ghana. Pathogens 2024; 13:583. [PMID: 39057810 PMCID: PMC11279407 DOI: 10.3390/pathogens13070583] [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: 06/29/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
The study was conducted to identify cluster patterns of enteric microorganisms with potential etiological relevance for infectious gastroenteritis in stool samples of individuals from Ghana, which is a known high-endemicity setting for infectious gastroenteritis. These patterns were compared to previous observations with specimens from Colombian indigenous people in order to assess potentially stable clustering for temporally and spatially distinct populations from high-endemicity regions. By doing so, the study aimed to identify stable clusters as markers of microbial interaction with potential importance for etiological relevance assignment in cases of multiple enteric pathogen detections. Stool samples from 1569 Ghanaian individuals (875 from HIV patients, 30 from HIV-negative control adult patients, and 644 from children < 2 years of age) were assessed for enteric microorganisms by applying real-time PCR. As a result, nucleic acids of bacterial microorganisms were most frequently detected, followed by protozoa, microsporidia, and helminths. Interestingly, the cluster assessment confirmed interaction patterns known from the previous analysis with Colombian indigenous people, demonstrating a high likelihood of Blastocystis hominis for clustering with other microorganisms and a prominent, potentially mediating role of Dientamoeba fragilis for microbial interactions within the clusters. In conclusion, the assessment confirmed conserved clustering of enteric microorganisms with potential etiological relevance for human infectious gastroenteritis over geographically distinct high-endemicity settings. Furthermore, the composition of abundant microorganisms is more important than regional factors for the determination of the interplay of enteric microorganisms in the human gut. Thereby, some microbial pathogens and commensals seem more susceptible to a changing microbial composition in the human gut than others.
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Affiliation(s)
- Joy Backhaus
- Statistical Consulting, 97074 Wuerzburg, Germany;
| | - Simone Kann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany;
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, 53127 Bonn, Germany
| | - Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany;
| | | | - Martin Blohm
- Laboratory Department, Bundeswehr Hospital Berlin, 10115 Berlin, Germany;
| | - Konstantin Tanida
- Institute for Microbiology, Virology and Hygiene, University Hospital Eppendorf, 20251 Hamburg, Germany;
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Fred Stephen Sarfo
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana;
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany;
| | - Ulrike Loderstädt
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Stephan Ehrhardt
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MA 21205, USA;
| | - Stefanie Schoppen
- Department of Health and Social Science, Hochschule Fresenius, 20148 Hamburg, Germany;
| | - Harry Tagbor
- School of Medicine, Department of Community Health, University of Health and Allied Sciences, Ho PMB 31, Ghana;
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany;
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
| | - Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center, 20359 Hamburg, Germany
- Division of Hygiene and Infectious Diseases, Institute of Hygiene and Environment, 20539 Hamburg, Germany
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Momo Cabrera P, Rachmühl C, Derrien M, Bourdet-Sicard R, Lacroix C, Geirnaert A. Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation. ISME COMMUNICATIONS 2024; 4:ycae033. [PMID: 38774131 PMCID: PMC11107946 DOI: 10.1093/ismeco/ycae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/10/2024] [Indexed: 05/24/2024]
Abstract
Iron fortification to prevent anemia in African infants increases colonic iron levels, favoring the growth of enteropathogens. The use of prebiotics may be an effective strategy to reduce these detrimental effects. Using the African infant PolyFermS gut model, we compared the effect of the prebiotics short-chain galacto- with long-chain fructo-oligosaccharides (scGOS/lcFOS) and native inulin, and the emerging prebiotic acacia gum, a branched-polysaccharide-protein complex consisting of arabinose and galactose, during iron supplementation on four Kenyan infant gut microbiota. Iron supplementation did not alter the microbiota but promoted Clostridioides difficile in one microbiota. The prebiotic effect of scGOS/lcFOS and inulin was confirmed during iron supplementation in all investigated Kenyan infant gut microbiota, leading to higher abundance of bifidobacteria, increased production of acetate, propionate, and butyrate, and a significant shift in microbiota composition compared to non-supplemented microbiota. The abundance of the pathogens Clostridium difficile and Clostridium perfringens was also inhibited upon addition of the prebiotic fibers. Acacia gum had no effect on any of the microbiota. In conclusion, scGOS/lcFOS and inulin, but not acacia gum, showed a donor-independent strong prebiotic potential in Kenyan infant gut microbiota. This study demonstrates the relevance of comparing fibers in vitro prior to clinical studies.
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Affiliation(s)
- Paula Momo Cabrera
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Muriel Derrien
- Danone Global Research & Innovation Center, 91190 Gif sur Yvette, France
- Present address: Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute KU, 3000 Leuven, Belgium
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
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Rachmühl C, Lacroix C, Cabrera PM, Geirnaert A. Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model. Sci Rep 2023; 13:20563. [PMID: 37996456 PMCID: PMC10667343 DOI: 10.1038/s41598-023-47131-7] [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: 06/23/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Appropriate in vitro models to investigate the impact of novel nutritional strategies on the gut microbiota of infants living in rural Africa are scarce. Here, we aimed to develop such a continuous gut fermentation model based on the PolyFermS platform, which allows controlled and stable long-term cultivation of colon microbiota in conditions akin the host. Nine immobilized Kenyan infant fecal microbiota were used as inoculum for continuous PolyFermS colon models fed with medium mimicking the weaning infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were investigated stepwise. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74-89%) and stable during 107 days of continuous cultivation. Community diversity was maintained and two distinct fermentation metabolite profiles of infant fecal microbiota were observed. Three propiogenic and one butyrogenic metabolite profile of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first rationally designed continuous cultivation model of African infant gut microbiota. This model will be important to assess the effect of dietary or environmental factors on the gut microbiota of African infants with high enteropathogen exposure.
