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Li J, Xiong A, Wang J, Wu X, Bai L, Zhang L, He X, Li G. Deciphering the microbial landscape of lower respiratory tract infections: insights from metagenomics and machine learning. Front Cell Infect Microbiol 2024; 14:1385562. [PMID: 38846353 PMCID: PMC11153674 DOI: 10.3389/fcimb.2024.1385562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Background Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Leveraging the advancements in metagenomic next-generation sequencing (mNGS) technology alongside the emergence of machine learning, it is now viable to compare the attributes of lower respiratory tract microbial communities among patients across diverse age groups, diseases, and infection types. Method We collected bronchoalveolar lavage fluid samples from 138 patients diagnosed with lower respiratory tract infections and conducted mNGS to characterize the lung microbiota. Employing various machine learning algorithms, we investigated the correlation of key bacteria in patients with concurrent bronchiectasis and developed a predictive model for hospitalization duration based on these identified key bacteria. Result We observed variations in microbial communities across different age groups, diseases, and infection types. In the elderly group, Pseudomonas aeruginosa exhibited the highest relative abundance, followed by Corynebacterium striatum and Acinetobacter baumannii. Methylobacterium and Prevotella emerged as the dominant genera at the genus level in the younger group, while Mycobacterium tuberculosis and Haemophilus influenzae were prevalent species. Within the bronchiectasis group, dominant bacteria included Pseudomonas aeruginosa, Haemophilus influenzae, and Klebsiella pneumoniae. Significant differences in the presence of Pseudomonas phage JBD93 were noted between the bronchiectasis group and the control group. In the group with concomitant fungal infections, the most abundant genera were Acinetobacter and Pseudomonas, with Acinetobacter baumannii and Pseudomonas aeruginosa as the predominant species. Notable differences were observed in the presence of Human gammaherpesvirus 4, Human betaherpesvirus 5, Candida albicans, Aspergillus oryzae, and Aspergillus fumigatus between the group with concomitant fungal infections and the bacterial group. Machine learning algorithms were utilized to select bacteria and clinical indicators associated with hospitalization duration, confirming the excellent performance of bacteria in predicting hospitalization time. Conclusion Our study provided a comprehensive description of the microbial characteristics among patients with lower respiratory tract infections, offering insights from various perspectives. Additionally, we investigated the advanced predictive capability of microbial community features in determining the hospitalization duration of these patients.
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Affiliation(s)
- Jiahuan Li
- Clinical Medicine Department, North Sichuan Medical College, Nanchong, China
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Junyi Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Xue Wu
- Clinical Medicine Department, North Sichuan Medical College, Nanchong, China
| | - Lingling Bai
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
- National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guoping Li
- Clinical Medicine Department, North Sichuan Medical College, Nanchong, China
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
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Aljabr W, Dandachi I, Abbas B, Karkashan A, Al-Amari A, AlShahrani D. Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities. Microbiol Spectr 2024; 12:e0416623. [PMID: 38557102 PMCID: PMC11237758 DOI: 10.1128/spectrum.04166-23] [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] [Received: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.
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Affiliation(s)
- Waleed Aljabr
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iman Dandachi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Basma Abbas
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Alaa Karkashan
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ahod Al-Amari
- Department of Basic Medical Sciences, College of Medicine, Dar Al-Uloom University, Riyadh, Saudi Arabia
| | - Dayel AlShahrani
- Pediatric infectious diseases, King Fahad Medical City, Riyadh, Saudi Arabia
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Buendia P, Fernandez K, Raley C, Rahnavard A, Crandall KA, Castro JG. Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics. Front Microbiol 2024; 15:1346762. [PMID: 38476940 PMCID: PMC10927822 DOI: 10.3389/fmicb.2024.1346762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA). Methods The saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received. Results Our study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis. Discussion Our results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient's salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.
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Affiliation(s)
| | | | - Castle Raley
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Ali Rahnavard
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Keith A. Crandall
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Jose Guillermo Castro
- Division of Infectious Diseases, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
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Liu S, Zhong M, Wu H, Su W, Wang Y, Li P. Potential Beneficial Effects of Naringin and Naringenin on Long COVID-A Review of the Literature. Microorganisms 2024; 12:332. [PMID: 38399736 PMCID: PMC10892048 DOI: 10.3390/microorganisms12020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused a severe epidemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Recent studies have found that patients do not completely recover from acute infections, but instead, suffer from a variety of post-acute sequelae of SARS-CoV-2 infection, known as long COVID. The effects of long COVID can be far-reaching, with a duration of up to six months and a range of symptoms such as cognitive dysfunction, immune dysregulation, microbiota dysbiosis, myalgic encephalomyelitis/chronic fatigue syndrome, myocarditis, pulmonary fibrosis, cough, diabetes, pain, reproductive dysfunction, and thrombus formation. However, recent studies have shown that naringenin and naringin have palliative effects on various COVID-19 sequelae. Flavonoids such as naringin and naringenin, commonly found in fruits and vegetables, have various positive effects, including reducing inflammation, preventing viral infections, and providing antioxidants. This article discusses the molecular mechanisms and clinical effects of naringin and naringenin on treating the above diseases. It proposes them as potential drugs for the treatment of long COVID, and it can be inferred that naringin and naringenin exhibit potential as extended long COVID medications, in the future likely serving as nutraceuticals or clinical supplements for the comprehensive alleviation of the various manifestations of COVID-19 complications.
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Affiliation(s)
- Siqi Liu
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Mengli Zhong
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Hao Wu
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Weiwei Su
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Yonggang Wang
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Peibo Li
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
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Ganesan SM, Peter TK, Withanage MHH, Boksa F, Zeng E, Martinez A, Dabdoub SM, Dhingra K, Hernandez-Kapila Y. COVID-19 associated oral and oropharyngeal microbiome: Systematic review and meta-analysis. Periodontol 2000 2024; 94:603-626. [PMID: 37277934 DOI: 10.1111/prd.12489] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/01/2023] [Indexed: 06/07/2023]
Abstract
Three years into the coronavirus disease 2019 (COVID-19) pandemic, there are still growing concerns with the emergence of different variants, unknown long- and short-term effects of the virus, and potential biological mechanisms underlying etiopathogenesis and increased risk for morbidity and mortality. The role of the microbiome in human physiology and the initiation and progression of several oral and systemic diseases have been actively studied in the past decade. With the proof of viral transmission, carriage, and a potential role in etiopathogenesis, saliva and the oral environment have been a focus of COVID-19 research beyond diagnostic purposes. The oral environment hosts diverse microbial communities and contributes to human oral and systemic health. Several investigations have identified disruptions in the oral microbiome in COVID-19 patients. However, all these studies are cross-sectional in nature and present heterogeneity in study design, techniques, and analysis. Therefore, in this undertaking, we (a) systematically reviewed the current literature associating COVID-19 with changes in the microbiome; (b) performed a re-analysis of publicly available data as a means to standardize the analysis, and (c) reported alterations in the microbial characteristics in COVID-19 patients compared to negative controls. Overall, we identified that COVID-19 is associated with oral microbial dysbiosis with significant reduction in diversity. However, alterations in specific bacterial members differed across the study. Re-analysis from our pipeline shed light on Neisseria as the potential key microbial member associated with COVID-19.
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Affiliation(s)
- Sukirth M Ganesan
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Tabitha K Peter
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Miyuraj H H Withanage
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Frank Boksa
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
| | - Erliang Zeng
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Department of Preventive and Community Dentistry, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - April Martinez
- Division of Periodontology, University of California at San Francisco School of Dentistry, San Francisco, California, USA
| | - Shareef M Dabdoub
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Kunaal Dhingra
- Periodontology Division, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Yvonne Hernandez-Kapila
- Section of Biosystems and Function Periodontics, University of California at Los Angeles School of Dentistry, Los Angeles, California, USA
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Banks JM, Capistrano KJ, Brandini DA, Zaidi F, Thakkar P, Rahat R, Schwartz J, Naqvi AR. Herpesviruses and SARS-CoV-2: Viral Association with Oral Inflammatory Diseases. Pathogens 2024; 13:58. [PMID: 38251365 PMCID: PMC10819702 DOI: 10.3390/pathogens13010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The oral cavity is a niche for diverse microbes, including viruses. Members of the Herpesviridae family, comprised of dsDNA viruses, as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an ssRNA virus, are among the most prevalent viruses infecting the oral cavity, and they exhibit clinical manifestations unique to oral tissues. Viral infection of oral mucosal epithelia triggers an immune response that results in prolonged inflammation. The clinical and systemic disease manifestations of HHV have been researched extensively, and several recent studies have illuminated the relationship between HHV and oral inflammatory diseases. Burgeoning evidence suggests the oral manifestation of SARS-CoV-2 infection includes xerostomia, dysgeusia, periodontal disease, mucositis, and opportunistic viral and bacterial infections, collectively described as oral post-acute sequelae of COVID-19 (PASC). These diverse sequelae could be a result of intensified immune responses initially due to the copious production of proinflammatory cytokines: the so-called "cytokine storm syndrome", facilitating widespread oral and non-oral tissue damage. This review explores the interplay between HHV, SARS-CoV-2, and oral inflammatory diseases such as periodontitis, endodontic disease, and peri-implantitis. Additionally, the review discusses proper diagnostic techniques for identifying viral infection and how viral diagnostics can lead to improved overall patient health.
