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Tikunov AY, Fedorets VA, Shrainer EV, Morozov VV, Bystrova VI, Tikunova NV. Intestinal Microbiome Changes and Clinical Outcomes of Patients with Ulcerative Colitis after Fecal Microbiota Transplantation. J Clin Med 2023; 12:7702. [PMID: 38137770 PMCID: PMC10743744 DOI: 10.3390/jcm12247702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND AND AIMS Ulcerative colitis (UC) is a chronic inflammatory disease that affects many people. One of the possible ways to treat UC is fecal microbiota transplantation (FMT). In this study, changes in the intestinal microbiome and clinical outcomes of 20 patients with UC after FMT were estimated. METHODS FMT enemas were administrated ten times, once a day, and fecal microbiota from three donors was used for each enema. The clinical outcomes were assessed after eight weeks and then via a patient survey. The 16S rRNA profiles of the gut microbiota were compared between three samplings: samples from 20 patients with UC before and after FMT and samples from 18 healthy volunteers. RESULTS Clinical remission was achieved in 19 (95%) patients at week 8. Adverse events occurred in five patients, including one non-responder. A significant increase in average biodiversity was shown in samples after FMT compared to samples before FMT, as well as a decrease in the proportion of some potentially pathogenic bacteria. CONCLUSION The efficacy of FMT for UC treatment was confirmed; however, the duration of remission varied substantially, possibly due to different characteristics of the initial microbiota of patients. Targeted analysis of a patient's microbiome before FMT could increase the treatment efficacy.
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Affiliation(s)
- Artem Y. Tikunov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria A. Fedorets
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Evgenia V. Shrainer
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Vitaliy V. Morozov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria I. Bystrova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Nina V. Tikunova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
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Gut Microbiota Host-Gene Interaction. Int J Mol Sci 2022; 23:ijms232213717. [PMID: 36430197 PMCID: PMC9698405 DOI: 10.3390/ijms232213717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
Studies carried out in the last ten years have shown that the metabolites made up from the gut microbiota are essential for multiple functions, such as the correct development of the immune system of newborns, interception of pathogens, and nutritional enrichment of the diet. Therefore, it is not surprising that alteration of the gut microbiota is the starting point of gastrointestinal infection, obesity, type 2 diabetes, inflammatory bowel disease, colorectal cancer, and lung cancer. Diet changes and antibiotics are the major factors damaging the gut microbiota. Early exposure of the newborns to antibiotics may prevent their correct development of the immune system, exposing them to pathogen infections, allergies, and chronic inflammatory diseases. We already know much on how host genes, microbiota, and the environment interact, owing to experiments in several model animals, especially in mice; advances in molecular technology; microbiota transplantation; and comparative metagenomic analysis. However, much more remains to be known. Longitudinal studies on patients undergoing to therapy, along with the identification of bacteria prevalent in responding patients may provide valuable data for improving therapies.
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Halla FF, Massawa SM, Joseph EK, Acharya K, Sabai SM, Mgana SM, Werner D. Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment. ENVIRONMENT INTERNATIONAL 2022; 167:107429. [PMID: 35914337 DOI: 10.1016/j.envint.2022.107429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Pit latrines provide essential onsite sanitation services to over a billion people, but there are concerns about their role in infectious disease transmission, and impacts on groundwater resources. We conducted fieldwork in an informal settlement in Dar es Salaam, where cholera is endemic. We combined plate counting with portable MinION sequencing and quantitative polymerase chain reaction (qPCR) methods for characterization of bacteria in pit latrine sludge, leachate, shallow and deep groundwater resources. Pit latrine sludge was characterized by log10 marker gene concentrations per 100 mL of 11.2 ± 0.2, 9.9 ± 0.9, 6.0 ± 0.3, and 4.4 ± 0.8, for total bacteria (16S rRNA), E. coli (rodA), human-host-associated Bacteroides (HF183), and Vibrio cholerae (ompW), respectively. The ompW gene observations suggested 5 % asymptomatic Vibrio cholerae carriers amongst pit latrine users. Pit leachate percolation through one-meter-thick sand beds attenuated bacterial hazard indicators by 1 to 4 log10 units. But first-order removal rates derived from these data substantially overestimated the longer-range hazard attenuation in the sand aquifers. Cooccurrence of human sewage marker gene HF183 in all shallow groundwater samples testing positive for ompW genes demonstrated the human origin of Vibrio cholerae hazards in the subsurface. All borehole water samples tested negative for ompW and HF183 genes, but 16S rRNA gene sequencing data suggested ingress of faecal pollution into boreholes at the peak of the "long rainy season". Quantitative microbial risk assessment (QMRA) predicted a gastrointestinal disease burden of 0.05 DALY per person per year for the community, well above WHO targets of 10-4-10-6 DALY for disease related to drinking water.
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Affiliation(s)
- Franella Francos Halla
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Said Maneno Massawa
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Elihaika Kengalo Joseph
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Shadrack Mwita Sabai
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Shaaban Mrisho Mgana
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania.
