The Association Between Smoking and Gut Microbiome in Bangladesh
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Bangladesh
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Pair of lungs Lungs,Lungs pair,Pulmones,Set of lungs,Pair of lungs
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- nicotine dependence , smoking behavior cigarette habituation, susceptibility to,Cigarette Smoking,Dependence, Nicotine,Dependence, Tobacco,Disorder, Nicotine Use,Disorder, Tobacco Use,Disorder, Tobacco-Use,Nicotine Addiction,nicotine addiction,nicotine addiction, susceptibility to,nicotine dependence,nicotine dependence, susceptibility to,NICOTINE USE DIS,Nicotine Use Disorder,Nicotine Use Disorders,smoking,smoking habit, susceptibility to,Smoking, Cigarette,Smoking, Tobacco,Smokings, Tobacco,susceptibility to tobacco addiction,tobacco addiction, susceptibility to,Tobacco Dependence,Tobacco Dependences,Tobacco Smoking,Tobacco Smokings,TOBACCO USE DIS,Tobacco Use Disorder,tobacco use disorder,Tobacco Use Disorders,Tobacco-Use Disorder,Use Disorder, Nicotine,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non smoker
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Current Smoker
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never-smokers.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 151
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month.
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
- Statistical test
- Logistic Regression
- Beta Binomial Regression
- Chi-Square
- 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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table 3
Description: The relative abundances of 14 taxa were nominally significantly associated with smoking status when comparing current smokers and never-smokers.
Abundance in Group 1: increased abundance in Current Smoker
Signature 2
Source: Table 4
Description: This table summarizes the odds ratio data of the presence or absence of specific bacterial taxa between current smokers and never smokers. According to this investigation, only Class Alphaproteobacteria is significantly enriched in the former group compared to the latter.
Abundance in Group 1: increased abundance in Current Smoker
NCBI | Quality Control | Links |
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Alphaproteobacteria |
Revision editor(s): Joyessa
Signature 3
Source: Table 5
Description: This table summarizes the odds ratio of mean relative abundances or presence or absence of bacterial taxa associated with one increase in packs of cigarette/bidi smoke.
Abundance in Group 1: increased abundance in Current Smoker
NCBI | Quality Control | Links |
---|---|---|
Catenibacterium | ||
Collinsella | ||
Erysipelotrichaceae | ||
Erysipelotrichales | ||
Mitsuokella | ||
Peptostreptococcaceae | ||
Slackia | ||
Erysipelotrichia |