How Lactobacillus plantarum shapes its transcriptome in response to contrasting habitats

Summary Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here...

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Bibliographic Details
Published in:Environmental microbiology 2018-10, Vol.20 (10), p.3700-3716
Main Authors: Filannino, Pasquale, De Angelis, Maria, Di Cagno, Raffaella, Gozzi, Giorgia, Riciputi, Ylenia, Gobbetti, Marco
Format: Article
Language:English
Subjects:
Adaptation
Amino acids
Carbohydrates
Catabolism
Cluster analysis
Clustering
Cultivation
Culture media
Data processing
Gene expression
Genomes
Habitats
Ion transport
Lactobacillus plantarum
Lipids
Metabolism
Metabolomics
Nucleic acids
Organic chemistry
Phages
Proteins
Proteolysis
Pyruvic acid
Ribonucleic acid
RNA
Transcription activation
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Summary:Summary Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA‐Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage‐ and prophage‐related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.
ISSN:1462-2912
1462-2920
DOI:10.1111/1462-2920.14372