Open access
6 January 2022

Draft Genome Sequences of Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, Isolated from a Beetroot Product


Lactic acid bacteria (LAB) participate in fermentation processes and have probiotic potential. The genomes of three LAB strains, Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei subsp. paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, isolated from a beetroot product, were characterized. The results contribute to our understanding of the beneficial properties of LAB.


The popularity of vegetarianism/veganism has led to a growing demand for nondairy probiotic products (1). Thus, broadening of the choice of commercially available products with probiotic potential is of high importance (2). Consuming fresh and fermented fruits and vegetables (including legumes) offers beneficial effects, as they are rich in carbohydrates, vitamins, antioxidants, and minerals and free from dairy allergens (1, 2). Probiotic lactic acid bacteria (LAB) help to improve the microbiological and keeping qualities of fermented food products (1, 2). Lacticaseibacillus rhamnosus and Lacticaseibacillus paracasei play an important role in fermentation processes and are among the most significant probiotic organisms (35). Until now, Lentilactobacillus otakiensis was described only from a traditional Japanese pickle (6, 7). Identification and characterization of strains found in various food products may help us to understand the background of their probiotic properties.
Here, we present the draft genome sequence of L. rhamnosus cek-R1, L. paracasei subsp. paracasei cek-R2, and L. otakiensis cek-R3. A beetroot product (beetroot prepared with sugar and vinegar and seasoned with horseradish) was purchased from a chemical-free farm in Dinnyés, Hungary. The sample was sliced and incubated overnight in brain heart infusion broth (Liofilchem, Italy) at 37°C; then, ∼20 μl was plated onto de Man-Rogosa-Sharpe (MRS) agar plates (Liofilchem) and incubated at 37°C for 2 days. Distinct colonies were identified as L. otakiensis, L. rhamnosus, and L. paracasei by matrix-assisted laser desorption ionization–time-of-flight (MALDI-TOF) mass spectrometry using a Microflex LT instrument (Bruker Daltonics, Germany). Isolates were stored at −20°C in tryptone soya broth (Liofilchem) containing 15% glycerol. For whole-genome sequencing, isolates were grown in MRS broth at 37°C for 4 to 5 days, and the genomic DNA was extracted using the Quick-DNA fungi/bacterial kit (Zymo Research, USA), according to the manufacturer’s protocol. The Illumina Nextera XT DNA library preparation kit was used to prepare Illumina-specific libraries (8). Genome sequencing was performed using an Illumina NextSeq 500 sequencer (USA). Quality check of the single-end reads was performed using FastQC v.0.11.9 (, and low-quality sequences and adaptors were removed using Cutadapt v.3.4 and fastp (9, 10). Then, the reads were corrected using Bloocoo (11). Default parameters were used unless otherwise specified. The quality-filtered reads were assembled de novo using SPAdes v.3.15.3, with error correction turned off, and MEGAHIT (12, 13), with automatic k-mer size selection. The assemblies were merged using GAM-NGS (14). The assembly quality was checked using BUSCO v.5.2.2 (15). Prokka (rapid prokaryotic genome annotation) was used for functional annotation (16). Information on the quality and genome features of the de novo assembly is presented in Table 1. Antimicrobial resistance (AMR) genes were predicted using the CARD Resistance Gene Identifier tool; AMR genes were not detectable with perfect or strict matches in our strains (17). Concatenated single-copy gene clusters of the novel and GenBank reference genomes were analyzed using Anvi’o (18), and the average nucleotide identity was calculated using pyANI (Fig. 1B) (19). The phylogenetic relationships were reconstructed using FastTree (Fig. 1A) (20). Both the pyANI and phylogenetic analyses suggested that the genomes described here grouped together and were closely related to reference sequences of the same LAB species.
FIG 1 (A) Approximate maximum likelihood phylogenetic tree of core genomes retrieved from representative Lacticaseibacillus sp. and Lentilactobacillus sp. strains. The phylogenomic analysis is based on the concatenated sequence alignment of protein sequences for the 341 single-copy core genes. All branches had support values of >0.98. The sequences identified in this study are shown in red. The members of Lacticaseibacillus are indicated by the blue branches; the Lentilactobacillus sp. strains are shown in green. (B) Heat map of the average nucleotide identities (ANIs) of representative Lacticaseibacillus sp. and Lentilactobacillus sp. strains. The cladogram above and left of the heat map represents the hierarchical clustering of strains as calculated by the pheatmap R package using the pairwise ANI values.
TABLE 1 Quality information and genome features of the de novo assembled strains Lentilactobacillus otakiensis cek-R3, Lacticaseibacillus rhamnosus cek-R1, and Lacticaseibacillus paracasei subsp. paracasei cek-R2, originating from beetroota
StrainTotal no. of readsGenBank accession no.SRA accession no.Genome coverage (×)No. of contigsNo. of coding sequencesNo. ofGenome size (bp)N50 (bp)GC content (%)BUSCOs (%)% ANI (reference strain)
cek-R17,250,258JAIPUO000000000SRS10102441277832,76241542,968,173137,35346.6599.297.2 (L. rhamnosus)
cek-R26,996,786JAIPUN000000000SRS101024422451662,88331513,033,51253,52146.1899.298.4 (L. paracasei)
cek-R34,084,504JAIPUM000000000SRS10102443219522,37031572,429,274137,31442.4199.299.8 (L. otakiensis)
tmRNAs, transfer-messenger RNAs; ANI, average nucleotide identity; BUSCOs, Benchmarking Universal Single-Copy Orthologs.
The features identified in the genomes of the described strains will assist us in better understanding their beneficial properties.

