Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients
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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.
Authors
Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W, Manne U
Journal
Heliyon
Year
2023
Keywords:
African American, Colorectal cancer, Egyptian, European American, Microbiome
PURPOSE: Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicities demonstrate distinct clinical behaviors. Thus, we investigated microbiome dysbiosis in Egyptian, African American (AA), and European American (EA) CRC patients. PATIENTS AND METHODS: CRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. DNA was isolated from frozen tissues, and the microbiome composition was analyzed by 16S rRNA sequencing. Differential microbial abundance, diversity, and metabolic pathways were identified using linear discriminant analysis (LDA) effect size analyses. Additionally, we compared these profiles with our previously published microbiome data derived from Kenyan CRC patients. RESULTS: Differential microbiome analysis of CRCs across all racial/ethnic groups showed dysbiosis. There were high abundances of Herbaspirillum and Staphylococcus in CRCs of Egyptians, Leptotrichia in CRCs of AAs, Flexspiria and Streptococcus in CRCs of EAs, and Akkermansia muciniphila and Prevotella nigrescens in CRCs of Kenyans (LDA score >4, adj. p-value <0.05). Functional analyses showed distinct microbial metabolic pathways in CRCs compared to normal tissues within the racial/ethnic groups. Egyptian CRCs, compared to normal tissues, showed lower l-methionine biosynthesis and higher galactose degradation pathways. CONCLUSIONS: Our findings showed altered mucosa-associated microbiome profiles of CRCs and their metabolic pathways across racial/ethnic groups. These findings provide a basis for future studies to link racial/ethnic microbiome differences with distinct clinical behaviors in CRC.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Subjects
- Location of subjects
- Egypt
- 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
- Colorectal mucosa Colorectal mucosa,colorectal mucosa
- 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 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal samples free from Colorectal Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Egyptian Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Egyptian Patients with colocrectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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).
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2A
Description: Fig.2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in Egyptians.
Abundance in Group 1: increased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Abyssicoccus albus | ||
| Bifidobacterium pseudolongum | ||
| Corynebacterium kroppenstedtii | ||
| Cutibacterium acnes | ||
| Eubacteriales | ||
| Kocuria | ||
| Lactobacillus helveticus | ||
| Tissierella creatinophila |
Revision editor(s): Chloe 256, Peace Sandy, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2A
Description: Figure 2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in egyptians.
Abundance in Group 1: decreased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Exiguobacterium | ||
| Kocuria palustris | ||
| Micrococcus | ||
| Neisseria | ||
| Pseudomonas viridiflava | ||
| Rothia aeria |
Revision editor(s): Chloe 256, Peace Sandy
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Location of subjects
- United States of America
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African American Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- African American Patients with Colorectal cancer.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2B
Description: Figure 2B shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African Americans.
Abundance in Group 1: increased abundance in African American Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens | ||
| Gardnerella | ||
| Granulicatella | ||
| Rhodobacter |
Revision editor(s): Chloe 256
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2B
Description: Figure 2B shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African American
Abundance in Group 1: decreased abundance in African American Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium |
Revision editor(s): Chloe 256
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- European American Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- European American Patients with colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2C
Description: Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.
Abundance in Group 1: increased abundance in European American Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Massilia |
Revision editor(s): Chloe 256
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2C
Description: Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.
Abundance in Group 1: decreased abundance in European American Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Gemmiger formicilis | ||
| Geobacter | ||
| Segatella copri | ||
| Mediterraneibacter gnavus |
Revision editor(s): Chloe 256, Iram jamshed
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- KeNyaN, African American and Egyptians patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of European American
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- sample of European Americans patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 53
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Source: Figure 3
Description: Differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in Tumor samples of European American
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Bacteroides ovatus | ||
| Clostridium perfringens | ||
| Comamonadaceae | ||
| Eggerthella lenta | ||
| Flexispira | ||
| Mycoplasma | ||
| Streptococcus | ||
| f_S24_7_9_s_f_S24_7_9_s_ | ||
| Lactobacillus iners |
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Location of subjects
- Kenya
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Egyptian, African American and European American Patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of kenyans
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor samples of kenyan patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Curated date: 2023/11/14
Curator: Chloe 256
Revision editor(s): Chloe 256, MyleeeA, Folakunmi, Joan Chuks
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in Tumor samples of kenyans
Revision editor(s): Chloe 256, MyleeeA, Folakunmi, Joan Chuks
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Location of subjects
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Egyptian, Kenyan and European American patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of African Americans
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sample of African American patients
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in Tumor samples of African Americans
Experiment 7
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Location of subjects
- Egypt
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- African American, Kenya and European American patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of Egyptians
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- sample of Egyptian patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in Tumor samples of Egyptians
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