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Affiliation(s)
- Jonathan M. Banks
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Kristelle J. Capistrano
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Daniela A. Brandini
- Department of Diagnosis and Surgery, School of Dentistry, São Paulo State University (UNESP), Araçatuba 16015-050, SP, Brazil;
| | - Filza Zaidi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Rani Rahat
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Joel Schwartz
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Afsar R. Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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Nardelli C, Aveta A, Pandolfo SD, Tripodi L, Russo F, Imbimbo C, Castaldo G, Pastore L. Microbiome Profiling in Bladder Cancer Patients Using the First-morning Urine Sample. EUR UROL SUPPL 2024; 59:18-26. [PMID: 38298766 PMCID: PMC10829607 DOI: 10.1016/j.euros.2023.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2023] [Indexed: 02/02/2024] Open
Abstract
Background Several studies support the interplay between the urinary microbiome (ie, urobiome) and bladder cancer (BCa). Specific urinary bacteria may be responsible for chronic inflammation, which in turn promotes carcinogenesis. Different signatures of urobiome in BCa patients were identified depending on tumor type, geographical area, age, and sex. Objective We explored the urobiome in BCa patients undergoing transurethral resection of bladder tumor (TURBT), to identify possible predictive biomarkers of cancer. Design setting and participants The urobiome analysis was conducted in 48 patients (13 females) undergoing TURBT, of whom 30 with BCa (five females) and 18 with benign bladder tumor, analyzing bacterial 16S rRNA by next-generation sequencing in first-morning (FM) urine samples. Forty-three cancer-free individuals and 17 prostate cancer patients were used as controls. Outcome measurements and statistical analysis First, we identified the better urine collection procedure to perform the urobiome analysis, comparing bacterial composition between catheterized (CAT) and FM urine samples in TURBT patients. Successively, we observed a specific urobiome in BCa patients rather than controls. A combined pipeline including the DESeq2 and linear discriminant analysis effect size tests was used to identify differential urinary taxa, strictly associated with BCa patients. Results and limitations The bacterial composition of CAT and FM urine samples was comparable, so the latter was used for the following analyses. An increased abundance of Porphyromonas and Porphyromonas somerae was found in BCa patients compared with controls. This signature seems to be more related (p <0.05) to male BCa patients over 50 yr old. Owing to the low biomass of urinary microbiota, several samples were excluded from the study, reducing the number of BCa patients considered. Conclusions FM urine samples represent a manageable specimen for a urobiome analysis; P. somerae is a specific biomarker of BCa risk. Patient summary Our study showed an increased abundance of Porphyromonas and Porphyromonas somerae in male bladder cancer (BCa) patients, supporting the use of a first-morning urine sample, a less invasive and low-cost collection method, for the urobiome analysis of patients at risk of BCa.
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Affiliation(s)
- Carmela Nardelli
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Achille Aveta
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Savio Domenico Pandolfo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
- Department of Urology, University of L'Aquila, L'Aquila, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Filippo Russo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Ciro Imbimbo
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
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Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A, Mukherjee S. Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups. Microbiol Spectr 2023; 11:e0236823. [PMID: 37905804 PMCID: PMC10715160 DOI: 10.1128/spectrum.02368-23] [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] [Received: 06/14/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies. The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. However, although it has been known that different SARS-CoV-2 variants manifest distinct transmissibility and mortality rates in human populations, their effect on the composition and diversity of the URT microbiome has not been studied to date. Unlike the older variant (Delta), the newer variant (Omicron) have become more transmissible with lesser mortality and the symptoms have also changed significantly. Hence, in the present study, we have investigated the change in the URT microbiome associated with Delta and Omicron variants and identified variant-specific signatures that will be useful in the assessment of lung health and can be utilized for nasal probiotic therapy in the future.
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Affiliation(s)
- Shankha Nath
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Mousumi Sarkar
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Debjit De
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Shouvik Paul
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Souradeep Dey
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Kuhu Pal
- Department of Microbiology, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Suman Kr. Roy
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Ayan Ghosh
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Sharmila Sengupta
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Nidhan K. Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Souvik Mukherjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
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9
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Abstract
The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.
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Affiliation(s)
- Sergio Candel
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Sylwia D. Tyrkalska
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Victoriano Mulero
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain, Victoriano Mulero ; Sergio Candel ; Sylwia D. Tyrkalska Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, 30120, Murcia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
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10
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Kim BG, Yu JY, Kim SY, Kim DH, Jhun BW. Changes in sputum microbiota during treatment for nontuberculous mycobacterial pulmonary disease. Sci Rep 2023; 13:19764. [PMID: 37957253 PMCID: PMC10643529 DOI: 10.1038/s41598-023-47230-5] [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] [Received: 09/18/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
Limited data exist on longitudinal changes in the sputum bacterial microbiome during treatment in nontuberculous mycobacterial pulmonary disease (NTM-PD) patients. We prospectively collected serial sputum samples from 14 NTM-PD patients during treatment, at the start (n = 14) and at 1 (n = 10), 3 (n = 10), 6 (n = 12), and 12 (n = 7) months. The bacterial microbiome changes were analyzed using 16S rRNA sequences (V3-V4 regions). Subgroup analysis included culture conversion (n = 9) and treatment refractory (n = 5) groups. In all patients, sputum alpha-diversity (ACE, Chao1, and Jackknife) significantly decreased during antibiotic treatment at 1, 3, 6, and 12 months compared to treatment initiation levels. Within the culture conversion group, genus/species-level beta-diversity showed differences at 1, 3, 6, and 12 months compared to treatment initiation (all p < 0.05). However, in the refractory group, there were no differences in beta-diversity at the genus/species levels in the sputum at any time point. In the linear discriminant analysis (LDA) effect sizes (LEfSe) analysis, the culture conversion group exhibited decreasing taxa at various levels (phylum/genus/species), but no significant increase in taxa was observed. LEfSe analysis of the refractory patient group revealed multiple taxa decreased during treatment. However, proportions of Veillonella dispar (LDA = 4.78), Fusobacterium periodonticum (LDA = 4.35), and Pseudomonas aeruginosa (LDA = 2.92) increased as the treatment period progressed in the refractory group. Sputum microbiota diversity decreases during NTM-PD treatment. In the culture conversion group, most taxa decrease, while some increase in the refractory group. These findings suggest that a distinct respiratory microbial community may exist in refractory NTM-PD patients compared to responsive antibiotic-treated patients.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Jin Young Yu
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea.
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11
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Bourumeau W, Tremblay K, Jourdan G, Girard C, Laprise C. Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection. Microorganisms 2023; 11:2703. [PMID: 38004715 PMCID: PMC10673573 DOI: 10.3390/microorganisms11112703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.
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Affiliation(s)
- William Bourumeau
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Karine Tremblay
- Pharmacology-Physiology Department, Université de Sherbrooke, Saguenay, QC J1K 2R1, Canada;
- Research Centre of Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay–Lac-Saint-Jean (CIUSSS-SLSJ), Saguenay, QC G7H 7K9, Canada
| | - Guillaume Jourdan
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Girard
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
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12
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Szabo D, Ostorhazi E, Stercz B, Makra N, Penzes K, Kristof K, Antal I, Rethelyi JM, Zsigmond RI, Birtalan E, Merkely B, Tamas L. Specific nasopharyngeal Corynebacterium strains serve as gatekeepers against SARS-CoV-2 infection. GeroScience 2023; 45:2927-2938. [PMID: 37338780 PMCID: PMC10643471 DOI: 10.1007/s11357-023-00850-1] [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] [Received: 04/10/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
The SARS-CoV-2 virus is still causing a worldwide problem. The virus settles primarily on the nasal mucosa, and the infection and its course depend on individual susceptibility. Our aim was to investigate the nasopharynx composition's role in the individual susceptibility. During the first phase of SARS-CoV-2 pandemic, nasopharyngeal microbiome samples of close contact unvaccinated patients were investigated by 16S rRNA analysis and by culturing. The whole genome of cultured Corynebacteria was sequenced. The relative expression of ACE2, TMPRSS2, and cathepsin L on Caco-2 cells and the strength of S1-ACE2 binding were determined in the presence of Corynebacteria. From 55 close contacts exposed to identical SARS-CoV-2 exposure, 26 patients became infected and 29 remained uninfected. The nasopharyngeal microbiome analysis showed significantly higher abundance of Corynebacteria in uninfected group. Corynebacterium accolens could be cultivated only from uninfected individuals and Corynebacterium propinquum from both infected and uninfected. Corynebacteria from uninfected patient significantly reduced the ACE2 and cathepsin L expression. C. accolens significantly reduced the TMPRSS2 expression compared to other Corynebacteria. Furthermore, Corynebacterium spp. weakened the binding of the S1-ACE2. Most C. accolens isolates harbored the TAG lipase LipS1 gene. Based on these results, the presence of Corynebacterium spp. in the nasopharyngeal microbiota, especially C. accolens strains, could reduce the individual susceptibility to SARS-CoV-2 infection by several mechanisms: by downregulation the ACE2, the TMPRSS2 receptors, and cathepsin L in the host; through the inhibition of S1-ACE2 binding; and lipase production. These results suggest the use of C. accolens strains as probiotics in the nasopharynx in the future.
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Affiliation(s)
- Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary.
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary.
| | - Eszter Ostorhazi
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Balazs Stercz
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Nora Makra
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Kinga Penzes
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Katalin Kristof
- Institute of Laboratory Medicine, Clinical Microbiology Laboratory, Semmelweis University, Budapest, Hungary
| | - Istvan Antal
- Department of Pharmaceutics, Semmelweis University, Budapest, Hungary
| | - Janos M Rethelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Reka I Zsigmond
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Ede Birtalan
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
| | - Bela Merkely
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Laszlo Tamas
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
- Department of Voice, Speech and Swallowing Therapy, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
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13
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Haldar S, Jadhav SR, Gulati V, Beale DJ, Balkrishna A, Varshney A, Palombo EA, Karpe AV, Shah RM. Unravelling the gut-lung axis: insights into microbiome interactions and Traditional Indian Medicine's perspective on optimal health. FEMS Microbiol Ecol 2023; 99:fiad103. [PMID: 37656879 PMCID: PMC10508358 DOI: 10.1093/femsec/fiad103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/05/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023] Open
Abstract
The microbiome of the human gut is a complex assemblage of microorganisms that are in a symbiotic relationship with one another and profoundly influence every aspect of human health. According to converging evidence, the human gut is a nodal point for the physiological performance matrixes of the vital organs on several axes (i.e. gut-brain, gut-lung, etc). As a result of COVID-19, the importance of gut-lung dysbiosis (balance or imbalance) has been realised. In view of this, it is of utmost importance to develop a comprehensive understanding of the microbiome, as well as its dysbiosis. In this review, we provide an overview of the gut-lung axial microbiome and its importance in maintaining optimal health. Human populations have successfully adapted to geophysical conditions through traditional dietary practices from around the world. In this context, a section has been devoted to the traditional Indian system of medicine and its theories and practices regarding the maintenance of optimally customized gut health.
