Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2023-10-26
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Alsulaiman RM, Al-Quorain AA, Al-Muhanna FA, Piotrowski S, Kurdi EA, Vatte C, Alquorain AA, Alfaraj NH, Alrezuk AM, Robinson F, Dowdell AK, Alamri TA, Hamilton L, Lad H, Gao H, Gandla D, Keating BJ, Meng R, Piening B, Al-Ali AK
Journal
BMC gastroenterology
Year
2023
Keywords:
Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis
BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16 S rRNA gene using the Swift Amplicon 16 S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16 S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.

Experiment 1


Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Chloe

Subjects

Location of subjects
Saudi Arabia
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
Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
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
ulcerative colitis (UC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)
Group 0 sample size Number of subjects in the control (unexposed) group
124
Group 1 sample size Number of subjects in the case (exposed) group
84
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V9
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).
raw counts
Statistical test
DESeq2
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


Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary File 14: Table S2

Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls

Abundance in Group 1: decreased abundance in ulcerative colitis (UC)

NCBI Quality ControlLinks
Agathobacter rectalis
Anaerostipes hadrus
Bacteroidaceae bacterium
Bacteroidales bacterium
Bacteroides stercoris
Dorea formicigenerans
Parabacteroides goldsteinii
Paraprevotella clara
Phocaeicola coprocola
Segatella copri
Trichuris trichiura

Revision editor(s): ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary File 14: Table S2

Description: Differential microbial abundance between ulcerative colitis (UC) and healthy controls

Abundance in Group 1: increased abundance in ulcerative colitis (UC)

NCBI Quality ControlLinks
Bacteroides ovatus
Blautia hansenii
Clostridiaceae bacterium
Clostridioides difficile
Clostridium perfringens
Comamonas kerstersii
Dialister invisus
Dialister micraerophilus
Dialister propionicifaciens
Dorea formicigenerans
Enterococcus durans
Escherichia sp.
Megamonas funiformis
Parabacteroides johnsonii
Porphyromonas asaccharolytica
Segatella oris
Punica granatum
Tyzzerella sp.
bacterium NLAE-zl-H31

Revision editor(s): ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
Group 1 name Corresponds to the case (exposed) group for case-control studies
Crohn's disease (CD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)
Group 1 sample size Number of subjects in the case (exposed) group
135

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary File 15: Table S3

Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls

Abundance in Group 1: decreased abundance in Crohn's disease (CD)

NCBI Quality ControlLinks
Anaerostipes hadrus
Bacteroides ovatus
Bacteroides stercoris
Collinsella aerofaciens
Dorea formicigenerans
Lactobacillus acidophilus
Lactobacillus gasseri
Leyella stercorea
Phocaeicola vulgatus
Prevotellaceae bacterium
Punica granatum
Segatella copri
Trichuris trichiura

Revision editor(s): ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary File 15: Table S3, Figure 4: left plot

Description: Differential microbial abundance between Crohn's disease (CD) and healthy controls

Abundance in Group 1: increased abundance in Crohn's disease (CD)

NCBI Quality ControlLinks
Bacteroides ovatus
Blautia hansenii
Clostridiaceae bacterium
Clostridioides difficile
Clostridium butyricum
Clostridium perfringens
Dialister invisus
Dialister micraerophilus
Dialister propionicifaciens
Dorea formicigenerans
Enterococcus durans
Escherichia sp.
Megamonas funiformis
Parabacteroides johnsonii
Porphyromonas asaccharolytica
Punica granatum
Streptococcus lutetiensis
Tyzzerella sp.
bacterium NLAE-zl-H31
Veillonella
Lachnoclostridium

Revision editor(s): ChiomaBlessing

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
ulcerative colitis (UC)
Group 0 sample size Number of subjects in the control (unexposed) group
84

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 4: right plot

Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)

Abundance in Group 1: increased abundance in Crohn's disease (CD)

NCBI Quality ControlLinks
Turicibacter

Revision editor(s): ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2023-10-26

Curated date: 2023/10/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Peace Sandy

Source: Figure 4, Plot 2

Description: Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD)

Abundance in Group 1: decreased abundance in Crohn's disease (CD)

NCBI Quality ControlLinks
Akkermansia
Anaerosporobacter
Butyricimonas
Candidatus Saccharimonadaceae
Christensenellaceae bacterium
Eubacterium coprostanoligenes
Fusobacterium
Harryflintia
Megamonas
Phascolarctobacterium
Sutterella
uncultured Lachnospira sp.
uncultured bacterium
MCG-2

Revision editor(s): ChiomaBlessing, Peace Sandy