Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-7

Curated date: 2021/10/16

Curator: Tislam

Revision editor(s): WikiWorks, Chloe, Tislam, Peace Sandy

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
Rheumatoid arthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid disease,Rheumatoid arthritis
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
Rheumatoid arthritis patient
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Rheumatoid arthritis patient
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
30
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-7

Curated date: 2021/10/16

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

Source: Figure 3B, text

Description: Discriminant analysis of LEfSe multistage species difference. (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.

Abundance in Group 1: increased abundance in Rheumatoid arthritis patient

NCBI Quality ControlLinks
Blautia
Eggerthella
Holdemanella
Lactobacillaceae
Lactobacillales
Micrococcaceae
Pseudomonadales
Pseudomonas
Streptococcaceae
Streptococcus
Rothia

Revision editor(s): Tislam, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-7

Curated date: 2021/10/19

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

Source: Figure 3, text

Description: Discriminant analysis of LEfSe multistage species difference. (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.

Abundance in Group 1: decreased abundance in Rheumatoid arthritis patient

NCBI Quality ControlLinks
Lachnoclostridium
Roseburia
Bacteroidales
Acidimicrobiales
Mycoplasmataceae
Erysipelotrichaceae
Microthrix
Mycoplasma
Mycoplasmatales
Gallicola
Kroppenstedtia
Veillonellaceae

Revision editor(s): Tislam, Peace Sandy