Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease

From BugSigDB
Needs review
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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Suwaiba

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Suwaiba

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

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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