Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Gao Z, Guo B, Gao R, Zhu Q, Wu W, Qin H
Journal
Molecular medicine reports
Year
2015
Studies using animal models have demonstrated that probiotics may have a beneficial role in the prevention of colorectal cancer (CRC); however, the underlying mechanism of the beneficial effects of interventional probiotic treatment on gut microbiota has remained elusive. In the present study, pyrosequencing of the V3 region of the 16S rRNA genes was conducted in order to determine the extent to which probiotics alter the microbiota. The observations of the present study indicated that the microbial structure of cancerous tissue differed significantly from that of healthy individuals and that the CRC microbiota exhibited lower diversity. It was indicated that interventional treatment with probiotics increased the density and diversity of mucosal microbes, and altered the mucosa‑associated microbiota. Pyrosequencing demonstrated that probiotics significantly reduced (5‑fold) the abundance of a bacterial taxon assigned to the genus Fusobacterium, which had been previously suggested to be a contributing factor to increase tumorigenesis. Accordingly, interventional probiotic therapy is suggested to be able to improve the composition of the mucosal microbial flora and significantly reduce the abundance of mucosa-associated pathogens in patients with CRC.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, LGeistlinger, Peace Sandy

Subjects

Location of subjects
China
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
Intestinal mucosa Bowel mucosa,Bowel mucosa of organ,Bowel mucous membrane,Bowel organ mucosa,Intestine mucosa,Intestine mucosa of organ,Intestine mucous membrane,Intestine organ mucosa,Mucosa of bowel,Mucosa of intestine,Mucosa of organ of bowel,Mucosa of organ of intestine,Mucous membrane of bowel,Mucous membrane of intestine,Organ mucosa of bowel,Organ mucosa of intestine,Tunica mucosa intestini,Intestinal mucosa,intestinal mucosa
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Nutraceutical Dietary Supplement,Food Supplementation,Nutritional supplement,Nutraceutical,nutraceutical
Group 0 name Corresponds to the control (unexposed) group for case-control studies
CGT group - colorectal cancer patients perioperative placebo
Group 1 name Corresponds to the case (exposed) group for case-control studies
PGT group - colorectal cancer patients perioperative probiotics
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days
Group 0 sample size Number of subjects in the control (unexposed) group
11
Group 1 sample size Number of subjects in the case (exposed) group
11
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Received antibiotics for the past 3 months prior to surgery

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: increased abundance in PGT group - colorectal cancer patients perioperative probiotics

NCBI Quality ControlLinks
Escherichia/Shigella sp.
Rhizobiaceae
Hyphomicrobiales
Rhizobium
Enterococcaceae
Enterococcus
Alphaproteobacteria
Prevotellaceae

Revision editor(s): Mary Bearkland, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: decreased abundance in PGT group - colorectal cancer patients perioperative probiotics

NCBI Quality ControlLinks
Fusobacteriaceae
Fusobacterium
Gemella
Bacillales Family X. Incertae Sedis
Peptostreptococcus
Anaerosporobacter

Revision editor(s): Mary Bearkland, Peace Sandy

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, LGeistlinger, Peace Sandy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HGT Group - Healthy controls
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
PGT group - colorectal cancer patients that received perioperative probiotics

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: increased abundance in PGT group - colorectal cancer patients perioperative probiotics

NCBI Quality ControlLinks
Escherichia/Shigella sp.
Rhizobium
Rhizobiaceae
Hyphomicrobiales
Rhizobium sp.
Enterococcaceae
Enterococcus
Alphaproteobacteria
Prevotellaceae

Revision editor(s): Mary Bearkland, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: decreased abundance in PGT group - colorectal cancer patients perioperative probiotics

NCBI Quality ControlLinks
Fusobacteriaceae
Fusobacterium
Gemella
Bacillales Family X. Incertae Sedis
Peptostreptococcus
Anaerosporobacter

Revision editor(s): Mary Bearkland, Peace Sandy

Experiment 3


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, LGeistlinger, Peace Sandy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HGT- Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
CGT- colorectal cancer patients that received perioperative placebo
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients that received perioperative placebos

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: increased abundance in CGT- colorectal cancer patients that received perioperative placebo

NCBI Quality ControlLinks
Fusobacteriaceae
Fusobacterium
Gemella
Bacillales Family X. Incertae Sedis
Peptostreptococcus
Anaerosporobacter

Revision editor(s): Mary Bearkland, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Aiyshaaaa, Peace Sandy

Source: Fig 4

Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT, and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.

Abundance in Group 1: decreased abundance in CGT- colorectal cancer patients that received perioperative placebo

NCBI Quality ControlLinks
Pseudomonadales
Pseudomonadota
Gammaproteobacteria
Pseudomonas
Pseudomonadaceae
Flavobacteriales
Flavobacteriaceae
Moraxellaceae

Revision editor(s): Mary Bearkland, Aiyshaaaa, Peace Sandy