Journal of Animal Science and Technology
Korean Society of Animal Sciences and Technology

Complete genome sequence of Limosilactobacillus fermentum JNU532 as a probiotic candidate for the functional food and feed supplements

Bogun Kim1,#, Ziayo Meng2,#, Xiaoyue Xu1, Seungwoo Baek1, Duleepa Pathiraja1, In-Geol Choi1,*, Sejong Oh2,*
1Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
2Division of Animal Science, Chonnam National University, Gwangju 61186, Korea

#These authors contributed equally to this work.

*Corresponding author: In-Geol Choi, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea. Tel: +82-2-3290-3152, E-mail:
*Corresponding author: Sejong Oh, Division of Animal Science, Chonnam National University, Gwangju 61186, Korea. Tel: +82-62-530-2116, E-mail:

© Copyright 2023 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Oct 02, 2022; Revised: Oct 23, 2022; Accepted: Oct 24, 2022

Published Online: Jan 31, 2023


Lactic acid bacteria (LAB) have been reported to possess various beneficial properties and are commonly used as probiotics. LAB play a crucial role in milk fermentation, industrial lactic acid fermentation, and health and medicine. Limosilactobacillus fermentum isolated from fermented dairy and food products is considered as ‘Generally Recognized as Safe’ by FDA. Limosilactobacillus fermentum plays an important role in modulation of the intestinal microbiota, enhancing the host immune system and improving feed digestibility. We isolated a probiotic candidate that was identified and named Limosilactobacillus fermentum JNU532. In a previous report, cell-free culture of L. fermentum JNU532 exhibited anti-melanogenic and antioxidant activities. In this study, we present the complete genome assembly of the bacterial strain JNU532. The final genome consists of one circular chromosome (2,077,416 base pairs) with a guanine + cytosine (GC) ratio of 51.5%.

Keywords: Limosilactobacillus fermentum; Probiotics; Food; Feed; Supplements

Recently, the genus Lactobacillus was divided into several genera [1], with the species Lactobacillus fermentum being assigned to the genus Limosilactobacillus.Limosilactobacillus fermentum is one of hetero-fermentatives and is used in the fermentation of milk, plants, and silage. Limosilactobacillus fermentum strains not only enhance the nutritional value and flavor of food but also its functional properties. This species has strong pH tolerance and good bile tolerance, and it can also reduce cholesterol content in the human body [2]. In addition, L. fermentum can inhibit harmful intestinal microbiota, lessen the activity of food allergens, reduce mutagenic and carcinogenic activities, display immunomodulatory activity, and lower cholesterol [3,4]. Limosilactobacillus fermentum JNU532 was isolated from local fermented kimchi in this study. In our previous study, an L. fermentum JNU532–derived fermentation broth demonstrated antioxidant properties and the ability to reduce melanin production by inhibiting the activity of tyrosinase in B16F10 melanoma cells. Therefore, L. fermentum JNU532 may be considered a natural depigmentation agent. [5].

L. fermentum JNU532 was cultivated in Man-Rogosa-Sharpe (MRS) medium (Becton, Dickinson, Franklin, USA) for 24 h at 37°C. Genomic DNA was extracted with a HiGeneTM Genomic DNA Prep kit (BIOFACT, Daejeon, South Korea), according to the manufacturer’s instructions.

The short-read sequencing library was prepared with an Illumina® DNA Prep kit (Illumina, San Diego, CA, USA). Sequencing was performed on the Illumina MiSeq platform (Illumina) using the Illumina MiSeq reagent kit V3 (300 bp, paired end). The long-read sequencing library was prepared using an Oxford Nanopore Ligation Sequencing Kit (Oxford Nanopore, Oxford, UK). Long-read sequencing was carried out on a MinION sequencing device (Oxford Nanopore) equipped with a MinION flow cell (R9.4.1, Oxford Nanopore). Illumina sequencing produced 1,244,607 paired end reads (433,289,083 bp), while 122,763 reads with an average length of 1,839 bases were obtained from Oxford Nanopore sequencing.

