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Yılmaz, B.; Punia, S.; Echegaray, N.; Suri, S.; Tomasevic, I.; Lorenzo, J.M.; Melekoglu, E.; Rocha, J.M.F.; Ozogul, F. Gene Sequencing for Lactiplantibacillus plantarum. Encyclopedia. Available online: https://encyclopedia.pub/entry/22074 (accessed on 18 January 2025).
Yılmaz B, Punia S, Echegaray N, Suri S, Tomasevic I, Lorenzo JM, et al. Gene Sequencing for Lactiplantibacillus plantarum. Encyclopedia. Available at: https://encyclopedia.pub/entry/22074. Accessed January 18, 2025.
Yılmaz, Birsen, Sneh Punia, Noemí Echegaray, Shweta Suri, Igor Tomasevic, Jose Manuel Lorenzo, Ebru Melekoglu, João Miguel Ferreira Rocha, Fatih Ozogul. "Gene Sequencing for Lactiplantibacillus plantarum" Encyclopedia, https://encyclopedia.pub/entry/22074 (accessed January 18, 2025).
Yılmaz, B., Punia, S., Echegaray, N., Suri, S., Tomasevic, I., Lorenzo, J.M., Melekoglu, E., Rocha, J.M.F., & Ozogul, F. (2022, April 21). Gene Sequencing for Lactiplantibacillus plantarum. In Encyclopedia. https://encyclopedia.pub/entry/22074
Yılmaz, Birsen, et al. "Gene Sequencing for Lactiplantibacillus plantarum." Encyclopedia. Web. 21 April, 2022.
Gene Sequencing for Lactiplantibacillus plantarum
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This entry is adapted from the peer-reviewed paper 10.3390/microorganisms10040826

Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is one of the Gram-positive lactic acid bacteria (LAB) species. Lb. plantarum has high ecological and metabolic adaptability that exists widely in a range of habitats including fermented dairy products, sourdoughs, fruits, vegetables, cereals, meat, fish, and the mammalian gastrointestinal tract.

Lactiplantibacillus plantarum lactic acid bacteria fermented food

1. Introduction

Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is one of the Gram-positive lactic acid bacteria (LAB) species [1]. Lb. plantarum has high ecological and metabolic adaptability that exists widely in a range of habitats including fermented dairy products, sourdoughs, fruits, vegetables, cereals, meat, fish, and the mammalian gastrointestinal tract [2]. In the production of various fermented foods, Lb. plantarum has been widely used as a starter culture that improves the flavor, texture and organoleptic properties of food products [3]. It also provides the functional properties of the fermented foods by producing a variety of bioactive components, including exopolysaccharides, γ-aminobutyric acid, riboflavin, folic acid, and vitamin B12 [4][5][6]. Moreover, Lb. plantarum is one of the most used bacterial strains in food processing and preservation as a food preservative through the production of diverse and potent bacteriocins (class I and II) and organic acid [7][8]. In particular, bacteriocins have a broad antimicrobial activity spectrum against Gram-positive and Gram-negative bacteria [9]. Lb. plantarum has a qualified presumption of safety (QPS) from the European Food Safety Authorities (EFSA) and is “generally recognized as safe” (GRAS) status by the United States Food and Drug Administration (US FDA) [10]. Since most of the LAB species are known as GRAS and QPS, bacteriocins are expected to be safe to use in the food industry as bio-preservatives [11][12].
It has greatly hastened the discovery of new strains of interest in the food industry and biotechnology since probiotic phenotypes may be traced back to specific genes and genetic clusters [13]. The whole-genome sequencing tries to explain genomic mapping of Lactobacillus species, isolated from different fermented foods. The characterisation of bacteriocin and the identification of probiotic genes can be explained through the studies. According to the genome sequence analysis, no pathogenic or antibiotic resistance genes were identified in Lb. plantarum. However, it has been reported that the Lb. plantarum genome (varies from 3.0 to 3.3 Mb) is greater than the other LAB species [14][15].

