Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients

Article Medicine, Research & Experimental

Lactobacillus plantarum induces innate cytokine responses that potentially provide a protective benefit against COVID-19: A single-arm, double-blind, prospective trial combined with an in vitro cytokine response assay

Yasunari Kageyama et al.

Summary: Intestinal dysbiosis is associated with COVID-19, and this study demonstrates that Lactobacillus plantarum can enhance immune response and reduce IL-6 levels, suggesting its potential as a probiotic for COVID-19.

EXPERIMENTAL AND THERAPEUTIC MEDICINE (2022)

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Article Immunology

Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types

Abhishek Gupta et al.

Summary: This study investigated the nasopharyngeal microbiome composition in infected and non-infected individuals using targeted amplicon sequencing. The results showed a decrease in microbial diversity in SARS-CoV-2 infected individuals and an increase in opportunistic pathogens. The study also found that host types and COVID-19 conditions influenced the microbial community in the upper respiratory tract.

MICROBES AND INFECTION (2022)

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Article Immunology

Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection

Yong-Lin Shi et al.

Summary: This study investigates the characteristics of oropharyngeal microbiota in mild COVID-19 patients and healthy controls. The results show distinct differences in the oropharyngeal microbiota composition of COVID-19 patients, with enrichment of opportunistic pathogens and depletion of certain bacteria. Several bacteria are found to be associated with COVID-19 severity and viral load. Furthermore, alterations in the oropharyngeal microbiota may impact the severity of COVID-19 by influencing microbial association patterns. The study highlights the potential role of oropharyngeal microbiota in COVID-19 infection and severity.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2022)

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Article Chemistry, Multidisciplinary

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut

Yifei Shen et al.

Summary: This study examines the role of respiratory tract microbes and the relationship between respiratory tract and gut microbiomes in COVID-19. The findings reveal differences in microbiota between ICU and non-ICU patients and identify potential biomarkers for disease severity. Understanding the dynamics of respiratory tract and gut microbial communities during COVID-19 progression can contribute to diagnosis and treatment strategies.

ADVANCED SCIENCE (2022)

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Article Medicine, General & Internal

Variation in the COVID-19 infection-fatality ratio by age, time, and geography during the pre-vaccine era: a systematic analysis

Reed J. D. Sorensen et al.

Summary: Understanding the determinants of IFR variation for COVID-19 is crucial for clinical practice, non-pharmaceutical interventions, and vaccine prioritization. IFR is a key parameter in COVID-19 dynamic transmission models.

LANCET (2022)

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Article Gastroenterology & Hepatology

Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19

Tao Zuo et al.

Summary: This study reveals active and prolonged 'quiescent' gastrointestinal infection of SARS-CoV-2 in patients with COVID-19, even without gastrointestinal manifestations and after recovery from respiratory infection. Patients with active SARS-CoV-2 gastrointestinal infection have a gut microbiota characterized by enrichment of opportunistic pathogens and an increased functional capacity for nucleotide and amino acid biosynthesis and carbohydrate metabolism.

GUT (2021)

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Article Dentistry, Oral Surgery & Medicine

Microbiome variations in preschool children with halitosis

Yu Zhang et al.

Summary: The study found that intra-oral halitosis in Chinese preschool children is associated with multi-microbial mutual interactions.

ORAL DISEASES (2021)

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Review Medicine, General & Internal

The Proportion of SARS-CoV-2 Infections That Are Asymptomatic A Systematic Review

Daniel P. Oran et al.

Summary: Available data suggests that at least one third of SARS-CoV-2 infections are asymptomatic. Longitudinal studies indicate that nearly three quarters of individuals who test positive via PCR but show no symptoms at the time of testing will remain asymptomatic. Control strategies for COVID-19 need to be adjusted considering the prevalence and transmission risk of asymptomatic SARS-CoV-2 infections.

ANNALS OF INTERNAL MEDICINE (2021)

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Article Pediatrics

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids

Erin Felton et al.

