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

From BugSigDB
Needs review
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


Needs review

Curated date: 2022/09/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Subjects

Location of subjects
China
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
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
NutraceuticalsNutraceuticals

Group 0 name Corresponds to the control (unexposed) group for case-control studies
colorectal cancer patients perioperative placebo
Group 1 name Corresponds to the case (exposed) group for case-control studies
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)
No antibiotics for 3 months preceding surgery

Lab analysis

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

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
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
increased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Needs review

Curated date: 2022/09/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

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

NCBI Quality ControlLinks
Acidovorax
Acinetobacter
Alphaproteobacteria
Brevundimonas
Buttiauxella
Caulobacter
Enhydrobacter
Enterococcus
Flavobacteriia
Gammaproteobacteria
Janthinobacterium
Nesterenkonia
Pseudomonadota
Pseudomonas
Psychrobacter
Rahnella
Rhizobium
Sphingobacteriia
Sphingobacterium
Stenotrophomonas
Nevskia

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

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

NCBI Quality ControlLinks
Coprococcus
Sphingomonas
Comamonas
Fusobacteriota

Revision editor(s): Mary Bearkland

Experiment 2


Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
increased

Signature 1

Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

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

NCBI Quality ControlLinks
Bacillota
Bacillus
Carnobacterium
Enterococcus
Rhizobium
Escherichia/Shigella sp.
Nevskia
Fusobacteriota
Rhodococcus

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

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

NCBI Quality ControlLinks
Acidovorax
Acinetobacter
Betaproteobacteria
Brevundimonas
Buttiauxella
Caulobacter
Enhydrobacter
Epilithonimonas
Flavobacteriia
Flavobacterium
Gammaproteobacteria
Janthinobacterium
Nesterenkonia
Pedobacter
Propionibacterium
Pseudomonas
Psychrobacter
Rahnella
Sphingobacteriia
Sphingobacterium
Sphingomonas
Pseudomonadota

Revision editor(s): Mary Bearkland

Experiment 3


Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
colorectal cancer patients perioperative placebo
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients in the CGT group received encapsulated maltodextrin (Haiyan Liuhe Pharmaceutical Industry Co., Ltd., Jiangsu, China) three times a day. During the study period, no parenteral or enteral nutritional

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

Signature 1

Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

Abundance in Group 1: increased abundance in colorectal cancer patients perioperative placebo

NCBI Quality ControlLinks
Enterococcus
Peptostreptococcus
Fusobacteriota
Fusobacterium

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2022/09/30

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Aiyshaaaa

Source: Table 3

Description: Comparison of gut microflora structure at phylum and genus levels.

Abundance in Group 1: decreased abundance in colorectal cancer patients perioperative placebo

NCBI Quality ControlLinks
Acidovorax
Acinetobacter
Alphaproteobacteria
Betaproteobacteria
Brevundimonas
Buttiauxella
Caulobacter
Enhydrobacter
Epilithonimonas
Flavobacterium
Gammaproteobacteria
Janthinobacterium
Nesterenkonia
Nevskia
Pedobacter
Propionibacterium
Pseudomonas
Psychrobacter
Rahnella
Rhodococcus
Sphingobacteriia
Sphingobacterium
Sphingomonas
Stenotrophomonas
Flavobacteriia

Revision editor(s): Mary Bearkland, Aiyshaaaa

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
colorectal cancer patients perioperative placebo
Group 1 name Corresponds to the case (exposed) group for case-control studies
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

Lab analysis

Statistical Analysis

Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
Not specified

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 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 colorectal cancer patients perioperative probiotics

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

Revision editor(s): Mary Bearkland

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Atrayees

Source: Figure 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 colorectal cancer patients perioperative probiotics

NCBI Quality ControlLinks
Fusobacterium
Fusobacteriaceae
Gemella
Peptostreptococcus
Anaerosporobacter

Revision editor(s): Mary Bearkland, Atrayees

Experiment 6


Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

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
colorectal cancer patients perioperative placebo
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients in the CGT group received encapsulated maltodextrin (Haiyan Liuhe Pharmaceutical Industry Co., Ltd., Jiangsu, China) three times a day. During the study period, no parenteral or enteral nutritional

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Merit

Source: Figure 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 colorectal cancer patients perioperative placebo

NCBI Quality ControlLinks
Anaerosporobacter
Fusobacteriaceae
Fusobacterium
Gemella
Peptostreptococcus

Revision editor(s): Mary Bearkland, Merit

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2022/10/07

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 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 colorectal cancer patients perioperative placebo

NCBI Quality ControlLinks
Pseudomonadales
Pseudomonadota
Gammaproteobacteria
Pseudomonas
Pseudomonadaceae
Flavobacteriales
Flavobacteriia
Moraxellaceae
Flavobacteriaceae

Revision editor(s): Mary Bearkland