Gut Pathogens最新文献

{"title":"Chronic hepatitis B virus infection imbalances short-chain fatty acids and amino acids in the liver and gut via microbiota modulation.","authors":"Wendi Zhang, Yuwei Wu, Min Cheng, Haiming Wei, Rui Sun, Hui Peng, Zhigang Tian, Yongyan Chen","doi":"10.1186/s13099-025-00695-3","DOIUrl":"10.1186/s13099-025-00695-3","url":null,"abstract":"<p><p>The commensal microbiota is closely related to HBV infection and HBV-related liver diseases; however, how HBV and viral components dynamically affect the targeted organ liver microbiota is not well-known. In this study, an HBV-carrier mouse model established by HBsAg⁺ hepatocyte replacement in Fah^-/- recipient mice, named HBs-HepR mice, was used to analyze the microbiota and metabolomics at the time of triggering the specific anti-HBV CD8⁺ T cell response in the liver. The composition and relative abundance of microbiota were both altered in the gut and liver of HBs-HepR mice. Particularly, increased Muribaculaceae and Alloprevotella, and decreased Lachnospiraceae-NK4A136 and Rikenella were observed in the gut; while increased Ralstonia and Geobacillus were observed in the liver of HBs-HepR mice. Furthermore, changes in microbial functions were revealed. There were no significant differences in the levels of SCFAs in fecal and serum; however, decreased propionic acid and acetic acid were detected in the livers of HBs-HepR mice, which was negatively related to the abundance of Geobacillus in the liver. Significantly decreased levels of 9 kinds of amino acids were detected in the feces of HBs-HepR mice, which was positively related to decreased Rikenella in the gut. A significant increase in L-glycine was observed in the liver and serum, positively related to the abundance of Geobaillus in the livers of HBs-HepR mice. In conclusion, chronic HBV infection imbalanced SCFA and amino acid metabolism by modulating microbiota in the liver, unlike in the gut, which was involved in the immune activation phase.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"18"},"PeriodicalIF":4.3,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clostridioides difficile concentration-dependant alterations in gut microbiota of asymptomatic infants.","authors":"Aleksander Mahnic, Jana Lozar Krivec, Darja Paro-Panjan, Andreja Valcl, Tanja Obermajer, Bojana Bogovič Matijašić, Evgen Benedik, Petra Bratina, Maja Rupnik","doi":"10.1186/s13099-025-00687-3","DOIUrl":"10.1186/s13099-025-00687-3","url":null,"abstract":"<p><strong>Background: </strong>Asymptomatic carriage of Clostridioides difficile is highly prevalent in early infancy, affecting approximately 40% of infants. This phenomenon offers a unique opportunity to study its impact on the gut microbiota without the confounding effects of disease. In this study, we analysed C. difficile-associated gut microbiome alterations in 76 asymptomatic infants, one year after receiving antibiotic treatment during early infancy. The presence and concentration of C. difficile were assessed in relation to gut microbiota structure and an extensive set of metadata.</p><p><strong>Results: </strong>Bacterial gut community structure was characterized using 16 S rRNA amplicon sequencing, while C. difficile concentration and the presence of the tcdB gene were quantified via digital PCR. C. difficile was detected in 36.8% of infants, with 10.5% testing positive for the tcdB gene. Significant alterations in gut microbiota were observed in relation to C. difficile concentration. Specifically, higher C. difficile loads were associated with reduced microbial diversity, greater deviations from average community structure, and co-occurrence with the genus Escherichia. Conversely, C. difficile colonization alone or the presence of the tcdB gene did not result in significant gut microbiota alterations. Additionally, no host-specific factors were significantly linked to C. difficile prevalence or concentration.</p><p><strong>Conclusions: </strong>Asymptomatic carriage of C. difficile in neonates is not associated with significant gut microbiota alterations unless pathogen concentration is considered. Our findings suggest that elevated C. difficile proliferation occurs in dysbiotic infant gut microbiota, characterized by reduced alpha diversity and an increase in Escherichia.