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Affiliation(s)
- Swati Haldar
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
| | - Snehal R Jadhav
- Consumer-Analytical-Safety-Sensory (CASS) Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - Vandana Gulati
- Biomedical Science, School of Science and Technology Faculty of Science, Agriculture, Business and Law, University of New England, Armidale, NSW 2351, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Acharya Balkrishna
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Patanjali Yog Peeth, Roorkee-Haridwar Road, Haridwar 249405, Uttarakhand, India
| | - Anurag Varshney
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Patanjali Yog Peeth, Roorkee-Haridwar Road, Haridwar 249405, Uttarakhand, India
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Avinash V Karpe
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Socio-Eternal Thinking for Unity (SETU), Melbourne, VIC 3805, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, ACT 2601, Australia
| | - Rohan M Shah
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora West, VIC 3083, Australia
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14
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Bose T, Wasimuddin, Acharya V, Pinna NK, Kaur H, Ranjan M, SaiKrishna J, Nagabandi T, Varma B, Tallapaka KB, Sowpati DT, Haque MM, Dutta A, Siva AB, Mande SS. A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India. Front Microbiol 2023; 14:1238829. [PMID: 37744900 PMCID: PMC10511876 DOI: 10.3389/fmicb.2023.1238829] [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: 06/12/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
Background Multiple variants of the SARS-CoV-2 virus have plagued the world through successive waves of infection over the past three years. Independent research groups across geographies have shown that the microbiome composition in COVID-19 positive patients (CP) differs from that of COVID-19 negative individuals (CN). However, these observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern. Methods The nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India and subjected to 16s rRNA gene amplicon - based sequencing. Findings We found variations in the microbiota of symptomatic vs. asymptomatic COVID-19 patients. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection. Interpretation To our knowledge, this is the first analytical cross-sectional study of this scale, which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Although no clear signatures were observed, this study shall pave the way for a better understanding of the disease pathophysiology and help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery.
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Affiliation(s)
- Tungadri Bose
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Wasimuddin
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Varnali Acharya
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Nishal Kumar Pinna
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Harrisham Kaur
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Manish Ranjan
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Jandhyala SaiKrishna
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Tulasi Nagabandi
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Binuja Varma
- TCS Genomics Lab, Tata Consultancy Services Limited, Noida, Uttar Pradesh, India
| | | | - Divya Tej Sowpati
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | | | - Anirban Dutta
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | | | - Sharmila S. Mande
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
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15
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Romani A, Sergi D, Zauli E, Voltan R, Lodi G, Vaccarezza M, Caruso L, Previati M, Zauli G. Nutrients, herbal bioactive derivatives and commensal microbiota as tools to lower the risk of SARS-CoV-2 infection. Front Nutr 2023; 10:1152254. [PMID: 37324739 PMCID: PMC10267353 DOI: 10.3389/fnut.2023.1152254] [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: 01/27/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
The SARS-CoV-2 outbreak has infected a vast population across the world, causing more than 664 million cases and 6.7 million deaths by January 2023. Vaccination has been effective in reducing the most critical aftermath of this infection, but some issues are still present regarding re-infection prevention, effectiveness against variants, vaccine hesitancy and worldwide accessibility. Moreover, although several old and new antiviral drugs have been tested, we still lack robust and specific treatment modalities. It appears of utmost importance, facing this continuously growing pandemic, to focus on alternative practices grounded on firm scientific bases. In this article, we aim to outline a rigorous scientific background and propose complementary nutritional tools useful toward containment, and ultimately control, of SARS-CoV-2 infection. In particular, we review the mechanisms of viral entry and discuss the role of polyunsaturated fatty acids derived from α-linolenic acid and other nutrients in preventing the interaction of SARS-CoV-2 with its entry gateways. In a similar way, we analyze in detail the role of herbal-derived pharmacological compounds and specific microbial strains or microbial-derived polypeptides in the prevention of SARS-CoV-2 entry. In addition, we highlight the role of probiotics, nutrients and herbal-derived compounds in stimulating the immunity response.
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Affiliation(s)
- Arianna Romani
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Domenico Sergi
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Enrico Zauli
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Rebecca Voltan
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giada Lodi
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Mauro Vaccarezza
- Curtin Medical School & Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Lorenzo Caruso
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Maurizio Previati
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialistic Hospital, Riyadh, Saudi Arabia
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16
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Ruiz-Tagle C, Ugalde JA, Naves R, Araos R, García P, Balcells ME. Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection. Sci Rep 2023; 13:7301. [PMID: 37147354 PMCID: PMC10160714 DOI: 10.1038/s41598-023-34052-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
The upper respiratory tract is an obliged pathway for respiratory pathogens and a healthy microbiota may support the host's mucosal immunity preventing infection. We analyzed the nasopharyngeal microbiome in tuberculosis household contacts (HHCs) and its association with latent tuberculosis infection (TBI). A prospective cohort of HHCs was established and latent TBI status was assessed by serial interferon-γ release assay (IGRA). Nasopharyngeal swabs collected at baseline were processed for 16S rRNA gene sequencing. The 82 participants included in the analysis were classified as: (a) non-TBI [IGRA negative at baseline and follow-up, no active TB (n = 31)], (b) pre-TBI [IGRA negative at baseline but converted to IGRA positive or developed active TB at follow-up (n = 16)], and (c) TBI [IGRA positive at enrollment (n = 35)]. Predominant phyla were Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota. TBI group had a lower alpha diversity compared to non-TBI (padj = 0.04) and pre-TBI (padj = 0.04). Only TBI and non-TBI had beta diversity differences (padj = 0.035). Core microbiomes' had unique genera, and genus showed differential abundance among groups. HHCs with established latent TBI showed reduced nasopharyngeal microbial diversity with distinctive taxonomical composition. Whether a pre-existing microbiome feature favors, are a consequence, or protects against Mycobacterium tuberculosis needs further investigation.
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Affiliation(s)
- Cinthya Ruiz-Tagle
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Republica 330, Santiago, Chile
| | - Rodrigo Naves
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rafael Araos
- Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
| | - Patricia García
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
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17
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Zafar H, Saier MH. Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery. Cells 2023; 12:cells12091213. [PMID: 37174613 PMCID: PMC10177376 DOI: 10.3390/cells12091213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) first emerged in 2019 in China and has resulted in millions of human morbidities and mortalities across the globe. Evidence has been provided that this novel virus originated in animals, mutated, and made the cross-species jump to humans. At the time of this communication, the Coronavirus disease (COVID-19) may be on its way to an endemic form; however, the threat of the virus is more for susceptible (older and immunocompromised) people. The human body has millions of bacterial cells that influence health and disease. As a consequence, the bacteriomes in the human body substantially influence human health and disease. The bacteriomes in the body and the immune system seem to be in constant association during bacterial and viral infections. In this review, we identify various bacterial spp. In major bacteriomes (oral, nasal, lung, and gut) of the body in healthy humans and compare them with dysbiotic bacteriomes of COVID-19 patients. We try to identify key bacterial spp. That have a positive effect on the functionality of the immune system and human health. These select bacterial spp. Could be used as potential probiotics to counter or prevent COVID-19 infections. In addition, we try to identify key metabolites produced by probiotic bacterial spp. That could have potential anti-viral effects against SARS-CoV-2. These metabolites could be subject to future therapeutic trials to determine their anti-viral efficacies.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Milton H Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
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Ancona G, Alagna L, Alteri C, Palomba E, Tonizzo A, Pastena A, Muscatello A, Gori A, Bandera A. Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID. Front Immunol 2023; 14:1080043. [PMID: 36969243 PMCID: PMC10030519 DOI: 10.3389/fimmu.2023.1080043] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
The gut microbiota plays a crucial role in human health and disease. Gut dysbiosis is known to be associated with increased susceptibility to respiratory diseases and modifications in the immune response and homeostasis of the lungs (the so-called gut-lung axis). Furthermore, recent studies have highlighted the possible role of dysbiosis in neurological disturbances, introducing the notion of the "gut-brain axis." During the last 2 years, several studies have described the presence of gut dysbiosis during coronavirus disease 2019 (COVID-19) and its relationship with disease severity, SARS-CoV-2 gastrointestinal replication, and immune inflammation. Moreover, the possible persistence of gut dysbiosis after disease resolution may be linked to long-COVID syndrome and particularly to its neurological manifestations. We reviewed recent evidence on the association between dysbiosis and COVID-19, investigating the possible epidemiologic confounding factors like age, location, sex, sample size, the severity of disease, comorbidities, therapy, and vaccination status on gut and airway microbial dysbiosis in selected studies on both COVID-19 and long-COVID. Moreover, we analyzed the confounding factors strictly related to microbiota, specifically diet investigation and previous use of antibiotics/probiotics, and the methodology used to study the microbiota (α- and β-diversity parameters and relative abundance tools). Of note, only a few studies focused on longitudinal analyses, especially for long-term observation in long-COVID. Lastly, there is a lack of knowledge regarding the role of microbiota transplantation and other therapeutic approaches and their possible impact on disease progression and severity. Preliminary data seem to suggest that gut and airway dysbiosis might play a role in COVID-19 and in long-COVID neurological symptoms. Indeed, the development and interpretation of these data could have important implications for future preventive and therapeutic strategies.
