Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis?
BackgroundCritically ill patients, including those with systemic inflammatory response syndrome (SIRS) and sepsis, frequently exhibit gut microbiota disruption due to physiological stress and broad-spectrum antimicrobial therapy (AT). Although antibiotics are essential for controlling infection, the...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| author | Rafaela Ramalho Guerra Rafaela Ramalho Guerra Rafaela Ramalho Guerra Patricia da Silva Fernandes Otávio von Ameln Lovison Otávio von Ameln Lovison Giovanna de Ross Forni Giovanna de Ross Forni Gabriel Silva de Oliveira Luana Cristina Viana Dariane Castro Pereira William Latosinski Matos William Latosinski Matos Miriane Melo Silveira Moretti Fabiana Zempulski Volpato Luciana Giordani Luciana Giordani Patricia Orlandi Barth Patricia Orlandi Barth Tarsila Vieceli Diego Rodrigues Falci Márcio Manozzo Boniatti Afonso Luís Barth Afonso Luís Barth Afonso Luís Barth Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins |
| author_facet | Rafaela Ramalho Guerra Rafaela Ramalho Guerra Rafaela Ramalho Guerra Patricia da Silva Fernandes Otávio von Ameln Lovison Otávio von Ameln Lovison Giovanna de Ross Forni Giovanna de Ross Forni Gabriel Silva de Oliveira Luana Cristina Viana Dariane Castro Pereira William Latosinski Matos William Latosinski Matos Miriane Melo Silveira Moretti Fabiana Zempulski Volpato Luciana Giordani Luciana Giordani Patricia Orlandi Barth Patricia Orlandi Barth Tarsila Vieceli Diego Rodrigues Falci Márcio Manozzo Boniatti Afonso Luís Barth Afonso Luís Barth Afonso Luís Barth Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins |
| author_sort | Rafaela Ramalho Guerra |
| collection | DOAJ |
| description | BackgroundCritically ill patients, including those with systemic inflammatory response syndrome (SIRS) and sepsis, frequently exhibit gut microbiota disruption due to physiological stress and broad-spectrum antimicrobial therapy (AT). Although antibiotics are essential for controlling infection, they can destabilize the gut microbiota and may contribute to poorer clinical outcomes. The characterization of the gut microbiota of these patients may inform microbiota-based interventions to mitigate antibiotic-induced dysbiosis.ObjectiveThis study aimed to identify key bacterial taxa that distinguish sepsis from non-sepsis patients.MethodsA total of 89 stool samples (51 non-sepsis, 38 sepsis) were evaluated by amplicon sequencing the 16S rRNA gene to assess microbiota diversity and differential abundance. Samples were stratified by antibiotic exposure time: early AT (within 5th days of initiation) and prolonged AT (6th to 10th days). Additionally, patients were also grouped based on their AT: beta-lactam combined with other antimicrobial classes (BL-combined) and beta-lactam monotherapy (BL).ResultsDuring early AT, alpha diversity (Shannon index) was significantly lower in sepsis patients compared to non-sepsis patients (2.48 vs. 3.0, p = 0.01), whereas no significant difference was observed after prolonged treatment (2.65 vs. 2.89, p = 0.58). Beta diversity analysis (Aitchison distance) revealed significant differences between groups early AT (PERMANOVA, p = 0.005), but not in the later phase (p = 0.54), suggesting that microbial communities converge over time. Early AT taxonomic profiling showed a decrease in Anaerobutyricum spp. and an increase in Holdemania spp. in the sepsis group. In the non-sepsis group, Veillonella spp. was impacted by time and beta-lactam combination. Turicibacter spp. showed a reduction in the prolonged AT sepsis group, while Klebsiella spp. was more abundant in the BL-combined sepsis patients.ConclusionsSepsis and non-sepsis patients showed distinct gut microbiota profiles in early AT. In sepsis, the loss of taxa involved in key metabolic functions, as short-chain fatty acid production, reflects dysbiosis and may contribute to worse outcomes. Prolonged antibiotic use may favor enteropathogen overgrowth and gut translocation. These findings highlight the potential of microbiota-based strategies to guide antimicrobial therapy and improve clinical outcomes in critically ill patients. |
| format | Article |
| id | doaj-art-dd6de79a7ad34d93981e14e4b94fcf7a |
| institution | Kabale University |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-dd6de79a7ad34d93981e14e4b94fcf7a2025-08-22T05:26:42ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-08-011510.3389/fcimb.2025.16228661622866Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis?Rafaela Ramalho Guerra0Rafaela Ramalho Guerra1Rafaela Ramalho Guerra2Patricia da Silva Fernandes3Otávio von Ameln Lovison4Otávio von Ameln Lovison5Giovanna de Ross Forni6Giovanna de Ross Forni7Gabriel Silva de Oliveira8Luana Cristina Viana9Dariane Castro Pereira10William Latosinski Matos11William Latosinski Matos12Miriane Melo Silveira Moretti13Fabiana Zempulski Volpato14Luciana Giordani15Luciana Giordani16Patricia Orlandi Barth17Patricia Orlandi Barth18Tarsila Vieceli19Diego Rodrigues Falci20Márcio Manozzo Boniatti21Afonso Luís Barth22Afonso Luís Barth23Afonso Luís Barth24Andreza Francisco Martins25Andreza Francisco Martins26Andreza Francisco Martins27Andreza Francisco