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"17"},"PeriodicalIF":4.3,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of pathogens associated with neonatal gastrointestinal infections: a systematic review and meta-analysis.","authors":"Xinyu Liu, Rui Zhang, Mengdie Wang, Chuncai Tang, Feifei Yang, Qingjuan Yang, Changyong Huang, Ying Zhang, Zhengmin Ren, Liqiao Liu, Guozhong Zhou, Jia Li","doi":"10.1186/s13099-025-00693-5","DOIUrl":"10.1186/s13099-025-00693-5","url":null,"abstract":"<p><p>Gastrointestinal infections represent a significant global health burden, ranking as the second leading cause of mortality among infants and children. Identifying of pathogens causing neonatal gastrointestinal infections has presented tough challenges. This study aimed to summarize the prevalence of common pathogens associated with neonatal gastrointestinal infections through a comprehensive systematic review and meta-analysis of published literature. The last search was performed on January 08, 2025, from databases including EMBASE, PubMed, Cochrane Libary, and Web of Science. The outcome variable was infection rate, and the detection methods used were blood culture, tissue culture, or molecular biology methods. Two researchers independently extracted the research data and evaluated its quality using the JBI Critical Appraisal Tools. Twenty-three studies met the inclusion criteria. The pooled prevalence rates of common pathogens were as follows: Bacteria, including Escherichia (22.2%; 95% CI 8.3-40.4%, I² = 98%), Clostridium (21.8%; 95% CI 2.2-53.8%, I² = 96%), Klebsiella (19.2%; 95% CI 8.3-33.4%, I² = 97%), Staphylococcus (13.6%; 95% CI 6.0-23.7%, I² = 91%), Enterococcus (12.4%; 95% CI 1.8-30.3%, I² = 96%), and Streptococcus (6.8%; 95% CI 2.5-12.9%, I² = 43%). Fungi, including Candida (3.8%; 95% CI 0.6-9.6%, I² = 84%). Viruses, including Rotavirus (11.6%; 95% CI 1.0-31.5%, I² = 94%) and Adenovirus (4.1%; 95% CI 0.5-11.0%, I² = 58%). Peritoneal culture methods demonstrated significantly higher positivity rates compared to other detection methods. Escherichia coli exhibited consistently high positivity rates across the three main detection methods. Klebsiella showed the highest positivity rates among bacterial isolates in both blood and peritoneal cultures. Pathogen detection and prevalence in necrotizing enterocolitis (NEC) cases were markedly higher compared to other conditions. This meta-analysis identifies key pathogens in gastrointestinal infections, including Klebsiella pneumoniae, Escherichia coli, Candida, Rotavirus, Adenovirus, and others that are suspected before clinical sample results are available. It also highlights that intestinal pathogen infections are linked to an increased risk of neonatal necrotizing enterocolitis (NEC) and emphasizes the advantages of peritoneal culture in detecting these infections.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"16"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Molecular characterization and risk analysis of Giardia duodenalis assemblages in corticosteroid-treated and non-treated patients in Ismailia, Arab Republic of Egypt.","authors":"Shahira Abdelaziz Ali Ahmed, Amira Bakr Mokhtar, Samar Farag Mohamed, Marwa Ibrahim Saad El-Din, Catherine O 'Dowd Phanis, Stefani Kazamia, Chad Schou, Paweł Gładysz, Anna Lass, Annalisa Quattrocchi, Panagiotis Karanis, Samer Eid Mohamed Gad","doi":"10.1186/s13099-025-00680-w","DOIUrl":"10.1186/s13099-025-00680-w","url":null,"abstract":"","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"15"},"PeriodicalIF":4.3,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular confirmation of Cryptosporidium and Cyclospora species in children with acute diarrhoea in Quindio region, Colombia.","authors":"Jessica Triviño-Valencia, Alejandro Nati-Castillo, Nancy Yhomara Cabeza, Fabiana Lora-Suarez, Jorge Gómez-Marín","doi":"10.1186/s13099-025-00685-5","DOIUrl":"10.1186/s13099-025-00685-5","url":null,"abstract":"<p><strong>Background: </strong>There are no reports with molecular confirmation of Cryptosporidium spp. and Cyclospora spp. in children consulting the emergency service due to diarrhoea in Colombia.</p><p><strong>Methods: </strong>A descriptive study was performed on 137 children who visited the Hospital San Juan de Dios Emergency Service in Armenia between April 1 and 31, 2022. Questionnaires and sampling were performed to identify parasites in the faecal samples. Fresh preparations were prepared with 1% iodine, and a modified Ziehl-Neelsen stain was used to identify pathogenic intestinal protozoa (Cryptosporidium spp. and Cyclospora spp.). PCR and sequencing of positive samples were performed to confirm infection.</p><p><strong>Results: </strong>The prevalence of Cryptosporidium spp. infection in children was 19,7%, and that of Cyclospora spp. was 10,9%. 59,2% of the children with cryptosporidiosis and 66,6% of the children with cyclosporiasis were hospitalized. PCR for Cryptosporidium spp. was positive in six of 28 (21%) samples and for Cyclospora in 11 of 15 (73%) samples. Cyclospora spp. SSU rRNA DNA sequences clustered 10 samples nearest to lineage A, two with lineage B, and one with lineage C.</p><p><strong>Conclusions: </strong>Cryptosporidiosis and cyclosporiasis are common in children with acute diarrhoea when consulting emergency services, and their search should be performed systematically.