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Martin-Castaño B, Diez-Echave P, García-García J, Hidalgo-García L, Ruiz-Malagon AJ, Molina-Tijeras JA, Rodríguez-Sojo MJ, Redruello-Romero A, Martínez-Zaldívar M, Mota E, Cobo F, Díaz-Villamarin X, Alvarez-Estevez M, García F, Morales-García C, Merlos S, Garcia-Flores P, Colmenero-Ruiz M, Hernández-Quero J, Nuñez M, Rodriguez-Cabezas ME, Carazo A, Martin J, Moron R, Rodríguez Nogales A, Galvez J. The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19. eLife 2025; 13:RP95292. [PMID: 39963971 PMCID: PMC11835386 DOI: 10.7554/elife.95292] [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] [Indexed: 02/20/2025] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicentre prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate (n = 51), and severe/critical (n = 31). Faecal and nasopharyngeal samples were taken, and the microbiota was analysed. Linear discriminant analysis identified Mycoplasma salivarium, Prevotella dentalis, and Haemophilus parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while Prevotella bivia and Prevotella timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.
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Affiliation(s)
- Benita Martin-Castaño
- Centro de Salud Las Gabias, Distrito Granada-MetropolitanoGranadaSpain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
| | - Patricia Diez-Echave
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - Jorge García-García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
- Servicio Microbiología, Hospital Universitario Clínico San CecilioGranadaSpain
| | - Laura Hidalgo-García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - Antonio Jesús Ruiz-Malagon
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - José Alberto Molina-Tijeras
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - María Jesús Rodríguez-Sojo
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | | | - Margarita Martínez-Zaldívar
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Centro de Salud “Salvador Caballero”, Distrito Granada-MetropolitanoGranadaSpain
| | - Emilio Mota
- Centro de Salud “Salvador Caballero”, Distrito Granada-MetropolitanoGranadaSpain
| | - Fernando Cobo
- Servicio Microbiología, Hospital Universitario Virgen de las NievesGranadaSpain
| | | | - Marta Alvarez-Estevez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio Microbiología, Hospital Universitario Clínico San CecilioGranadaSpain
- CIBER de Enfermedades Infecciosas (CIBER-Infecc), Instituto de Salud Carlos IIIMadridSpain
| | - Federico García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio Microbiología, Hospital Universitario Clínico San CecilioGranadaSpain
- CIBER de Enfermedades Infecciosas (CIBER-Infecc), Instituto de Salud Carlos IIIMadridSpain
| | | | - Silvia Merlos
- Respiratory Medicine Department, Hospital Universitario Virgen de las NievesGranadaSpain
| | - Paula Garcia-Flores
- Respiratory Medicine Department, Hospital Universitario Virgen de las NievesGranadaSpain
| | - Manuel Colmenero-Ruiz
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio de Medicina Intensiva, Hospital Universitario Clínico San CecilioGranadaSpain
| | - José Hernández-Quero
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio de Enfermedades Infecciosas, Hospital Universitario Clínico San CecilioGranadaSpain
| | - Maria Nuñez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio Farmacia Hospitalaria, Hospital Universitario Clínico San CecilioGranadaSpain
- CIBER de Epidemiología y Salud Pública (CIBER-ESP), Instituto de Salud Carlos IIIMadridSpain
| | - Maria Elena Rodriguez-Cabezas
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - Angel Carazo
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio Microbiología, Hospital Universitario Clínico San CecilioGranadaSpain
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSICGranadaSpain
| | - Rocio Moron
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Servicio Farmacia Hospitalaria, Hospital Universitario Clínico San CecilioGranadaSpain
| | - Alba Rodríguez Nogales
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
| | - Julio Galvez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA)GranadaSpain
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of GranadaGranadaSpain
- CIBER de Enfermedades Hepáticas y Digestivas (CIBER-EHD), Instituto de Salud Carlos IIIMadridSpain
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Chung RS, Wong S, Lin D, Kokot NC, Sinha UK, Han AY. Mechanisms of crosstalk between the oropharyngeal microbiome and human papillomavirus in oropharyngeal carcinogenesis: a mini review. Front Oncol 2024; 14:1425545. [PMID: 39211550 PMCID: PMC11357953 DOI: 10.3389/fonc.2024.1425545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 09/04/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer globally. Notably, human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) is on the rise, accounting for 70% of all OPSCC cases. Persistent high-risk HPV infection is linked to various cancers, but HPV infection alone is not sufficient to cause cancer. Advances in next-generation sequencing have improved our understanding of changes in the human microbiome of cancerous environments. Yet, there remains a dearth of knowledge on the impact of HPV-microbiome crosstalk in HPV-positive OPSCC. In this review, we examine what is known about the oropharyngeal microbiome and the compositional shifts in this microbiome in HPV-positive OPSCC. We also review potential mechanisms of crosstalk between HPV and specific microorganisms. Additional research is needed to understand these interactions and their roles on cancer development and progression.
