Association of suboptimal health status with intestinal microbiota in Chinese youths

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31808612

DOI Digital object identifier for electronic documents.

10.1111/jcmm.14880

URI

Authors

Sun Q, Xu X, Zhang J, Sun M, Tian Q, Li Q, Cao W, Zhang X, Wang H, Liu J, Zhang J, Meng X, Wu L, Song M, Liu H, Wang W, Wang Y

Journal

Journal of cellular and molecular medicine

Year

2020

Keywords:

16S rRNA, LEfSe analysis, intestinal microbiota, random forest tree, suboptimal health status

Suboptimal health status (SHS), a physical state between health and disease, is a subclinical and reversible stage of chronic disease. Previous studies have shown alterations in the intestinal microbiota in patients with some chronic diseases. This study aimed to investigate the association between SHS and intestinal microbiota in a case-control study with 50 SHS individuals and 50 matched healthy controls. Intestinal microbiota was analysed by MiSeq 250PE. Alpha diversity of intestinal microbiota in SHS individuals was higher compared with that of healthy controls (Simpson index, W = 2238, P = .048). Beta diversity was different between SHS and healthy controls (P = .018). At the phylum level, the relative abundance of Verrucomicrobia was higher in the SHS group than that in the controls (W = 2201, P = .049). Compared with that of the control group, nine genera were significantly higher and five genera were lower in abundance in the SHS group (all P < .05). The intestinal microbiota, analysed by a random forest model, was able to distinguish individuals with SHS from the controls, with an area under the curve of 0.79 (95% confidence interval: 0.77-0.81). We demonstrated that the alteration of intestinal microbiota occurs with SHS, an early stage of disease, which might shed light on the importance of intestinal microbiota in the primary prevention of noncommunicable chronic diseases.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, 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: Health trait Health trait,health trait

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: suboptimal health status

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: subjects with SHSQ-25 (SHS score >= 35)

Group 0 sample size Number of subjects in the control (unexposed) group: 50

Group 1 sample size Number of subjects in the case (exposed) group: 50

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: 16S

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

Matched on Factors on which subjects have been matched on in a case-control study: age, body mass index, sex

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 5

Description: LDA score of LEfSe analysis between suboptimal health status (SHS) and control group

Abundance in Group 1: increased abundance in suboptimal health status

NCBI	Quality Control	Links
Chryseobacterium
Cyanobacteriota
Oscillospira
Oscillospiraceae
Peptococcaceae
Rikenellaceae
Roseburia
Ruminococcus
Verrucomicrobiota
Clostridiales bacterium
Fusobacteriaceae