1
|
Missa KF, Diallo K, Bla KB, Tuo KJ, Gboko KDT, Tiémélé LS, Ouattara AF, Gragnon BG, Ngoi JM, Wilkinson RJ, Awandare GA, Bonfoh B. Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire. Front Microbiol 2024; 15:1412923. [PMID: 38993497 PMCID: PMC11238735 DOI: 10.3389/fmicb.2024.1412923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/29/2024] [Indexed: 07/13/2024] Open
Abstract
Introduction The oropharyngeal microbiome plays an important role in protection against infectious agents when in balance. Despite use of vaccines and antibiotic therapy to prevent respiratory tract infections, they remain one of the major causes of mortality and morbidity in Low- and middle-income countries. Hence the need to explore other approaches to prevention by identifying microbial biomarkers that could be leveraged to modify the microbiota in order to enhance protection against pathogenic bacteria. The aim of this study was to analyze the oropharyngeal microbiome (OPM) of schoolchildren in Côte d'Ivoire presenting symptoms of upper respiratory tract infections (URTI) for better prevention strategy. Methods Primary schools' children in Korhogo (n = 37) and Abidjan (n = 39) were followed for six months with monthly oropharyngeal sampling. Clinical diagnostic of URT infection was performed and nucleic acid extracted from oropharyngeal swabs were used for 16S rRNA metagenomic analysis and RT-PCR. Results The clinical examination of children's throat in Abidjan and Korhogo identified respectively 17 (43.59%) and 15 (40.54%) participants with visible symptoms of URTIs, with 26 episodes of infection in Abidjan and 24 in Korhogo. Carriage of Haemophilus influenzae (12%), Streptococcus pneumoniae (6%) and SARS-CoV-2 (6%) was confirmed by PCR. A significant difference in alpha diversity was found between children colonized by S. pneumoniae and those that were not (p = 0.022). There was also a significant difference in alpha diversity between children colonised with H. influenzae and those who were not (p = 0.017). No significant difference was found for SARS-CoV-2. Sphingomonas, Ralstonia and Rothia were significantly enriched in non-carriers of S. pneumoniae; Actinobacillus was significantly enriched in non-carriers of H. influenzae; Actinobacillus and Porphyromonas were significantly enriched in non-carriers of SARS-CoV-2 (p < 0.001). Discussion Nearly 40% of children showed clinical symptoms of infection not related to geographical location. The OPM showed an imbalance during H. influenzae and S. pneumoniae carriage. This study provides a baseline understanding of microbiome markers in URTIs in children for future research, to develop targeted interventions aimed at restoring the microbial balance and reducing the symptoms associated with RTIs.
Collapse
Affiliation(s)
- Kouassi Firmin Missa
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kanny Diallo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Kouakou Brice Bla
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kolotioloman Jérémie Tuo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Microbiologie, Biotechnologies et Bio-informatique, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Kossia Debia Thérèse Gboko
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Laurent-Simon Tiémélé
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Allassane Foungoye Ouattara
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Biego Guillaume Gragnon
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | | | - Robert J Wilkinson
- Laboratoire National d'Appui au Développement Agricole, Laboratoire Régional de Korhogo, Korhogo, Côte d'Ivoire
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Bassirou Bonfoh
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| |
Collapse
|
2
|
Wei Y, Yu W, Zhang Z, Liu S, Xue J, Wu C, Gao Z, Guo S. Comparative analysis of oropharyngeal microbiota in healthcare workers post-COVID-19. Front Cell Infect Microbiol 2024; 14:1347345. [PMID: 38828262 PMCID: PMC11140064 DOI: 10.3389/fcimb.2024.1347345] [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: 11/30/2023] [Accepted: 04/25/2024] [Indexed: 06/05/2024] Open
Abstract
Background To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored. Methods Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated. Results The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications. Conclusion During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.
Collapse
Affiliation(s)
- Yue Wei
- Nursing of school, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Zhixia Zhang
- Nursing Department, Linfen Central Hospital, Shanxi, China
| | - Siqin Liu
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jianbo Xue
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Chunyan Wu
- Nursing of school, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
- Institute of Chest and Lung Diseases, Shanxi Medical University, Linfen, Shanxi, China
| | - Shuming Guo
- Nursing of school, Shanxi Medical University, Taiyuan, Shanxi, China
- Nursing Department, Linfen Central Hospital, Shanxi, China
| |
Collapse
|
3
|
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 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.
