Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches

Study information

Reviewed Marked as Reviewed by Folakunmi on 2023-12-21

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37077242

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2023.1113174

URI

https://pubmed.ncbi.nlm.nih.gov/37077242/

Authors

Huang D, Wang J, Zeng Y, Li Q, Wang Y

Journal

Frontiers in microbiology

Year

2023

Keywords:

bone mineral density, feature selection, gut microbiota, microbial biomarker, postmenopausal osteoporosis

Osteoporosis (OP) is a metabolic bone disorder characterized by low bone mass and deterioration of micro-architectural bone tissue. The most common type of OP is postmenopausal osteoporosis (PMOP), with fragility fractures becoming a global burden for women. Recently, the gut microbiota has been connected to bone metabolism. The aim of this study was to characterize the gut microbiota signatures in PMOP patients and controls. Fecal samples from 21 PMOP patients and 37 controls were collected and analyzed using amplicon sequencing of the V3-V4 regions of the 16S rRNA gene. The bone mineral density (BMD) measurement and laboratory biochemical test were performed on all participants. Two feature selection algorithms, maximal information coefficient (MIC) and XGBoost, were employed to identify the PMOP-related microbial features. Results showed that the composition of gut microbiota changed in PMOP patients, and microbial abundances were more correlated with total hip BMD/T-score than lumbar spine BMD/T-score. Using the MIC and XGBoost methods, we identified a set of PMOP-related microbes; a logistic regression model revealed that two microbial markers (Fusobacteria and Lactobacillaceae) had significant abilities in disease classification between the PMOP and control groups. Taken together, the findings of this study provide new insights into the etiology of OP/PMOP, as well as modulating gut microbiota as a therapeutic target in the diseases. We also highlight the application of feature selection approaches in biological data mining and data analysis, which may improve the research in medical and life sciences.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-21

Curated date: 2023/12/20

Curator: Aleru002

Revision editor(s): Aleru002, Folakunmi

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: Postmenopausal osteoporosis Bone Loss, Perimenopausal,Bone Loss, Postmenopausal,Bone Losses, Perimenopausal,Bone Losses, Postmenopausal,bone mineral density quantitative trait locus,Osteoporoses, Post-Menopausal,Osteoporoses, Postmenopausal,Osteoporosis, Post Menopausal,Osteoporosis, Post-Menopausal,Osteoporosis, Postmenopausal,osteoporosis, postmenopausal,Perimenopausal Bone Loss,Perimenopausal Bone Losses,Post-Menopausal Osteoporoses,Post-Menopausal Osteoporosis,Postmenopausal Bone Loss,Postmenopausal Bone Losses,Postmenopausal Osteoporoses,postmenopausal osteoporosis,Postmenopausal osteoporosis

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: Postmenopausal osteoporosis (PMOP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Postmenopausal osteoporosis (PMOP)

Group 0 sample size Number of subjects in the control (unexposed) group: 37

Group 1 sample size Number of subjects in the case (exposed) group: 21

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Subjects who were on antibiotics one (1) month preceding the sample collection were excluded from the study

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

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): 0.1

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

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Curated date: 2023/12/20

Curator: Aleru002

Revision editor(s): Aleru002, Folakunmi

Source: Table S2, Figure 1

Description: Gut microbiota compositions between healthy controls and patients with postmenopausal osteoporosis (PMOP)

Abundance in Group 1: increased abundance in Postmenopausal osteoporosis (PMOP) patients

NCBI	Quality Control	Links
Bacilli
Clostridium disporicum
Erysipelotrichia
Fusobacteriia
Lactobacillaceae
Lactobacillales
Lactobacillus
Erysipelotrichales
Ligilactobacillus salivarius
unclassified Eubacteriales