{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Emilie Thivat"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001001794"],"host":["EGA"],"description":["EGA DAC EGAC00001001794"],"repository":["EGA"],"email":["Emilie.THIVAT@clermont.unicancer.fr"],"pubmed_abstract":["<h4>Background</h4>While well-characterised on its molecular base, non-small cell lung cancer (NSCLC) and its interaction with local microbiota remains scarcely explored. Moreover, current studies vary in source of lung microbiota, from bronchoalveolar lavage fluid (BAL) to tissue, introducing potentially differing results. Therefore, the objective of this study was to provide detailed characterisation of the oral and multi-source lung microbiota of direct interest in lung cancer research. Since lung tumours in lower lobes (LL) have been associated with decreased survival, characteristics of the microbiota in upper (UL) and lower tumour lobes have also been examined.<h4>Methods</h4>Using 16S rRNA gene sequencing technology, we analysed microbiota in saliva, BAL (obtained directly on excised lobe), non-malignant, peritumoural and tumour tissue from 18 NSCLC patients eligible for surgical treatment. Detailed taxonomy, diversity and core members were provided for each microbiota, with analysis of differential abundance on all taxonomical levels (zero-inflated binomial general linear model with Benjamini-Hochberg correction), between samples and lobe locations.<h4>Results</h4>Diversity and differential abundance analysis showed clear separation of oral and lung microbiota, but more importantly, of BAL and lung tissue microbiota. Phylum Proteobacteria dominated tissue samples, while Firmicutes was more abundant in BAL and saliva (with class Clostridia and Bacilli, respectively). However, all samples showed increased abundance of phylum Firmicutes in LL, with decrease in Proteobacteria. Also, clades Actinobacteria and Flavobacteriia showed inverse abundance between BAL and extratumoural tissues depending on the lobe location. While tumour microbiota seemed the least affected by location, peritumoural tissue showed the highest susceptibility with markedly increased similarity to BAL microbiota in UL. Differences between the three lung tissues were however very limited.<h4>Conclusions</h4>Our results confirm that BAL harbours unique lung microbiota and emphasise the importance of the sample choice for lung microbiota analysis. Further, limited differences between the tissues indicate that different local tumour-related factors, such as tumour type, stage or associated immunity, might be the ones responsible for microbiota-shaping effect. Finally, the \"shift\" towards Firmicutes in LL might be a sign of increased pathogenicity, as suggested in similar malignancies, and connected to worse prognosis of the LL tumours.<h4>Trial registration</h4>ClinicalTrials.gov ID: NCT03068663. Registered February 27, 2017."],"pubmed_title":["Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial."],"pubmed_authors":["Bingula Rea R, Filaire Edith E, Molnar Ioana I, Delmas Eve E, Berthon Jean-Yves JY, Vasson Marie-Paule MP, Bernalier-Donadille Annick A, Filaire Marc M"],"name_synonyms":["fbwd4, Microbiome., Microbial Community Composition, l(2)04454, DmelCG1772, Community Composition, dac, pulmo, CIB1, lung parenchyma, p21[dacapo], Microbial, dactylin, Human, E130112M23Rik, cdi4, dactylyn, parenchyma of lung, p21, lung, CG1772, FBWD4, Cdi4, CDI4, p27, Decapo, neoplasm, neoplasms, Microbial Communities, Microbiome, MIC-A, Microbiomes, Microbial Community Compositions, Microbial Community, shsf3, Microbial Community Structure, shfm3, Community Structure, E(Sev-CycE)2B, Fbw4, FBW4, PERB11.1, Dach, CDKN2B, Composition, SHFM3, Ica, Dac, DAC, p27[Dap], mICA, pulmonary, dacapo/cyclin-dependent kinase interactor 4, AI182278, Microbial Community Structures, Dap, Microbiotas, CES5A1, Lungs, P15, fbw4, SHSF3, Human Microbiomes, Community, Human Microbiome"],"pubmed_title_synonyms":["Microbial Community Composition, Carcinoma, Community Composition, Lung, Bronchial Lavage Fluids, non-small cell lung