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Affiliation(s)
| | | | | | | | | | - Albert Y. Han
- Department of Otolaryngology—Head and Neck Surgery, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
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Yan T, Bao Y, Cao S, Jiang P, Zhang Z, Li L, Kang Y, Wu Q. The investigation of the role of oral-originated Prevotella-induced inflammation in childhood asthma. Front Microbiol 2024; 15:1400079. [PMID: 38863747 PMCID: PMC11165567 DOI: 10.3389/fmicb.2024.1400079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/26/2024] [Indexed: 06/13/2024] Open
Abstract
Background and objectives The oral and gut microbiota play significant roles in childhood asthma pathogenesis. However, the communication dynamics and pathogenic mechanisms by which oral microbiota influence gut microbiota and disease development remain incompletely understood. This study investigated potential mechanisms by which oral-originated gut microbiota, specifically Prevotella genus, may contribute to childhood asthma etiology. Methods Oral swab and fecal samples from 30 asthmatic children and 30 healthy controls were collected. Microbiome composition was characterized using 16S rRNA gene sequencing and metagenomics. Genetic distances identified potential oral-originated bacteria in asthmatic children. Functional validation assessed pro-inflammatory properties of in silico predicted microbial mimicry peptides from enriched asthma-associated species. Fecal metabolome profiling combined with metagenomic correlations explored links between gut microbiota and metabolism. HBE cells treated with Prevotella bivia culture supernatant were analyzed for lipid pathway impacts using UPLC-MS/MS. Results Children with asthma exhibited distinct oral and gut microbiota structures. Prevotella bivia, P. disiens, P. oris and Bacteroides fragilis were enriched orally and intestinally in asthmatics, while Streptococcus thermophilus decreased. P. bivia, P. disiens and P. oris in asthmatic gut likely originated orally. Microbial peptides induced inflammatory cytokines from immune cells. Aberrant lipid pathways characterized asthmatic children. P. bivia increased pro-inflammatory and decreased anti-inflammatory lipid metabolites in HBE cells. Conclusion This study provides evidence of Prevotella transfer from oral to gut microbiota in childhood asthma. Prevotella's microbial mimicry peptides and effects on lipid metabolism contribute to disease pathogenesis by eliciting immune responses. Findings offer mechanistic insights into oral-gut connections in childhood asthma etiology.
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Affiliation(s)
- Tongtong Yan
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuling Bao
- Department of Respiratory Medicine, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Shuyuan Cao
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ping Jiang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhan Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Li
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yulin Kang
- Institute of Environmental Information, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Qian Wu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, China
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Siasios P, Giosi E, Ouranos K, Christoforidi M, Dimopoulou I, Leshi E, Exindari M, Anastassopoulou C, Gioula G. Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study. J Pers Med 2024; 14:369. [PMID: 38672996 PMCID: PMC11051038 DOI: 10.3390/jpm14040369] [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: 02/27/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.
