Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Bucher-Johannessen C, Birkeland EE, Vinberg E, Bemanian V, Hoff G, Berstad P, Rounge TB
Journal
Frontiers in oncology
Year
2023
Keywords:
16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing
BACKGROUND: The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross-sectional studies. However, there is a lack of studies using prospectively collected samples. METHODS: From the Norwegian Colorectal Cancer Prevention (NORCCAP) trial, we analyzed 144 archived fecal samples from participants who were diagnosed with CRC or high-risk adenoma (HRA) at screening and from participants who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all the samples and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity and differential abundance. RESULTS: Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls. Phascolarctobacterium succinatutens was more abundant in CRC compared with healthy controls in both the 16S and metagenome data. The abundance of Bifidobacterium and Lachnospiraceae spp. was associated with time to CRC diagnosis. CONCLUSION: Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/19

Curator: Yjung24

Revision editor(s): Yjung24, Davvve, Folakunmi

Subjects

Location of subjects
Norway
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
Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
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
HRA (high-risk adenoma)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.
Group 0 sample size Number of subjects in the control (unexposed) group
53
Group 1 sample size Number of subjects in the case (exposed) group
63

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
Negative Binomial Regression
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
age, time, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, geographic area

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/19

Curator: Yjung24

Revision editor(s): Yjung24, Davvve, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: decreased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Azospirillum sp. 47_25
Escherichia/Shigella sp.
Pseudomonadota

Revision editor(s): Yjung24, Davvve, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/19

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Bacillota

Revision editor(s): Yjung24, Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
CRC (participants diagnosed with colorectal cancer)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.
Group 1 sample size Number of subjects in the case (exposed) group
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in CRC (participants diagnosed with colorectal cancer)

NCBI Quality ControlLinks
Bacillota
unclassified Phascolarctobacterium

Revision editor(s): Yjung24, Folakunmi

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal adenoma , Colorectal cancer adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma,cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.
Group 1 sample size Number of subjects in the case (exposed) group
91

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
geographic area, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group

NCBI Quality ControlLinks
Bacillota

Revision editor(s): Yjung24

Experiment 4


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
Group 1 name Corresponds to the case (exposed) group for case-control studies
HRA (high-risk adenoma)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.
Group 1 sample size Number of subjects in the case (exposed) group
63

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, geographic area

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between HRA and healthy controls.

Abundance in Group 1: increased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Lacrimispora saccharolytica

Revision editor(s): Yjung24, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between HRA and healthy controls.

Abundance in Group 1: decreased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Parasutterella

Revision editor(s): Yjung24, Folakunmi

Experiment 5


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
CRC (participants diagnosed with colorectal cancer)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.
Group 0 sample size Number of subjects in the control (unexposed) group
22
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
geographic area, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in CRC (participants diagnosed with colorectal cancer)

NCBI Quality ControlLinks
Acidaminococcus
Acidaminococcus intestini
Coprococcus eutactus
Firmicutes bacterium CAG:95
[Lactobacillus] rogosae
Phascolarctobacterium succinatutens

Revision editor(s): Yjung24

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: decreased abundance in CRC (participants diagnosed with colorectal cancer)

NCBI Quality ControlLinks
Bacteroides finegoldii
Monoglobus pectinilyticus
Roseburia sp. CAG:303
Veillonella parvula

Revision editor(s): Yjung24

Experiment 6


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal adenoma , Colorectal cancer adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma,cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.
Group 1 sample size Number of subjects in the case (exposed) group
25

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, geographic area

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group

NCBI Quality ControlLinks
Lacrimispora saccharolytica

Revision editor(s): Yjung24

Experiment 7


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/26

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Time Time,time
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colorectal cancer diagnosed at time of screening
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colorectal cancer diagnosed during 17-year follow-up/post screening
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Diagnosed with colorectal cancer at screening in the beginning of the Norwegian Colorectal Cancer Prevention Trial
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
23

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study
Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/26

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: increased abundance in Colorectal cancer diagnosed during 17-year follow-up/post screening

NCBI Quality ControlLinks
Bifidobacterium
Lachnospiraceae

Revision editor(s): Yjung24

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/26

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.

Abundance in Group 1: decreased abundance in Colorectal cancer diagnosed during 17-year follow-up/post screening

NCBI Quality ControlLinks
Lachnospiraceae

Revision editor(s): Yjung24