Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Ma HQ, Yu TT, Zhao XJ, Zhang Y, Zhang HJ
Journal
World journal of gastroenterology
Year
2018
AIM: To analyze the alterations of fecal microbiota in Chinese patients with inflammatory bowel disease (IBD). METHODS: Fecal samples from 15 patients with Crohn's disease (CD) (11 active CD, 4 inactive CD), 14 patients with active ulcerative colitis (UC) and 13 healthy individuals were collected and subjected to 16S ribosomal DNA (rDNA) gene sequencing. The V4 hypervariable regions of 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Quality control and operational taxonomic units classification of reads were calculated with QIIME software. Alpha diversity and beta diversity were displayed with R software. RESULTS: Community richness (chao) and microbial structure in both CD and UC were significantly different from those in normal controls. At the phyla level, analysis of the microbial compositions revealed a significantly greater abundance of Proteobacteria in IBD as compared to that in controls. At the genera level, 8 genera in CD and 23 genera in UC (in particular, the Escherichia genus) showed significantly greater abundance as compared to that in normal controls. The relative abundance of Bacteroidetes in the active CD group was markedly lower than that in the inactive CD group. The abundance of Proteobacteria in patients with active CD was nominally higher than that in patients with inactive CD; however, the difference was not statistically significant after correction. Furthermore, the relative abundance of Bacteroidetes showed a negative correlation with the CD activity index scores. CONCLUSION: Our study profiles specific characteristics and microbial dysbiosis in the gut of Chinese patients with IBD. Bacteroidetes may have a negative impact on inflammatory development.
Experiment 1
Needs review
Subjects
- Location of subjects
- China
- 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
- 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
- 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
- Patients with Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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
- Statistical test
- Kruskall-Wallis
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Needs review
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: increased abundance in Patients with Crohn's disease
| NCBI | Links |
|---|---|
| Abiotrophia | |
| Escherichia | |
| Pseudomonadota | |
| Pseudoramibacter ⚠ | |
| unidentified rumen bacterium RFN20 |
Revision editor(s): Claregrieve1, Suwaiba
Signature 2
Needs review
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
| NCBI | Links |
|---|---|
| Butyricicoccus | |
| Mitsuokella | |
| Haemophilus | |
| Victivallis |
Revision editor(s): Claregrieve1
Experiment 2
Needs review
Subjects
- Location of subjects
- China
- 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
- 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
- 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
- Patients with ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with ulcerative colitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: increased abundance in Patients with ulcerative colitis
| NCBI | Links |
|---|---|
| Granulicatella | |
| Peptostreptococcus | |
| Schwartzia | |
| Capnocytophaga | |
| Pseudomonadota | |
| Escherichia | |
| Janthinobacterium ⚠ | |
| Campylobacter | |
| Actinomyces | |
| Eggerthella | |
| Corynebacterium | |
| Spirochaetota |
Revision editor(s): Claregrieve1
Signature 2
Needs review
Source: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with ulcerative colitis
| NCBI | Links |
|---|---|
| Holdemania ⚠ | |
| 02d0602d06 | |
| Lachnobacterium | |
| Megamonas | |
| Mitsuokella | |
| Alistipes | |
| Butyricimonas | |
| Prevotella | |
| Desulfovibrio | |
| Oxalobacter ⚠ | |
| Pyramidobacter | |
| Synergistes | |
| Lentisphaerota | |
| Victivallis |
Revision editor(s): Claregrieve1
Experiment 3
Needs review
Subjects
- Location of subjects
- China
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
Signature 1
Needs review
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: increased abundance in Patients with Crohn's disease
| NCBI | Links |
|---|---|
| Desulfovibrio | |
| Pseudoramibacter ⚠ | |
| Slackia | |
| 02d0602d06 | |
| Abiotrophia defectiva |
Revision editor(s): Claregrieve1, Suwaiba
Signature 2
Needs review
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
| NCBI | Links |
|---|---|
| Butyricicoccus | |
| Moryella | |
| Staphylococcus | |
| Capnocytophaga | |
| Haemophilus | |
| Janthinobacterium ⚠ | |
| Cardiobacterium | |
| Lautropia | |
| Propioniferax innocua | |
| Shewanella ⚠ | |
| Corynebacterium |
Revision editor(s): Claregrieve1
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