Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells

Abstract

Background Lactiplantibacillus plantarum (L. plantarum), a dominant strain in traditional fermented foods, is widely used in fermentation industry because of its fast acid production. However, L. plantarum is easily inactivated due to acidity, high temperature and other factors. The formation of biofilm by bacteria can effectively increase environmental tolerance. Therefore, it is important to improve the environmental tolerance of L. plantarum by studying its biofilm formation conditions and regulatory mechanisms. Methods After determining a suitable NaCl concentration for promoting biofilm formation, L. plantarum was grown with 48 g L−1 NaCl. Differential gene expressions in L. plantarum biofilm vs. planktonic cells were analyzed using RNA sequencing and validated using qPCR. Result L. plantarum RS66CD biofilm formation formed highest amount of when grown at 48 g L−1 NaCl. Altogether 447 genes were up-regulated and 426 genes were down-regulated in the biofilm. KEGG pathway analysis showed that genes coding for D-Alanine metabolism, peptidoglycan biosynthesis, two-component system, carbon metabolism, bacterial secretion system, lysine biosynthesis and fatty acid metabolism were crucial for biofilm formation. In addition, eight other genes related to biofilm formation were differentially expressed. Our results provide insights into the differential gene expression involved in biofilm formation, which can help to reveal gene regulation during L. plantarum biofilm formation.

Deep Shotgun metagenomic and 16S rRNA analysis revealed the microbial diversity of lactic acid bacteria in traditional fermented foods of eastern Hainan, China

“…23 The results of microbial metabolic pathways predicted showed that the microbial metabolic activities in traditional fermented foods in the eastern coastal area of Hainan, China were very active, including amino acid transport and metabolism, energy metabolism, carbohydrate transport and metabolism, lipid transport and metabolism, nucleotide metabolism and glycolysis IV. Since the fermentation system itself is a micro-ecological environment, the decomposition of the fermentation substrate matrix can provide carbon and nitrogen sources for the growth of microorganisms, so the carbohydrate metabolism and amino acid metabolism of microorganisms in the fermentation samples are at a high level, 56 which is consistent with the observed results that the metabolic activity of microorganisms in traditional fermented foods in eastern Hainan remained consistent. In addition, the biosynthesis of fatty acids, glycogen and amino acids in traditional fermented foods in eastern Hainan is also very active, including fatty acid biosynthesis initiation (mitochondria), l -valine biosynthesis, glycogen biosynthesis I (from ADP- d -glucose), l -valine biosynthesis-methionine biosynthesis IV, superpathway of l -cysteine biosynthesis (mammalian) and ectoine biosynthesis.…”

Comparative Transcriptome Analysis of Shewanella putrefaciens WS13 Biofilms Under Cold Stress

“…For energy metabolism, approximately 10 DEGs were significantly down-regulated (0.01 fold to 0.48 fold) at 30°C. For example, expression of the ppsA gene was increased by 2.62 fold in S. putrefaciens at 4°C which can promote biofilm formation by enhancing bacterial adhesion ( Ao et al., 2020 ). Moreover, approximately 11 DEGs involved in aminoacyl-tRNA biosynthesis were highly down-regulated (2.02 fold to 5.15 fold) in S. putrefaciens WS13 biofilm at 4°C, which may have released amino acids to feed the energy-providing pathways ( Bénédicte et al., 2009 ), and benefited the survival of S. putrefaciens WS13 under the cold stress.…”

“…Mature biofilm cells of S. putrefaciens WS13 at 4°C and 30°C were harvested at 24h, and 84h, respectively. RNA extraction, cDNA library preparation, and RNA sequencing were carried out as described previously ( Ao et al., 2020 ).…”

“…These results suggested QS plays an important role in the biofilm formation of S. putrefaciens at the cold stress. (Ao et al, 2020). Moreover, approximately 11 DEGs involved in aminoacyl-tRNA biosynthesis were highly downregulated (2.02 fold to 5.15 fold) in S. putrefaciens WS13 biofilm at 4°C, which may have released amino acids to feed the energyproviding pathways (Beńedicte et al, 2009), and benefited the survival of S. putrefaciens WS13 under the cold stress.…”

“…With increased breakthrough of sequeneing technology, RNA-Sequencing (RNA-Seq) technique has been use to study bacterial differential express genes (DEGs), transcript structures, new transcripts and isomers, and alternative splicing and allele-specific expression under adverse circumstances, such as Clostridium acetobutylicum in a high-salt environment ( Ao et al., 2020 ), and Escherichia coli under different heating methods. In recent years, gene expression between biofilm cells and planktonic cells under stress conditions ( Charlebois et al., 2016 ; Ao et al., 2020 ), has been investigated at the transcriptomic level in Clostridium acetobutylicum ( Dong et al., 2015 ), Porphyromonas gingivalis ( Lo et al., 2009 ), and Gardnerella vaginalis ( Castro et al., 2017 ). However, current literature on the molecular mechanism of biofilm formation of spoilage bacteria under the cold stress is still rare.…”