E-MTAB-5499
Transcriptome profiling during interactions between food-spoilage-associated lactic acid bacteria: Leuconostoc gelidum, Lactococcus piscium and Lactobacillus oligofermentans
Mostly, lactic acid bacteria (LAB), including food-spoilage-associated, grow in communities consisting of several microbial species. The interspecies interactions eventually shape the structure and global activity of a given microbial community. Generally, the knowledge on system level responses of LAB (especially food-spoilage-associated) during such interactions is very limited.  To study transcriptome responses during interactions between three MAP meat-spoilage-associated LAB (Leuconostoc gelidum subsp. gasicomitatum LMG 18811T, Lactococcus piscium MKFS47 and Lactobacillus oligofermentans LMG 22743T) we grew them separately in individual cultures and in mixed cultures pairwise (three combinations) and all together (triple culture) in three replicates on a glucose-containing growth medium (MRS) under microaerobic conditions at 25 °C, samples were taken at three time points (3, 5 and 11 h) and extracted RNA were sequenced.   The experiments were performed in two batches. At first (batch 1), co-cultivation of Le. gelidum and Lc. piscium accompanied with their individual cultures was performed and processed. The raw RNA-seq data for the individual culture of Lc. piscium from the batch 1 were uploaded earlier and are available in the ArrayExpress database under accession number E-MTAB-3245.  Later (batch 2), two other pairwise cultures (Le. gelidum + Lb. oligofermentans and Lc. piscium + Lb. oligofermentans) and the triple culture were grown together with the individual cultures of all three LAB.  Designations used for the sample names: \"G\": Le. gelidum; \"P\": Lc. piscium; \"O\": Lb. oligofermentans;  \"GO\", \"PO\", \"PG\": pairwise cultures of the corresponding species; \"OPG\": triple culture; \"b1\": batch 1; \"b2\": batch 2.  Example: \"3G2_b1\":  3 h, Le. gelidum, 2nd replicate, batch 1; \"11PO3_b2\": 11 h, pairwise culture of Lc. piscium and Lb. oligofermentans, 3d replicate, batch 2.  One sample (5PO3_b2) had very low number of reads ~ 9000, and, therefore, was not uploaded under this project.  RNA extraction and library construction were done analogously as in the study (Andreevskaya M et al., 2015. Appl. Environ. Microbiol. 81:3800–3811, doi: 10.1128/AEM.00320-15). Ribosomal RNA was omitted.  Libraries were sequenced in five lanes using SOLiD 5500XL (Life technologies, Foster City, Ca, USA) to produce 75 bp single-end reads.  For the data submission, xsq files obtained from SOLiD 5500XL machine, were converted into fastq files. Adapter sequences were removed using cutadapt 1.4.1.
Mostly, lactic acid bacteria (LAB), including food-spoilage-associated, grow in communities consisting of several microbial species. The interspecies interactions eventually shape the structure and global activity of a given microbial community. Generally, the knowledge on system level responses of LAB (especially food-spoilage-associated) during such interactions is very limited.  To study transcriptome responses during interactions between three MAP meat-spoilage-associated LAB (Leuconostoc gelidum subsp. gasicomitatum LMG 18811T, Lactococcus piscium MKFS47 and Lactobacillus oligofermentans LMG 22743T) we grew them separately in individual cultures and in mixed cultures pairwise (three combinations) and all together (triple culture) in three replicates on a glucose-containing growth medium (MRS) under microaerobic conditions at 25 °C, samples were taken at three time points (3, 5 and 11 h) and extracted RNA were sequenced.   The experiments were performed in two batches. At first (batch 1), co-cultivation of Le. gelidum and Lc. piscium accompanied with their individual cultures was performed and processed. The raw RNA-seq data for the individual culture of Lc. piscium from the batch 1 were uploaded earlier and are available in the ArrayExpress database under accession number E-MTAB-3245.  Later (batch 2), two other pairwise cultures (Le. gelidum + Lb. oligofermentans and Lc. piscium + Lb. oligofermentans) and the triple culture were grown together with the individual cultures of all three LAB.  Designations used for the sample names: \"G\": Le. gelidum; \"P\": Lc. piscium; \"O\": Lb. oligofermentans;  \"GO\", \"PO\", \"PG\": pairwise cultures of the corresponding species; \"OPG\": triple culture; \"b1\": batch 1; \"b2\": batch 2.  Example: \"3G2_b1\":  3 h, Le. gelidum, 2nd replicate, batch 1; \"11PO3_b2\": 11 h, pairwise culture of Lc. piscium and Lb. oligofermentans, 3d replicate, batch 2.  One sample (5PO3_b2) had very low number of reads ~ 9000, and, therefore, was not uploaded under this project.  RNA extraction and library construction were done analogously as in the study (Andreevskaya M et al., 2015. Appl. Environ. Microbiol. 81:3800–3811, doi: 10.1128/AEM.00320-15). Ribosomal RNA was omitted.  Libraries were sequenced in five lanes using SOLiD 5500XL (Life technologies, Foster City, Ca, USA) to produce 75 bp single-end reads.  For the data submission, xsq files obtained from SOLiD 5500XL machine, were converted into fastq files. Adapter sequences were removed using cutadapt 1.4.1.