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"14"},"PeriodicalIF":4.3,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salivary shield: Rhodnius prolixus salivary glandular extract reduces intestinal immunopathology and protects against Toxoplasma gondii infection.","authors":"Roberto Augusto Pereira Sousa, Jean Henrique Nunes de Paula, Rafaela José Silva, Samuel Cota Teixeira, Flávia Batista Ferreira França, Amanda Helena Leão Gonçalves, Túlio Rodrigues Oliveira Silva, Maria Julia Granero-Rosa, Murilo Vieira Silva, Marcos de Lucca Moreira Gomes, Marcos Vinícius Silva, Virmondes Rodrigues Junior, José Roberto Mineo, Bellisa Freitas Barbosa, Eloisa Amália Vieira Ferro, Carlo José Freire Oliveira, Angelica Oliveira Gomes","doi":"10.1186/s13099-024-00676-y","DOIUrl":"10.1186/s13099-024-00676-y","url":null,"abstract":"<p><p>C57BL/6 mice, orally infected with T. gondii, experience pronounced severe intestinal inflammation, causing necrosis, weight loss, and bacterial translocation. In addition, immunomodulatory molecules such as lipocalins, nitrophorins, and apyrases are present in R. prolixus saliva. Our objective was to assess the immunomodulatory effects of the salivary gland extract (SGE) of R. prolixus in mice orally infected by T. gondii. Experimental groups received no treatment (PBS) or SGE (10 µg and 30 µg) in the chronic infection phase and (30 µg) in the acute infection phase. Control groups were non-infected and treated or not treated with SGE (30 µg). SGE was injected intraperitoneally daily, and mice were infected by gavage with 20 cysts of T. gondii (ME-49 strain) on the third treatment day. The treatment duration for the experiment was 23 days for the chronic infection phase (corresponding to 20 days of infection) and 12 days for the acute infection phase (corresponding to 9 days of infection). SGE-treated mice showed reduced small intestine shortening, weight loss, clinical scores, and higher survival rates. Treated mice also exhibited increased secretion of regulatory and protective cytokines (IL-4, IL-2, IL-10, IL-22) and higher levels of IL-4 (chronic phase), IL-2, and IL-22 (acute phase) in the gut. SGE treatment (30 µg) demonstrated protective effects in both the duodenum and ileum of T. gondii-infected mice. Treated animals showed better-preserved villus architecture, increased goblet and Paneth cell counts, and shallower crypts. Correlation data revealed that treated animals exhibited a more regulated and protective immune response. Overall, SGE contributed to the preservation of intestinal integrity and the reduction of inflammation. Thus, we conclude that SGE induces a regulatory response, mitigating inflammation and protecting against T. gondii infection.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"13"},"PeriodicalIF":4.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of a rapid fluorescence immunoassay for detecting Campylobacter antigens in stool samples.","authors":"Lucie Bénéjat, Astrid Ducournau, Juliette Gebhart, Emilie Bessede, Juergen Becker, Marine Jauvain, Philippe Lehours","doi":"10.1186/s13099-025-00686-4","DOIUrl":"10.1186/s13099-025-00686-4","url":null,"abstract":"<p><strong>Background: </strong>The species most frequently causing campylobacteriosis are Campylobacter jejuni and Campylobacter coli, followed by Campylobacter fetus, Campylobacter upsaliensis, and Campylobacter lari. Although polymerase chain reaction (PCR) can be used to detect Campylobacter DNA in stool samples, PCR assays are often validated for C. jejuni and C. coli only, and coproculture results can take several days to receive. For laboratories that do not have access to PCR technology, rapid antigen tests can be of the utmost importance for early diagnosis of the disease. We evaluated the performance of the Sofia Campylobacter Fluorescence Immunoassay (SCFIA) for rapid detection of Campylobacter antigens in stool.</p><p><strong>Methods: </strong>In total, 94 frozen and 205 fresh stool specimens were included in retrospective and prospective evaluations, respectively. The linearity of the assay and its limit of detection for different Campylobacter species was evaluated using serial dilutions. Cross reactivity to phylogenetically related species was also investigated. The PCR results from the BD MAX Enteric Panel were considered the gold standard.</p><p><strong>Results: </strong>The sensitivity of the SCFIA was 97.87% and 96.88% in retrospective and prospective evaluations, respectively. The specificity was 98.84%. The assay exhibited high linearity in serial dilutions for C. coli, C. jejuni, C. armoricus, C. ornithocola, C. lari, and C. upsaliensis, with correlation coefficients of 0.991-0.999, whereas C. fetus was not detected. No cross-reactivity was detected for Aliarcobacter butzleri, Helicobacter cinaedi, or Helicobacter pullorum. The minimum concentration for a positive result at the assay-specific cut-off was 4-17 million CFU/mL. The limit of detection ranged from 10⁶ to 10⁷ CFU/mL.</p><p><strong>Conclusion: </strong>SCFIA results are highly correlated with PCR results, with no cross-reactivity with phylogenetically related species. The linear correlation between fluorescence and CFU/mL results was strong. The assay's ability to detect antigens of various Campylobacter species can aid early diagnosis. However, the inability to detect C. fetus must be considered.