Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Abstract

Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial against specific food processes. To augment our genomic understanding of L.paraplantarum and uncover metabolic differences and lifestyle adaptations between strains (DSM10667, L-ZS9, AS-7) to better utilize these species in food bioprocesses. In-silico genomic approach applied using JGI’s IMG/MER, and PATRIC to compare DSM10667, L-ZS9 and AS-7 genomes. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software respectively. BRIG was used to identify alignments of strains to each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and amino-acid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14 and 3.01 M bp, respectively. Unique genes were found to predict evolutionary adaptation of strains against their corresponding micro-niche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9 while dextran-sucrase encoding gene was unique to beer contaminant DSM10667. All three strains predicted to carry plnAEFJ operon for plantaricin biosynthesis and AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region still showing the plasticity of the genome. Genome analysis predicted isolation sources might potentially affect the metabolic capabilities of strains part of adaptation of the strains to their habitats. Our findings put forth new insights into the genomics of L.paraplantarum for future studies and uncovering potential strain manipulation elements for better use in commercial processing environment.

Keywords

• Lactiplantibacillus paraplantarum
• comparative genomics
• bacteriocin
• prophage
• carbohydrate
• adaptation

References

1. [1]. H. Nishioka, T. Ohno, H. Iwahashi, and M. Horie, "Diversity of Lactic Acid Bacteria Involved in the Fermentation of Awa-bancha," Microbes Environ, vol. 36, 2021. [Online]. Available: https://doi.org/10.1264/jsme2.ME21029.
2. [2]. J. Zheng, S. Wittouck, E. Salvetti, 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., vol. 70, 2020. [Online]. Available: https://doi.org/10.1099/ijsem.0.004107.
3. [3]. Reale, T. Zotta, R. G. Ianniello, et al., "Selection criteria of lactic acid bacteria to be used as starter for sweet and salty leavened baked products," LWT, vol. 133, p. 110092, 2020. [Online]. Available: https://doi.org/10.1016/j.lwt.2020.110092.
4. [4]. S. Akbulut, M. O. Baltaci, G. Adiguzel, and A. Adiguzel, "Identification and biotechnological characterization of Lactic Acid Bacteria Isolated from White Cheese Samples," Research Square, 2021.
5. [5]. S. Nishida, M. Ishii, Y. Nishiyama, et al., "Lactobacillus paraplantarum 11-1 Isolated from Rice Bran Pickles Activated Innate Immunity and Improved Survival in a Silkworm Bacterial Infection Model," Front. Microbiol., vol. 8, 2017.
6. [6]. W. J. Park, K. H. Lee, J. M. Lee, et al., "Characterization of pC7 from Lactobacillus paraplantarum C7 derived from Kimchi and development of lactic acid bacteria--Escherichia coli shuttle vector," Plasmid, vol. 52, pp. 84–88, 2004. [Online]. Available: https://doi.org/10.1016/j.plasmid.2004.05.001.
7. [7]. W. E. Hussein, E. Huang, I. Ozturk, and A. E. Yousef, "Draft Genome Sequence of Lactobacillus paraplantarum OSY-TC318, a Producer of the Novel Lantibiotic Paraplantaracin TC318," Microbiol. Resour. Announc., vol. 8, p. e00274-19, 2019. [Online]. Available: https://doi.org/10.1128/MRA.00274-19.
8. [8]. K. Sharma, N. Sharma, S. Handa, and S. Pathania, "Purification and characterization of novel exopolysaccharides produced from Lactobacillus paraplantarum KM1 isolated from human milk and its cytotoxicity," J. Genet. Eng. Biotechnol., vol. 18, p. 56, 2020. [Online]. Available: https://doi.org/10.1186/s43141-020-00063-5.

