ABSTRACT
Here, we report the draft genome sequence of Pediococcus acidilactici RTMP1 isolated from fecal samples of Speckled goats. This bacterium (scaffolds = 54; genome size = 1,973,216 bp; coding sequences = 1,870; N50 = 59,077; GC content = 42%) encodes for genes attributed to probiotic characteristics.
KEYWORDS: Pediococcus acidilactici, Speckled goats, genome assembly, probiotic activities
ANNOUNCEMENT
Pediococcus acidilactici is a lactic acid bacterium (LAB) that has presence in diverse habitats, including gastrointestinal systems and fermented foods (1). This bacterium has received a lot of interest due to its diversity and prospective uses in biotechnology and food preservation (2). Its resilience to acidic and bile conditions, along with its ability to produce antimicrobial compounds, makes it a promising candidate for probiotic applications in livestock animal health (3, 4). Therefore, studying the genome of this bacteria may help predict the genes responsible for the above-mentioned valuable traits.
We sequenced the genome of P. acidilactici strain RTMP1, isolated from goat fecal samples. A total of 20 fresh goat fecal samples were collected from the Small-Stock Division of the Agricultural Research Council, Animal Production Unit in Irene, Gauteng, South Africa (25°53′59.60″S, 28°12′51.60″E). Fecal collection was observed based on the protocol reviewed and approved by the Agricultural Research Council-Animal Production Institute Ethics Committee (APIEC24/04) and Tshwane University of Technology Animal Research Ethics Committee (AREC-010411-009). Bacterial cells were isolated through 10-fold serial dilution of each sample (1 g in 9 mL) in sterile 0.85% saline solution, and thereafter, plated on de Man, Rogosa Sharpe (MRS) agar, incubated anaerobically using an Anaerobic Gas Pack (Oxoid) for a period of 48 h at 37°C. After incubation, discrete colonies were sub-cultured onto MRS agar, before being streaked for pure culture. The pure culture in MRS broth was then stored in 50% (vol/vol) glycerol at −80°C.
The genome of RTMP1 was extracted from overnight culture in MRS broth using a Quick-DNA miniprep kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions. A NanoDrop (ThermoFisher Scientific, Carlsbad, CA, USA) was used to determine the concentration of extracted DNA. A sequencing library was prepared using the NEBNext Ultra II FS DNA library prep kit (New England Biolabs, Ipswich, MA) and sequenced on an Illumina NextSeq 550 platform with standard operating procedures. A total of 9,054,313 paired-end 2 × 150 bp reads generated were analyzed via KBase platform (5). The quality of the reads was evaluated using FastQC v0.11.5 (6), and sequence adaptors and low-quality reads were removed using Trimmomatic v0.36 (7). The genome was assembled de novo using SPAdes v3.13.0 (8) yielding 54 scaffolds with a coverage of 1,376.6×. The assembly produced a genome sequence of 1,973,216 bp long, with a G + C content of 42% and an N50 value of 59,077. Genome completeness and contamination were performed using CheckM v1.2.2 (9) and were 88.72% and 1.54%, respectively. Gene annotation was performed using the PGAP v6.3 (10) identifying 1,870 protein-coding genes, 50 tRNAs and 54 RNA as well as discovering probiotic genes involved in immunomodulation against pathogens, stress tolerance, acid tolerance, bile salt tolerance, adhesion to epithelial cells, and antioxidant production (Fig. 1 and Table 1), all potentially related to probiotic actions (11, 12). The genome was assigned to P. acidilactici via GTDB-Tk v2.3.2 (13) and had the pairwise ANI value of 99.15% average nucleotide identity (ANI) with P. acidilactici DSM 20284 (GCF_000146325.1), confirming its affiliation to the Pediococcus acidilactici taxonomic group. In each step, default parameters were used except where otherwise noted.
Fig 1.
Circular representation of P. acidilactici RTMP1 genome, highlighting annotated features, such as gene distribution, CDS, tRNA, tmRNA, and GC Content. Figure created using ProkSee (https://proksee.ca).
TABLE 1.