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"12"},"PeriodicalIF":4.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intestinal mucus: the unsung hero in the battle against viral gastroenteritis.","authors":"Waqar Saleem, Ateeqa Aslam, Mehlayl Tariq, Hans Nauwynck","doi":"10.1186/s13099-025-00684-6","DOIUrl":"10.1186/s13099-025-00684-6","url":null,"abstract":"<p><p>Intestinal mucus plays a crucial role in defending against enteric infections by protecting the vulnerable intestinal epithelial cells both physically and through its various constituents. Despite this, numerous gastroenteritis-causing viruses, such as rotavirus, coronavirus, adenovirus, astrovirus, calicivirus, and enterovirus, continue to pose significant threats to humans and animals. While several studies have examined the interactions between these viruses and intestinal mucus, significant gaps remain in understanding the full protective potential of intestinal mucus against these pathogens. This review aims to elucidate the protective role of intestinal mucus in viral gastroenteritis. It begins with a comprehensive literature overview of (i) intestinal mucus, (ii) enteric viruses of medical and veterinary importance, and (iii) the known interactions between various enteric viruses and intestinal mucus. Following this, a case study is presented to highlight the age-dependent blocking effect of porcine intestinal mucus against transmissible gastroenteritis virus, a porcine coronavirus. Finally, the review discusses future investigation directions to further explore the potential of intestinal mucus as a defense mechanism against viral gastroenteritis to stimulate further research in this dynamic and critical area.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"11"},"PeriodicalIF":4.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota dysbiosis and associated immune response in systemic lupus erythematosus: impact of disease and treatment.","authors":"Aya Y Ali, Sara A Zahran, Mervat Eissa, Mona T Kashef, Amal Emad Ali","doi":"10.1186/s13099-025-00683-7","DOIUrl":"10.1186/s13099-025-00683-7","url":null,"abstract":"<p><strong>Background: </strong>Gut microbial dysbiosis and leaky gut play a role in systemic lupus erythematosus (SLE). Geographical location and dietary habits affect the microbiome composition in diverse populations. This study explored the gut microbiome dysbiosis, leaky gut, and systemic immune response to gut bacterial consortium in patients with SLE exhibiting mild/moderate and severe disease activity.</p><p><strong>Methods: </strong>Fecal and blood samples were collected from patients with SLE and healthy volunteers. Genomic DNA was extracted from the stool samples and subjected to 16S rRNA amplicon sequencing and microbiome profiling. Additionally, enzyme-linked immunosorbent assays were employed to determine the serum lipopolysaccharide level, as an assessment of gut permeability, and the systemic immune response against gut bacteria.</p><p><strong>Results: </strong>Patients with SLE showed significantly lower gut bacterial richness and diversity, indicated by observed OTUs (56.6 vs. 74.44; p = 0.0289), Shannon (3.05 vs. 3.45; p = 0.017) and Simpson indices (0.91 vs. 0.94; p = 0.033). A lower Firmicutes-to-Bacteroidetes ratio (1.07 vs. 1.69; p = 0.01) was observed, with reduced genera such as Ruminococcus 2 (0.003 vs. 0.026; p = 0.0009) and Agathobacter (0.003 vs. 0.012; p < 0.0001) and elevated Escherichia-Shigella (0.04 vs. 0.006; p < 0.0001) and Bacteroides (0.206 vs. 0.094; p = 0.033). Disease severity was associated with a higher relative abundance of Prevotella (0.001 vs. 0.0001; p = 0.04). Medication effects included lower Romboutsia (0.0009 vs. 0.011; p = 0.005) with azathioprine and higher Prevotella (0.003 vs. 0.0002; p = 0.038) with cyclophosphamide. Furthermore, categorization by prednisolone dosage revealed significantly higher relative abundances of Slackia (0.0007 vs. 0.00002; p = 0.0088), Romboutsia (0.009 vs. 0.002; p = 0.0366), and Comamonas (0.002 vs. 0.00007; p = 0.0249) in patients receiving high-dose prednisolone (> 10 mg/day). No differences in serum lipopolysaccharide levels were found, but SLE patients exhibited elevated serum gut bacterial antibody levels, suggesting a systemic immune response.</p><p><strong>Conclusion: </strong>This study confirms the gut microbiome dysbiosis in patients with SLE, influenced by disease severity and specific medication usage.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"10"},"PeriodicalIF":4.3,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda.","authors":"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","doi":"10.1186/s13099-025-00678-4","DOIUrl":"10.1186/s13099-025-00678-4","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"17 1","pages":"9"},"PeriodicalIF":4.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}