Collapse
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
| |
Collapse
|
4
|
Cui G, Sun Y, Zou Y, Sun R, Gao Y, Liu X, Zhou Y, Zhang D, Wang X, Li Y, Liu L, Zhang G, Rao B, Yu Z, Ren Z. Dynamic changes of Bacterial Microbiomes in Oropharynx during Infection and Recovery of COVID-19 Omicron Variant. PLoS Pathog 2024; 20:e1012075. [PMID: 38568937 PMCID: PMC10990182 DOI: 10.1371/journal.ppat.1012075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Oropharyngeal microbiomes play a significant role in the susceptibility and severity of COVID-19, yet the role of these microbiomes play for the development of COVID-19 Omicron variant have not been reported. A total of 791 pharyngeal swab samples were prospectively included in this study, including 297 confirmed cases of Omicron variant (CCO), 222 confirmed case of Omicron who recovered (CCOR), 73 confirmed cases of original strain (CCOS) and 199 healthy controls (HC). All samples completed MiSeq sequencing. The results showed that compared with HC, conditional pathogens increased in CCO, while acid-producing bacteria decreased. Based on six optimal oropharyngeal operational taxonomy units (OTUs), we constructed a marker microbial classifier to distinguish between patients with Omicron variant and healthy people, and achieved high diagnostic efficiency in both the discovery queue and the verification queue. At same time, we introduced a group of cross-age infection verification cohort and Omicron variant subtype XBB.1.5 branch, which can be accurately distinguished by this diagnostic model. We also analyzed the characteristics of oropharyngeal microbiomes in two subgroups of Omicron disease group-severity of infection and vaccination times, and found that the change of oropharyngeal microbiomes may affect the severity of the disease and the efficacy of the vaccine. In addition, we found that some genera with significant differences gradually increased or decreased with the recovery of Omicron variant infection. The results of Spearman analysis showed that 27 oropharyngeal OTUs were closely related to 6 clinical indexes in CCO and HC. Finally, we found that the Omicron variant had different characterization of oropharyngeal microbiomes from the original strain. Our research characterizes oropharyngeal microbiomes of Omicron variant cases and rehabilitation cases, successfully constructed and verified the non-invasive diagnostic model of Omicron variant, described the correlation between microbial OTUs and clinical indexes. It was found that the infection of Omicron variant and the infection of original strain have different characteristics of oropharyngeal microbiomes.
Collapse
Affiliation(s)
- Guangying Cui
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yawen Zou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ranran Sun
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanxia Gao
- Emergency Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaorui Liu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongjian Zhou
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Donghua Zhang
- Anyang City Fifth People’s Hospital, Long An District, Anyang, China
| | - Xueqing Wang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yonghong Li
- Anyang City Fifth People’s Hospital, Long An District, Anyang, China
| | - Liwen Liu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guizhen Zhang
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Benchen Rao
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
5
|
Sawaswong V, Chanchaem P, Klomkliew P, Rotcheewaphan S, Meesawat S, Kemthong T, Kaewparuehaschai M, Noradechanon K, Ekatat M, Kanitpun R, Srilohasin P, Warit S, Chaiprasert A, Malaivijitnond S, Payungporn S. Full-length 16S rDNA sequencing based on Oxford Nanopore Technologies revealed the association between gut-pharyngeal microbiota and tuberculosis in cynomolgus macaques. Sci Rep 2024; 14:3404. [PMID: 38337025 PMCID: PMC10858278 DOI: 10.1038/s41598-024-53880-w] [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: 11/29/2023] [Accepted: 02/06/2024] [Indexed: 02/12/2024] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the Mycobacterium tuberculosis complex (Mtbc), which develops from asymptomatic latent TB to active stages. The microbiome was purposed as a potential factor affecting TB pathogenesis, but the study was limited. The present study explored the association between gut-pharyngeal microbiome and TB stages in cynomolgus macaques using the full-length 16S rDNA amplicon sequencing based on Oxford Nanopore Technologies. The total of 71 macaques was divided into TB (-) control, TB (+) latent and TB (+) active groups. The differential abundance analysis showed that Haemophilus hemolyticus was decreased, while Prevotella species were increased in the pharyngeal microbiome of TB (+) macaques. In addition, Eubacterium coprostanoligenes in the gut was enriched in TB (+) macaques. Alteration of these bacteria might affect immune regulation and TB severity, but details of mechanisms should be further explored and validated. In summary, microbiota may be associated with host immune regulation and affect TB progression. The findings suggested the potential mechanisms of host-microbes interaction, which may improve the understanding of the role of microbiota and help develop therapeutics for TB in the future.