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Affiliation(s)
- Giuseppe Ancona
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Alagna
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Bambino Gesù Children Hospital (IRCCS), Rome, Italy
| | - Emanuele Palomba
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Anna Tonizzo
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Andrea Pastena
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
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Yasir M, Al-Sharif HA, Al-Subhi T, Sindi AA, Bokhary DH, El-Daly MM, Alosaimi B, Hamed ME, Karim AM, Hassan AM, AlShawdari MM, Alawi M, El-Kafrawy SA, Azhar EI. Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia. J Infect Public Health 2023; 16:680-688. [PMID: 36934642 PMCID: PMC9984237 DOI: 10.1016/j.jiph.2023.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/11/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. METHODS A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. RESULTS No significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. CONCLUSIONS Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Hessa A Al-Sharif
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tagreed Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Pulmonary & Critical Care Consultant, International Medical Center, Jeddah 21589, Saudi Arabia
| | - Diyaa H Bokhary
- Emergency Medicine Department, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mai M El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bandar Alosaimi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maaweya E Hamed
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Asad Mustafa Karim
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, the Republic of Korea
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mustafa M AlShawdari
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maha Alawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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20
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SeyedAlinaghi S, Afzalian A, Pashaei Z, Varshochi S, Karimi A, Mojdeganlou H, Mojdeganlou P, Razi A, Ghanadinezhad F, Shojaei A, Amiri A, Dashti M, Ghasemzadeh A, Dadras O, Mehraeen E, Afsahi AM. Gut microbiota and COVID-19: A systematic review. Health Sci Rep 2023; 6:e1080. [PMID: 36721396 PMCID: PMC9881458 DOI: 10.1002/hsr2.1080] [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: 10/19/2022] [Revised: 12/24/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Background and Aims Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS-CoV-2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS-CoV-2 infection and its severity and the impact that SARS-CoV-2 could have on the gut microbiota. Methods We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full-text screening. The data of the eligible studies were extracted into a pre-designed word table. This study adhered to the PRISMA checklist and Newcastle-Ottawa Scale Bias Assessment tool. Results Sixty-three publications were included in this review. Our study shows that among COVID-19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID-19 disease would probably also be influenced by the gut, and lung microbiota's composition. Conclusion Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID-19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID-19 and human microbiome.
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Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Arian Afzalian
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Zahra Pashaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Sanaz Varshochi
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | | | - Armin Razi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | - Alireza Shojaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Ava Amiri
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Mohsen Dashti
- Department of RadiologyTabriz University of Medical SciencesTabrizIran
| | | | - Omid Dadras
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
- Department of Global Public Health and Primary CareUniversity of BergenBergenNorway
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyKhalkhal University of Medical SciencesKhalkhalIran
| | - Amir Masoud Afsahi
- Department of RadiologyUniversity of California, San Diego (UCSD)CaliforniaUSA
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21
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Mańkowska-Wierzbicka D, Zuraszek J, Wierzbicka A, Gabryel M, Mahadea D, Baturo A, Zakerska-Banaszak O, Slomski R, Skrzypczak-Zielinska M, Dobrowolska A. Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing. Biomedicines 2023; 11:biomedicines11020367. [PMID: 36830905 PMCID: PMC9953267 DOI: 10.3390/biomedicines11020367] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/13/2022] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
It is crucial to consider the importance of the microbiome and the gut-lung axis in the context of SARS-CoV-2 infection. This pilot study examined the fecal microbial composition of patients with COVID-19 following a 3-month recovery. Using for the first time metagenomic analysis based on all hypervariable regions (V1-V9) of the 16S rRNA gene, we have identified 561 microbial species; however, 17 were specific only for the COVID-19 group (n = 8). The patients' cohorts revealed significantly greater alpha diversity of the gut microbiota compared to healthy controls (n = 14). This finding has been demonstrated by operational taxonomic units (OTUs) richness (p < 0.001) and Chao1 index (p < 0.01). The abundance of the phylum Verrucomicrobia was 30 times higher in COVID-19 patients compared to healthy subjects. Accordingly, this disproportion was also noted at other taxonomic levels: in the class Verrucomicrobiae, the family Verrucomicrobiaceae, and the genus Akkermansia. Elevated pathobionts such as Escherichia coli, Bilophila wadsworthia, and Parabacteroides distasonis were found in COVID-19 patients. Considering the gut microbiota's ability to disturb the immune response, our findings suggest the importance of the enteric microbiota in the course of SARS-CoV-2 infection. This pilot study shows that the composition of the microbial community may not be fully restored in individuals with SARS-CoV-2 following a 3-month recovery.
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Affiliation(s)
- Dorota Mańkowska-Wierzbicka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
- Correspondence: (D.M.-W.); (M.S.-Z.)
| | - Joanna Zuraszek
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Adrianna Wierzbicka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Marcin Gabryel
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Dagmara Mahadea
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Alina Baturo
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | | | - Ryszard Slomski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Marzena Skrzypczak-Zielinska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
- Correspondence: (D.M.-W.); (M.S.-Z.)
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznan, Poland
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22
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Nardelli C, Scaglione GL, Testa D, Setaro M, Russo F, Di Domenico C, Atripaldi L, Zollo M, Corrado F, Salvatore P, Pinchera B, Gentile I, Capoluongo E. Nasal Microbiome in COVID-19: A Potential Role of Corynebacterium in Anosmia. Curr Microbiol 2023; 80:53. [PMID: 36583787 PMCID: PMC9802018 DOI: 10.1007/s00284-022-03106-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/31/2022] [Indexed: 12/31/2022]
Abstract
The evolution and the development of the symptoms of Coronavirus disease 19 (COVID-19) are due to different factors, where the microbiome plays a relevant role. The possible relationships between the gut, lung, nasopharyngeal, and oral microbiome with COVID-19 have been investigated. We analyzed the nasal microbiome of both positive and negative SARS-CoV-2 individuals, showing differences in terms of bacterial composition in this niche of respiratory tract. The microbiota solution A (Arrow Diagnostics) was used to cover the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. MicrobAT Suite and MicrobiomeAnalyst program were used to identify the operational taxonomic units (OTUs) and to perform the statistical analysis, respectively. The main taxa identified in nasal microbiome of COVID-19 patients and in Healthy Control subjects belonged to three distinct phyla: Proteobacteria (HC = 14%, Cov19 = 35.8%), Firmicutes (HC = 28.8%, Cov19 = 30.6%), and Actinobacteria (HC = 56.7%, Cov19 = 14.4%) with a relative abundance > 1% in all groups. A significant reduction of Actinobacteria in Cov19 group compared to controls (P < 0.001, FDR = 0.01) was found. The significant reduction of Actinobacteria was identified in all taxonomic levels down to the genus (P < 0.01) using the ANOVA test. Indeed, a significantly reduced relative abundance of Corynebacterium was found in the patients compared to healthy controls (P = 0.001). Reduced abundance of Corynebacterium has been widely associated with anosmia, a common symptom of COVID-19 as suffered from our patients. Contrastingly, the Corynebacterium genus was highly represented in the nasal mucosa of healthy subjects. Further investigations on larger cohorts are necessary to establish functional relationships between nasal microbiota content and clinical features of COVID-19.
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Affiliation(s)
- Carmela Nardelli
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Giovanni Luca Scaglione
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Istituto Dermopatico Dell'Immacolata IDI-IRCSS, Rome, Italy
| | - Domenico Testa
- Department of Otorhinolaryngology, Luigi Vanvitelli University of Naples, Naples, Italy
| | - Mario Setaro
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
| | - Filippo Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
| | | | - Lidia Atripaldi
- Clinical Biochemistry Unit, AORN Ospedale Dei Colli, Naples, Italy
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
| | - Federica Corrado
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Naples, Italy
| | - Paola Salvatore
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate S.C.a R.L., Naples, Italy
| | - Biagio Pinchera
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ivan Gentile
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
- Department of Clinical Pathology and Genomics, Azienda Ospedaliera Per L'Emergenza Cannizzaro, Catania, Italy.
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23
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Mycobiome profiling of nasopharyngeal region of SARS-CoV-2 infected individuals. Microbes Infect 2023; 25:105059. [PMID: 36241143 PMCID: PMC9553963 DOI: 10.1016/j.micinf.2022.105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 02/07/2023]
Abstract
The present cross-sectional study aims to understand the fungal community composition of the nasopharyngeal region of SARS-CoV-2 infected individuals and how the infection influences the mycobiome therein. The infection significantly (p < 0.05) influenced the alpha diversity. Interestingly, a higher abundance of Cladosporium and Alternaria was noted in the infected individuals and inter-individual variation in mycobiome composition was well supported by beta dispersion analysis (p < 0.05). Moreover, decrease in Aspergillus abundance was observed in infected patients across the four age groups. This study provides insight into the alteration in mycobiome during the viral disease progression and demands continuous investigation to monitor fungal infections.
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24
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Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS, Chen Z. Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients. Microbiol Spectr 2022; 10:e0219622. [PMID: 36350127 PMCID: PMC9769582 DOI: 10.1128/spectrum.02196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022] Open
Abstract
Numerous studies have reported dysbiosis in the naso- and/or oro-pharyngeal microbiota of COVID-19 patients compared with healthy individuals; however, only a few small-scale studies have also included a disease control group. In this study, we characterized and compared the bacterial communities of pooled nasopharyngeal and throat swabs from hospitalized COVID-19 patients (n = 76), hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses (n = 69), and local community controls (n = 76) using 16S rRNA gene V3-V4 amplicon sequencing. None of the subjects received antimicrobial therapy within 2 weeks prior to sample collection. Both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls. However, the microbial communities in the two hospitalized patient groups did not differ significantly from each other. Differential abundance analysis revealed the enrichment of nine bacterial genera in the COVID-19 patients compared with local controls; however, six of them were also enriched in the non-COVID-19 patients. Bacterial genera uniquely enriched in the COVID-19 patients included Alloprevotella and Solobacterium. In contrast, Mogibacterium and Lactococcus were dramatically decreased in COVID-19 patients only. Association analysis revealed that Alloprevotella in COVID-19 patients was positively correlated with the level of the inflammation biomarker C-reactive protein. Our findings reveal a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients and suggest that Alloprevotella and Solobacterium are more specific biomarkers for COVID-19 detection. IMPORTANCE Our results showed that while both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls, the microbial communities in the two hospitalized patient groups did not differ significantly from each other, indicating a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients. Besides, we identified Alloprevotella and Solobacterium as bacterial genera uniquely enriched in COVID-19 patients, which may serve as more specific biomarkers for COVID-19 detection.