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Affiliation(s)
- Carole Rachmühl
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
| | - Paula Momo Cabrera
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
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Rachmühl C, Lacroix C, Cabrera PM, Geirnaert A. Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model. RESEARCH SQUARE 2023:rs.3.rs-3101157. [PMID: 37461546 PMCID: PMC10350169 DOI: 10.21203/rs.3.rs-3101157/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Appropriate in vitro models to investigate the impact of novel nutritional strategies on the gut microbiota of infants living in rural Africa are scarce. Here, we aimed to develop such a continuous gut fermentation model based on the PolyFermS platform. Eight immobilized Kenyan infant fecal microbiota were used as inoculum for continuous PolyFermS colon models fed with medium mimicking the weaning infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were stepwise investigated. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74-89%) and stable during 107 days of continuous cultivation. Community diversity was maintained, and two distinct fermentation metabolite profiles, propiogenic and butyrogenic, of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first rationally designed and accurate continuous cultivation model of African infant gut microbiota. This model will be important to assess the effect of dietary or environmental factors on the gut microbiota of African infants with high enteropathogen exposure.
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Farahmand M, Khales P, Salavatiha Z, Sabaei M, Hamidzade M, Aminpanah D, Tavakoli A. Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis. Microb Pathog 2023:106209. [PMID: 37385570 DOI: 10.1016/j.micpath.2023.106209] [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: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/01/2023]
Abstract
AIM Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis. METHODS Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis. RESULTS Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I2 = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%). CONCLUSION The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Salavatiha
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Milad Sabaei
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Hamidzade
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Danesh Aminpanah
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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Eberhardt KA, Sarfo FS, Klupp EM, Dompreh A, Di Cristanziano V, Osei Kuffour E, Boateng R, Norman B, Phillips RO, Aepfelbacher M, Feldt T. Intestinal Colonization with Tropheryma whipplei-Clinical and Immunological Implications for HIV Positive Adults in Ghana. Microorganisms 2021; 9:1781. [PMID: 34442860 PMCID: PMC8400997 DOI: 10.3390/microorganisms9081781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Recent studies demonstrated higher prevalence rates of Tropheryma whipplei (T. whipplei) in HIV positive than in HIV negative subjects. However, associations with the immune status in HIV positive participants were conflicting. METHODS For this cross-sectional study, stool samples of 906 HIV positive and 98 HIV negative individuals in Ghana were tested for T. whipplei. Additionally, sociodemographic parameters, clinical symptoms, medical drug intake, and laboratory parameters were assessed. RESULTS The prevalence of T. whipplei was 5.85% in HIV positive and 2.04% in HIV negative participants. Within the group of HIV positive participants, the prevalence reached 7.18% in patients without co-trimoxazole prophylaxis, 10.26% in subjects with ART intake, and 12.31% in obese participants. Frequencies of clinical symptoms were not found to be higher in HIV positive T. whipplei carriers compared to T. whipplei negative participants. Markers of immune activation were lower in patients colonized with T. whipplei. Multivariate regression models demonstrated an independent relationship of a high CD4+ T cell count, a low HIV-1 viral load, and an obese body weight with the presence of T. whipplei. CONCLUSIONS Among HIV positive individuals, T. whipplei colonization was associated with a better immune status but not with clinical consequences. Our data suggest that the withdrawal of co-trimoxazole chemoprophylaxis among people living with HIV on stable cART regimen may inadvertently increase the propensity towards colonization with T. whipplei.
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Affiliation(s)
- Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Fred Stephen Sarfo
- Department of Medicine, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Department of Medicine, Komfo Anokye Teaching Hospital, 00233 Kumasi, Ghana
| | - Eva-Maria Klupp
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany; (E.-M.K.); (M.A.)
| | - Albert Dompreh
- Department of Clinical Microbiology, Komfo Anokye Teaching Hospital, 00233 Kumasi, Ghana; (A.D.); (R.B.)
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany;
| | - Edmund Osei Kuffour
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA;
| | - Richard Boateng
- Department of Clinical Microbiology, Komfo Anokye Teaching Hospital, 00233 Kumasi, Ghana; (A.D.); (R.B.)
| | - Betty Norman
- Department of Medicine, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Department of Medicine, Komfo Anokye Teaching Hospital, 00233 Kumasi, Ghana
| | - Richard Odame Phillips
- Department of Medicine, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Department of Medicine, Komfo Anokye Teaching Hospital, 00233 Kumasi, Ghana
- Kumasi Center for Collaborative Research in Tropical Medicine, 00233 Kumasi, Ghana
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany; (E.-M.K.); (M.A.)
| | - Torsten Feldt
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, 40225 Düsseldorf, Germany;
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