Transcriptomic analysis of Lacticaseibacillus paracasei Zhang in transition to the viable but non-culturable state by RNA sequencing

Qiuhua Bao; Xuebo Ma; Xiaoyu Bo; Jing Pang; Lixia Dai; Huiying Wang; Yongfu Chen; Lai-Yu Kwok

doi:10.3389/fmicb.2023.1280350

Transcriptomic analysis of Lacticaseibacillus paracasei Zhang in transition to the viable but non-culturable state by RNA sequencing

Front Microbiol. 2023 Dec 21:14:1280350. doi: 10.3389/fmicb.2023.1280350. eCollection 2023.

Authors

Qiuhua Bao^#^{1

2

3}, Xuebo Ma^#^{1

2

3}, Xiaoyu Bo^{1

2

3}, Jing Pang^{1

2

3}, Lixia Dai^{1

2

3}, Huiying Wang^{1

2

3}, Yongfu Chen^{1

2

3}, Lai-Yu Kwok^{1

2

3}

Affiliations

¹ Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China.
² Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China.
³ Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.

^# Contributed equally.

Abstract

Background: Some bacteria enter the viable but non-culturable (VBNC) state to survive harsh environmental conditions and external stresses. This alters cell physiology and has implications for the food industry as some bacteria, such as lactobacilli, undergo similar changes during food processing.

Methods: This study aimed to investigate the transcriptomic changes of a probiotic strain, Lacticaseibacillus paracasei Zhang (L. paracasei Zhang), upon transition to the VBNC state using high throughput RNA sequencing (RNA-seq).

Results: Bacteria were inoculated into the de Man, Rogosa, and Sharpe medium and maintained at low temperature and pH to induce cell transition to the VBNC state. Cells were harvested for analysis at five stages of VBNC induction: 0, 3, 30, and 180 days after induction and 210 days when the cells entered the VBNC state. Our results showed that the expression of 2,617, 2,642, 2,577, 2,829, and 2,840 genes was altered at these five different stages. The function of differentially expressed genes (DEGs, compared to healthy cells collected at day 0) and their encoded pathways were analyzed by the Gene Ontology Consortium and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. A total of 10 DEGs were identified in cells that entered the VBNC state: five continuously upregulated (LCAZH_0621, LCAZH_1986, LCAZH_2038, LCAZH_2040, and LCAZH_2174) and five continuously downregulated (LCAZH_0024, LCAZH_0210, LCAZH_0339, LCAZH_0621, and LCAZH_0754).

Conclusions: This study proposes a molecular model of the VBNC mechanism in L. paracasei Zhang, highlighting that changes in cell metabolism improve substrate utilization efficiency, thereby enhancing bacterial survival under adverse conditions. These data may be useful for improving the survival of probiotics in industrial food processing.

Keywords: Lacticaseibacillus paracasei Zhang; high-throughput RNA sequencing; induction; transcriptomics; viable but non-culturable (VBNC).

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the Science and Technology Plan Project Assignment of the Food Science and Engineering College of the Inner Mongolia Agricultural University (SPKJ202205), the National Natural Science Foundation of China (31860434 and 31972083), the Inner Mongolia Autonomous Region Science & Technology Project (2020GG0101), Inner Mongolia Autonomous Region 2022 Leading Scientific and Technological Talents Team Project (2022LJRC0003), and the Inner Mongolia Natural Science Foundation Project (2023MS03046).