IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation
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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
Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P, Brigidi P
Journal
Gut microbes
Year
2012
IBS is a prevalent functional gastrointestinal disorder, in which the microbiota has been demonstrated to play a role. An increasing number of studies have suggested how probiotics may alleviate IBS symptoms and several mechanisms of action have been proposed. In the present study we characterized the intestinal microbiota of 19 subjects suffering from diagnosed IBS using a fully validated High Taxonomic Fingerprint Microbiota Array (HTF-Microbi.Array). We demonstrated that the IBS microbiota is different from that of healthy individuals due to an unbalance in a number of commensal species, with an increase in relative abundance of lactobacilli, B. cereus and B. clausii, bifidobacteria, Clostridium cluster IX and E. rectale, and a decrease in abundance of Bacteroides/Prevotella group and Veillonella genus. Additionally, we demonstrated that some bacterial groups of the human intestinal microbiota, recently defined as pathobionts, are increased in concentration in the IBS microbiota. Furthermore, we aimed at investigating if the daily administration of a novel probiotic yogurt containing B. animalis subsp lactis Bb12 and K. marxianus B0399, recently demonstrated to have beneficial effects in the management of IBS symptoms, could impact on the biostructure of IBS microbiota, modulating its composition to counteract putative dysbiosis found in IBS subjects. Notably, we demonstrated that the beneficial effects associated to the probiotic preparation are not related to significant modifications in the composition of the human intestinal microbiota.
Experiment 1
Needs review
Subjects
- 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
- 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
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fulfilled the Rome III criteria for the diagnosis of IBS.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- HTF-Microbi.Array
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: increased abundance in IBS
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: decreased abundance in IBS
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Bacteroides | |
| Veillonella |
Revision editor(s): Kwekuamoo
Experiment 2
Needs review
Subjects
- 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
- 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
- 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-C
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- HTF-Microbi.Array
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: increased abundance in IBS-C
| NCBI | Links |
|---|---|
| Alkalihalobacillus clausii | |
| Bifidobacteriaceae |
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: decreased abundance in IBS-C
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Bacteroides |
Revision editor(s): Kwekuamoo
Experiment 3
Needs review
Subjects
- 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
- 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
- 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-D
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- HTF-Microbi.Array
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: increased abundance in IBS-D
Revision editor(s): Kwekuamoo
Signature 2
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: decreased abundance in IBS-D
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Bacteroides |
Revision editor(s): Kwekuamoo
Experiment 4
Needs review
Subjects
- 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
- 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
- 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-M
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fulfilled the Rome III criteria for the diagnosis of IBS. Mixed IBS (IBS-M).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- HTF-Microbi.Array
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1.
Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)
Abundance in Group 1: increased abundance in IBS-M
| NCBI | Links |
|---|---|
| Alkalihalobacillus clausii | |
| Bifidobacteriaceae | |
| Campylobacter | |
| Enterobacteriaceae | |
| Enterococcus faecium | |
| Lentilactobacillus buchneri |
Revision editor(s): Kwekuamoo
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