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Affiliation(s)
- Christopher K. C. Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace C. Y. Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Y. K. Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Rita W. Y. Ng
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hiu Ching Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Apple C. M. Yeung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wendy C. S. Ho
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siaw Shi Boon
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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25
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Neag MA, Vulturar DM, Gherman D, Burlacu CC, Todea DA, Buzoianu AD. Gastrointestinal microbiota: A predictor of COVID-19 severity? World J Gastroenterol 2022; 28:6328-6344. [PMID: 36533107 PMCID: PMC9753053 DOI: 10.3748/wjg.v28.i45.6328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by a severe acute respiratory syndrome coronavirus 2 infection, has raised serious concerns worldwide over the past 3 years. The severity and clinical course of COVID-19 depends on many factors (e.g., associated comorbidities, age, etc) and may have various clinical and imaging findings, which raises management concerns. Gut microbiota composition is known to influence respiratory disease, and respiratory viral infection can also influence gut microbiota. Gut and lung microbiota and their relationship (gut-lung axis) can act as modulators of inflammation. Modulating the intestinal microbiota, by improving its composition and diversity through nutraceutical agents, can have a positive impact in the prophylaxis/treatment of COVID-19.
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Affiliation(s)
- Maria Adriana Neag
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania
| | - Damiana-Maria Vulturar
- Department of Pneumology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400332, Romania
| | - Diana Gherman
- Department of Radiology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400347, Romania
| | - Codrin-Constantin Burlacu
- Faculty of Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca 400347, Romania
| | - Doina Adina Todea
- Department of Pneumology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400332, Romania
| | - Anca Dana Buzoianu
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania
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Jitvaropas R, Mayuramart O, Sawaswong V, Kaewsapsak P, Payungporn S. Classification of salivary bacteriome in asymptomatic COVID-19 cases based on long-read nanopore sequencing. Exp Biol Med (Maywood) 2022; 247:1937-1946. [PMID: 36082397 PMCID: PMC9742750 DOI: 10.1177/15353702221118091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The coronavirus (COVID-19) global pandemic has impacted the health of almost everyone, including changes in their salivary microbiota. Since 2019, there has been an increase in the number of new COVID-19 cases in Thailand. Therefore, COVID-19 active case finding is important for early detection and epidemic control. Moreover, the dynamic changes of salivary bacteriome in asymptomatic COVID-19 cases are largely unknown. This research aimed to investigate and compare the salivary bacteriome and the co-infectious bacterial pathogens in the asymptomatic COVID-19 positive group to the negative group, based on novel nanopore sequencing. This cohort was a cross-sectional study including saliva samples collected from 82 asymptomatic participants (39 COVID-19 positive and 43 COVID-19 negative cases). All samples were sequenced for the full-length bacterial 16S rDNA. The alpha and beta diversity analyses were not significantly different between groups. The three major species in salivary bacteriome including Veillonella parvula, Streptococcus mitis, and Prevotella melaninogenica were observed in both groups. Interestingly, Lautropia mirabilis was a significantly enriched species in the saliva of the asymptomatic COVID-19-positive cases based on linear discriminant analysis effect size (LEfSe) analysis. The results suggested that L. mirabilis was a co-infectious agent in the asymptomatic COVID-19 group. However, the potential role of L. mirabilis should be validated in further experimental studies.
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Affiliation(s)
- Rungrat Jitvaropas
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 10120, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. PLoS One 2022; 17:e0275815. [PMID: 36240246 PMCID: PMC9565700 DOI: 10.1371/journal.pone.0275815] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022] Open
Abstract
Objectives The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral infection, as well as disease severity. Several studies have assessed whether compositional alterations in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection. However, the results of these studies were varied, and many did not account for disease severity. This study aims to examine whether compositional differences in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection status and disease severity. Methods We performed Nanopore full-length 16S rRNA sequencing on 194 nasopharyngeal swab specimens from hospitalized and community-dwelling SARS-CoV-2-infected and uninfected individuals. Sequence data analysis was performed using the BugSeq 16S analysis pipeline. Results We found significant beta (PERMANOVA p < 0.05), but not alpha (Kruskal-Wallis p > 0.05) diversity differences in the nasopharyngeal microbiota among our study groups. We identified several differentially abundant taxa associated with SARS-CoV-2 infection status and disease severity using ALDEx2. Finally, we observed a trend towards higher abundance of Enterobacteriaceae in specimens from hospitalized SARS-CoV-2-infected patients. Conclusions This study identified several alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. Understanding the role of the microbiome in infection susceptibility and severity may open new avenues of research for disease prevention and treatment.
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Starikova EV, Galeeva JS, Andreev DN, Sokolov PS, Fedorov DE, Manolov AI, Pavlenko AV, Klimina KM, Veselovsky VA, Zaborovsky AV, Evdokimov VV, Andreev NG, Devkota MK, Fomenko AK, Khar'kovskii VA, Asadulin PO, Kucher SA, Cheremushkina AS, Yanushevich OO, Maev IV, Krikheli NI, Levchenko OV, Ilina EN, Govorun VM. [Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity]. TERAPEVT ARKH 2022; 94:963-972. [PMID: 36286976 DOI: 10.26442/00403660.2022.08.201780] [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: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
AIM To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity. MATERIALS AND METHODS The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV). RESULTS When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often. CONCLUSION We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.
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Affiliation(s)
| | - J S Galeeva
- Research Institute of Systemic Biology and Medicine
| | - D N Andreev
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - P S Sokolov
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - D E Fedorov
- Research Institute of Systemic Biology and Medicine
| | - A I Manolov
- Research Institute of Systemic Biology and Medicine
| | - A V Pavlenko
- Research Institute of Systemic Biology and Medicine
| | - K M Klimina
- Federal Scientific and Clinical Center for Physical and Chemical Medicine
| | - V A Veselovsky
- Federal Scientific and Clinical Center for Physical and Chemical Medicine
| | - A V Zaborovsky
- Yevdokimov Moscow State University of Medicine and Dentistry, Moscow
| | - V V Evdokimov
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - N G Andreev
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - M K Devkota
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - A K Fomenko
- Yevdokimov Moscow State University of Medicine and Dentistry
| | | | - P O Asadulin
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - S A Kucher
- Yevdokimov Moscow State University of Medicine and Dentistry
| | | | - O O Yanushevich
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - I V Maev
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - N I Krikheli
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - O V Levchenko
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - E N Ilina
- Research Institute of Systemic Biology and Medicine
| | - V M Govorun
- Research Institute of Systemic Biology and Medicine
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29
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He C, Liao Q, Fu P, Li J, Zhao X, Zhang Q, Gui Q. Microbiological characteristics of different tongue coatings in adults. BMC Microbiol 2022; 22:214. [PMID: 36085010 PMCID: PMC9461261 DOI: 10.1186/s12866-022-02626-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Tongue coating is an important health indicator in traditional Chinese medicine (TCM). The tongue coating microbiome can distinguish disease patients from healthy controls. To study the relationship between different types of tongue coatings and health, we analyzed the species composition of different types of tongue coatings and the co-occurrence relationships between microorganisms in Chinese adults.
From June 2019 to October 2020, 158 adults from Hangzhou and Shaoxing City, Zhejiang Province, were enrolled. We classified the TCM tongue coatings into four different types: thin white tongue fur (TWF), thin yellow tongue fur (TYF), white greasy tongue fur (WGF), and yellow greasy tongue fur (YGF). Tongue coating specimens were collected and used for 16S rRNA gene sequencing using the Illumina MiSeq system. Wilcoxon rank-sum and permutational multivariate analysis of variance tests were used to analyze the data. The microbial networks in the four types of tongue coatings were inferred independently using sparse inverse covariance estimation for ecological association inference.
Results
The microbial composition was similar among the different tongue coatings; however, the abundance of microorganisms differed. TWF had a higher abundance of Fusobacterium periodonticum and Neisseria mucosa, the highest α-diversity, and a highly connected community (average degree = 3.59, average closeness centrality = 0.33). TYF had the lowest α-diversity, but the most species in the co-occurrence network diagram (number of nodes = 88). The platelet-to-lymphocyte ratio (PLR) was associated with tongue coating (P = 0.035), and the YGF and TYF groups had higher PLR values. In the co-occurrence network, Aggregatibacter segnis was the “driver species” of the TWF and TYF groups and correlated with C-reactive protein (P < 0.05). Streptococcus anginosus was the “driver species” in the YGF and TWF groups and was positively correlated with body mass index and weight (P < 0.05).
Conclusion
Different tongue coatings have similar microbial compositions but different abundances of certain bacteria. The co-occurrence of microorganisms in the different tongue coatings also varies. The significance of different tongue coatings in TCM theory is consistent with the characteristics and roles of the corresponding tongue-coating microbes. This further supports considering tongue coating as a risk factor for disease.
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Crovetto F, Selma-Royo M, Crispi F, Carbonetto B, Pascal R, Larroya M, Casas I, Tortajada M, Escudero N, Muñoz-Almagro C, Gomez-Roig MD, González-Torres P, Collado MC, Gratacos E. Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection. Sci Rep 2022; 12:13404. [PMID: 35927569 PMCID: PMC9352760 DOI: 10.1038/s41598-022-17542-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/27/2022] [Indexed: 12/18/2022] Open
Abstract
We aimed to analyze the nasopharyngeal microbiota profiles in pregnant women with and without SARS-CoV-2 infection, considered a vulnerable population during COVID-19 pandemic. Pregnant women were enrolled from a multicenter prospective population-based cohort during the first SARS-CoV-2 wave in Spain (March-June 2020 in Barcelona, Spain) in which the status of SARS-CoV-2 infection was determined by nasopharyngeal RT–PCR and antibodies in peripheral blood. Women were randomly selected for this cross-sectional study on microbiota. DNA was extracted from nasopharyngeal swab samples, and the V3-V4 region of the 16S rRNA of bacteria was amplified using region-specific primers. The differential abundance of taxa was tested, and alpha/beta diversity was evaluated. Among 76 women, 38 were classified as positive and 38 as negative for SARS-CoV-2 infection. All positive women were diagnosed by SARS-CoV-2 IgG and IgM/IgA antibodies, and 14 (37%) also had a positive RT–PCR. The overall composition of the nasopharyngeal microbiota differ in pregnant women with SARS-CoV-2 infection (positive SARS-CoV-2 antibodies), compared to those without the infection (negative SARS-CoV-2 antibodies) (p = 0.001), with a higher relative abundance of the Tenericutes and Bacteroidetes phyla and a higher abundance of the Prevotellaceae family. Infected women presented a different pattern of microbiota profiling due to beta diversity and higher richness (observed ASV < 0.001) and evenness (Shannon index < 0.001) at alpha diversity. These changes were also present in women after acute infection, as revealed by negative RT–PCR but positive SARS-CoV-2 antibodies, suggesting a potential association between SARS-CoV-2 infection and long-lasting shift in the nasopharyngeal microbiota. No significant differences were reported in mild vs. severe cases. This is the first study on nasopharyngeal microbiota during pregnancy. Pregnant women with SARS-CoV-2 infection had a different nasopharyngeal microbiota profile compared to negative cases.
