Complete genome sequence of Pediococcus acidilactici CACC 537 isolated from canine

Jung-Ae Kim1,2, Hyun-Jun Jang1, Dae-Hyuk Kim1,3, Youn Kyoung Son4, Yangseon Kim1,*
Author Information & Copyright
1Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea
2Department of Bioactive Material Science, Jeonbuk National University, Jeonju 54896, Korea
3Department of Molecular Biology, Department of Bioactive Material Science, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Korea
4Biologicla and Genetic Reources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
*Corresponding author: Yangseon Kim, Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea. Tel: +82-63-536-6712, 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 17, 2022; Revised: Nov 03, 2022; Accepted: Nov 12, 2022

Published Online: Sep 30, 2023


Pedi coccus acidilactici CACC 537 was isolated from canine feces and reported to have probiotic properties. We aimed to characterize the potential probiotic properties of this strain by functional genomic analysis. Complete genome sequencing of P. acidilactici CACC 537 was performed using a PacBio RSII and Illumina platform, and contained one circular chromosome (2.0 Mb) with a 42% G + C content. The sequences were annotation revealed 1,897 protein-coding sequences, 15 rRNAs, and 56 tRNAs. It was determined that P. acidilactici CACC 537 genome carries genes known to be involved in the immune system, defense mechanisms, restriction-modification (R-M), and the CRISPR system. CACC 537 was shown to be beneficial in preventing pathogen infection during the fermentation process, help host immunity, and maintain intestinal health. These results provide for a comprehensive understanding of P. acidilactici and the development of industrial probiotic feed additives that can help improve host immunity and intestinal health.

Keywords: Pediococcus acidilactici; Canine; Whole-genome sequencing

Lactic acid bacteria (LAB) are mostly used as probiotics in functional foods and feed additives [1]. Among them, Pediococcus sp. is used as a beneficial microorganism in the context of food and livestock microbiology, and it has been reported that P. acidilactici CACC 537 (KACC 8198BP) has acid and bile tolerance, intestinal adhesion activity, and antibacterial activity against livestock pathogens [2].

This study attempted to genetically determine the useful effects and functions of CACC537 using whole-genome sequencing. The complete genome of CACC 537 was sequenced using a PacBio RS II (Pacific Biosciences, Menlo Park, CA, USA) and Illumina (San Diego, CA, USA) platform with a SMRTbellTM template at Macrogen (Seoul, Korea), and the reads were assembled of the using HGAP version 3.0 [3]. The annotation of the sequence used automatic results from the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) and analyzing Rapid Annotations using Subsystems Technology (RAST) tools [4]. The complete genome of CACC537 consists of one circular chromosome with a total length of 2,035,984 bp and a DNA G + C content of 42.0%. it includes 1,897 protein-coding genes (CDSs) and 71 RNA genes (15 rRNA and 56 tRNA genes) (Table 1 and Fig. 1A). The 1,782 genes were categorized as functional proteins based on designations through the Clusters of Orthologous Groups (COGs) database. Most assigned CDSs were found to be involved in carbohydrate transport and metabolism; transcription; translation, ribosomal structure and biogenesis; replication, recombination and repair; and cell wall/membrane/envelope biogenesis (225, 146, 142, 107, and 104 genes, respectively) (Fig. 1B).

Table 1. Genome overview of Pediococcus acidilactici CACC 537
Feature Values
Genome size (bp) 2,035,984
No. of contigs 1
GC content 42.0 %
Protein-coding genes (CDSs) 1,897
rRNA 15
tRNA 56
Genbank Acession No. CP048019

bp, base pair.

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Fig. 1. Genome features of Pediococcus acidilactici CACC 537. (A) Circular genome maps of the P. acidilactici CACC537 chromosome. Circles from the outside to the center denote rRNA and tRNA genes, reverse strand CDSs, forward strand CDSs, GC skew, and GC content. (B) COG functional category annotation numbers on CACC 537 genome. CDS, coding sequences; GC, guanine cytosine; COG, clusters of orthologous groups.
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In the genome of strain CACC 537, the presence of ldhD, ldhL, pyk, eno, fbaA, pfk, and pgi, which are involved in lactic acid production as key genes of homo-fermentation in the Embden-Meyerhof-Parnas (EMP) pathway, was detected [5]. We also identified genes encoding lysozymes, chitinases, and proteases, commonly predicted as able to exert antibacterial functions against pathogens; and the fab gene cluster, in charge of producing fatty acids that can protect the intestinal mucosal from pathogens. Interestingly, the short-chain fatty acids (SCFA) produced as metabolic by-products play an important role in intestinal homeostasis and have been reported to be associated with immune enhancement and liver function improvement [68]. In addition, we identified a type II-A CRISPR/CRISPR-related (Cas) gene with two CRISPR (1 and 2) regions, and a CRISPR 9 region; and genes involved in immune and defense mechanisms, including some for restriction-modification (R-M) systems. This strain prevents fermentation failure due to bacterial phage and pathogen infection in the fermentation process, and has an intestinal function to help host immunity and maintain intestinal health [910] (Table 2).

