The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-30
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

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 ControlLinks
Enterocloster bolteae
unclassified Coprococcus

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

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 ControlLinks
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