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Affiliation(s)
- Francesca Crovetto
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain. .,Institut de Recerca Sant Joan de Deu, Barcelona, Spain. .,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain.
| | - Marta Selma-Royo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Fàtima Crispi
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca August Pi Sunyer, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases, Barcelona, Spain
| | | | - Rosalia Pascal
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Larroya
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Irene Casas
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Marta Tortajada
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | | | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Ciber of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Maria Dolores Gomez-Roig
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Eduard Gratacos
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Institut de Recerca August Pi Sunyer, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases, Barcelona, Spain
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Oral dysbiosis and its linkage with SARS-CoV-2 infection. Microbiol Res 2022; 261:127055. [PMID: 35597076 PMCID: PMC9065653 DOI: 10.1016/j.micres.2022.127055] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 01/21/2023]
Abstract
The human oral cavity harbours complex microbial communities with various commensal microorganisms that play pivotal roles in maintaining host health and immunity but can elicit local and systemic diseases. The role of commensal microorganisms in SARS-CoV-2 infection and disease susceptibility and enrichment of opportunistic pathobionts in the oral cavity is poorly understood. The present study aims to understand the altered landscape of the oral microbiome and mycobiome in SARS-CoV-2 infected patients (n = 30) and its correlation with risk factors compared to non-infected individuals (n = 24) using targeted amplicon sequencing. Diminution of species richness, an elevated abundance of opportunistic pathogens (Veillonella, Acinetobacter, Klebsiella, Prevotella, Gemella, and Streptococcus) and impaired metabolic pathways were observed in the COVID-19 patients. Similarly, altered oral mycobiome with enrichment of known respiratory disease causing pathogenic fungi were observed in the infected individuals. The data further suggested that reduction in immunomodulatory microorganisms lowers the protection of individuals from SARS-CoV-2. Linear discriminant analysis identified several differentially abundant taxa associated with risk factors (ageing and co-morbidities). We also observed distinct bacterial and fungal community structures of elderly infected patients compared to the younger age group members making them highly vulnerable to SARS-CoV-2 infection and disease severity. Furthermore, we also assessed the dynamics of the oral microbiome and mycobiome in symptomatic and asymptomatic patients, host types, co-morbidities, and viral load in the augmentation of specific pathobionts. Overall, the present study demonstrates the microbiome and mycobiome profiling of the COVID-19 infected individuals, the data further suggests that the SARS-CoV-2 infection triggers the prevalence of specific pathobiont.
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32
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Rocafort M, Henares D, Brotons P, Launes C, Fernandez de Sevilla M, Fumado V, Barrabeig I, Arias S, Redin A, Ponomarenko J, Mele M, Millat-Martinez P, Claverol J, Balanza N, Mira A, Garcia-Garcia JJ, Bassat Q, Jordan I, Muñoz-Almagro C. Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home. Viruses 2022; 14:v14071521. [PMID: 35891502 PMCID: PMC9315980 DOI: 10.3390/v14071521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023] Open
Abstract
The increased incidence of COVID-19 cases and deaths in Spain in March 2020 led to the declaration by the Spanish government of a state of emergency imposing strict confinement measures on the population. The objective of this study was to characterize the nasopharyngeal microbiota of children and adults and its relation to SARS-CoV-2 infection and COVID-19 severity during the pandemic lockdown in Spain. This cross-sectional study included family households located in metropolitan Barcelona, Spain, with one adult with a previous confirmed COVID-19 episode and one or more exposed co-habiting child contacts. Nasopharyngeal swabs were used to determine SARS-CoV-2 infection status, characterize the nasopharyngeal microbiota and determine common respiratory DNA/RNA viral co-infections. A total of 173 adult cases and 470 exposed children were included. Overall, a predominance of Corynebacterium and Dolosigranulum and a limited abundance of common pathobionts including Haemophilus and Streptococcus were found both among adults and children. Children with current SARS-CoV-2 infection presented higher bacterial richness and increased Fusobacterium, Streptococcus and Prevotella abundance than non-infected children. Among adults, persistent SARS-CoV-2 RNA was associated with an increased abundance of an unclassified member of the Actinomycetales order. COVID-19 severity was associated with increased Staphylococcus and reduced Dolosigranulum abundance. The stringent COVID-19 lockdown in Spain had a significant impact on the nasopharyngeal microbiota of children, reflected in the limited abundance of common respiratory pathobionts and the predominance of Corynebacterium, regardless of SARS-CoV-2 detection. COVID-19 severity in adults was associated with decreased nasopharynx levels of healthy commensal bacteria.
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Affiliation(s)
- Muntsa Rocafort
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Desiree Henares
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Mariona Fernandez de Sevilla
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Victoria Fumado
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Irene Barrabeig
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Epidemiological Surveillance Unit, Department of Health, Generalitat de Catalunya, 08907 Barcelona, Spain
| | - Sara Arias
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alba Redin
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Maria Mele
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Pere Millat-Martinez
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Joana Claverol
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
| | - Nuria Balanza
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain
| | - Juan J. Garcia-Garcia
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Quique Bassat
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça Maputo 1929, Mozambique
| | - Iolanda Jordan
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
- Correspondence: ; Tel.: +34-673302405; Fax: +34-932803626
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Ferrari L, Favero C, Solazzo G, Mariani J, Luganini A, Ferraroni M, Montomoli E, Milani GP, Bollati V. Nasopharyngeal Bacterial Microbiota Composition and SARS-CoV-2 IgG Antibody Maintenance in Asymptomatic/Paucisymptomatic Subjects. Front Cell Infect Microbiol 2022; 12:882302. [PMID: 35873175 PMCID: PMC9297915 DOI: 10.3389/fcimb.2022.882302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), ranging from asymptomatic conditions to severe/fatal lung injury and multi-organ failure. Growing evidence shows that the nasopharyngeal microbiota composition may predict the severity of respiratory infections and may play a role in the protection from viral entry and the regulation of the immune response to the infection. In the present study, we have characterized the nasopharyngeal bacterial microbiota (BNM) composition and have performed factor analysis in a group of 54 asymptomatic/paucisymptomatic subjects who tested positive for nasopharyngeal swab SARS-CoV-2 RNA and/or showed anti-RBD-IgG positive serology at the enrolment. We investigated whether BNM was associated with SARS-CoV-2 RNA positivity and serum anti-RBD-IgG antibody development/maintenance 20–28 weeks after the enrolment. Shannon’s entropy α-diversity index [odds ratio (OR) = 5.75, p = 0.0107] and the BNM Factor1 (OR = 2.64, p = 0.0370) were positively associated with serum anti-RBD-IgG antibody maintenance. The present results suggest that BNM composition may influence the immunological memory against SARS-CoV-2 infections. To the best of our knowledge, this is the first study investigating the link between BNM and specific IgG antibody maintenance. Further studies are needed to unveil the mechanisms through which the BNM influences the adaptive immune response against viral infections.
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Affiliation(s)
- Luca Ferrari
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
- Department of Preventive Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Favero
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Giulia Solazzo
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Jacopo Mariani
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Anna Luganini
- Laboratory of Microbiology and Virology, Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Turin, Italy
| | - Monica Ferraroni
- Branch of Medical Statistics, Biometry, and Epidemiology "G. A. Maccacaro", Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, Università degli Studi di Siena, Siena, Italy
| | - Gregorio Paolo Milani
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Pediatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Bollati
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
- Department of Preventive Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- *Correspondence: Valentina Bollati,
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Kao M, Yang J, Balasubramaniam A, Traisaeng S, Jackson Yang A, Yang JJ, Salamon BP, Herr DR, Huang C. Colonization of nasal cavities by Staphylococcus epidermidis mitigates SARS-CoV-2 nucleocapsid phosphoprotein-induced interleukin (IL)-6 in the lung. Microb Biotechnol 2022; 15:1984-1994. [PMID: 35426250 PMCID: PMC9111282 DOI: 10.1111/1751-7915.13994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 11/19/2021] [Accepted: 12/02/2021] [Indexed: 11/27/2022] Open
Abstract
Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can trigger excessive interleukin (IL)-6 signalling, leading to a myriad of biological effects including a cytokine storm that contributes to multiple organ failure in severe coronavirus disease 2019 (COVID-19). Using a mouse model, we demonstrated that nasal inoculation of nucleocapsid phosphoprotein (NPP) of SARS-CoV-2 increased IL-6 content in bronchoalveolar lavage fluid (BALF). Nasal administration of liquid coco-caprylate/caprate (LCC) onto Staphylococcus epidermidis (S. epidermidis)-colonized mice significantly attenuated NPP-induced IL-6. Furthermore, S. epidermidis-mediated LCC fermentation to generate electricity and butyric acid that promoted bacterial colonization and activated free fatty acid receptor 2 (Ffar2) respectively. Inhibition of Ffar2 impeded the effect of S. epidermidis plus LCC on the reduction of NPP-induced IL-6. Collectively, these results suggest that nasal S. epidermidis is part of the first line of defence in ameliorating a cytokine storm induced by airway infection of SARS-CoV-2.