carcinoma, BAL cell, Salivas, Non-Small Cell Lung Cancer, Non-Small-Cell Lung, non-small cell carcinoma of the lung, Microbial, Bronchoalveolar, Client, bronchioalveolar lavage, Intervention Study., Human, non-small cell lung cancer, non-small cell cancer of the lung, Lung Carcinomas, Lavage Fluid, saliva molecularis, Non-Small-Cell Lung Carcinoma, simple tissue, NSCLC - non-small cell lung cancer, Non-small cell lung cancer, Non-Small Cell Lung Carcinoma, bronchoalveolar lavage fluid, Bronchial Lavage Fluid, Pulmonary Lavage Fluids, non-small cell lung carcinoma (disease), Bronchial Alveolar Lavage Fluid, Microbial Communities, Lavage Fluids, Pulmonary, Microbiome, Carcinomas, Microbiomes, Microbial Community Compositions, Microbial Community, Microbial Community Structure, saliva atomaris, Alveolar Lavage Fluids, Tissue, Community Structure, 2-D projection, Pulmonary Lavage Fluid, Non-Small Cell Lung, Lung Lavage Fluids, Non Small Cell Lung Carcinoma, Lung Carcinoma, Non Small Cell Lung, Composition, non-small cell carcinoma of lung, Alveolar, NSCLC, Lung Lavage Fluid, cross-sectional, Patient, Clients, Bronchoalveolar Lavage Fluids, Nonsmall Cell Lung Cancer, Microbial Community Structures, Alveolar Lavage Fluid, Microbiotas, sailva normalis, Bronchial, non-small cell cancer of lung, other neoplasm, Non-Small-Cell Lung Carcinomas, Human Microbiomes, Community, Human Microbiome, Non-Small-Cell"],"pubmed_abstract_synonyms":["Proteobacteria, mixed phenotype acute leukaemia, MGC130048, Malignant tumor of lung, Bile salt-stimulated lipase, sulfactin, Activity, determination, Laboratory, Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980), neoplasia, Non-Small Cell Lung Cancer, A4, malignant tumor of lung, PRAS40, malignant neoplasm of the lung, Tumor, FCAALL.51, Bronchoalveolar, infectivity, bronchioalveolar lavage, Pancreatic lysophospholipase, Lung Carcinomas, Techniques, parenchyma of lung, Method, RNA Genes, Cholate--CoA ligase, Non-Small-Cell Lung Carcinoma, 3-mercaptopropan-1-ol, 1, NEOPL., 2, Non-Small Cell Lung Carcinoma, Research Activity, Pulmonary Lavage Fluids, Laboratory Research, present in fewer numbers in organism, Bronchial Alveolar Lavage Fluid, placement, Pulmonary cancer, Priorities, treatment, ARTD9, gamma sarcoglycan, Lung Cancer, increased, 3-hydroxy-1, Ribosomal, Immune Processes, Immune Responses, Prognoses, cell process disease, tumor disease, alveolar cell carcinoma, Solute carrier family 27 member 5, neoplasm (disease), bases, Microbial Community Structure, Alveolar Lavage Fluids, Tissue, Basen, 2-dimercapto-3-propanol, Pulmonary Lavage Fluid, Non-Small Cell Lung, Ribosomal RNA, Lung Cancers, procedures, Non Small Cell Lung Carcinoma, Alveolar, Lobel, Lung Lavage Fluid, resistance to, decreased, proteobacteria, Immune, Malignant neoplasm of lung, Methodological Studies, sample, acute leukaemia of undetermined lineage, disease management, Microbial Community Structures, Therapies, gamma-sarcoglycan, dithioglycerol, stage, BSSL, Research Priority, tumor, purple photosynthetic bacteria and relatives, associated, 1110012J22Rik, somatic mutation, Very long-chain acyl-CoA synthetase-related protein, Tumors, Therapy, dimercaprolum, Carcinoma, dimercaptopropanol, Lung cancer, pulmo, Process, Nucleobase, Arts, SG-gamma, lung parenchyma, Cancer of Lung, Salivas, Research Priorities, Bssl, neoplastic disease, Purple Bacteria, Procedure, Microbial, somatic, results, tumours, non-small cell lung cancer, cancer of lung, Lavage Fluid, ALL with myeloid markers, Carboxyl ester lipase, Base2, Base1, Pathogenicity, 3-Mercaptopropanol, Malignant lung tumor, malignant tumour of lung, sarcoglycan, simple tissue, relational spatial quality, VLACSR, non-small cell lung carcinoma (disease), AI227026, Microbial Communities, neoplasms, Lavage Fluids, Carcinomas, Research and Development, Lung malignant tumors, Industrial, low G+C Gram-positive bacteria, Cholesterol esterase, malignant lung neoplasm, Actinobacteraeota, Factors, Industrial Arts, death rate, Microbial Community Compositions, adenocarcinoma of lung, Prognostic, susceptibility