Summary: Long-chain fatty acid biosynthesis pathways were upregulated in follow-up samples compared to the end of treatment, and Achromobacter xylosoxidans and Escherichia sp. were more prevalent in follow-up. LCFAs may be associated with persistent infection of opportunistic pathogens. Future studies should investigate the role of bacterial production of LCFAs in CF patients' transition from baseline wellness to PEx.

PEDIATRIC RESEARCH (2021)

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Article Immunology

Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum?

Carmela Nardelli et al.

Summary: SARS-CoV-2 infection leads to significant differences in the nasopharyngeal microbiome composition between patients and controls. The reduction of certain bacteria, such as Fusobacterium periodonticum (FP), may affect the pathogenesis of SARS-CoV-2 infection. Further research is needed to elucidate the specific role of FP in COVID-19.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2021)

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Article Biology

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults

Rong Xu et al.

Summary: This study conducted longitudinal analyses of throat and anal microbiomes in 35 COVID-19 patients and 19 healthy controls. Results showed lower bacterial diversity in COVID-19 patients, but observed a synchronous restoration of upper respiratory and gut microbiomes in some mild patients.

COMMUNICATIONS BIOLOGY (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Tzipi Braun et al.

Summary: Despite the rapid spread of COVID-19 around the world, a study on nasopharyngeal swab samples found that SARS-CoV-2 does not have a significant effect on the microbial community in the nasopharynx.

SCIENTIFIC REPORTS (2021)

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Article Microbiology

Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

Maria Paz Ventero et al.

Summary: This study investigated the nasopharynx microbial community of patients with different severity levels of COVID-19, revealing differences in composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances could potentially serve as biomarkers for COVID-19 severity, but validation with larger sample sizes is needed.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Virology

Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19

Dongyan Xiong et al.

Summary: This study conducted metagenomic sequencing of pharyngeal swabs from COVID-19 and Non-COVID-19 patients, revealing 81 bacterial species enriched in the COVID-19 group, with 51 species enriched more than 8 folds. Some of the enriched bacteria contain opportunistic pathogens.

VIROLOGICA SINICA (2021)

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Article Immunology

Distinct systemic and mucosal immune responses during acute SARS-CoV-2 infection

Nikaia Smith et al.

Summary: This study conducted a paired analysis of nasopharyngeal and systemic immune responses in COVID-19 patients, revealing distinct compartmentalization of immunity and shifts in the microbiome.

NATURE IMMUNOLOGY (2021)

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Article Microbiology

Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome

Carter Merenstein et al.

Summary: The study found that patients with COVID-19 have dysbiosis in the respiratory tract microbiome, with significant changes over time, and the diversity of oropharyngeal microbiome at the initial stage is inversely correlated with disease severity. Additionally, microbiome composition is associated with systemic immune parameters, and machine learning analysis indicates early microbiome features can effectively discriminate COVID-19 severity.

MBIO (2021)

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Article Chemistry, Multidisciplinary

Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients

Ming Gao et al.

Summary: The study characterizes the oropharyngeal microbiota in recovered COVID-19 cases and suspected cases for the first time, successfully constructs and validates a diagnostic model for COVID-19, and depicts correlations between microbial OTUs and clinical indicators.

ADVANCED SCIENCE (2021)

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Article Biotechnology & Applied Microbiology

Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization

Yongjian Wu et al.

Summary: This study investigated the dynamics of oral and gut flora in 53 COVID-19 patients before and after the clearance of SARS-CoV-2, comparing them with 76 healthy individuals. The findings revealed a potential association between SARS-CoV-2 infection and alterations in the microbiome community, suggesting new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

NPJ BIOFILMS AND MICROBIOMES (2021)

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Article Medicine, Research & Experimental

Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID

John P. Haran et al.

Summary: In a study, it was found that patients with long COVID had higher abundance of bacteria in the oral microbiome that can induce inflammation, such as Prevotella and Veillonella genera. These microbes may be related to the development of ongoing symptoms in patients, and the oral microbiome of long COVID patients resembled that of patients with chronic fatigue syndrome.

