The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

35411293

DOI Digital object identifier for electronic documents.

10.34172/bi.2021.23378

URI Uniform resource identifier for web resources.

Authors

Han Y, Jia Z, Shi J, Wang W, He K

Journal

BioImpacts : BI

Year

2022

Keywords:

COVID-19, Faecalibacterium prausnitzii, Lactic acid bacteria, Microbiota, SARS-CoV-2

Introduction: With the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the interaction between the host and SARS-CoV-2 was widely studied. However, it is unclear whether and how SARS-CoV-2 infection affects lung microflora, which contribute to COVID-19 complications. Methods: Here, we analyzed the metatranscriptomic data of bronchoalveolar lavage fluid (BALF) of 19 COVID-19 patients and 23 healthy controls from 6 independent projects and detailed the active microbiota landscape in both healthy individuals and COVID-19 patients. Results: The infection of SARS-CoV-2 could deeply change the lung microbiota, evidenced by the α-diversity, β-diversity, and species composition analysis based on bacterial microbiota and virome. Pathogens (e.g., Klebsiella oxytoca causing pneumonia as well), immunomodulatory probiotics (e.g., lactic acid bacteria and Faecalibacterium prausnitzii, a butyrate producer), and Tobacco mosaic virus (TMV) were enriched in the COVID-19 group, suggesting a severe microbiota dysbiosis. The significant correlation between Rothia mucilaginosa, TMV, and SARS-CoV-2 revealed drastic inflammatory battles between the host, SARS-CoV-2, and other microbes in the lungs. Notably, TMV only existed in the COVID-19 group, while human respirovirus 3 (HRV 3) only existed in the healthy group. Our study provides insights into the active microbiota in the lungs of COVID-19 patients and would contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. Conclusion: SARS-COV-2 infection deeply altered the lung microbiota of COVID-19 patients. The enrichment of several other pathogens, immunomodulatory probiotics (lactic acid or butyrate producers), and TMV in the COVID-19 group suggests a complex and active lung microbiota disorder.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

Curated date: 2021/06/11

Curator: Claregrieve1

Revision editor(s): WikiWorks, Claregrieve1, Peace Sandy, Aleru Divine

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Lung Pulmo,Lung,lung

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 infected patients

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 19

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Sequencing platform: "IDseq" is not in the list (DNA-DNA Hybridization, Human Intestinal Tract Chip, Illumina, Ion Torrent, Non-quantitative PCR, PacBio RS, PhyloChip, Roche454, RT-qPCR, Mass spectrometry, ...) of allowed values.IDseq

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

Curated date: 2021/06/12

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Davvve, WikiWorks

Source: Supplementary Table 2

Description: Differential microbial abundance between the COVID-19 patients and the healthy controls

Abundance in Group 1: increased abundance in COVID-19 cases

NCBI	Quality Control	Links
Actinomyces pacaensis
Anaerocolumna sedimenticola
Anaerotignum propionicum
Bacillus cereus
Chryseobacterium cucumeris
Citrobacter braakii
Citrobacter freundii
Citrobacter freundii complex sp. CFNIH3
Clostridiales bacterium
Clostridiales bacterium CCNA10
Clostridium beijerinckii
Clostridium carboxidivorans
Comamonas terrigena
Comamonas testosteroni
Enterobacter asburiae
Enterobacter bugandensis
Enterobacter cancerogenus
Enterobacter cloacae
Enterobacter cloacae complex sp.
Enterobacter hormaechei
Enterobacter kobei
Enterobacter oligotrophicus
Enterobacter roggenkampii
Enterobacter soli
Enterobacter sp. 638
Enterobacter sp. E76
Enterobacter sp. ODB01
Enterobacter sp. T2
Faecalibacterium prausnitzii
Filimonas lacunae
Flavonifractor plautii
Klebsiella michiganensis
Klebsiella oxytoca
Lachnoclostridium phytofermentans
Lacrimispora saccharolytica
Lacrimispora sphenoides
Lactiplantibacillus plantarum
Lactobacillus delbrueckii
Lactobacillus johnsonii
Latilactobacillus curvatus
Leclercia adecarboxylata
Leclercia sp. 29361
Leclercia sp. J807
Leclercia sp. LSNIH1
Leclercia sp. W17
Lelliottia amnigena
Lelliottia jeotgali
Lelliottia sp. WB101
Ligilactobacillus salivarius
Limosilactobacillus fermentum
Limosilactobacillus reuteri
Lysinibacillus sp. B2A1
Lysinibacillus sphaericus
Mesomycoplasma hyorhinis
Methylobacterium sp. DM1
Paenibacillus graminis
Paenibacillus guangzhouensis
Pantoea sp. SO10
Peribacillus frigoritolerans
Phyllobacterium myrsinacearum
Pluralibacter gergoviae
Pseudomonas alkylphenolica
Pseudomonas oryzihabitans
Pseudomonas rhodesiae
Pseudomonas sp.
Pseudomonas sp. JY-Q
Pseudomonas sp. MRSN 12121
Pseudomonas sp. PONIH3
Pseudomonas sp. XWY-1
Rahnella aquatilis
Ralstonia pickettii
Rothia aeria
Rothia mucilaginosa
Ruminobacter amylophilus
Schaalia meyeri
Sphingobacterium sp. B29
Sphingobacterium sp. G1-14
Sphingomonas sp. FARSPH
Stenotrophomonas sp. LM091
Streptococcus salivarius
Streptococcus sanguinis
Streptococcus sp. oral taxon 064
Succinivibrio dextrinosolvens
Suicoccus acidiformans
Variovorax boronicumulans
Variovorax paradoxus
Variovorax sp. PBL-H6
Variovorax sp. PMC12
Vibrio anguillarum
Mediterraneibacter gnavus
uncultured Variovorax sp.