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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Chaima D, Hart J, Pickering H, Burr S, Maleta K, Kalua K, Bailey R, Holland M. Association between intestinal bacterial carriage, biomarkers of environmental enteric dysfunction, and stunting in rural Malawian children. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13671.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background. Available data from murine studies suggest that intestinal bacteria may have a role in modulating growth phenotypes in the host. We investigated the prevalence of four gut bacteria known in murine models to impair growth (Bifidobacterium longum, Faecalibacterium prausnitzii, Dorea formicigenerans, and Akkermansia muciniphila), the level of fecal biomarkers of environmental enteric dysfunction (EED) and stunting in rural Malawian children. Methods. DNA and protein were extracted from fecal samples of rural Malawian children (aged 1-59 months) at a baseline cross-sectional survey in the Mangochi district of Malawi conducted within the framework of the Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) trial. Intestinal carriage of bacteria was measured by PCR. Neopterin (NEO), myeloperoxidase (MPO), and alpha-1 antitrypsin (AAT), biomarkers of EED, were measured by an enzyme-linked immunosorbent assay (ELISA) test. Height-for-age Z (HAZ) score <-2 defined stunting. Tests of proportions and regression models were used to explore the relationship between bacterial carriage, EED, and stunting. Results. Fecal samples from 613 children were available for laboratory analyses. F. prausnitzii and D. formicigenerans were prevalent in over 70% of children while B. longum was the least prevalent. B. longum carriage in younger children was associated with elevated EED biomarkers. Two thirds of children had elevated NEO, 33% had elevated MPO, and 16% had elevated AAT. Stunting was found in 38%. No significant associations were found between EED biomarkers or intestinal bacteria carriage and stunting. Conclusion. Intestinal carriage of these four bacteria was not associated with stunting in Malawian children. Carriage was also not associated with EED, nor EED biomarker levels associated with stunting. Further factors acting in concert are necessary to impact EED, perturb growth, and alter gut bacterial carriage.
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Crane RJ, Parker EP, Fleming S, Gwela A, Gumbi W, Ngoi JM, de Laurent ZR, Nyatichi E, Ngari M, Wambua J, Uhlig HH, Berkley JA. Cessation of exclusive breastfeeding and seasonality, but not small intestinal bacterial overgrowth, are associated with environmental enteric dysfunction: A birth cohort study amongst infants in rural Kenya. EClinicalMedicine 2022; 47:101403. [PMID: 35497062 PMCID: PMC9046123 DOI: 10.1016/j.eclinm.2022.101403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/18/2022] Open
Abstract
Background Environmental Enteric Dysfunction (EED) is a chronic intestinal inflammatory disorder of unclear aetiology prevalent amongst children in low-income settings and associated with stunting. We aimed to characterise development of EED and its putative risk factors amongst rural Kenyan infants. Methods In a birth cohort study in Junju, rural coastal Kenya, between August 2015 and January 2017, 100 infants were each followed for nine months. Breastfeeding status was recorded weekly and anthropometry monthly. Acute illnesses and antibiotics were captured by active and passive surveillance. Intestinal function and small intestinal bacterial overgrowth (SIBO) were assessed by monthly urinary lactulose mannitol (LM) and breath hydrogen tests. Faecal alpha-1-antitrypsin, myeloperoxidase and neopterin were measured as EED biomarkers, and microbiota composition assessed by 16S sequencing. Findings Twenty nine of the 88 participants (33%) that underwent length measurement at nine months of age were stunted (length-for-age Z score <-2). During the rainy season, linear growth was slower and LM ratio was higher. In multivariable models, LM ratio, myeloperoxidase and neopterin increased after cessation of continuous-since-birth exclusive breastfeeding. For LM ratio this only occurred during the rainy season. EED markers were not associated with antibiotics, acute illnesses, SIBO, or gut microbiota diversity. Microbiota diversified with age and was not strongly associated with complementary food introduction or linear growth impairment. Interpretation Our data suggest that intensified promotion of uninterrupted exclusive breastfeeding amongst infants under six months during the rainy season, where rainfall is seasonal, may help prevent EED. Our findings also suggest that therapeutic strategies directed towards SIBO are unlikely to impact on EED in this setting. However, further development of non-invasive diagnostic methods for SIBO is required. Funding This research was funded in part by the Wellcome Trust (Research Training Fellowship to RJC (103376/Z/13/Z)). EPKP was supported by the MRC/DfID Newton Fund (MR/N006259/1). JAB was supported by the MRC/DFiD/Wellcome Trust Joint Global Health Trials scheme (MR/M007367/1) and the Bill & Melinda Gates Foundation (OPP1131320). HHU was supported by the NIHR Oxford Biomedical Research Centre (IS-BRC-1215-20008).
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Affiliation(s)
- Rosie J. Crane
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7LG, UK
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
| | - Edward P.K. Parker
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Simon Fleming
- Royal Cornwall Hospitals NHS Trust, Treliske, Truro TR1 3LQ, UK
| | - Agnes Gwela
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
| | - Wilson Gumbi
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
| | - Joyce M. Ngoi
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Accra, Ghana
| | | | - Emily Nyatichi
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
| | - Moses Ngari
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, P.O Box 43640 – 00100, Nairobi, Kenya
| | - Juliana Wambua
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - James A. Berkley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7LG, UK
- KEMRI Wellcome Trust Research Programme, PO Box 80108-230, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, P.O Box 43640 – 00100, Nairobi, Kenya
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