Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches/Experiment 2

From BugSigDB


Needs review

Curated date: 2025/05/08

Curator: Shulamite

Revision editor(s): Shulamite, Anne-mariesharp

Subjects

Location of subjects
Taiwan
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
Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal (N-like group)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Case (OB-like group)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with a Body Mass Index ≥ 27
Group 0 sample size Number of subjects in the control (unexposed) group
45
Group 1 sample size Number of subjects in the case (exposed) group
36

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
Fisher's Exact Test
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

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Needs review

Curated date: 2025/05/08

Curator: Shulamite

Revision editor(s): Shulamite, Anne-mariesharp

Source: Table 3 and S2

Description: Genera & species with a significantly different presence between normal and case samples

Abundance in Group 1: increased abundance in Case (OB-like group)

NCBI Quality ControlLinks
Acinetobacter
Aliivibrio
Aliivibrio fischeri
Apilactobacillus kunkeei
Marinomonas
Parabacteroides distasonis
Pseudoalteromonas
Shewanella
Shewanella algae
Marinomonas posidonica
Pseudoalteromonas piscicida

Revision editor(s): Shulamite, Anne-mariesharp

Signature 2

Needs review

Curated date: 2025/05/08

Curator: Shulamite

Revision editor(s): Shulamite, Anne-mariesharp

Source: Table 3 and S2

Description: Genera & species with a significantly different presence between normal and case samples

Abundance in Group 1: decreased abundance in Case (OB-like group)

NCBI Quality ControlLinks
Agathobaculum desmolans
Alistipes shahii
Blautia producta
Citrobacter
Citrobacter amalonaticus
Clostridium sp. Clone-17
Cronobacter
Cronobacter sakazakii
Enterobacter cloacae
Enterobacter hormaechei
Enterocloster aldenensis
Lachnobacterium bovis
Leclercia
Leclercia adecarboxylata
Parabacteroides merdae
Pectinatus cerevisiiphilus
Rahnella
Rahnella sp. EMA-83
Ruminococcus albus
Ruminococcus sp. ID1
Serratia proteamaculans
Serratia sp. DAP4
Serratia sp. M1
Shigella
Sutterella wadsworthensis
Tatumella
Tatumella sp. L3-179
uncultured Lachnospira sp.
uncultured Serratia sp.
uncultured Shigella sp.
Butyricimonas
Butyrivibrio
Lachnobacterium
Lachnospira
Syntrophococcus
Pectinatus
Comamonas
Butyricimonas virosa
Syntrophococcus sucromutans
Comamonas testosteroni
Desulfovibrio sp. enrichment culture clone Jdgsrb011
Citrobacter sp. I91-10
Erwinia rhapontici

Revision editor(s): Shulamite, Anne-mariesharp