Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda
Abstract Background Infection with the COVID-19-causing pathogen SARS-CoV-2 is associated with disruption in the human gut microbiome. The gut microbiome enables protection against diverse pathogens and exhibits dysbiosis during infectious and autoimmune disease. Studies based in the United States a...
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2025-02-01
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| Series: | Gut Pathogens |
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| Online Access: | https://doi.org/10.1186/s13099-025-00678-4 |
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| author | Carolina Agudelo David Patrick Kateete Emmanuel Nasinghe Rogers Kamulegeya Christopher Lubega Monica Mbabazi Noah Baker Kathryn Y. Lin Chang C. Liu Arthur Shem Kasambula Edgar Kigozi Kevin Komakech John Mukisa Kassim Mulumba Patricia Mwachan Brenda Sharon Nakalanda Gloria Patricia Nalubega Julius Nsubuga Diana Sitenda Henry Ssenfuka Giana T. Cirolia Jeshua T. Gustafson Ruohong Wang Moses Luutu Nsubuga Fahim Yiga Sarah A. Stanley Bernard Ssentalo Bagaya Alison Elliott Moses Joloba Ashley R. Wolf |
| author_facet | Carolina Agudelo David Patrick Kateete Emmanuel Nasinghe Rogers Kamulegeya Christopher Lubega Monica Mbabazi Noah Baker Kathryn Y. Lin Chang C. Liu Arthur Shem Kasambula Edgar Kigozi Kevin Komakech John Mukisa Kassim Mulumba Patricia Mwachan Brenda Sharon Nakalanda Gloria Patricia Nalubega Julius Nsubuga Diana Sitenda Henry Ssenfuka Giana T. Cirolia Jeshua T. Gustafson Ruohong Wang Moses Luutu Nsubuga Fahim Yiga Sarah A. Stanley Bernard Ssentalo Bagaya Alison Elliott Moses Joloba Ashley R. Wolf |
| author_sort | Carolina Agudelo |
| collection | DOAJ |
| description | Abstract Background Infection with the COVID-19-causing pathogen SARS-CoV-2 is associated with disruption in the human gut microbiome. The gut microbiome enables protection against diverse pathogens and exhibits dysbiosis during infectious and autoimmune disease. Studies based in the United States and China have found that severe COVID-19 cases have altered gut microbiome composition when compared to mild COVID-19 cases. We present the first study to investigate the gut microbiome composition of COVID-19 cases in a population from Sub-Saharan Africa. Given the impact of geography and cultural traditions on microbiome composition, it is important to investigate the microbiome globally and not draw broad conclusions from homogenous populations. Results We used stool samples in a Ugandan biobank collected from COVID-19 cases during 2020–2022. We profiled the gut microbiomes of 83 symptomatic individuals who tested positive for SARS-CoV-2 along with 43 household contacts who did not present any symptoms of COVID-19. The inclusion of healthy controls enables us to generate hypotheses about bacterial strains potentially related to susceptibility to COVID-19 disease, which is highly heterogeneous. Comparison of the COVID-19 patients and their household contacts revealed decreased alpha diversity and blooms of Enterococcus and Eggerthella in COVID-19 cases. Conclusions Our study finds that the microbiome of COVID-19 individuals is more likely to be disrupted, as indicated by decreased diversity and increased pathobiont levels. This is either a consequence of the disease or may indicate that certain microbiome states increase susceptibility to COVID-19 disease. Our findings enable comparison with cohorts previously published in the Global North, as well as support new hypotheses about the interaction between the gut microbiome and SARS-CoV-2 infection. |
| format | Article |
| id | doaj-art-441b4b37a8a04a858eb7dcaddcefbbdd |
| institution | Kabale University |
| issn | 1757-4749 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Gut Pathogens |
