Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Microbiome Inference
2.3. Checking for Genus Coverage, Richness and Evenness
2.4. Phylogenetic Analyses
2.5. Evaluating Microbiota Composition in Gastric Tumorigenesis
2.6. Host-Genome and Microbiome Associations
3. Results
3.1. Quality Control of RNASeq Data for Microbiome Inference
3.2. Microbiome Composition in Cancer vs. Non-Cancer Samples from European Ancestry
3.3. Microbiome Profiling in Function of Host Geographic Origin
3.4. Identification of Host Genetic Variation Associated with the Microbiome
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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SNP | Genus | GeneID | p-Value | q-Value | Genotype Frequency | Fst (p-Values) | |||||
MAF_EUR | MAF_EAS | MAF_AFR | EUR_AFR | EUR_EAS | EAS_AFR | ||||||
TCGA-EUROPE | rs1131600 | Corynebacterium | DPH1 | 7.97104 × 10−8 | 0.01501 | G|G: 0.028 A|G: 0.252 A|A: 0.720 | G|G: 0.004 A|G: 0.105 A|A: 0.891 | A|G: 0.020 A|A: 0.980 | 0.14323 (0.00000 ± 0.0000) | 0.04831 (0.00000 ± 0.0000) | 0.0359 (0.00000 ± 0.0000) |
TCGA-EUROPE | rs61997220 | Lactobacillus | ZC3H12D | 3.07635 × 10−7 | 0.02414 | T|T: 0.907 C|T: 0.093 | T|T: 1.000 | T|T: 0.995 C|T: 0.005 | 0.04507 (0.00000 ± 0.0000) | 0.04582 (0.00000 ± 0.0000) | 0.00113 (0.25978 + 0.0048) |
TCGA-EUROPE | rs9262143 | Acinetobacter | PPP1R18 | 5.68970 × 10−7 | 0.02414 | C|C: 0.845 C|T: 0.151 T|T: 0.004 | C|C: 1.000 | C|C: 0.995 C|T: 0.005 | 0.08232 (0.00000 ± 0.0000) | 0.07868 (0.00000 ± 0.0000) | 0.00113 (0.26255 ± 0.0046) |
TCGA-EUROPE | rs17350674 | Cloacibacterium | KIF24 | 5.97391 × 10−7 | 0.02414 | C|C: 0.614 A|A: 0.050 A|C: 0.336 | C|C: 0.988 A|A: 0.002 A|C: 0.010 | C|C: 0.980 A|C: 0.020 | 0.21379 (0.00000 ± 0.0000) | 0.19977 (0.00000 ± 0.0000) | 0 (0.52688 ± 0.0052) |
TCGA-EUROPE | rs2219078 | Acinetobacter | SULT1C3 | 6.40940 × 10−7 | 0.02414 | G|G: 0.658 A|G: 0.300 A|A: 0.042 | G|G: 0.097 A|G: 0.452 A|A: 0.450 | G|G: 0.472 A|G: 0.443 A|A: 0.085 | 0.03291 (0.00000 ± 0.0000) | 0.38529 (0.00000 ± 0.0000) | 0.24086 (0.00000 ± 0.0000) |
TCGA-EUROPE | rs2523989 | Acinetobacter | TRIM31 | 1.03982 × 10−6 | 0.03263 | C|C: 0.775 C|T: 0.209 T|T: 0.016 | C|C: 0.905 C|T: 0.093 T|T: 0.002 | C|C: 0.903 C|T: 0.095 T|T: 0.002 | 0.03296 (0.00000 ± 0.0000) | 0.03172 (0.00000 ± 0.0000) | 0 (0.99990 ± 0.0000) |
TCGA-EUROPE | rs7198494 | Achromobacter | C16orf46 | 1.75767 × 10−6 | 0.04728 | A|A: 0.648 A|G: 0.294 G|G: 0.058 | A|A: 0.962 A|G: 0.036 G|G: 0.002 | A|A: 0.526 A|G: 0.389 G|G: 0.085 | 0.01389 (0.00010 ± 0.0001) | 0.15724 (0.00000 ± 0.0000) | 0.21452 (0.00000 ± 0.0000) |
TCGA-EUROPE | rs61997220 | Fusobacterium | ZC3H12D | 2.66174 × 10−6 | 0.05857 | T|T: 0.907 C|T: 0.093 | T|T: 1.000 | T|T: 0.995 C|T: 0.005 | 0.04507 (0.00000 ± 0.0000) | 0.04582 (0.00000 ± 0.0000) | 0.00113 (0.25978 ± 0.0048) |
