Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
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

Curated date: 2023/10/08

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

Curated date: 2023/10/12

Curator: Chloe 256

Revision editor(s): Chloe 256, Peace Sandy, Folakunmi

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 ControlLinks
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

Curated date: 2023/10/12

Curator: Chloe 256

Revision editor(s): Chloe 256, Peace Sandy

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 ControlLinks
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

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256

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 ControlLinks
Clostridium perfringens
Gardnerella
Granulicatella
Rhodobacter

Revision editor(s): Chloe 256

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-20

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256

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 ControlLinks
Bradyrhizobium

Revision editor(s): Chloe 256

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-2-21

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256

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 ControlLinks
Massilia

Revision editor(s): Chloe 256

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-20

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256, Iram jamshed

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 ControlLinks
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

Curated date: 2023/11/06

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

Curated date: 2023/11/14

Curator: Chloe 256

Revision editor(s): Chloe 256, MyleeeA, Folakunmi

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 ControlLinks
Anaeroplasma
Bacteroides ovatus
Clostridium perfringens
Comamonadaceae
Eggerthella lenta
Flexispira
Mycoplasma
Streptococcus
f_S24_7_9_s_f_S24_7_9_s_
Lactobacillus iners

Revision editor(s): Chloe 256, MyleeeA, Folakunmi

Experiment 5


Reviewed Marked as Reviewed by Folakunmi on 2024-2-21

Curated date: 2023/11/14

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

NCBI Quality ControlLinks
Akkermansia muciniphila
Alloalcanivorax dieselolei
Denitrobacter
Inquilinus
Prevotella
Prevotella nigrescens
Sporobacterium sp. WAL 1855D
Verrucomicrobiaceae
g_p_75_as_s_g_p_75_as_s_
MogibacteriaceaeMogibacteriaceae

Revision editor(s): Chloe 256, MyleeeA, Folakunmi, Joan Chuks

Experiment 6


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

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

Curated date: 2023/11/14

Curator: Chloe 256

Revision editor(s): Chloe 256, MyleeeA, Folakunmi

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

NCBI Quality ControlLinks
Corynebacterium
Enhydrobacter
Facklamia
Flavobacterium succinicans
Lactobacillus
Lactococcus
Leptotrichia
Peptoniphilus
Pseudomonas
Rhodobacter
Rothia dentocariosa
Lactobacillaceae

Revision editor(s): Chloe 256, MyleeeA, Folakunmi

Experiment 7


Reviewed Marked as Reviewed by Folakunmi on 2024-2-21

Curated date: 2023/11/15

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

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

Curated date: 2023/11/15

Curator: Chloe 256

Revision editor(s): Chloe 256, MyleeeA, Folakunmi

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

NCBI Quality ControlLinks
Acinetobacter
Acinetobacter lwoffii
Acinetobacter schindleri
Bacillaceae
Bradyrhizobium
Brevundimonas diminuta
Herbaspirillum
Heyndrickxia acidicola
Hydrogenophilus
Lysobacter
Meiothermus
Micrococcus
Paenibacillus
Phyllobacterium
Proteus
Serratia marcescens
Sphingomonas
Staphylococcus
Stenotrophomonas geniculata

Revision editor(s): Chloe 256, MyleeeA, Folakunmi