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Affiliation(s)
- Panagiotis Siasios
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Evangelia Giosi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Konstantinos Ouranos
- Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Maria Christoforidi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Ifigenia Dimopoulou
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Enada Leshi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Maria Exindari
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Cleo Anastassopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia Gioula
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
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Xu H, Kang Y, Liang T, Lu S, Xia X, Lu Z, Hu L, Guo L, Zhang L, Huang J, Ye L, Jiang P, Liu Y, Xinyi L, Zhai J, Wang Z, Liu Y. SNP-based and haplotype-based genome-wide association on drug dependence in Han Chinese. BMC Genomics 2024; 25:255. [PMID: 38448893 PMCID: PMC10919046 DOI: 10.1186/s12864-024-10117-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Drug addiction is a serious problem worldwide and is influenced by genetic factors. The present study aimed to investigate the association between genetics and drug addiction among Han Chinese. METHODS A total of 1000 Chinese users of illicit drugs and 9693 healthy controls were enrolled and underwent single nucleotide polymorphism (SNP)-based and haplotype-based association analyses via whole-genome genotyping. RESULTS Both single-SNP and haplotype tests revealed associations between illicit drug use and several immune-related genes in the major histocompatibility complex (MHC) region (SNP association: log10BF = 15.135, p = 1.054e-18; haplotype association: log10BF = 20.925, p = 2.065e-24). These genes may affect the risk of drug addiction via modulation of the neuroimmune system. The single-SNP test exclusively reported genome-wide significant associations between rs3782886 (SNP association: log10BF = 8.726, p = 4.842e-11) in BRAP and rs671 (SNP association: log10BF = 7.406, p = 9.333e-10) in ALDH2 and drug addiction. The haplotype test exclusively reported a genome-wide significant association (haplotype association: log10BF = 7.607, p = 3.342e-11) between a region with allelic heterogeneity on chromosome 22 and drug addiction, which may be involved in the pathway of vitamin B12 transport and metabolism, indicating a causal link between lower vitamin B12 levels and methamphetamine addiction. CONCLUSIONS These findings provide new insights into risk-modeling and the prevention and treatment of methamphetamine and heroin dependence, which may further contribute to potential novel therapeutic approaches.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100028, China
| | - Yulin Kang
- Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Sifen Lu
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaolin Xia
- Office of Academic Affairs, The National Police University for Criminal Justice, Baoding, 071000, China
| | - Zuhong Lu
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, 211189, China
| | - Lingming Hu
- Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Li Guo
- School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210003, China
| | - Lishu Zhang
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100028, China
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100028, China
| | - Lin Ye
- Cheung Hong School of Journalism and Communication, Shantou University, Shantou, 515060, China
| | - Peiye Jiang
- Office of International Cooperation and Exchanges, Nanjing University, Nanjing, 210023, China
| | - Yi Liu
- Jiangsu Taihu Institute of Addiction Rehabilitation, Suzhou, 215111, China
| | - Li Xinyi
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100028, China
| | - Jin Zhai
- Department of Social Work, Changzhou University, Changzhou, 213164, China
| | - Zi Wang
- School of Music, Nanjing Normal University, Nanjing, 210097, China
| | - Yangyang Liu
- Department of Psychology, Nanjing University, Nanjing, 210023, China.
- School of Education, Tianjin University, Tianjin, 200350, China.
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Brīvība M, Silamiķele L, Birzniece L, Ansone L, Megnis K, Silamiķelis I, Pelcmane L, Borisova D, Rozenberga M, Jagare L, Elbere I, Kloviņš J. Gut Microbiome Composition and Dynamics in Hospitalized COVID-19 Patients and Patients with Post-Acute COVID-19 Syndrome. Int J Mol Sci 2024; 25:567. [PMID: 38203738 PMCID: PMC10779053 DOI: 10.3390/ijms25010567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of coronavirus disease 2019 (COVID-19). We aimed to investigate the dynamics and compositional changes in the gut microbiome of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of post-COVID-19 conditions. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for cross-sectional and longitudinal analyses with one- and three-month follow-ups. We observed a decline in taxonomic diversity among hospitalized COVID-19 patients compared to healthy controls, while a subsequent increase in alpha diversity was shown during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process and suggested a potential significance of population-specificity in the early gut microbiome markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, pinpointing potential modulators of the disease progression.
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Affiliation(s)
- Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (L.S.); (L.B.); (L.A.); (K.M.); (I.S.); (L.P.); (D.B.); (I.E.); (J.K.)
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