Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome

From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2021/07/16
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S, de Vos WM
Journal
Gastroenterology
Year
2011
BACKGROUND & AIMS: Irritable bowel syndrome (IBS) has been associated with disruptions to the intestinal microbiota, but studies have had limited power, coverage, and depth of analysis. We aimed to define microbial populations that can be used discriminate the fecal microbiota of patients with IBS from that of healthy subjects and correlate these with IBS intestinal symptom scores. METHODS: The microbiota composition was assessed by global and deep molecular analysis of fecal samples from 62 patients with IBS patients and 46 healthy individuals (controls). We used a comprehensive and highly reproducible phylogenetic microarray in combination with quantitative polymerase chain reaction. RESULTS: The intestinal microbiota of IBS patients differed significantly (P = .0005) from that of controls. The microbiota of patients, compared with controls, had a 2-fold increased ratio of the Firmicutes to Bacteroidetes (P = .0002). This resulted from an approximately 1.5-fold increase in numbers of Dorea, Ruminococcus, and Clostridium spp (P < .005); a 2-fold decrease in the number of Bacteroidetes (P < .0001); a 1.5-fold decrease in numbers of Bifidobacterium and Faecalibacterium spp (P < .05); and, when present, a 4-fold lower average number of methanogens (3.50 × 10(7) vs 8.74 × 10(6) cells/g feces; P = .003). Correlation analysis of the microbial groups and IBS symptom scores indicated the involvement of several groups of Firmicutes and Proteobacteria in the pathogenesis of IBS. CONCLUSIONS: Global and deep molecular analysis of fecal samples indicates that patients with IBS have a different composition of microbiota. This information might be used to develop better diagnostics and ultimately treatments for IBS.

Experiment 1


Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

Subjects

Location of subjects
Finland
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
Irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel,Irritable bowel syndrome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-A
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A)
Group 0 sample size Number of subjects in the control (unexposed) group
46
Group 1 sample size Number of subjects in the case (exposed) group
19

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Human Intestinal Tract Chip

Statistical Analysis

Statistical test
T-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)?
Yes


Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: decreased abundance in IBS-A

NCBI Quality ControlLinks
Alistipes
Alloprevotella tannerae
Bacteroides fragilis
Bacteroides intestinalis
Phocaeicola plebeius DSM 17135
Bacteroides uniformis
Faecalibacterium
Odoribacter
Parabacteroides
Phocaeicola vulgatus
Tannerella

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: increased abundance in IBS-A

NCBI Quality ControlLinks
Blautia
Clostridioides difficile
Coprococcus eutactus
Dialister
Dorea
Lacrimispora sphenoides
Marvinbryantia
Papillibacter
Ruminococcus
Ruminococcus callidus
Streptococcus intermedius
[Clostridium] nexile
[Clostridium] symbiosum
Mediterraneibacter gnavus
[Ruminococcus] lactaris
uncultured Clostridia bacterium

Revision editor(s): Kwekuamoo

Experiment 2


Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-C
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C)
Group 1 sample size Number of subjects in the case (exposed) group
18

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: decreased abundance in IBS-C

NCBI Quality ControlLinks
Alistipes
Alloprevotella tannerae
Bacteroides fragilis
Bacteroides intestinalis
Bacteroides ovatus
Phocaeicola plebeius DSM 17135
Bacteroides uniformis
Odoribacter
Parabacteroides
Phocaeicola vulgatus
Hoylesella oralis
Xylanibacter ruminicola
Tannerella
uncultured Bacteroidetes bacterium

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: increased abundance in IBS-C

NCBI Quality ControlLinks
Anaerotruncus
Anaerovorax
Aneurinibacillus
Clostridioides difficile
Coprococcus eutactus
Dorea
Flavonifractor plautii
Lachnospira
Marvinbryantia
Papillibacter
Peptococcus
Ruminococcus bromii
Sporobacter
[Clostridium] nexile
[Clostridium] cellulosi
[Clostridium] leptum
[Clostridium] symbiosum
Mediterraneibacter gnavus

Revision editor(s): Kwekuamoo

Experiment 3


Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-D
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D)
Group 1 sample size Number of subjects in the case (exposed) group
25

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: decreased abundance in IBS-D

NCBI Quality ControlLinks
Alloprevotella tannerae
Bacteroides intestinalis
Odoribacter
Parabacteroides
Phocaeicola plebeius
Phocaeicola vulgatus
Hoylesella oralis
Tannerella

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: increased abundance in IBS-D

NCBI Quality ControlLinks
Butyrivibrio
Clostridioides difficile
Dorea
Flavonifractor plautii
Lachnospira
Peptococcus
Roseburia
[Clostridium] nexile
[Clostridium] symbiosum
Mediterraneibacter gnavus
[Ruminococcus] lactaris

Revision editor(s): Kwekuamoo

Experiment 4


Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS (All patients)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
IBS patients fulfilled the Rome II criteria. All IBS patients.
Group 1 sample size Number of subjects in the case (exposed) group
62

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Figure 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: decreased abundance in IBS (All patients)

NCBI Quality ControlLinks
Bifidobacterium
Alistipes
Bacteroides fragilis
Bacteroides intestinalis
Bacteroides ovatus
Bacteroides stercoris
Bacteroides uniformis
Phocaeicola plebeius
Phocaeicola vulgatus
Odoribacter
Parabacteroides
Hoylesella oralis
Xylanibacter ruminicola
Alloprevotella tannerae
Tannerella
uncultured Bacteroidetes bacterium
uncultured Clostridia bacterium

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2021/07/16

Curated date: 2021/07/15

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.

Abundance in Group 1: increased abundance in IBS (All patients)

NCBI Quality ControlLinks
Aneurinibacillus
Streptococcus intermedius
[Clostridium] leptum
Flavonifractor plautii
Papillibacter
Dialister
Peptococcus
Anaerovorax
Clostridioides difficile
Blautia
Marvinbryantia
[Clostridium] nexile
[Clostridium] symbiosum
Coprococcus eutactus
Dorea
Lachnospira
Roseburia
Mediterraneibacter gnavus
[Ruminococcus] lactaris

Revision editor(s): Kwekuamoo