TCGA-EUROPE | rs62572859 | Lactobacillus | C9orf129 | 2.79953 × 10−6 | 0.05857 | C|C: 0.750 C|T: 0.221 T|T: 0.030 | C|C: 0.919 C|T: 0.081 | C|C: 0.433 C|T: 0.475 T|T: 0.092 | 0.09115 (0.00000 ± 0.0000) | 0.05751 (0.00000 ± 0.0000) | 0.22638 (0.00000 ± 0.0000) |
TCGA-EUROPE | rs1014867 | Lactobacillus | FAT4 | 5.53680 × 10−6 | 0.09807 | C|C: 0.895 C|T: 0.103 T|T: 0.002 | C|C: 0.885 C|T: 0.109 T|T: 0.006 | C|C: 0.865 C|T: 0.126 T|T: 0.009 | 0.00188 (0.09425 ± 0.0026) | 0 (0.56796 ± 0.0055) | 0.00016 (0.33403 ± 0.0052) |
TCGA-EUROPE | rs1782360 | Lactobacillus | LRBA | 6.08310 × 10−6 | 0.09807 | G|G: 0.855 C|C: 0.012 C|G: 0.133 | G|G: 0.754 C|C: 0.022 C|G: 0.224 | G|G: 0.495 C|C: 0.077 C|G: 0.428 | 0.13144 (0.00000 ± 0.0000) | 0.01505 (0.00040 ± 0.0002) | 0.06804 (0.00000 ± 0.0000) |
TCGA-EUROPE | rs4963198 | Corynebacterium | LRRC56 | 6.84488 × 10−6 | 0.09914 | G|G: 0.109 A|A: 0.437 A|G: 0.453 | G|G: 0.022 A|A: 0.768 A|G: 0.210 | G|G: 0.319 A|A: 0.194 A|G: 0.487 | 0.09743 (0.00000 ± 0.0000) | 0.11482 (0.00000 ± 0.0000) | 0.33553 (0.00000 ± 0.0000) |
GTEx | rs61733127 | Streptococcus | PHLPP2 | 3.22625 × 10−11 | 0.00001 | G|G: 0.024 A|G: 0.249 A|A: 0.728 | G|G: 0.012 A|G: 0.109 A|A: 0.879 | A|G: 0.056 A|A: 0.944 | 0.09268 (0.00000 ± 0.0000) | 0.03325 (0.00000 ± 0.0000) | 0.01635 (0.00000 ± 0.0000) |
GTEx | rs74344827 | Streptococcus | TAT | 9.87962 × 10−8 | 0.01160 | G|G: 0.700 A|G: 0.274 A|A: 0.026 | G|G: 0.905 A|G: 0.087 A|A: 0.008 | G|G: 0.663 A|G: 0.309 A|A: 0.029 | 0.00052 (0.22265 ± 0.0035) | 0.06188 (0.00000 ± 0.0000) | 0.07456 (0.00000 ± 0.0000) |
GTEx | rs73229817 | Corynebacterium | PDLIM2 | 2.60383 × 10−7 | 0.02039 | C|C: 0.901 C|T: 0.097 T|T: 0.002 | C|C: 1.000 | C|C: 0.998 C|T: 0.002 | 0.05466 (0.00000 ± 0.0000) | 0.0498 (0.00000 ± 0.0000) | 0 (0.99990 ± 0.0000) |
GTEx | rs12807209 | Nevskia | MUC6 | 5.79755 × 10−7 | 0.03405 | G|G: 0.998 C|G: 0.002 | G|G: 1.000 | G|G: 0.750 C|C: 0.018 C|G: 0.231 | 0.11679 (0.00000 ± 0.0000) | 0 (0.50579 ± 0.0054) | 0.11913 (0.00000 ± 0.0000) |
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Cavadas, B.; Camacho, R.; Ferreira, J.C.; Ferreira, R.M.; Figueiredo, C.; Brazma, A.; Fonseca, N.A.; Pereira, L. Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci. Microorganisms 2020, 8, 1196. https://doi.org/10.3390/microorganisms8081196
Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L. Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci. Microorganisms. 2020; 8(8):1196. https://doi.org/10.3390/microorganisms8081196
Chicago/Turabian StyleCavadas, Bruno, Rui Camacho, Joana C. Ferreira, Rui M. Ferreira, Ceu Figueiredo, Alvis Brazma, Nuno A. Fonseca, and Luísa Pereira. 2020. "Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci" Microorganisms 8, no. 8: 1196. https://doi.org/10.3390/microorganisms8081196