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Affiliation(s)
- Ming‐Shan Kao
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
| | - Jen‐Ho Yang
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
| | - Arun Balasubramaniam
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
| | | | - Albert Jackson Yang
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
| | - John Jackson Yang
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
| | | | - Deron R. Herr
- Department of BiologySan Diego State UniversitySan DiegoCA92182USA
| | - Chun‐Ming Huang
- Department of Biomedical Sciences and EngineeringNational Central UniversityTaoyuan32001Taiwan
- Department of Biomedical Science and Environment BiologyKaohsiung Medical UniversityKaohsiung80708Taiwan
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Rovito R, Augello M, Ben-Haim A, Bono V, d'Arminio Monforte A, Marchetti G. Hallmarks of Severe COVID-19 Pathogenesis: A Pas de Deux Between Viral and Host Factors. Front Immunol 2022; 13:912336. [PMID: 35757770 PMCID: PMC9231592 DOI: 10.3389/fimmu.2022.912336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
Two years into Coronavirus Disease 2019 (COVID-19) pandemic, a comprehensive characterization of the pathogenesis of severe and critical forms of COVID-19 is still missing. While a deep dysregulation of both the magnitude and functionality of innate and adaptive immune responses have been described in severe COVID-19, the mechanisms underlying such dysregulations are still a matter of scientific debate, in turn hampering the identification of new therapies and of subgroups of patients that would most benefit from individual clinical interventions. Here we review the current understanding of viral and host factors that contribute to immune dysregulation associated with COVID-19 severity in the attempt to unfold and broaden the comprehension of COVID-19 pathogenesis and to define correlates of protection to further inform strategies of targeted therapeutic interventions.
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Affiliation(s)
- Roberta Rovito
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Matteo Augello
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Assaf Ben-Haim
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Antonella d'Arminio Monforte
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
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Prasad P, Mahapatra S, Mishra R, Murmu KC, Aggarwal S, Sethi M, Mohapatra P, Ghosh A, Yadav R, Dodia H, Ansari SA, De S, Singh D, Suryawanshi A, Dash R, Senapati S, Beuria TK, Chattopadhyay S, Syed GH, Swain R, Raghav SK, Parida A. Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: a potential source of co-infection. Mol Omics 2022; 18:490-505. [PMID: 35506682 DOI: 10.1039/d2mo00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx, which may be involved in co-infection in COVID-19 patients. The 16S rRNA variable regions, V1-V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in the COVID-19 NP microbiome with an increase in the abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggests their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.
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Affiliation(s)
- Punit Prasad
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Soumendu Mahapatra
- Institute of Life Sciences, Bhubaneswar, Odisha, India. .,Kalinga Institute of Industrial Technology (KIIT), School of Biotechnology, Bhubaneswar, Odisha, India
| | | | | | | | - Manisha Sethi
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Arup Ghosh
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Rina Yadav
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Hiren Dodia
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Saikat De
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Deepak Singh
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Rupesh Dash
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | | | | | | | - Rajeeb Swain
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Ajay Parida
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
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Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients. Biomedicines 2022; 10:biomedicines10050982. [PMID: 35625719 PMCID: PMC9138573 DOI: 10.3390/biomedicines10050982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/23/2022] Open
Abstract
The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited at microbiota genus level and by the lack of functional interpretation. Our study, therefore, characterized the URT bacterial microbiome at species level and their encoded pathways in patients with COVID-19 and correlated these to clinical outcomes. Whole metagenome sequencing was performed on nasopharyngeal samples from hospitalized patients with critical COVID-19 (n = 37) and SARS-CoV-2-negative individuals (n = 20). Decreased bacterial diversity, a reduction in commensal bacteria, and high abundance of pathogenic bacteria were observed in patients compared to negative controls. Several bacterial species and metabolic pathways were associated with better respiratory status and lower inflammation. Strong correlations were found between species biomarkers and metabolic pathways associated with better clinical outcome, especially Moraxella lincolnii and pathways of vitamin K2 biosynthesis. Our study demonstrates correlations between the URT microbiome and COVID-19 patient outcomes; further studies are warranted to validate these findings and to explore the causal roles of the identified microbiome biomarkers in COVID-19 pathogenesis.
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De R, Dutta S. Role of the Microbiome in the Pathogenesis of COVID-19. Front Cell Infect Microbiol 2022; 12:736397. [PMID: 35433495 PMCID: PMC9009446 DOI: 10.3389/fcimb.2022.736397] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were available in early 2020. Subsequent whole-genome sequencing revealed that the virus had accumulated several mutations in genes associated with viral replication and pathogenesis. These variants showed enhanced transmissibility and infectivity. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. Thereafter, several variants emerged, which were found to harbor mutations in essential viral genes encoding proteins that could act as drug and vaccine targets. Numerous vaccines have been successfully developed to assuage the burden of COVID-19. These have different rates of efficacy, including, although rarely, a number of vaccinated individuals exhibiting side effects like thrombosis. However, the recent emergence of the Britain strain with 70% more transmissibility and South African variants with higher resistance to vaccines at a time when several countries have approved these for mass immunization has raised tremendous concern regarding the long-lasting impact of currently available prophylaxis. Apart from studies addressing the pathophysiology, pathogenesis, and therapeutic targets of SARS-CoV-2, analysis of the gut, oral, nasopharyngeal, and lung microbiome dysbiosis has also been undertaken to find a link between the microbiome and the pathogenesis of COVID-19. Therefore, in the current scenario of skepticism regarding vaccine efficacy and challenges over the direct effects of currently available drugs looming large, investigation of alternative therapeutic avenues based on the microbiome can be a rewarding finding. This review presents the currently available understanding of microbiome dysbiosis and its association with cause and consequence of COVID-19. Taking cues from other inflammatory diseases, we propose a hypothesis of how the microbiome may be influencing homeostasis, pro-inflammatory condition, and the onset of inflammation. This accentuates the importance of a healthy microbiome as a protective element to prevent the onset of COVID-19. Finally, the review attempts to identify areas where the application of microbiome research can help in reducing the burden of the disease.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkota, India
- Division of Immunology, National Institute of Cholera and Enteric Diseases, Kolkota, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkota, India
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Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y, Sharma A. Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types. Microbes Infect 2022; 24:104880. [PMID: 34425246 PMCID: PMC8379005 DOI: 10.1016/j.micinf.2021.104880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/09/2023]
Abstract
The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n = 63) and non-infected (n = 26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p < 0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acinetobacter, Moraxella, Corynebacterium 1, Gemella, Ralstonia, and Pseudomonas) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. In this study, we also performed the assesment of microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.
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Affiliation(s)
- Abhishek Gupta
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Rajesh Karyakarte
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Suvarna Joshi
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Rashmita Das
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Kunal Jani
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Yogesh Shouche
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Sharma
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India.
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Shilts MH, Rosas-Salazar C, Strickland BA, Kimura KS, Asad M, Sehanobish E, Freeman MH, Wessinger BC, Gupta V, Brown HM, Boone HH, Patel V, Barbi M, Bottalico D, O’Neill M, Akbar N, Rajagopala SV, Mallal S, Phillips E, Turner JH, Jerschow E, Das SR. Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome. Front Cell Infect Microbiol 2022; 11:781968. [PMID: 35141167 PMCID: PMC8819187 DOI: 10.3389/fcimb.2021.781968] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background The upper respiratory tract (URT) is the portal of entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-CoV-2 likely interacts with the URT microbiome. However, understanding of the associations between the URT microbiome and the severity of coronavirus disease 2019 (COVID-19) is still limited. Objective Our primary objective was to identify URT microbiome signature/s that consistently changed over a spectrum of COVID-19 severity. Methods Using data from 103 adult participants from two cities in the United States, we compared the bacterial load and the URT microbiome between five groups: 20 asymptomatic SARS-CoV-2-negative participants, 27 participants with mild COVID-19, 28 participants with moderate COVID-19, 15 hospitalized patients with severe COVID-19, and 13 hospitalized patients in the ICU with very severe COVID-19. Results URT bacterial load, bacterial richness, and within-group microbiome composition dissimilarity consistently increased as COVID-19 severity increased, while the relative abundance of an amplicon sequence variant (ASV), Corynebacterium_unclassified.ASV0002, consistently decreased as COVID-19 severity increased. Conclusions We observed that the URT microbiome composition significantly changed as COVID-19 severity increased. The URT microbiome could potentially predict which patients may be more likely to progress to severe disease or be modified to decrease severity. However, further research in additional longitudinal cohorts is needed to better understand how the microbiome affects COVID-19 severity.
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Affiliation(s)
- Meghan H. Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christian Rosas-Salazar
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Britton A. Strickland
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Kyle S. Kimura
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mohammad Asad
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Esha Sehanobish
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Michael H. Freeman
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bronson C. Wessinger
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Veerain Gupta
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Hunter M. Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Helen H. Boone
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Viraj Patel
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mali Barbi
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Danielle Bottalico
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meaghan O’Neill
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Nadeem Akbar
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Simon Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Justin H. Turner
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Elina Jerschow
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Suman R. Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
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41
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Wang H, Wang H, Sun Y, Ren Z, Zhu W, Li A, Cui G. Potential Associations Between Microbiome and COVID-19. Front Med (Lausanne) 2022; 8:785496. [PMID: 35004750 PMCID: PMC8727742 DOI: 10.3389/fmed.2021.785496] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has plunged the world into a major crisis. The disease is characterized by strong infectivity, high morbidity, and high mortality. It is still spreading in some countries. Microbiota and their metabolites affect human physiological health and diseases by participating in host digestion and nutrition, promoting metabolic function, and regulating the immune system. Studies have shown that human microecology is associated with many diseases, including COVID-19. In this research, we first reviewed the microbial characteristics of COVID-19 from the aspects of gut microbiome, lung microbime, and oral microbiome. We found that significant changes take place in both the gut microbiome and airway microbiome in patients with COVID-19 and are characterized by an increase in conditional pathogenic bacteria and a decrease in beneficial bacteria. Then, we summarized the possible microecological mechanisms involved in the progression of COVID-19. Intestinal microecological disorders in individuals may be involved in the occurrence and development of COVID-19 in the host through interaction with ACE2, mitochondria, and the lung-gut axis. In addition, fecal bacteria transplantation (FMT), prebiotics, and probiotics may play a positive role in the treatment of COVID-19 and reduce the fatal consequences of the disease.