Martins28Bacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, BrazilInfectious Diseases Department, Hospital de Clínicas de Porto Alegre, Porto Alegre, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilBioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilDepartment of Critical Care, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, BrazilDepartment of Biosciences, Federal University of Paraná - Palotina Sector, Palotina, Paraná, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilInfectious Diseases Department, Hospital de Clínicas de Porto Alegre, Porto Alegre, BrazilInfectious Diseases Department, Hospital de Clínicas de Porto Alegre, Porto Alegre, BrazilDepartment of Critical Care, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBacterial Resistance Research Laboratory (LABRESIS), Hospital de clínicas de Porto Alegre (HCPA), Experimental Research Center, Porto Alegre, BrazilPostgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, BrazilPostgraduate Program in Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, BrazilBackgroundCritically ill patients, including those with systemic inflammatory response syndrome (SIRS) and sepsis, frequently exhibit gut microbiota disruption due to physiological stress and broad-spectrum antimicrobial therapy (AT). Although antibiotics are essential for controlling infection, they can destabilize the gut microbiota and may contribute to poorer clinical outcomes. The characterization of the gut microbiota of these patients may inform microbiota-based interventions to mitigate antibiotic-induced dysbiosis.ObjectiveThis study aimed to identify key bacterial taxa that distinguish sepsis from non-sepsis patients.MethodsA total of 89 stool samples (51 non-sepsis, 38 sepsis) were evaluated by amplicon sequencing the 16S rRNA gene to assess microbiota diversity and differential abundance. Samples were stratified by antibiotic exposure time: early AT (within 5th days of initiation) and prolonged AT (6th to 10th days). Additionally, patients were also grouped based on their AT: beta-lactam combined with other antimicrobial classes (BL-combined) and beta-lactam monotherapy (BL).ResultsDuring early AT, alpha diversity (Shannon index) was significantly lower in sepsis patients compared to non-sepsis patients (2.48 vs. 3.0, p = 0.01), whereas no significant difference was observed after prolonged treatment (2.65 vs. 2.89, p = 0.58). Beta diversity analysis (Aitchison distance) revealed significant differences between groups early AT (PERMANOVA, p = 0.005), but not in the later phase (p = 0.54), suggesting that microbial communities converge over time. Early AT taxonomic profiling showed a decrease in Anaerobutyricum spp. and an increase in Holdemania spp. in the sepsis group. In the non-sepsis group, Veillonella spp. was impacted by time and beta-lactam combination. Turicibacter spp. showed a reduction in the prolonged AT sepsis group, while Klebsiella spp. was more abundant in the BL-combined sepsis patients.ConclusionsSepsis and non-sepsis patients showed distinct gut microbiota profiles in early AT. In sepsis, the loss of taxa involved in key metabolic functions, as short-chain fatty acid production, reflects dysbiosis and may contribute to worse outcomes. Prolonged antibiotic use may favor enteropathogen overgrowth and gut translocation. These findings highlight the potential of microbiota-based strategies to guide antimicrobial therapy and improve clinical outcomes in critically ill patients.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1622866/fullamplicon sequencingbiomarkergut microbiotasepsisSIRS |
| spellingShingle | Rafaela Ramalho Guerra Rafaela Ramalho Guerra Rafaela Ramalho Guerra Patricia da Silva Fernandes Otávio von Ameln Lovison Otávio von Ameln Lovison Giovanna de Ross Forni Giovanna de Ross Forni Gabriel Silva de Oliveira Luana Cristina Viana Dariane Castro Pereira William Latosinski Matos William Latosinski Matos Miriane Melo Silveira Moretti Fabiana Zempulski Volpato Luciana Giordani Luciana Giordani Patricia Orlandi Barth Patricia Orlandi Barth Tarsila Vieceli Diego Rodrigues Falci Márcio Manozzo Boniatti Afonso Luís Barth Afonso Luís Barth Afonso Luís Barth Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins Andreza Francisco Martins Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? Frontiers in Cellular and Infection Microbiology amplicon sequencing biomarker gut microbiota sepsis SIRS |
| title | Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? |
| title_full | Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? |
| title_fullStr | Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? |
| title_full_unstemmed | Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? |
| title_short | Microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome: can we use gut bacteria as potential biomarkers to characterize sepsis? |
| title_sort | microbial diversity and composition in the gut microbiome of patients during systemic inflammatory response syndrome can we use gut bacteria as potential biomarkers to characterize sepsis |
| topic | amplicon sequencing biomarker gut microbiota sepsis SIRS |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1622866/full |
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