| spelling | doaj-art-441b4b37a8a04a858eb7dcaddcefbbdd2025-02-09T12:38:51ZengBMCGut Pathogens1757-47492025-02-0117111310.1186/s13099-025-00678-4Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in UgandaCarolina Agudelo0David Patrick Kateete1Emmanuel Nasinghe2Rogers Kamulegeya3Christopher Lubega4Monica Mbabazi5Noah Baker6Kathryn Y. Lin7Chang C. Liu8Arthur Shem Kasambula9Edgar Kigozi10Kevin Komakech11John Mukisa12Kassim Mulumba13Patricia Mwachan14Brenda Sharon Nakalanda15Gloria Patricia Nalubega16Julius Nsubuga17Diana Sitenda18Henry Ssenfuka19Giana T. Cirolia20Jeshua T. Gustafson21Ruohong Wang22Moses Luutu Nsubuga23Fahim Yiga24Sarah A. Stanley25Bernard Ssentalo Bagaya26Alison Elliott27Moses Joloba28Ashley R. Wolf29Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyCollege of Engineering, University of California, BerkeleyCollege of Engineering, University of California, BerkeleyDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesMRC/UVRI and LSHTM Uganda Research UnitDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health SciencesDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, BerkeleyAbstract Background Infection with the COVID-19-causing pathogen SARS-CoV-2 is associated with disruption in the human gut microbiome. The gut microbiome enables protection against diverse pathogens and exhibits dysbiosis during infectious and autoimmune disease. Studies based in the United States and China have found that severe COVID-19 cases have altered gut microbiome composition when compared to mild COVID-19 cases. We present the first study to investigate the gut microbiome composition of COVID-19 cases in a population from Sub-Saharan Africa. Given the impact of geography and cultural traditions on microbiome composition, it is important to investigate the microbiome globally and not draw broad conclusions from homogenous populations. Results We used stool samples in a Ugandan biobank collected from COVID-19 cases during 2020–2022. We profiled the gut microbiomes of 83 symptomatic individuals who tested positive for SARS-CoV-2 along with 43 household contacts who did not present any symptoms of COVID-19. The inclusion of healthy controls enables us to generate hypotheses about bacterial strains potentially related to susceptibility to COVID-19 disease, which is highly heterogeneous. Comparison of the COVID-19 patients and their household contacts revealed decreased alpha diversity and blooms of Enterococcus and Eggerthella in COVID-19 cases. Conclusions Our study finds that the microbiome of COVID-19 individuals is more likely to be disrupted, as indicated by decreased diversity and increased pathobiont levels. This is either a consequence of the disease or may indicate that certain microbiome states increase susceptibility to COVID-19 disease. Our findings enable comparison with cohorts previously published in the Global North, as well as support new hypotheses about the interaction between the gut microbiome and SARS-CoV-2 infection.https://doi.org/10.1186/s13099-025-00678-4COVID-19SARS-CoV-2Gut microbiomeEnterococcusUganda |
| spellingShingle | Carolina Agudelo David Patrick Kateete Emmanuel Nasinghe Rogers Kamulegeya Christopher Lubega Monica Mbabazi Noah Baker Kathryn Y. Lin Chang C. Liu Arthur Shem Kasambula Edgar Kigozi Kevin Komakech John Mukisa Kassim Mulumba Patricia Mwachan Brenda Sharon Nakalanda Gloria Patricia Nalubega Julius Nsubuga Diana Sitenda Henry Ssenfuka Giana T. Cirolia Jeshua T. Gustafson Ruohong Wang Moses Luutu Nsubuga Fahim Yiga Sarah A. Stanley Bernard Ssentalo Bagaya Alison Elliott Moses Joloba Ashley R. Wolf Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda Gut Pathogens COVID-19 SARS-CoV-2 Gut microbiome Enterococcus Uganda |
| title | Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda |
| title_full | Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda |
| title_fullStr | Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda |
| title_full_unstemmed | Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda |
| title_short | Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda |
| title_sort | enterococcus and eggerthella species are enriched in the gut microbiomes of covid 19 cases in uganda |
| topic | COVID-19 SARS-CoV-2 Gut microbiome Enterococcus Uganda |
| url | https://doi.org/10.1186/s13099-025-00678-4 |
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