to, Firmicutes, DL4475C, Low G+C firmicutes, alpha, Methodological, gamma (35kDa dystrophin-associated glycoprotein), Lung Lavage Fluids, Methodological Study, rRNA gene, Treatments, Non Small Cell Lung, Activities, non-small cell carcinoma of lung, Composition, response to tyrosine kinase inhibitor in, Terrabacteria, DMDA, hyaline, pulmonary, Patient, acute leukemia of undetermined lineage, 35kD dystrophin-associated glycoprotein, rRNA Gene, Base, Bronchoalveolar Lavage Fluids, BACS, AML with lymphoid markers, Purple, Cancer of the Lung, lung neoplasm, 3-Dimercapto-1-propanol, other neoplasm, location, Human Microbiomes, accessory, Community, base, Prognostic Factor, Cancer of the lung, Lobe, Microbial Community Composition, Lung, Sterol esterase, SGCG_HUMAN, Procedures, non-small cell lung carcinoma, clostridial firmicutes, malignant lung tumor, Neoplasms, developmental stage, lung cancer, Gene, Prognostic Factors, Non-Small-Cell Lung, non-small cell carcinoma of the lung, autosomal dominant, supernumerary, firmicutes, TYPE, NEOPL, Human, DAGA4, non-small cell cancer of the lung, 3-dithiopropanol, British antilewisite, reduced, CONSTITUTIVE 1, subnumerary, 3-dimercaptopropanol, Firmacutes, 35DAG, lung, Studies, saliva molecularis, SUPPRESSOR OF NPR1-1, rRNA Genes, NSCLC - non-small cell lung cancer, AW214463, 2-propanedithiol, Proteobacteriota, bronchoalveolar lavage fluid, Pulmonary Cancer, MAM, gamma-SG, neoplasm, SCG3, Technique, Pulmonary, 3-dimercaptol-1-propanol, dimercaprol, study, Ribosomal RNA Gene, malignant tumour of the lung, Research, High G+C Gram-Positive Bacteria, saliva atomaris, LNCR, Bacillus/Clostridium group, mixed phenotype acute leukemia, rBAL-1, tumour, decreased number, Bacteria, Lung Carcinoma, Study, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), NSCLC, Actinomycete, Immune Response, Bacillus/Lactobacillus/Streptococcus group, Lung Neoplasm, 2-dithioglycerol, time of survival, Gram-Positive Bacteria, malignant neoplasm of lung, Clients, Nonsmall Cell Lung Cancer, FATP-5, rDNA, BA-CoA ligase, Development and Research, Immune Process, Non-Small-Cell Lung Carcinomas, Terrabacterida, Firmicuteota, Neoplastic Growth, Human Microbiome, Cancer, Community Composition, Pulmonary Neoplasms, Bronchial Lavage Fluids, Actinobacteriota, 35 kDa dystrophin-associated glycoprotein, Firmibacteria, BAL cell, beta-dithioglycerol, biphenotypic acute leukemia, VLACS-related, Factor, Bagl, Client, 1810036E18Rik, SGCG, LGMD2C, actinobacteria, 6.2.1.7, \"Alphaproteobacteriota\" Whitman et al. 2018, Alphaproteobacteriota, neoplastic growth, Priority, survival, Ribosomal RNA Genes, British anti-Lewisite, chemical analysis, Research Activities, malignant lung tumour, Nonsmall cell lung cancer, Neoplasm, British anti-lewisite, core, background, 3-dimercapto-1-propanol, techniques, Non-small cell lung cancer, Bronchial Lavage Fluid, Microbiome, 3.1.1.13, susceptibility, Bile acid-CoA ligase, malignant tumor of the lung, Genes, Microbiomes, DMDA1, Microbial Community, biphenotypic acute leukaemia, Pulmonary Neoplasm, increased number, Community Structure, Cancers, Bacillota corrig. Gibbons and Murray 2021, Actinobacteria, 3.1.1.3, disease of cellular proliferation, Bacillaeota, sample population, introduction, BALL, present in greater numbers in organism, PARP-9, nonsmall cell lung cancer, RNA Gene, rRNA, Clostridium group firmicutes, clear, Therapeutic, air-filled, Bal, BAL, BC003281, High G+C, SCARMD2, dithioglycerine, Alveolar Lavage Fluid, Response, Fatty acid transport protein 5, Microbiotas, protection against, Treatment, Lungs, Pulmonary Cancers, virulence, nucleobases, sailva normalis, assay, non-small cell cancer of lung, Bronchial, Actinomycetes, NEOPLASMS BENIGN, Neoplasia, methodology, Non-Small-Cell"],"additional_accession":[]},"is_claimable":false,"name":"DAC - MICA Pchir lung microbiota","description":"Data Access Committee EGAC00001001794","dates":{"output":"2025-1-9"},"accession":"EGAC00001001794","cross_references":{"TAXONOMY":["9606"],"pubmed":["32450847"],"EGA":["EGAS00001004728","EGAD00001006567"]}}