Collapse
Affiliation(s)
- Vorthon Sawaswong
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Prangwalai Chanchaem
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
| | - Pavit Klomkliew
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
| | - Suwatchareeporn Rotcheewaphan
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suthirote Meesawat
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Mutchamon Kaewparuehaschai
- Wildlife Conservation Office, Department of National Parks Wildlife and Plant Conservation, Bangkok, 10900, Thailand
| | - Kirana Noradechanon
- Wildlife Conservation Office, Department of National Parks Wildlife and Plant Conservation, Bangkok, 10900, Thailand
| | - Monya Ekatat
- National Institute of Animal Health (NIAH), Bangkok, 10900, Thailand
| | - Reka Kanitpun
- National Institute of Animal Health (NIAH), Bangkok, 10900, Thailand
| | - Prapaporn Srilohasin
- Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Saradee Warit
- Industrial Tuberculosis Team, Industrial Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Angkana Chaiprasert
- Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Brzychczy- Sroka B, Talaga-Ćwiertnia K, Sroka-Oleksiak A, Gurgul A, Zarzecka-Francica E, Ostrowski W, Kąkol J, Zarzecka J, Brzychczy-Włoch M. Oral microbiota study of the patients after hospitalisation for COVID-19, considering selected dental indices and antibiotic therapy using the next generation sequencing method (NGS). J Oral Microbiol 2023; 15:2264591. [PMID: 37840855 PMCID: PMC10569355 DOI: 10.1080/20002297.2023.2264591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023] Open
Abstract
Background Poor oral hygiene and the increased incidence and severity of periodontitis may exacerbate SARS-CoV-2 infection. The aim was to evaluate the oral microbiota of 60 participants divided into groups: COVID-19 convalescents who received antibiotics during hospitalization (I), COVID-19 convalescents without antibiotic therapy (II) and healthy individuals (III). Materials and Methods Dental examination was conducted, and oral health status was evaluated using selected dental indexes. Clinical samples (saliva, dorsal swabs, supragingival and subgingival plaque) were collected and used for metagenomic library to the next-generation sequencing (NGS) preparation. Results Each of the clinical materials in particular groups of patients showed a statistically significant and quantitatively different bacterial composition. Patients from group I showed significantly worse oral health, reflected by higher average values of dental indexes and also a higher percentage of Veillonella, Tannerella, Capnocytophaga and Selenomonas genera in comparison to other groups. Additionally, a statistically significant decrease in the amount of Akkermansia type in both groups with COVID-19 was observed for all materials. Conclusions The primary factor affecting the composition of oral microbiota was not the SARS-CoV-2 infection itself, but the use of antibiotic therapy. The increased percentage of pro-inflammatory pathogens observed in COVID-19 patients underscores the importance of preventing periodontal disease and improving oral hygiene in the future.
Collapse
Affiliation(s)
- Barbara Brzychczy- Sroka
- Department of Conservative Dentistry with Endodontics, Institute of Dentistry, Jagiellonian University Medical College, Kraków, Poland
| | - Katarzyna Talaga-Ćwiertnia
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Agnieszka Sroka-Oleksiak
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Kraków, Poland
| | - Elżbieta Zarzecka-Francica
- Department of Prosthodontics and Orthodontics, Institute of Dentistry, Jagiellonian University Medical College, Kraków, Poland
| | - Wojciech Ostrowski
- Department of Conservative Dentistry with Endodontics, Institute of Dentistry, Jagiellonian University Medical College, Kraków, Poland
| | | | - Joanna Zarzecka
- Department of Conservative Dentistry with Endodontics, Institute of Dentistry, Jagiellonian University Medical College, Kraków, Poland
| | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| |
Collapse
|
8
|
Lazar V, Oprea E, Ditu LM. Resistance, Tolerance, Virulence and Bacterial Pathogen Fitness-Current State and Envisioned Solutions for the Near Future. Pathogens 2023; 12:pathogens12050746. [PMID: 37242416 DOI: 10.3390/pathogens12050746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The current antibiotic crisis and the global phenomena of bacterial resistance, inherited and non-inherited, and tolerance-associated with biofilm formation-are prompting dire predictions of a post-antibiotic era in the near future. These predictions refer to increases in morbidity and mortality rates as a consequence of infections with multidrug-resistant or pandrug-resistant microbial strains. In this context, we aimed to highlight the current status of the antibiotic resistance phenomenon and the significance of bacterial virulence properties/fitness for human health and to review the main strategies alternative or complementary to antibiotic therapy, some of them being already clinically applied or in clinical trials, others only foreseen and in the research phase.
