Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

33603076

DOI Digital object identifier for electronic documents.

10.1038/s42003-021-01796-w

URI

Authors

Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z, Zhang C

Journal

Communications biology

Year

2021

SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.

Experiment 1

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Curated date: 2021/06/28

Curator: Claregrieve1

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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: Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

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 H)

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 6 COVID-19 patients, 10 non-COVID-19 patients, 2 healthy controls

Group 0 sample size Number of subjects in the control (unexposed) group: 13

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: ANOSIM

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

Pielou Quantifies how equal the community is numerically: unchanged

Richness Number of species: decreased

Experiment 2

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Community Type I Patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 16 COVID-19 patients, 2 healthy controls

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

Richness Number of species: unchanged

Experiment 3

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Curated date: 2021/06/28

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Community Type II patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 47 COVID-19 patients, 1 healthy control

Group 1 sample size Number of subjects in the case (exposed) group: 48

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

Richness Number of species: decreased

Experiment 4

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Community Type III patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 10 COVID-19 patients, 1 healthy control

Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Richness Number of species: decreased

Experiment 5

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Community Type IV patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 4 COVID-19 patients

Group 1 sample size Number of subjects in the case (exposed) group: 4

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Richness Number of species: decreased

Experiment 6

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Curated date: 2021/07/10

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Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Group I - High Diversity COVID-19 patients

Group 1 name Corresponds to the case (exposed) group for case-control studies: Group II - Medium Diversity COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with medium microbial diversity in rectal samples

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 24

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

Richness Number of species: decreased

Experiment 7

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Curated date: 2021/07/10

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Group III - Low Diversity COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with low microbial diversity in rectal swab samples

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Richness Number of species: decreased