Data availability.

The draft genome sequences of Lacticaseibacillus sp. strains cek-R1 and cek-R2 and Lentilactobacillus sp. strain cek-R3 have been deposited in GenBank under accession numbers JAIPUO000000000.1, JAIPUN000000000, and JAIPUM000000000, respectively. The raw reads can be found in the SRA under BioProject accession number PRJNA761968.


E.K. was supported by the New National Excellence Program of the Ministry for Innovation and Technology (ÚNKP-20-4-I-DE-277) through funds provided by the National Research, Development, and Innovation Fund. The work is supported by project GINOP-2.3.4-15-2020-00008. The project is cofinanced by the European Union and the European Regional Development Fund.


Malik M, Bora J, Sharma V. 2019. Growth studies of potentially probiotic lactic acid bacteria (Lactobacillus plantarum, Lactobacillus acidophilus, and Lactobacillus casei) in carrot and beetroot juice substrates. J Food Process Preserv 43:e14214.
Panghal A, Virkar K, Kumar V, Dhull SB, Gat Y, Chhikara N. 2017. Development of probiotic beetroot drink. Curr Res Nutr Food Sci 5:257–262.
Kingston JJ, Radhika M, Roshini PT, Raksha MA, Murali HS, Batra HV. 2010. Molecular characterization of lactic acid bacteria recovered from natural fermentation of beet root and carrot Kanji. Indian J Microbiol 50:292–298.
Vanderhoof JA, Whitney DB, Antonson DL, Hanner TL, Lupo JV, Young RJ. 1999. Lactobacillus GG in the prevention of antibiotic-associated diarrhea in children. J Pediatr 135:564–568.
Balzaretti S, Taverniti V, Rondini G, Marcolegio G, Minuzzo M, Remagni MC, Fiore W, Arioli S, Guglielmetti S. 2015. The vaginal isolate Lactobacillus paracasei LPC-S01 (DSM 26760) is suitable for oral administration. Front Microbiol 6:952.
Watanabe K, Fujimoto J, Tomii Y, Sasamoto M, Makino H, Kudo Y, Okada S. 2009. Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 59:754–760.
Doi K, Mori K, Mutaguchi Y, Tashiro K, Fujino Y, Ohmori T, Kuhara S, Ohshima T. 2013. Draft genome sequence of d-branched-chain amino acid producer Lactobacillus otakiensis JCM 15040T, isolated from a traditional Japanese pickle. Genome Announc 1:e00546-13.
Fehér E, Jakab S, Bali K, Kaszab E, Nagy B, Ihász K, Bálint Á, Palya V, Bányai K. 2021. Genomic epidemiology and evolution of duck hepatitis A virus. Viruses 13:1592.
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12.
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890.
Benoit G, Lavenier D, Lemaitre C, Rizk G. 2015. Bloocoo, a memory efficient read corrector.
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70:e102.
Li D, Liu CM, Luo R, Sadakane K, Lam TW. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676.
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A. 2013. GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics 14:S6.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FSL, Wright GD, McArthur AG. 2017. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 45:D566–D573.
Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD. 2021. Community-led, integrated, reproducible multi-omics with anvi'o. Nat Microbiol 6:3–6.
Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. 2016. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12–24.
Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650.

Information & Contributors


Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 11Number 120 January 2022
eLocator: e00921-21
Editor: David A. Baltrus, University of Arizona
PubMed: 34989623


Received: 16 September 2021
Accepted: 30 November 2021
Published online: 6 January 2022



Veterinary Medical Research Institute, Budapest, Hungary
Levente Laczkó
Department of Metagenomics, University of Debrecen, Debrecen, Hungary
MTA-DE “Lendület” Evolutionary Phylogenomics Research Group, Debrecen, Hungary
Krisztina Bali
Veterinary Medical Research Institute, Budapest, Hungary
Eszter Fidrus
Department of Metagenomics, University of Debrecen, Debrecen, Hungary
Krisztián Bányai
Veterinary Medical Research Institute, Budapest, Hungary
Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
Gábor Kardos
Department of Metagenomics, University of Debrecen, Debrecen, Hungary


David A. Baltrus
University of Arizona


The authors declare no conflict of interest.

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

View options



Get Access

Buy Article
Microbiology Resource Announcements Vol.11 • Issue 1 • ASM Journals Pay Per View, PPV 25
Journal Subscription
Microbiology Resource Announcements
ASM members can purchase subscriptions to journals.
Join or renew

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy