IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation

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Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/17

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks, Atrayees

Subjects

Location of subjects
Italy
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
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)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V2-V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
HTF-Microbi.Array

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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

NCBI Quality ControlLinks
Shouchella clausii
Bacillus cereus
Bifidobacteriaceae
Bifidobacterium adolescentis
Bifidobacterium breve
Bifidobacterium longum
Campylobacter
Clostridioides difficile
Enterobacteriaceae
Enterococcus faecium
Lactobacillaceae
Lentilactobacillus buchneri
Ligilactobacillus salivarius
Peptostreptococcaceae
Agathobacter rectalis

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Atrayees

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 Quality ControlLinks
Bacteroides
Veillonella
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks, Atrayees

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
Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C)
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 Quality ControlLinks
Shouchella clausii
Bifidobacteriaceae

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Atrayees

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 Quality ControlLinks
Bacteroides
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks, Atrayees

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
Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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

NCBI Quality ControlLinks
Shouchella clausii
Bacillus cereus
Bifidobacteriaceae
Bifidobacterium adolescentis
Bifidobacterium breve
Bifidobacterium longum
Clostridioides difficile
Enterobacteriaceae
Enterococcus faecium
Lactobacillaceae
Ligilactobacillus salivarius
Peptostreptococcaceae
Agathobacter rectalis

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Atrayees

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 Quality ControlLinks
Bacteroides
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): LGeistlinger, Kwekuamoo, WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

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 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

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 Quality ControlLinks
Shouchella clausii
Bifidobacteriaceae
Campylobacter
Enterobacteriaceae
Enterococcus faecium
Lentilactobacillus buchneri

Revision editor(s): Kwekuamoo