Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

BMC Genomics

Research Article

Stéphane Cruveiller¹  Vincent Navratil²  Audrey Dubost³  Cindy Garnier⁴  Delphine Thevenot-Sergentet⁵  Wessam Galia⁶  Stéphanie Blanquet-Diot⁷  Francoise Leriche⁸ 

[1] Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute Genoscope & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, Evry, France;PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France;UMR 5557 Ecologie Microbienne, CNRS, Université de Lyon, Lyon, France;UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France;UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France;Reference Laboratory for Escherichia coli including Shiga Toxin-Producing E. coli, VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, Marcy l’Etoile, Lyon, France;UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France;Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France;UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France;VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France;UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France;Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France;VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France;

关键词: RNA-Seq;    EHEC;    Ground beef;    Natural microbiota;    16S metagenomics analysis;   

DOI  :  10.1186/s12864-017-3957-2

 received in 2017-03-13, accepted in 2017-07-24,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundEnterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef.ResultsBased on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota’s inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota.ConclusionIn the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.

【 授权许可】

CC BY   
© The Author(s). 2017