Alterations in the human oral and gut microbiomes and lipidomics in COVID-19

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q, Li L
Journal
Gut
Year
2021
Keywords:
COVID-19, intestinal microbiology, lipid metabolism
OBJECTIVE: To characterise the oral microbiome, gut microbiome and serum lipid profiles in patients with active COVID-19 and recovered patients; evaluate the potential of the microbiome as a non-invasive biomarker for COVID-19; and explore correlations between the microbiome and lipid profile. DESIGN: We collected and sequenced 392 tongue-coating samples, 172 faecal samples and 155 serum samples from Central China and East China. We characterised microbiome and lipid molecules, constructed microbial classifiers in discovery cohort and verified their diagnostic potential in 74 confirmed patients (CPs) from East China and 37 suspected patients (SPs) with IgG positivity. RESULTS: Oral and faecal microbial diversity was significantly decreased in CPs versus healthy controls (HCs). Compared with HCs, butyric acid-producing bacteria were decreased and lipopolysaccharide-producing bacteria were increased in CPs in oral cavity. The classifiers based on 8 optimal oral microbial markers (7 faecal microbial markers) achieved good diagnostic efficiency in different cohorts. Importantly, diagnostic efficacy reached 87.24% in the cross-regional cohort. Moreover, the classifiers successfully diagnosed SPs with IgG antibody positivity as CPs, and diagnostic efficacy reached 92.11% (98.01% of faecal microbiome). Compared with CPs, 47 lipid molecules, including sphingomyelin (SM)(d40:4), SM(d38:5) and monoglyceride(33:5), were depleted, and 122 lipid molecules, including phosphatidylcholine(36:4p), phosphatidylethanolamine (PE)(16:0p/20:5) and diglyceride(20:1/18:2), were enriched in confirmed patients recovery. CONCLUSION: This study is the first to characterise the oral microbiome in COVID-19, and oral microbiomes and lipid alterations in recovered patients, to explore their correlations and to report the successful establishment and validation of a diagnostic model for COVID-19.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/06/1

Curated date: 2021/06/21

Curator: Claregrieve1

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

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
Tongue Glossus,Tongue,tongue
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
Confirmed COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Suspected COVID-19 cases with one of the following etiological or serological evidence: (1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid. (2) Viral gene sequencing finds highly homologous to COVID-19 virus
Group 0 sample size Number of subjects in the control (unexposed) group
100
Group 1 sample size Number of subjects in the case (exposed) group
48
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/21

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1

Source: Supplementary Figures 1E and 1G

Description: Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients

Abundance in Group 1: decreased abundance in Confirmed COVID-19 patients

NCBI Quality ControlLinks
Bacteroidota
Candidatus Gracilibacteria
Candidatus Saccharibacteria genomosp. TM7-H1
Candidatus Saccharimonas
Cardiobacterium
Catonella
Corynebacterium
Eubacteriales Family XIII. Incertae Sedis
Filifactor
Fusobacterium
Gemella
Haemophilus
Mogibacterium
Oribacterium
Parvimonas
Peptostreptococcaceae incertae sedis
Peptostreptococcus
Porphyromonas
Pseudomonadota
Solobacterium
Streptococcus
Mycoplasmatota
candidate division SR1 bacterium
candidate division TM7 genomosp. GTL1

Revision editor(s): Fatima, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/21

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1

Source: Supplementary Figures 1E and 1G

Description: Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients

Abundance in Group 1: increased abundance in Confirmed COVID-19 patients

NCBI Quality ControlLinks
Campylobacter
Cyanobacteriota
Granulicatella
Leptotrichia
Megasphaera
Ruminococcus sp.
Selenomonas
Spirochaeta
Tannerella

Revision editor(s): Fatima, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/22

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovered COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Confirmed COVID-19 patients who recovered
Group 0 sample size Number of subjects in the control (unexposed) group
150
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls

Abundance in Group 1: decreased abundance in Recovered COVID-19 patients

NCBI Quality ControlLinks
Candidatus Saccharimonas
Eubacteriales Family XIII. Incertae Sedis
Haemophilus
Parvimonas
Porphyromonas

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls

Abundance in Group 1: increased abundance in Recovered COVID-19 patients

NCBI Quality ControlLinks
Centipeda
Leptotrichia
Megasphaera
Selenomonas

Revision editor(s): Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Suspected COVID-19 cases with one of the following etiological or serological evidence: (1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid. (2) Viral gene sequencing finds highly homologous to COVID-19 virus
Group 0 sample size Number of subjects in the control (unexposed) group
48
Group 1 sample size Number of subjects in the case (exposed) group
24

Lab analysis

Statistical Analysis

Statistical test
LEfSe

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Lwaldron, Claregrieve1

Source: Figure 5c, S3E, S3G -Supp 05

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

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

NCBI Quality ControlLinks
Alistipes
Bacteroides
Bilophila
Blautia
Clostridium
Collinsella
Coprococcus
Dialister
Dorea
Faecalibacterium
Haemophilus
Holdemania
Intestinimonas
Klebsiella
Lachnospira
Odoribacter
Parabacteroides
Parasutterella
Pseudobutyrivibrio
Roseburia
Ruminococcus
Sphingomonas
Sutterella
Turicibacter
bacterium
uncultured Oscillospiraceae bacterium

Revision editor(s): Lwaldron, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 5c

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

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

NCBI Quality ControlLinks
Akkermansia
Bifidobacterium
Enterococcus
Lachnospiraceae incertae sedis
Streptococcus
Rothia
Halomonas
Anaerostipes
Oribacterium
Veillonella
Solobacterium
Atopobium
Flavonifractor
Pelagibacterium
Gemella
Granulicatella

Revision editor(s): Claregrieve1