Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis

Study information

EditHistoryDelete

Mark reviewed

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36350161

DOI Digital object identifier for electronic documents.

https://doi.org/10.1128/spectrum.01926-22

URI Uniform resource identifier for web resources.

Authors

Li S, Guo J, Liu R, Zhang F, Wen S, Liu Y, Ren W, Zhang X, Shang Y, Gao M, Lu J, Pang Y

Journal

Microbiology spectrum

Year

2022

Tuberculous meningitis (TBM), the most lethal and disabling form of tuberculosis (TB), may be related to gut microbiota composition, warranting further study. Here we systematically compared gut microbiota compositions and blood cytokine profiles of TBM patients, pulmonary TB patients, and healthy controls. Notably, the significant gut microbiota dysbiosis observed in TBM patients was associated with markedly high proportions of Escherichia-Shigella species as well as increased blood levels of tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). Next, we obtained a fecal bacterial isolate from a TBM patient and administered it via oral gavage to mice in order to develop a murine gut microbiota dysbiosis model for use in exploring mechanisms underlying the observed relationship between gut microbial dysbiosis and TBM. Thereafter, cells of commensal Escherichia coli (E. coli) were isolated and administered to model mice by gavage and then mice were inoculated with Mycobacterium tuberculosis (M. tuberculosis). Subsequently, these mice exhibited increased blood TNF-α levels accompanied by downregulated expression of tight junction protein claudin-5, increased brain tissue bacterial burden, and elevated central nervous system inflammation relative to corresponding indicators in controls administered PBS by gavage. Thus, our results demonstrated that a signature dysbiotic gut microbiome profile containing a high proportion of E. coli was potentially associated with an increased circulating TNF-α level in TBM patients. Collectively, these results suggest that modulation of dysbiotic gut microbiota holds promise as a new strategy for preventing or alleviating TBM. IMPORTANCE As the most severe form of tuberculosis, the pathogenesis of tuberculous meningitis (TBM) is still unclear. Gut microbiota dysbiosis plays an important role in a variety of central nervous system diseases. However, the relationship between gut microbiota and TBM has not been identified. In our study, significant dysbiosis in gut microbiota composition with a high proportion of E. coli and increased levels of TNF-α in plasma was noted in TBM patients. A commensal E. coli was isolated and shown to increase the plasma level of TNF-α and downregulate brain tight junction protein claudin-5 in the murine model. Gavage administration of E. coli aggravated the bacterial burden and increased the inflammatory responses in the central nervous system after M. tuberculosis infection. Dysbiosis of gut microbiota may be a promising therapeutic target and biomarker for TBM prevention or treatment.

Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Subjects

Location of subjects

China

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

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

meningeal tuberculosis meningeal tuberculosis,TB meningitis

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

Healthy Control (HC)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Tuberculosis Meningitis (TBM)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

TBM patients enrolled from January - June 2019 at Beijing Chest Hospital.

TBM was diagnosed based on expert consensus. TBM patients were aged 18 - 70, tested positive for M. tuberculosis complex bacilli in cerebrospinal fluid (CSF) by GeneXpert MTB/RIF assay

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

9

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

9

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

proof of extensive antibiotic therapy for 1+ week in previous 6 months.

also, prior treatment of systemic antituberculous therapy for more than 1 week.

Lab analysis

Sequencing type

16S

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

V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Statistical test

PERMANOVA

Welch's T-Test

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

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3B

Description: Stack diagram of relative phylum-level gut microbiota abundance difference between TMB patients and HCs.

Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Pseudomonadota

Revision editor(s): Chondatondaponda

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3B

Description: Stack diagram of relative phylum-level gut microbiota abundance difference between TMB patients and HCs.

Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Actinomycetota
Bacteroidota
Firmicutes bacterium ASF500

Revision editor(s): Chondatondaponda

Signature 3

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3D

Description: Stack diagram at genus-level of relative gut microbiota abundance between TMB patients and HCs.

Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Escherichia/Shigella sp.

Revision editor(s): Chondatondaponda

Signature 4

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3D

Description: Stack diagram at genus-level of relative gut microbiota abundance between TMB patients and HCs.

Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Blautia �
Bifidobacterium �
Fusicatenibacter �
Anaerostipes �

Revision editor(s): Chondatondaponda

Experiment 2

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Pulmonary tuberculosis (PTB)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

PTB patients enrolled from January - June 2019 at Beijing Chest Hospital.

PTB patient criteria: 1. age 18 - 70 2. positive M. tuberculosis results from either smears, cultures, or positive GeneXpert MTB/RIF results 3. pulmonary imaging features indicative of TB

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

13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

therapy for 1+ week in previous 6 months.

also, prior treatment of systemic antituberculous therapy for more than 1 week.

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3B

Description: Stack diagram of relative phylum-level gut microbiota abundance difference between PTB patients and HCs.

Abundance in Group 1: increased abundance in Pulmonary tuberculosis (PTB)

NCBI	Links
Pseudomonadota

Revision editor(s): Chondatondaponda

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Figure 3B

Description: Stack diagram of relative phylum-level gut microbiota abundance difference between PTB patients and HCs.

Abundance in Group 1: decreased abundance in Pulmonary tuberculosis (PTB)

NCBI	Links
Actinomycetota
Bacteroidota
Firmicutes bacterium ASF500

Revision editor(s): Chondatondaponda

Experiment 3

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Differences from previous experiment shown

Subjects

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

Pulmonary tuberculosis (PTB)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Tuberculosis Meningitis (TBM)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

TBM patients enrolled from January - June 2019 at Beijing Chest Hospital.

TBM was diagnosed based on expert consensus. TBM patients were aged 18 - 70, tested positive for M. tuberculosis complex bacilli in cerebrospinal fluid (CSF) by GeneXpert MTB/RIF assay

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

9

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

proof of extensive antibiotic therapy for 1+ week in previous 6 months.

also, prior treatment of systemic antituberculous therapy for more than 1 week.

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/21

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Supplementary Figure 1.C

Description: Comparisons between PTB and TBM microbiota compositions at phylum level

Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Pseudomonadota

Revision editor(s): Chondatondaponda

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/21

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Supplementary Figure 1.C

Description: Comparisons between PTB and TBM microbiota compositions at phylum level.

Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Firmicutes bacterium ASF500
Bacteroidota
Actinomycetota

Revision editor(s): Chondatondaponda

Signature 3

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/21

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Supplementary Figure 2.C

Description: Comparisons between PTB and TBM microbiota compositions at genus level.

Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Escherichia/Shigella sp.

Revision editor(s): Chondatondaponda

Signature 4

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/21

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda

Source: Supplementary Figure 2.C

Description: Comparisons between PTB and TBM microbiota compositions at genus level

Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)

NCBI	Links
Blautia �
Bacteroides �

Revision editor(s): Chondatondaponda