The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture

Abstract

To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the host, it is important to study them using transcriptomics. In this study, we applied the RNA-Seq technique to study global gene expression of B. longum at different growth phases in order to better understand the response of bifidobacterial cells to the specific conditions of the human gut. We have shown that in the lag phase, ABC transporters, whose function may be linked to active substrate utilization, are increasingly expressed due to preparation for cell division. In the exponential phase, the functions of activated genes include synthesis of amino acids (alanine and arginine), energy metabolism (glycolysis/gluconeogenesis and nitrogen metabolism), and translation, all of which promote active cell division, leading to exponential growth of the culture. In the stationary phase, we observed a decrease in the expression of genes involved in the control of the rate of cell division and an increase in the expression of genes involved in defense-related metabolic pathways. We surmise that the latter ensures cell survival in the nutrient-deprived conditions of the stationary growth phase.

The Role of luxS in Campylobacter jejuni Beyond Intercellular Signaling

“…Specifically, when the luxS gene is deleted, survival under starvation conditions is better because other metabolic pathways are upregulated, including oxidative phosphorylation, carbon metabolism, citrate cycle, and biosynthesis of secondary metabolites and different essential amino acids ( 29 , 30 ). Veselovsky et al ( 31 ) stated that during the exponential phase, synthesis of different essential molecules encourages cell growth. The same was determined with proteomic analysis and the Pearson’s correlation test, which confirmed a strong correlation between transcriptomic and proteomic data (Fig.…”

Impact of electro-activated whey on growth, acid and bile resistance of Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus ATCC 4356

“…Moreover, genes of lipid transport and metabolism ( accC , accD , fabA , fabF , fabH , fabZ2 ), energy production and conversion ( atpA , atpD , atpF , atpG , atpH , citC , citD , citF , citM , iolA , oadA , oadB ), and ribosomal genes ( rplJ , rplL , rplR , rpmA , rpsC , rpsD , rpsE , rpsF , rpsI , rpsR ) were also downregulated in the EAW sample. The decrease in the expression level of these genes may be primarily related to the transition of the culture from exponential to stationary growth [ 36 ]. Bacteria entering the lag phase dramatically transform their transcriptome and proteome to produce the cellular components that are needed to accumulate biomass and divide [ 37 ].…”

Study of the binding of ΔFN3.1 fragments of the Bifidobacterium longum GT15 with TNFα and prevalence of domain-containing proteins in groups of bacteria of the human gut microbiota

“…The genome of B. longum subsp. longum GT15 was sequenced (status complete, NZ_CP006741.1) [31] . We conducted RNA-Seq analysis [25,32] .…”

“…The strain B. longum subsp. longum GT15 was cultivated anaerobically (HiAnaerobic SystemeMark III, HiMedia, India) in agar and MRS broth (HiMedia, India) supplemented with cysteine (0.5 g/L) at 37 °C for 24-48 h. E. coli strains were cultivated in Luria-Bertani (LB) broth [31] . Ampicillin (150 μg/mL) was used as a selective marker for cells containing plasmids.…”

“…longum GT15 was isolated using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich, USA). Isolation of plasmid DNA, obtaining competent E. coli cells, transformation and analysis of recombinant plasmids were performed using standard methods [31] .…”