Genes potentially related to probiotic functions of Pediococcus cidilactici RTMP1a
| Gene | Function | Locus tag | NCBI protein accession no. | Product |
|---|---|---|---|---|
| dltD | Immunomodulation | ACSR7A_00875 | MGL3993017.1 | D-alanyl-lipoteichoic acid biosynthesis protein DltD |
| dltC | ACSR7A_00880 | MGL3993018.1 | D-alanine—poly (phosphoribitol) ligase subunit DltC | |
| dltB | ACSR7A_00885 | MGL3993019.1 | D-alanyl-lipoteichoic acid biosynthesis protein DltB | |
| dltA | ACSR7A_00890 | MGL3993020.1 | D-alanine—poly(phosphoribitol) ligase subunit DltA | |
| clpB | Stress tolerance | ACSR7A_01290 | MGL3993100.1 | ATP-dependent chaperone clpB |
| groES | ACSR7A_06825 | MGL3994183.1 | Co-chaperone GroES | |
| hslV | ACSR7A_01805 | MGL3993202.1 | ATP-dependent protease subunit hslV | |
| hslU | ACSR7A_01810 | MGL3993203.1 | ATP-dependent protease ATPase subunit hslU | |
| dnaJ | ACSR7A_02235 | MGL3993287.1 | Molecular chaperone dnaJ | |
| dnaK | ACSR7A_02240 | MGL3993288.1 | Molecular chaperone dnaK | |
| hrcA | ACSR7A_02250 | MGL3993290.1 | Heat inducible transcriptional repressor hrcA | |
| clpP | ACSR7A_06655 | MGL3994150.1 | ATP-dependent Clp endopeptidase proteolytic subunit ClpP | |
| clpX | ACSR7A_07790 | MGL3994365.1 | ATP-dependent Clp protease ATP-binding subunit ClpX | |
| pyk | Acid tolerance | ACSR7A_01310 | MGL3993104.1 | pyruvate kinase |
| atpD | ACSR7A_04685 | MGL3993769.1 | F0F1 ATP synthase subunit beta | |
| atpA | ACSR7A_04695 | MGL3993771.1 | F0F1 ATP synthase subunit alpha | |
| atpH | ACSR7A_04700 | MGL3993772.1 | ATP synthase F1 subunit delta | |
| atpF | ACSR7A_04705 | MGL3993773.1 | F0F1 ATP synthase subunit B | |
| atpE | ACSR7A_04710 | MGL3993774.1 | F0F1 ATP synthase subunit C | |
| atpB | ACSR7A_04715 | MGL3993775.1 | F0F1 ATP synthase subunit A | |
| rplI | Bile salt tolerance | ACSR7A_00285 | MGL3992920.1 | Large ribosomal protein L9 |
| rpsU | ACSR7A_01225 | MGL3993087.1 | Small ribosomal protein S21 | |
| rpsA | ACSR7A_01370 | MGL3993116.1 | small ribosomal protein S1 | |
| rpsB | ACSR7A_02335 | MGL3993307.1 | Small ribosomal protein S2 | |
| rplS | ACSR7A_02465 | MGL3993333.1 | Large ribosomal protein L19 | |
| rpsP | ACSR7A_02490 | MGL3993338.1 | Small ribosomal protein S16 | |
| rpmB | ACSR7A_02545 | MGL3993349.1 | Large ribosomal protein L28 | |
| rpmA | ACSR7A_02665 | MGL3993373.1 | Large ribosomal protein L27 | |
| rplU | ACSR7A_02765 | MGL3993375.1 | Large ribosomal protein L21 | |
| glnA | ACSR7A_02715 | MGL3993382.1 | Type I glutamate—ammonia ligase | |
| rpmF | ACSR7A_02860 | MGL3993411.1 | Large ribosomal protein L32 | |
| rplT | ACSR7A_02910 | MGL3993421.1 | Large ribosomal protein L20 | |
| rpmI | ACSR7A_02915 | MGL3993422.1 | Large ribosomal protein L35 | |
| rpsD | ACSR7A_04580 | MGL3993749.1 | Small ribosomal protein S4 | |
| GNAT | ACSR7A_06575 | MGL3994134.1 | GNAT family N-acetyltransferase | |
| LPXTG | Adhesion | ACSR7A_01735 | MGL3993188.1 | LPXTG cell wall anchor domain-containing protein |
| lspA | ACSR7A_02035 | MGL3993248.1 | Signal peptidase II | |
| tpiA | ACSR7A_06625 | MGL3994144.1 | Triose-phosphate isomerase | |
| celB | ACSR7A_07315 | MGL3994279.1 | PTS cellobiose transporter subunit IIC | |
| tuf | ACSR7A_07780 | MGL3994363.1 | Elongation factor Tu | |
| trxA | Antioxidant | ACSR7A_00180 | MGL3992899.1 | Thioredoxin |
| msrB | ACSR7A_01870 | MGL3993215.1 | Peptide-methionine (R)-S-oxide reductase MsrB | |
| msrA | ACSR7A_01875 | MGL3993216.1 | Peptide-methionine (S)-S-oxide reductase MsrA | |
| nrdH | ACSR7A_05580 | MGL3993938.1 | Glutaredoxin-like protein NrdH | |
| trxB | ACSR7A_06705 | MGL3994159.1 | Thioredoxin-disulfide reductase |
NCBI, National Center for Biotechnolgy Information.