Collapse
Affiliation(s)
- Veronica Lazar
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 1-3 Portocalelor Street, 060101 Bucharest, Romania
| | - Eliza Oprea
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 1-3 Portocalelor Street, 060101 Bucharest, Romania
| | - Lia-Mara Ditu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 1-3 Portocalelor Street, 060101 Bucharest, Romania
| |
Collapse
|
9
|
Wei N, Zhu G, Zhao T, Wang Y, Lou H, Li H, Yang Z, Zhang Z, Wang Q, Han M, Lin Z, Li S. Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients. BMC Microbiol 2023; 23:123. [PMID: 37158877 PMCID: PMC10166687 DOI: 10.1186/s12866-023-02872-3] [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: 12/04/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
COVID-19 has emerged as a global pandemic, challenging the world's economic and health systems. Human oral microbiota comprises the second largest microbial community after the gut microbiota and is closely related to respiratory tract infections; however, oral microbiomes of patients who have recovered from COVID-19 have not yet been thoroughly studied. Herein, we compared the oral bacterial and fungal microbiota after clearance of SARS-CoV-2 in 23 COVID-19 recovered patients to those of 29 healthy individuals. Our results showed that both bacterial and fungal diversity were nearly normalized in recovered patients. The relative abundance of some specific bacteria and fungi, primarily opportunistic pathogens, decreased in recovered patients (RPs), while the abundance of butyrate-producing organisms increased in these patients. Moreover, these differences were still present for some organisms at 12 months after recovery, indicating the need for long-term monitoring of COVID-19 patients after virus clearance.
Collapse
Affiliation(s)
- Nana Wei
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Guangqi Zhu
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Tingxiao Zhao
- Department of Infectious Disease, Zhejiang University Zhoushan Hospital, Zhoushan, 316021, China
| | - Yan Wang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Haifei Lou
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Haoxuan Li
- Wenzhou-Kean University, Wenzhou, 325060, China
| | - Zhejuan Yang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Zheen Zhang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Qiujing Wang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Mingfang Han
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Zhibing Lin
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shibo Li
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China.
| |
Collapse
|
10
|
Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z, Ren Z. Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2205058. [PMID: 37119437 DOI: 10.1002/advs.202205058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/15/2023] [Indexed: 06/19/2023]
Abstract
The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19). However, the oral fungal microbiota in COVID-19 remains unclear. This article aims to characterize the oral mycobiome in COVID-19 and recovered patients. Tongue coating specimens of 71 COVID-19 patients, 36 suspected cases (SCs), 22 recovered COVID-19 patients, 36 SCs who recovered, and 132 controls from Henan are collected and analyzed using internal transcribed spacer sequencing. The richness of oral fungi is increased in COVID-19 versus controls, and beta diversity analysis reveals separate fungal communities for COVID-19 and control. The ratio of Ascomycota and Basidiomycota is higher in COVID-19, and the opportunistic pathogens, including the genera Candida, Saccharomyces, and Simplicillium, are increased in COVID-19. The classifier based on two fungal biomarkers is constructed and can distinguish COVID-19 patients from controls in the training, testing, and independent cohorts. Importantly, the classifier successfully diagnoses SCs with positive specific severe acute respiratory syndrome coronavirus 2 immunoglobulin G antibodies as COVID-19 patients. The correlation between distinct fungi and bacteria in COVID-19 and control groups is depicted.. These data suggest that the oral mycobiome may play a role in COVID-19.