De novo genome sequence assembly was assembled performed using a Flye assembler (v. 2.9) [6] with default options. Adapter sequences from short reads were removed using TrimGalore (v. 0.6.7) [7] with the ‘paired’ parameter. Errors in the draft genome assembly were corrected with Pilon (v. 1.24) [8] with default parameters. Gene prediction of the chromosomal sequence was performed with Prokka (v. 1.14.5) [9]. The completeness of the genome assembly was assessed using BUSCO (v. 5.2.2) [10] with the OrthoDB v10 bacterial (bacteria_odb10) database.

The complete genome sequence of L. fermentum JNU532 consisted of one circular chromosome with a guanine + cytosine (GC) ratio of 51.5% (Table 1). A total of 2,113 genes, including 15 rRNA and 57 tRNA, were predicted in the genome (Fig. 1). The genomic information of L. fermentum JNU532 could provide insight to future research on the characteristics of this strain for functional food and feed supplements (Table 1).

Table 1. Genome features of Limosilactobacillus fermentum JNU532
L. fermentum JNU532
Total genome length (bp) 2,077,416
GC content (%) 51.5
Depth 96.0
Genome completeness (%) 99.2
Protein-coding genes 2,041
tRNA 57
rRNA 15

bp, base pair; G, guanine; C, cytosine; tRNA, transfer RNA; rRNA, ribosomal RNA.

Download Excel Table
Fig. 1. Circular chromosome map of Limosilactobacillus fermentum JNU532. From the periphery to the center, marked features are as follows: protein--coding sequences on the forward strand, protein--coding sequences on the reverse strand, tRNA, rRNA, GC ratio, and GC skew. bp, base pair; G, guanine; C, cytosine; tRNA, transfer RNA; rRNA, ribosomal RNA.
Download Original Figure


The complete genome sequence has been deposited in the National Center for Biotechnology Information (NCBI) GenBank under the accession number GCA_024800585.1. The BioProject accession number is PRJNA872884 and the BioSample accession number is SAMN30472492.

Competing interests

No potential conflict of interest relevant to this article was reported.

Funding sources

This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through High Value-added Food Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (grant 321034051HD020) and was supported by the National Research Foundation (NRF) grant funded by the Korea government (2021R1A4A1031220).


Not applicable.

Availability of data and material

Upon reasonable request, the datasets of this study can be available from the corresponding author.

Authors’ contributions

Conceptualization: Choi IG, Oh S.

Data curation: Kim B, Choi IG, Oh S.

Formal analysis: Kim B, Meng Z.

Methodology: Kim B, Meng Z.

Software: Kim B, Xu X, Baek S.

Validation: Pathiraja D.

Investigation: Kim B, Meng Z, Choi IG.

Writing - original draft: Choi IG, Oh S.

Writing - review & editing: Kim B, Meng Z, Xu X, Baek S, Pathiraja D, Choi IG, Oh S.

Ethics approval and consent to participate

This manuscript does not require IRB/IACUC approval because there are no human and animal participants.



Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, et al. A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol. 2020; 70:2782-858


Pan DD, Zeng XQ, Yan YT. Characterisation of Lactobacillus fermentum SM-7 isolated from koumiss, a potential probiotic bacterium with cholesterol-lowering effects. J Sci Food Agric. 2011; 91:512-8


Naghmouchi K, Belguesmia Y, Bendali F, Spano G, Seal BS, Drider D. Lactobacillus fermentum: a bacterial species with potential for food preservation and biomedical applications. Crit Rev Food Sci Nutr. 2020; 60:3387-99


Swain MR, Anandharaj M, Ray RC, Parveen Rani R. Fermented fruits and vegetables of Asia: a potential source of probiotics. Biotechnol Res Int. 2014; 2014:250424


Meng Z, Oh S. Antioxidant and antimelanogenic activities of kimchi-derived Limosilactobacillus fermentum JNU532 in B16F10 melanoma cells. J Microbiol Biotechnol. 2021; 31:990-8


Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019; 37:540-6


Krueger F, James F, Ewels P, Afyounian E, Schuster-Boeckler B. FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo [Internet]. Zenodo. 2021[cited 2022 Feb 23]


Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS ONE. 2014; 9e112963


Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30:2068-9


Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021; 38:4647-54