Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36523636

DOI Digital object identifier for electronic documents.

https://doi.org/10.3389/fcimb.2022.943609

URI

https://www.frontiersin.org/articles/10.3389/fcimb.2022.943609/full

Authors

Morales C, Rojas G, Rebolledo C, Rojas-Herrera M, Arias-Carrasco R, Cuadros-Orellana S, Maracaja-Coutinho V, Saavedra K, Leal P, Lanas F, Salazar LA, Saavedra N

Journal

Frontiers in cellular and infection microbiology

Year

2022

Keywords:

16S rRNA sequencing, LDL cholesterol, LEfSe analysis, gut microbiota, microbial signature

INTRODUCTION: In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition. METHODS: Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe). RESULTS: Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (α=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups. CONCLUSION: Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

Curated date: 2024/03/07

Curator: Abiola-Salako

Revision editor(s): Abiola-Salako, Folakunmi

Subjects

Location of subjects: Chile

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: Hypercholesterolemia Elevated serum cholesterol,Elevated total cholesterol,High cholesterol,Increased total cholesterol,Hypercholesterolemia,hypercholesterolemia

Group 0 name Corresponds to the control (unexposed) group for case-control studies: normocholesterolemic individuals (controls)

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L)

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 27

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 Months

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: LEfSe

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

Curated date: 2024/03/08

Curator: Abiola-Salako

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Source: Figure 3

Description: Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05

Abundance in Group 1: decreased abundance in hypercholesterolemic (cases)

NCBI	Quality Control	Links
Faecalibacterium
Selenomonas
Victivallis

Revision editor(s): Abiola-Salako, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

Curated date: 2024/03/08

Curator: Abiola-Salako

Revision editor(s): Abiola-Salako, Folakunmi

Source: Figure 3

Description: Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05.

Abundance in Group 1: increased abundance in hypercholesterolemic (cases)

NCBI	Quality Control	Links
Bacillaceae
Chromatiales
Coriobacteriaceae
Eubacteriales
Methanosphaera
Rothia

Revision editor(s): Abiola-Salako, Folakunmi