9. [9]. S. M. Devi, N. K. Kurrey, and P. M. Halami, "In vitro anti-inflammatory activity among probiotic Lactobacillus species isolated from fermented foods," J. Funct. Foods, vol. 47, pp. 19–27, 2018. [Online]. Available: https://doi.org/10.1016/j.jff.2018.05.036.
10. [10]. R. J. da Costa, F. L. S. Voloski, R. G. Mondadori, et al., "Preservation of Meat Products with Bacteriocins Produced by Lactic Acid Bacteria Isolated from Meat," J. Food Qual., vol. 2019, p. e4726510, 2019. [Online]. Available: https://doi.org/10.1155/2019/4726510.
11. [11]. L. Liu and P. Li, "Complete genome sequence of Lactobacillus paraplantarum L-ZS9, a probiotic starter producing class II bacteriocins," J. Biotechnol., vol. 222, pp. 15–16, 2016. [Online]. Available: https://doi.org/10.1016/j.jbiotec.2016.02.003.
12. [12]. "IMG," [Online]. Available: https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2922794270. Accessed: Sep. 4, 2023.
13. [13]. L. C. Reimer, A. Vetcininova, J. S. Carbasse, et al., "Bac Dive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis," Nucleic Acids Res., vol. 47, pp. D631–D636, 2019. [Online]. Available: https://doi.org/10.1093/nar/gky879.
14. [14]. H. Nordberg, M. Cantor, S. Dusheyko, et al., "The genome portal of the Department of Energy Joint Genome Institute: 2014 updates," Nucleic Acids Res., vol. 42, pp. D26-31, 2014. [Online]. Available: https://doi.org/10.1093/nar/gkt1069.
15. [15]. J.-Y. Chun, W.-J. Jeong, J.-S. Kim, et al., "Hydrolysis of Isoflavone Glucosides in Soymilk Fermented with Single or Mixed Cultures of Lactobacillus paraplantarum KM, Weissella sp. 33, and Enterococcus faecium 35 Isolated from Humans," J. Microbiol. Biotechnol., vol. 18, pp. 573–578, 2008.
16. [16]. R. Kant, J. Blom, A. Palva, et al., "Comparative genomics of Lactobacillus," Microb. Biotechnol., vol. 4, pp. 323–332, 2011. [Online]. Available: https://doi.org/10.1111/j.1751-7915.2010.00215.
17. [17]. M. Schmid, J. Muri, D. Melidis, et al., "Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level," Front. Microbiol., vol. 9, p. 63, 2018. [Online]. Available: https://doi.org/10.3389/fmicb.2018.00063.
18. [18]. S. Wuyts, C. N. Allonsius, S. Wittouck, et al., "Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group," Microb. Genomics, vol. 5, p. e000286, 2019. [Online]. Available: https://doi.org/10.1099/mgen.0.000286.
19. [19]. M. C. Curk, J. C. Hubert, and F. Bringel, "Lactobacillus paraplantarum sp. nov., a new species related to Lactobacillus plantarum," Int. J. Syst. Bacteriol., vol. 46, pp. 595–598, 1996. [Online]. Available: https://doi.org/10.1099/00207713-46-2-595.
20. [20]. S. Mukherjee, D. Stamatis, J. Bertsch, et al., "Genomes OnLine Database (GOLD) v.8: overview and updates," Nucleic Acids Res., vol. 49, pp. D723–D733, 2021. [Online]. Available: https://doi.org/10.1093/nar/gkaa983.
21. [21]. N.-F. Alikhan, N. Petty, N. Ben Zakour, and S. Beatson, "BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons," BMC Genomics, vol. 12, p. 402, 2011. [Online]. Available: https://doi.org/10.1186/1471-2164-12-402.
22. [22]. Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, "A greedy algorithm for aligning DNA sequences," J. Comput. Biol. J. Comput. Mol. Cell Biol., vol. 7, pp. 203–214, 2000. [Online]. Available: https://doi.org/10.1089/10665270050081478.
23. [23]. R. Wattam, D. Abraham, O. Dalay, et al., "PATRIC, the bacterial bioinformatics database and analysis resource," Nucleic Acids Res., vol. 42, pp. D581–D591, 2014.
24. [24]. de Jong, S. A. F. T. van Hijum, J. J. E. Bijlsma, et al., "BAGEL: a web-based bacteriocin genome mining tool," Nucleic Acids Res., vol. 34, pp. W273–W279, 2006. [Online]. Available: https://doi.org/10.1093/nar/gkl237.
25. [25]. J. Zhang and T. L. Madden, "PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation," Genome Res., vol. 7, pp. 649–656, 1997. [Online]. Available: https://doi.org/10.1101/gr.7.6.649.
26. [26]. D. Arndt, J. R. Grant, A. Marcu, et al., "PHASTER: a better, faster version of the PHAST phage search tool," Nucleic Acids Res., vol. 44, pp. W16-21, 2016. [Online]. Available: https://doi.org/10.1093/nar/gkw387.
27. [27]. G. Marçais, A. L. Delcher, A. M. Phillippy, et al., "MUMmer4: A fast and versatile genome alignment system," PLOS Comput. Biol., vol. 14, p. e1005944, 2018. [Online]. Available: https://doi.org/10.1371/journal.pcbi.1005944.
28. [28]. I.-M. A. Chen, K. Chu, K. Palaniappan, et al., "The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities," Nucleic Acids Res., vol. 49, pp. D751–D763, 2021. [Online]. Available: https://doi.org/10.1093/nar/gkaa939.
29. [29]. D. Couvin, A. Bernheim, C. Toffano-Nioche, et al., "CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins," Nucleic Acids Res., vol. 46, pp. W246–W251, 2018. [Online]. Available: https://doi.org/10.1093/nar/gky425.
30. [30]. H. Zhang, T. Yohe, L. Huang, et al., "dbCAN2: a meta server for automated carbohydrate-active enzyme annotation," Nucleic Acids Res., vol. 46, pp. W95–W101, 2018. [Online]. Available: https://doi.org/10.1093/nar/gky418.
31. [31]. S. Mukherjee, R. Seshadri, N. J. Varghese, et al., "1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life," Nat. Biotechnol., vol. 35, pp. 676–683, 2017. [Online]. Available: https://doi.org/10.1038/nbt.3886.
32. [32]. W. E. Hussein, E. Huang, I. Ozturk, et al., "Genome-Guided Mass Spectrometry Expedited the Discovery of Paraplantaricin TC318, a Lantibiotic Produced by Lactobacillus paraplantarum Strain Isolated From Cheese," Front. Microbiol., vol. 11, p. 1381, 2020. [Online]. Available: https://doi.org/10.3389/fmicb.2020.01381.
33. [33]. S.-C. Yang, C.-H. Lin, C. T. Sung, and J.-Y. Fang, "Antibacterial activities of bacteriocins: application in foods and pharmaceuticals," Front. Microbiol., vol. 5, 2014.
34. [34]. E. Evanovich, P. J. de Souza Mendonça Mattos, and J. F. Guerreiro, "Comparative Genomic Analysis of Lactobacillus plantarum: An Overview," Int. J. Genomics, vol. 2019, p. e4973214, 2019. [Online].
35. [35]. Al-Farga A, Abed S. Production of dextrans and their applications in human health and nutrition– Review. Eur Acad Res 29. (2016) [36]. “Type Strain Genome Server,” Dsmz.de, 2019. https://tygs.dsmz.de/ (accessed Aug. 07, 2023).