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Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiwei Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Hursitoglu M, Isıksacan N, Erismis B, Karandere F, Kural A, Kumbasar AB, Kart Yasar K. In-vitro cytokine production and nasopharyngeal microbiota composition in the early stage of COVID-19 infection. Cytokine 2022; 149:155757. [PMID: 34763156 PMCID: PMC8570934 DOI: 10.1016/j.cyto.2021.155757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/26/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND To determine and compare nasopharyngeal microbiota (NM) composition, in vitro basal (Nil tube), provoked (Mitogen tube) production of cytokines at the early stage of COVID-19. METHODS This cross-sectional study included 4 age and sex-matched study groups; group 1 (recovered COVID-19) (n = 26), group 2 (mild COVID-19) (n = 24), group 3 (severe COVID-19) (n = 25), and group 4 (healthy controls) (n = 25). The study parameters obtained from the COVID-19 (group 2, and 3) at the early phase of hospital admission. RESULTS The results from the reaserch deoicted that the Mean ± SD age was 53.09 ± 14.51 years. Some of the in vitro cytokines production was significantly different between the study groups. Some of the findinggs on cytokines depicted a significant differences between study groups were interleukin (IL)-1β Nil, IL-1β Mitogen, and their subtraction (i.e Mitogen-Nil). Regarding IL-10, and IL-17a levels, Mitogen, and Mitogen-Nil tube production levels were significantly different between the groups. Surprisingly, most of these measures were lowest in the severe COVID-19 patients' group. Using discriminant analysis effect size (LEfSe), Taxa of NM with significant abundance was determined. About 20 taxa with an LDA score > 4 were identified as candidate biomarkers. Some of these taxa showed a significant correlation with IL-1β and IL-10 Mitogen and Mitogen- Nil levels (R > 0.3 or < -0.3, p < 0.05). CONCLUSIONS The findings of this perticular study regarting the early stage of COVID-19 showed that in vitro cytokines production, studies might be more useful than the ordinary cytokines' blood level measurement. Besides, the study identified some NM species that could be candidate biomarkers in managing this infection. However, further detailed studies are needed in these fields.
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Affiliation(s)
- Mehmet Hursitoglu
- Internal Medicine Department, Basaksehir Cam & Sakura Sehir Hospital, University of Health Sciences, Istanbul, Turkey; Internal Medicine Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey.
| | - Nilgun Isıksacan
- Biochemistry Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Betul Erismis
- Internal Medicine Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Faruk Karandere
- Internal Medicine Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Alev Kural
- Biochemistry Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - A Baki Kumbasar
- Internal Medicine Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Kadriye Kart Yasar
- Clinical Microbiology and Infectious Diseases Department, Bakirkoy Dr. Sadi Konuk Training & Research Hospital, University of Health Sciences, Istanbul, Turkey
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Liu TFD, Philippou E, Kolokotroni O, Siakallis G, Rahima K, Constantinou C. Gut and airway microbiota and their role in COVID-19 infection and pathogenesis: a scoping review. Infection 2021; 50:815-847. [PMID: 34671922 PMCID: PMC8528184 DOI: 10.1007/s15010-021-01715-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/09/2021] [Indexed: 12/24/2022]
Abstract
Background The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. Researchers have been studying the pathogenesis of the virus with the aim to improve our current diagnosis and management strategies. The microbiota have been proposed to play a key role in the pathogenesis of the disease. Purpose To investigate and report on the current available evidence on any associations between the gut and/or airway microbiota and the pathogenesis of COVID-19. Methods Using a predefined protocol in compliance with the PRISMA guidelines, a search was conducted on MEDLINE, Science Direct, DOAJ and Cochrane databases on primary research studies assessing the association between COVID-19 infection and the gut and/or airway microbiota. Results Twenty-two studies were included in the current review; nineteen studies concluded an association between the gut and/or airway dysbiosis and SARS-CoV-2, while 3 studies failed to observe a significant association between the airway microbiome and SARS-CoV-2 infection. Specifically, most studies reported a decrease in microbial diversity and therefore development of intestinal dysbiosis in COVID-19-positive patients compared to healthy controls as well as a possible association between increased intestinal dysbiosis and disease severity. Conclusion During infection with SARS-CoV-2, there are significant changes in the composition of the gut and airway microbiota. Furthermore, the gut microbiota may have a more important role than the airway microbiota in COVID-19 infection. In the future, studies should be more carefully designed to derive more conclusive evidence on the role of the gut and airway microbiota following infection with SARS-CoV-2 which will lead to the formulation of better management strategies in combating COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-021-01715-5.
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Affiliation(s)
- Tik Fung Dave Liu
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Elena Philippou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
- Department of Nutrition and Dietetics, King's College London, London, UK
| | - Ourania Kolokotroni
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Georgios Siakallis
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Kenan Rahima
- Queen Elizabeth The Queen Mother Hospital, Margate, UK
| | - Constantina Constantinou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus.
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44
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Understanding the link between the oral microbiome and the development and progression of head and neck squamous cell carcinoma. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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45
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Rhoades NS, Pinski AN, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I. Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose. Cell Rep 2021; 36:109637. [PMID: 34433082 PMCID: PMC8361213 DOI: 10.1016/j.celrep.2021.109637] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Research conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and coronavirus disease 2019 (COVID-19) generally focuses on the systemic host response, especially that generated by severely ill patients, with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2-positive patients (CoV+, n = 68) at the time of diagnosis is unique when compared to CoV− healthcare workers (n = 45) and CoV− outpatients (n = 21). This shift is marked by an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa, which is also positively associated with viral RNA load. Additionally, we observe a robust host transcriptional response in the nasal epithelia of CoV+ patients, indicative of an antiviral innate immune response and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.
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Affiliation(s)
- Nicholas S Rhoades
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Alisha N Monsibais
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Allen Jankeel
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Isaac R Cinco
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Izabela Ibraim
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
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46
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Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.
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47
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Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19. Synth Syst Biotechnol 2021; 6:135-143. [PMID: 34151035 PMCID: PMC8200311 DOI: 10.1016/j.synbio.2021.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2, the causative agent for COVID-19, infect human mainly via respiratory tract, which is heavily inhabited by local microbiota. However, the interaction between SARS-CoV-2 and nasopharyngeal microbiota, and the association with metabolome has not been well characterized. Here, metabolomic analysis of blood, urine, and nasopharyngeal swabs from a group of COVID-19 and non-COVID-19 patients, and metagenomic analysis of pharyngeal samples were used to identify the key features of COVID-19. Results showed lactic acid, l-proline, and chlorogenic acid methyl ester (CME) were significantly reduced in the sera of COVID-19 patients compared with non-COVID-19 ones. Nasopharyngeal commensal bacteria including Gemella morbillorum, Gemella haemolysans and Leptotrichia hofstadii were notably depleted in the pharynges of COVID-19 patients, while Prevotella histicola, Streptococcus sanguinis, and Veillonella dispar were relatively increased. The abundance of G. haemolysans and L. hofstadii were significantly positively associated with serum CME, which might be an anti-SARS-CoV-2 bacterial metabolite. This study provides important information to explore the linkage between nasopharyngeal microbiota and disease susceptibility. The findings were based on a very limited number of patients enrolled in this study; a larger size of cohort will be appreciated for further investigation.
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48
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Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A, Voigt RM. Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients. Biol Proced Online 2021; 23:10. [PMID: 34058978 PMCID: PMC8166531 DOI: 10.1186/s12575-021-00148-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
We investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed significant microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection samples already collected for SARS-CoV-2 testing (viral transport media) and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.
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Affiliation(s)
- Phillip A Engen
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, 1725 W. Harrison St. STE 206, Chicago, IL, 60612, USA
| | - Ankur Naqib
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, 1725 W. Harrison St. STE 206, Chicago, IL, 60612, USA
| | - Cheryl Jennings
- Department of Molecular Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, USA
| | - Alan Landay
- Department of Internal Medicine, Division of Geriatrics and Palliative Medicine, Rush Medical College, Chicago, IL, USA
| | - Ali Keshavarzian
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, 1725 W. Harrison St. STE 206, Chicago, IL, 60612, USA.,Department of Physiology, Rush University Medical Center, Chicago, IL, USA.,Department of Medicine, Rush University Medical Center, IL, Chicago, USA
| | - Robin M Voigt
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, 1725 W. Harrison St. STE 206, Chicago, IL, 60612, USA. .,Department of Medicine, Rush University Medical Center, IL, Chicago, USA.
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Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I. Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34031657 DOI: 10.1101/2021.05.20.445008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Much of the research conducted on SARS-CoV-2 and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients. Very few studies have investigated the impact of acute SARS-CoV-2 within the nasopharynx, the site of initial infection and viral replication. In this study we profiled changes in the nasal microbial communities as well as in host transcriptional profile during acute SARS-CoV-2 infection using 16S amplicon sequencing and RNA sequencing. These analyses were coupled to viral genome sequencing. Our microbiome analysis revealed that the nasal microbiome of COVID patients was unique and was marked by an expansion of bacterial pathogens. Some of these microbes (i.e. Acinetobacter ) were shared with COVID negative health care providers from the same medical center but absent in COVID negative outpatients seeking care at the same institutions suggesting acquisition of nosocomial respiratory pathogens. Specifically, we report a distinct increase in the prevalence and abundance of the pathogen Pseudomonas aeruginosa in COVID patients that correlated with viral RNA load. These data suggest that the inflammatory environment caused by SARS-CoV-2 infection and potentially exposure to the hospital environment leads to an expansion of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections. Additionally, we observed a robust host transcriptional response in the nasal epithelia of COVID patients, indicative of an antiviral innate immune repones and neuronal damage. Finally, analysis of viral genomes did not reveal an association between viral loads and viral sequences.
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