The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-30

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31001490

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2019.00090

URI

Authors

Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B, Sun Z

Journal

Frontiers in cellular and infection microbiology

Year

2019

Keywords:

human gut microbiota, metabolic potential, metagenomic sequencing, microbial diversity, tuberculosis

Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-30

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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: 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis

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: Tuberculosis (TB) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.

Group 0 sample size Number of subjects in the control (unexposed) group: 31

Group 1 sample size Number of subjects in the case (exposed) group: 30

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: Illumina

Statistical Analysis

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

Statistical test: Mann-Whitney (Wilcoxon)

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: decreased

Richness Number of species: decreased

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-30

Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 2A, Text (results)

Description: (A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.

Abundance in Group 1: increased abundance in Tuberculosis (TB) patients

NCBI	Quality Control	Links
Enterocloster bolteae
unclassified Coprococcus

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-30

Curated date: 2021/01/10

Curator: Yu Wang

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

Source: Figure 2A, Text (results)

Description: (A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.

Abundance in Group 1: decreased abundance in Tuberculosis (TB) patients

NCBI	Quality Control	Links
Agathobacter rectalis
Akkermansia muciniphila
Bifidobacterium adolescentis
Bifidobacterium longum subsp. longum
Bifidobacterium pseudocatenulatum
Blautia obeum
Collinsella aerofaciens
Coprococcus comes
Coprococcus sp.
Coprococcus sp. ART55/1
Dorea formicigenerans
Dorea longicatena
Haemophilus parainfluenzae
Lachnospira eligens
Megamonas funiformis
Megamonas hypermegale
Megamonas rupellensis
Roseburia hominis
Roseburia intestinalis
Roseburia inulinivorans
Sutterella wadsworthensis
[Ruminococcus] lactaris

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