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Open AccessArticle

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

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i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
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IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
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FEUP-Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
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INESC TEC—Instituto de Engenharia de Sistemas e Computadores, Tecnologia e Ciência, Universidade do Porto, 4200-465 Porto, Portugal
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Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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CIBIO—Centro de Investigação em Biodiversidade e Recursos Genético, Universidade do Porto, 4485-661 Vairão, Portugal
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(8), 1196; https://doi.org/10.3390/microorganisms8081196
Received: 14 July 2020 / Revised: 31 July 2020 / Accepted: 2 August 2020 / Published: 6 August 2020
(This article belongs to the Special Issue From Host-Pathogen Interaction to Host-Directed Therapies)
The human gastrointestinal tract harbors approximately 100 trillion microorganisms with different microbial compositions across geographic locations. In this work, we used RNASeq data from stomach samples of non-disease (164 individuals from European ancestry) and gastric cancer patients (137 from Europe and Asia) from public databases. Although these data were intended to characterize the human expression profiles, they allowed for a reliable inference of the microbiome composition, as confirmed from measures such as the genus coverage, richness and evenness. The microbiome diversity (weighted UniFrac distances) in gastric cancer mimics host diversity across the world, with European gastric microbiome profiles clustering together, distinct from Asian ones. Despite the confirmed loss of microbiome diversity from a healthy status to a cancer status, the structured profile was still recognized in the disease condition. In concordance with the parallel host-bacteria population structure, we found 16 human loci (non-synonymous variants) in the European-descendent cohorts that were significantly associated with specific genera abundance. These microbiome quantitative trait loci display heterogeneity between population groups, being mainly linked to the immune system or cellular features that may play a role in enabling microbe colonization and inflammation. View Full-Text
Keywords: gastric microbiome; gastric cancer; European and Asian diversity; biomarkers; microbiome quantitative trait loci; miQTL gastric microbiome; gastric cancer; European and Asian diversity; biomarkers; microbiome quantitative trait loci; miQTL
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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.

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