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Transcriptome profiling during interactions between food-spoilage-associated lactic acid bacteria: Leuconostoc gelidum, Lactococcus piscium and Lactobacillus oligofermentans

ABSTRACT: Transcriptome profiling during interactions between food-spoilage-associated lactic acid bacteria: Leuconostoc gelidum, Lactococcus piscium and Lactobacillus oligofermentans

PROVIDER: PRJEB19612 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1855030.fastq.gz	Fastqsanger.gz
	ERR1855040.fastq.gz	Fastqsanger.gz
	ERR1855050.fastq.gz	Fastqsanger.gz
	ERR1855060.fastq.gz	Fastqsanger.gz
	ERR1855070.fastq.gz	Fastqsanger.gz

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Project description: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. 81:38003811, 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.

Project description:Oxygen and carbon dioxide are common protective gases used in modified atmosphere packaging (MAP) of meat. Within the package, they selectively suppress members of the spoilage microbiome, reshaping it to adapted species concomitantly growing upon MAP. Thus, this species must exhibit adaptation mechanisms to withstand the inhibitory effect of carbon dioxide and oxygen, and cope with selective nutrition on MAP meat. In order to uncover these mechanisms, the typical representative meat-spoiling bacteria Brochothrix (B.) thermosphacta TMW2.2101 and four lactic acid bacteria (LAB) Carnobacterium (C.) divergens TMW2.1577, C. maltaromaticum TMW2.1581, Leuconostoc (L.) gelidum subsp. gelidum TMW2.1618 and L. gelidum subsp. gasicomitatum TMW2.1619 were grown in a meat simulation medium under a controlled, sterile environment, aerated constantly with either air, 100%_N2, 30%_CO2/70%_O2 or 30%_CO2/70%_N2. Growth dynamics were monitored and a label-free quantitative mass spectrometric approach was employed to determine changes within the bacterial proteomes in response to the different gas atmospheres. Revealed bacterial tolerance to modified atmospheres (MA) comprise two possible scenarios: Either bacteria were intrinsically adapted to MA, exhibiting no proteomic regulation of enzymes (L. gelidum subsp. gelidum and gasicomitatum) or, tolerance was provided by varying specific metabolic adaptation (B. thermosphacta, C. divergens, C. maltaromaticum). In detail, metabolic adaptation mechanisms to oxygen comprised an enhanced oxidative stress reduction response, adjustment of the pyruvate metabolism and catabolic oxygen consuming reactions. Adaptation to carbon dioxide was characterized by an upregulation of proteins involved in intracellular pH homeostasis, maintenance of osmotic balance and alteration of the fatty acid composition of the cell membrane. We furthermore predict species-specific strategies for different and preferential carbon source utilization enabling a non-competitive coexistence on meat and resulting in a synergistic spoilage. We conclude that a gas atmosphere containing 30%_CO2/70%_O2 has no inhibitory effect on the analyzed prominent meat-spoiling bacteria whereas 30%_CO2/70%_N2 predictively inhibits C. divergens TMW21577 and B. thermosphacta TMW2.2101 but not the other three species. This gives a mechanistically explanation of their acknowledged status as typical spoilage organisms on packaged meats.

Dataset Information

Transcriptome profiling during interactions between food-spoilage-associated lactic acid bacteria: Leuconostoc gelidum, Lactococcus piscium and Lactobacillus oligofermentans

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