This genome offers a platform for future comprehensive comparative genomic analysis of Pediococcus species and understanding of deeper insights into functional annotation and evolutionary relationships.
ACKNOWLEDGMENTS
The authors would like to acknowledge the Tshwane University of Technology and the Agricultural Research Council (ARC) of South Africa for research platform. The authors are grateful to the Small Stock Section team of ARC-AP for goats animal welfare and assistance with fecal samples collection.
This research was supported by the Department of Agriculture of South Africa (grant number A148/API012403000048).
AFTER EPUB
[This article was published on 13 October 2025 with errors in the Acknowledgements and Data Availability statement. These production errors were corrected in the current version, posted on 10 November 2025.]
Contributor Information
Goitsemang Makete, Email: Makete@arc.agric.za.
Kazeem Adekunle Alayande, Email: jkadekunle2@gmail.com.
Tshifhiwa Paris Mamphogoro, Email: MamphogoroT@arc.agric.za.
Julie C. Dunning Hotopp, University of Maryland School of Medicine, Baltimore, Maryland, USA
DATA AVAILABILITY
This whole-genome shotgun sequencing project has been deposited at DDBJ/ENA/GenBank under the accession number JBPURR000000000. The version described in this paper is the first version. The SRA accession number is SRR34674031, the BioProject accession number is PRJNA1291987, and the BioSample accession number is SAMN49984124.
REFERENCES
- 1. Porto MCW, Kuniyoshi TM, Azevedo POS, Vitolo M, Oliveira RPS. 2017. Pediococcus spp.: an important genus of lactic acid bacteria and pediocin producers. Biotechnol Adv 35:361–374. doi: 10.1016/j.biotechadv.2017.03.004 [DOI] [PubMed] [Google Scholar]
- 2. Aziz T, Naveed M, Shabbir MA, Naseeb J, Sarwar A, Zhao L, Yang Z, Haiying C, Lin L, Shami A, Al-Asmari F. 2025. Genomic profiling of pediococcus acidilactici BCB1H and identification of its key features for biotechnological innovation, food technology and medicine. Sci Rep 15:6050. doi: 10.1038/s41598-025-90633-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Sachdeva A, Tomar T, Malik T, Bains A, Karnwal A. 2025. Exploring probiotics as a sustainable alternative to antimicrobial growth promoters: mechanisms and benefits in animal health. Front Sustain Food Syst 8:1523678. doi: 10.3389/fsufs.2024.1523678 [DOI] [Google Scholar]
- 4. Olajugbagbe TE, Elugbadebo OE, Omafuvbe BO. 2020. Probiotic potentials of Pediococuss acidilactici isolated from wara; A Nigerian unripened soft cheese. Heliyon 6:e04889. doi: 10.1016/j.heliyon.2020.e04889 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, et al. 2018. KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 36:566–569. doi: 10.1038/nbt.4163 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Cambridge, United Kingdom: Babraham Institute. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. [Google Scholar]
- 7. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Oh YJ, Kim S-A, Yang SH, Kim DH, Cheng Y-Y, Kang JI, Lee SY, Han N 2. 2022. Integrated genome-based assessment of safety and probiotic characteristics of Lactiplantibacillus plantarum PMO 08 isolated from kimchi. PLoS One 17:e0273986. doi: 10.1371/journal.pone.0273986 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Kandasamy S, Lee K-H, Yoo J, Yun J, Kang HB, Kim JE, Oh M-H, Ham J-S. 2024. Whole genome sequencing of Lacticaseibacillus casei KACC92338 strain with strong antioxidant activity, reveals genes and gene clusters of probiotic and antimicrobial potential. Front Microbiol 15:1458221. doi: 10.3389/fmicb.2024.1458221 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2022. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38:5315–5316. doi: 10.1093/bioinformatics/btac672 [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This whole-genome shotgun sequencing project has been deposited at DDBJ/ENA/GenBank under the accession number JBPURR000000000. The version described in this paper is the first version. The SRA accession number is SRR34674031, the BioProject accession number is PRJNA1291987, and the BioSample accession number is SAMN49984124.