Collapse
Affiliation(s)
- Xiaobo Hu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Haiyu Wang
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Bo Yu
- Henan Key Laboratory of Ion-beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 455004, P. R. China
| | - Jia Yu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Department of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, P. R. China
| | - Junyi Sun
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Ying Sun
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Yawen Zou
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Hong Luo
- Department of Infectious Diseases, Guangshan County People's Hospital, Guangshan County, Xinyang, Henan, 465450, P. R. China
| | - Zhaohai Zeng
- Department of Infectious Diseases, Guangshan County People's Hospital, Guangshan County, Xinyang, Henan, 465450, P. R. China
| | - Shanshuo Liu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| | - Yan Jiang
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Zhongwen Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Department of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, P. R. China
| | - Zhigang Ren
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, Zhengzhou, 450052, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, P. R. China
| |
Collapse
|
11
|
Wei J, Dai W, Pan X, Zhong Y, Xu N, Ye P, Wang J, Li J, Yang F, Luo J, Luo M. Identifying the Novel Gut Microbial Metabolite Contributing to Metabolic Syndrome in Children Based on Integrative Analyses of Microbiome-Metabolome Signatures. Microbiol Spectr 2023; 11:e0377122. [PMID: 36794949 PMCID: PMC10101147 DOI: 10.1128/spectrum.03771-22] [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: 09/15/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
The pathogenesis of gut microbiota and their metabolites in the development of metabolic syndrome (MS) remains unclear. This study aimed to evaluate the signatures of gut microbiota and metabolites as well as their functions in obese children with MS. A case-control study was conducted based on 23 MS children and 31 obese controls. The gut microbiome and metabolome were measured using 16S rRNA gene amplicon sequencing and liquid chromatography-mass spectrometry. An integrative analysis was conducted, combining the results of the gut microbiome and metabolome with extensive clinical indicators. The biological functions of the candidate microbial metabolites were validated in vitro. We identified 9 microbiota and 26 metabolites that were significantly different from the MS and the control group. The clinical indicators of MS were correlated with the altered microbiota Lachnoclostridium, Dialister, and Bacteroides, as well as with the altered metabolites all-trans-13,14-dihydroretinol, DL-dipalmitoylphosphatidylcholine (DPPC), LPC 24: 1, PC (14:1e/10:0), and 4-phenyl-3-buten-2-one, etc. The association network analysis further identified three MS-linked metabolites, including all-trans-13,14-dihydroretinol, DPPC, and 4-phenyl-3-buten-2-one, that were significantly correlated with the altered microbiota. Bio-functional validation showed that all-trans-13, 14-dihydroretinol could significantly upregulate the expression of lipid synthesis genes and inflammatory genes. This study identified a new biomarker that may contribute to MS development. These findings provided new insights regarding the development of efficient therapeutic strategies for MS. IMPORTANCE Metabolic syndrome (MS) has become a health concern worldwide. Gut microbiota and metabolites play an important role in human health. We first endeavored to comprehensively analyze the microbiome and metabolome signatures in obese children and found the novel microbial metabolites in MS. We further validated the biological functions of the metabolites in vitro and illustrated the effects of the microbial metabolites on lipid synthesis and inflammation. The microbial metabolite all-trans-13, 14-dihydroretinol may be a new biomarker in the pathogenesis of MS, especially in obese children. These findings were not available in previous studies, and they provide new insights regarding the management of metabolic syndrome.
Collapse
Affiliation(s)
- Jia Wei
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Wen Dai
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Xiongfeng Pan
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Yan Zhong
- Institute of Children Health, Hunan Children’s Hospital, Changsha, Hunan, China
| | - Ningan Xu
- Institute of Children Health, Hunan Children’s Hospital, Changsha, Hunan, China
| | - Ping Ye
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Jie Wang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Jina Li
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Fei Yang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, China
| | - Jiayou Luo
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| | - Miyang Luo
- Xiangya School of Public Health, Central South University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan, China
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections. Biomolecules 2022; 13:biom13010006. [PMID: 36671391 PMCID: PMC9856197 DOI: 10.3390/biom13010006] [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: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein-Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.
Collapse
|
15
|
Jiang X, Zhang Y, Wang H, Wang Z, Hu S, Cao C, Xiao H. In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer. Research (Wash D C) 2022; 2022:9781578. [PMID: 36320634 PMCID: PMC9590273 DOI: 10.34133/2022/9781578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method, the number of interfering peptides decreased by 52.87%, whereas the bacterial peptides and species increased by 94.97% and 44.90%, respectively, compared to the conventional metaproteomics approach. We identified 3647 bacterial proteins, which is the most comprehensive oral metaproteomics study to date. Lung cancer-associated bacteria were validated among an independent cohort. The imbalanced Fusobacterium nucleatum and Prevotella histicola and their dysregulated functions in inhibiting immune response and maintaining cell redox homeostasis were revealed. The FFIEF-MS may serve as a valuable strategy to study the mechanisms between human diseases and microbiomes with broader applications.