Table 2. Predicted genes involved in probiotic potency in Pediococcus acidilactici CACC537
Predicted function Pediococcus acidilactici CACC 537
Predicted genes Products Gene position Length (bp)
Homolactic-fermentation related
ldhD D-Lactate dehydrolase 195437..196432 996
ldhL L-Lactate dehydrolase 940686..941657 972
c(1521565..1522485) 921
pyk Pyruvate kinase c(408957..410720) 1,764
eno Phosphopyruvate hydratase c(1111207..1112493) 1,287
1802875..1804197 1,323
fbaA Fructose-bisphosphate aldolase 730570..731433 864
pfk 6-Phosphofructokinase c(410797..411765) 969
c(552661..553572) 912
pgi Glucose-6-phosphate isomerase c(727794..729146) 1,353
Antimicrobial resistance-related
Bacteriolytic enzyme
- Lysozyme c(465359..466543) 1,185
- Chitinase 1707522..1708034 513
2026125..2027144 1,020
glup Rhomboid protease 125912..126601 690
Fatty acid biosynthesis (Clusters)
fabI Enoyl-(acyl-carrier-protein) reductase 187972..188730 759
accA,D,C Acetyl-CoA carboxylase 184990..187955 2,966
fabZ1 3-Hydroxyacyl-(acyl-carrier-protein) dehydratase 184563..184973 411
accB Acetyl-CoA carboxylase 184125..184550 426
fabF,G,D β-Ketoacyl-ACP synthase II, β-ketoacyl-ACP reductase, acyl-carrier protein 181121..184120 3,000
acpP Acyl carrier protein 180858..181094 237
fabH,Z2 β-Ketoacyl-ACP synthase III, β-hydroxyacyl-ACP dehydratase 179410..180831 1,422
Restriction-modification system
hsdR Type I site-specific deoxyribonuclease 1445338..1448211 2,874
hsdM Site-specific DNA-methyltransferase 1448232..1449824 1,593
hsdS Type I site-specific deoxyribonuclease 1449821..1453105 3,284
Immune system
cas9 CRISPR-associated endonuclease 1747125..1751225 4,101
cas1 CRISPR-associated endonuclease 1751443..1752348 906
cas2 CRISPR-associated endoribonuclease 1752326..1752631 306
yajC Immunogenic membrane protein c(647443..647826) 384
cfa Cyclopropane-fatty-acyl-phospholipid synthase 1113749..1114924 1,176
dacA Diadenylate cyclase 1814096..1814947 852
myh6 TNF receptor protein 1730618..1733290 2,673

bp, base pair; c, complement.

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This study on the complete genome sequence of P. acidilactici CACC 537 showed that it has potential probiotic effects, and thus may be useful for the development of health-promoting products.

Nucleotide sequence accession number

The complete genome of P. acidilactici CACC 537 has been deposited in the NCBI GenBank database under the accession number CP048019.

Competing interests

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

Funding sources

This research was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through the 2022 Technology Commercialization Support Project and Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (122037-02, 918002-4). This work was also supported by the INNOPOLIS FOUNDATION through the Science and Technology Project Opens the Future of the Region, funded by the Ministry of Science and ICT (2022-DD-UP-0333), and supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Korea (NIBR202322101).


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: Kim Y.

Data curation: Kim JA, Jang HJ.

Formal analysis: Kim JA.

Methodology: Kim JA, Son YK.

Software: Kim JA.

Validation: Kim JA, Kim DH.

Investigation: Kim Y.

Writing - original draft: Kim Y.

Writing - review & editing: Kim JA, Jang HJ, Kim DH, Son YK, Kim Y.

Ethics approval and consent to participate

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



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