JCI INSIGHT (2021)

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Article Biochemistry & Molecular Biology

Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19

Shengli Ma et al.

Summary: Our analysis of oropharyngeal microbiota revealed distinct compositions in COVID-19 patients compared to flu patients and healthy controls, with Veillonella identified as a prominent biomarker for COVID-19. Additionally, alterations in oropharyngeal microbiota may impact COVID-19 severity by influencing inflammatory response and amino acid metabolism. The study suggests the potential of oropharyngeal microbiota as a target for future research into COVID-19 management.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

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Article Immunology

Association Between the Respiratory Microbiome and Susceptibility to Influenza Virus Infection

Tim K. Tsang et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Immunology

Clinical Characteristics of Imported Cases of Coronavirus Disease 2019 (COVID-19) in Jiangsu Province: A Multicenter Descriptive Study

Jian Wu et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Markus Hoffmann et al.

CELL (2020)

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Article Immunology

The Oral Microbiota May Have Influence on Oral Cancer

Ling Zhang et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

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Letter Infectious Diseases

Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19

Grace Lui et al.

JOURNAL OF INFECTION (2020)

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Article Medicine, General & Internal

SARS-CoV-2 and viral sepsis: observations and hypotheses

Hui Li et al.

LANCET (2020)

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Article Microbiology

Disruption of Cross-Feeding Inhibits Pathogen Growth in the Sputa of Patients with Cystic Fibrosis

Jefferey M. Flynn et al.

MSPHERE (2020)

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Letter Biotechnology & Applied Microbiology

PICRUSt2 for prediction of metagenome functions

Gavin M. Douglas et al.

NATURE BIOTECHNOLOGY (2020)

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Review Dentistry, Oral Surgery & Medicine

Oral-lung microbiome interactions in lung diseases

Manoj J. Mammen et al.

PERIODONTOLOGY 2000 (2020)

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Article Biochemical Research Methods

Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients

Flavio De Maio et al.

BIOLOGICAL PROCEDURES ONLINE (2020)

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Review Microbiology

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

Lirong Bao et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Public, Environmental & Occupational Health

Coronavirus Disease 2019 Case Surveillance - United States, January 22-May 30, 2020

Erin K. Stokes et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2020)

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Article Immunology

Prospective Study Comparing Deep Throat Saliva With Other Respiratory Tract Specimens in the Diagnosis of Novel Coronavirus Disease 2019

Christopher K. C. Lai et al.

JOURNAL OF INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms

Hao Li et al.

NATURE COMMUNICATIONS (2020)

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Review Medical Laboratory Technology

Gastrointestinal symptoms associated with COVID-19: impact on the gut microbiome

Sonia Villapol

TRANSLATIONAL RESEARCH (2020)

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Review Biology

The Microbiota/Host Immune System Interaction in the Nose to Protect from COVID-19

Arianna Di Stadio et al.

LIFE-BASEL (2020)

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Review Multidisciplinary Sciences

Small, but smelly: the importance of Solobacterium moorei in halitosis and other human infections

Ibrahim Barrak et al.

HELIYON (2020)

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Article Microbiology

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling

Zigui Chen et al.

MSYSTEMS (2019)

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Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

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Article Dentistry, Oral Surgery & Medicine

Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus

Yan Li et al.

INTERNATIONAL JOURNAL OF ORAL SCIENCE (2019)

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Article Dentistry, Oral Surgery & Medicine

Oral bacteriome of HIV-1-infected children from Rio de Janeiro, Brazil: Next-generation DNA sequencing analysis

Lucio Souza Goncalves et al.

JOURNAL OF CLINICAL PERIODONTOLOGY (2019)

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PLOS ONE (2019)

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Review Microbiology

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Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection

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Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease

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PLOS PATHOGENS (2016)

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Review Immunology

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NATURE IMMUNOLOGY (2015)

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Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project

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AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY (2010)

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Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients

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