Collapse
Affiliation(s)
- Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shen Hu
- School of Dentistry and Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles 90095, USA
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
16
|
Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. MICROBIOME 2022; 10:165. [PMID: 36195943 PMCID: PMC9532226 DOI: 10.1186/s40168-022-01342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown-did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions. Video Abstract.
Collapse
Affiliation(s)
- Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| |
Collapse
|
17
|
Gang J, Wang H, Xue X, Zhang S. Microbiota and COVID-19: Long-term and complex influencing factors. Front Microbiol 2022; 13:963488. [PMID: 36033885 PMCID: PMC9417543 DOI: 10.3389/fmicb.2022.963488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). According to the World Health Organization statistics, more than 500 million individuals have been infected and more than 6 million deaths have resulted worldwide. Although COVID-19 mainly affects the respiratory system, considerable evidence shows that the digestive, cardiovascular, nervous, and reproductive systems can all be involved. Angiotensin-converting enzyme 2 (AEC2), the target of SARS-CoV-2 invasion of the host is mainly distributed in the respiratory and gastrointestinal tract. Studies found that microbiota contributes to the onset and progression of many diseases, including COVID-19. Here, we firstly conclude the characterization of respiratory, gut, and oral microbial dysbiosis, including bacteria, fungi, and viruses. Then we explore the potential mechanisms of microbial involvement in COVID-19. Microbial dysbiosis could influence COVID-19 by complex interactions with SARS-CoV-2 and host immunity. Moreover, microbiota may have an impact on COVID-19 through their metabolites or modulation of ACE2 expression. Subsequently, we generalize the potential of microbiota as diagnostic markers for COVID-19 patients and its possible association with post-acute COVID-19 syndrome (PACS) and relapse after recovery. Finally, we proposed directed microbiota-targeted treatments from the perspective of gut microecology such as probiotics and prebiotics, fecal transplantation and antibiotics, and other interventions such as traditional Chinese medicine, COVID-19 vaccines, and ACE2-based treatments.
Collapse
Affiliation(s)
- Jiaqi Gang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangsheng Xue
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
- *Correspondence: Xiangsheng Xue,
| | - Shu Zhang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Shu Zhang,
| |
Collapse
|
18
|
Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R. Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiol Spectr 2022; 10:e0231121. [PMID: 35579429 PMCID: PMC9241827 DOI: 10.1128/spectrum.02311-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/17/2022] [Indexed: 12/13/2022] Open
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.
Collapse
Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kriti Khare
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sujeet Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
19
|
Shi YL, He MZ, Han MZ, Gui HY, Wang P, Yu JL, Ge YL, Sun Y, Huang SH. Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:824578. [PMID: 35372134 PMCID: PMC8965315 DOI: 10.3389/fcimb.2022.824578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.
Collapse
Affiliation(s)
- Yong-Lin Shi
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Mao-Zhang He
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Mao-Zhen Han
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Hong-Ya Gui
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Peng Wang
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Jun-Ling Yu
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Ying-Lu Ge
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Yong Sun
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
- *Correspondence: Sheng-Hai Huang, ; Yong Sun,
| | - Sheng-Hai Huang
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- School of Life Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Sheng-Hai Huang, ; Yong Sun,
| |
Collapse
|
20
|
Li X, Wang Q, Hu X, Liu W. Current Status of Probiotics as Supplements in the Prevention and Treatment of Infectious Diseases. Front Cell Infect Microbiol 2022; 12:789063. [PMID: 35360101 PMCID: PMC8964067 DOI: 10.3389/fcimb.2022.789063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/03/2022] [Indexed: 12/20/2022] Open
Abstract
Probiotics play an important role against infectious pathogens via their effects on the epithelium, the production of antimicrobial compounds, and competitive exclusion. Administration of probiotic supplements may reduce the risk of infectious diseases and the use of antibiotics, hence contributing to a reduction or a delay of the development of multi-resistant bacteria. Infection is a constant concern for people who experience recurrent infections, and antibiotic treatment usually fails due to antibiotic resistance. Therefore, an infection can lead to severe illness and hospitalization if left untreated. A growing number of studies have demonstrated promising results for a variety of probiotic strains used to prevent or treat acute and recurrent infectious diseases, but additional standardized clinical research is needed.
Collapse
Affiliation(s)
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, China
| | | | | |
Collapse
|