The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes/Experiment 1
Curated date: 2021/06/17
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, 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
- Diabetes mellitus Diabetes,diabetes,diabetes mellitus,diabetes mellitus (disease),Diabetes mellitus (disorder),Diabetes mellitus, NOS,Diabetes NOS,DM,DM - Diabetes mellitus,Diabetes mellitus
- 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
- Individuals diagnosed with Type 2 Diabetes Mellitus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019; The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 179
- Group 1 sample size Number of subjects in the case (exposed) group
- 137
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long-term antibiotic application
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Curated date: 2021/06/27
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, Aiyshaaaa, Peace Sandy
Source: Figure 2
Description: Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
Revision editor(s): Madhubani Dey, Aiyshaaaa, Peace Sandy
Signature 2
Curated date: 2021/06/27
Curator: Madhubani Dey
Revision editor(s): Lwaldron, Madhubani Dey, Peace Sandy
Source: Figure 2
Description: Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
Revision editor(s): Lwaldron, Madhubani Dey, Peace Sandy
