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

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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


Needs review

Curated date: 2021/06/11

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects
China
Switzerland
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Lung Pulmo,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
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
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

Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
1e-11
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

Needs review

Curated date: 2021/06/12

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 2

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

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

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

Revision editor(s): Claregrieve1

Signature 2

Needs review

Curated date: 2021/06/12

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 2

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

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

NCBI Quality ControlLinks
Campylobacter gracilis
Campylobacter rectus
Campylobacter showae
Treponema putidum

Revision editor(s): Claregrieve1