2. Genomic Mapping and Gene Locations of Lactiplantibacillus plantarum

Lb. plantarum is one of the promising LAB species, which is extensively utilized in the food industry for its use as a probiotic and starter culture [16]. Owing to its vast history of safe application in human foods, most LAB species, especially Lb. plantarum, are incorporated in the QPS recommendations of the European Food Safety Authority [17][18].
As per the literature, the Lb. plantarum genome (3.3 Mb) is greater than the distinctive genome of other LAB species (2–2.7 Mb). The larger genome size of Lb. plantarum advocates a very high level of genetic diversity within the species, which is attributed to this species’ nomadic life, inhabiting a wide variety of habitats and exhibiting great metabolic diversity [19][20][21]. Due to the high intraspecies diversity, it is difficult to classify the strains of Lb. plantarum based on simple characteristic traits. Previous studies of comparative genomic analysis have repetitively confirmed the progression of Lb. plantarum is not associated with the source of isolation or the geographic location of the strains belonging to this species [19]. Nonetheless, alterations in some gene clusters were found among Lb. plantarum strains. A comparison of 23 strains of Lb. plantarum showed that they evolved to comprise interspaced short palindromic repeats, antimicrobial action, and detoxification activity [22]. Six strains of Lb. plantarum were studied, and a significant difference was found in prophages, transposase, IS elements, and plantaricin biosynthesis genes among the strains. Furthermore, a high variation was observed in capsular plus extracellular polysaccharide biosynthesis genes [23].
A more recent study described the genomic properties of the Lb. plantarum strain UTNGt2 was obtained from wild copoazu (Theobroma grandiflorum), also known as white cacao. They also studied the variation in the genes of Lb. plantarum UTNGt2 strain through diverse hypervariable CRISPR (clustered regularly interspaced short palindromic repeats)/Cas systems. Based on the results of gene prediction and annotation, 9.4% of proteins were observed to be involved in carbohydrate transport as well as metabolism, 8.46% were involved in transcription, 2.36% were involved in defence mechanisms, and 0.5% carried out secondary metabolite biosynthesis, transport, and catabolism, whereas the remaining 25.11% had an unknown action. The genome study reveals the occurrence of genes engaged in riboflavin and folic acid production. Besides, the presence of CRISPR/Cas genes, phage sequences, the nonexistence of acquired antibiotic resistance genes, pathogenicity, and virulence factors indicated that the UTNGt2 is a safe strain. Its high antibacterial activity is associated with the existence of two bacteriocin clusters (class IIc), the sactipeptide class (contig 4) and the plantaricin E class (contig 22). The research demonstrates that UTNGt2 is a non-pathogenic, nonvirulent strain and can be used as a probiotic in food applications [24]. Similarly, the characterization of Lb. plantarum R23 and its bacteriocin were conducted. The genome sequence of Lb. plantarum was done by whole-genome sequencing (WGS). No pathogenic or antibiotic resistance genes were identified in Lb. plantarum. Four proteins that are 100% identical to Class II bacteriocins (Plantaricin E, Plantaricin F, Pediocin PA1 (Pediocin AcH), and Coagulin A) were detected through WGS analysis. The small (<6.5 kDa) R23 bacteriocin was observed to be stable at varying pH values (range 2–8), temperature (4–100 °C), detergents (all excluding Triton X100 as well as Triton X114 at 0.01 g/mL), and enzymes (catalase and α-amylase). In addition, they do not adsorb to producer cells, have a bacteriostatic mode of action, and their maximum activity (12,800 AU/mL) against the two Listeria monocytogenes strains is between 15–21 h of Lb. plantarum R23 growth. This research indicated that Lb. plantarum R23 is safe and promising as a bio-conservative culture because it produces stable bacteriocins [25].
Likewise, a group of researchers drafted the genomic sequence of Lb. plantarum L125. The entire genome of Lb. plantarum L125 comprises 3,354,135 bp, has a GC content of 44.34%, contains prophage regions, and does not contain CRISPR arrays. The 3220 predicted genes comprised protein-coding sequences (3024), pseudogenes (126), tRNA genes (62), rRNA genes (4), and ncRNAs (4). Lb. plantarum L125, usually isolated from meat-based foodstuffs, adapts to different niches, as indicated by the fact that 88 of its genes are mapped to the KEGG microbial metabolism in various environmental pathways. Lb. plantarum strains can colonize various habitats, including the human gastrointestinal tract, vegetables, meat, fish, dairy products, and other fermented foodstuffs (Figure 1). This kind of nomadic life of Lb. plantarum is reflected in the vast genetic diversity of the Lb. plantarum strain [13].
Figure 1. The functionality of Lb. plantarum strains.
In a recent study, Lb. plantarum X7021 was isolated from the Chinese fermented stinky tofu. To examine the applicability of this strain in the food industry, researchers investigated genomic and metabolic properties using comparative genomics as well as transcriptional assays. The results show that Lb. plantarum X7021 is safe for application in food. Lb. plantarum X7021 was found to have 25 complete transporters of the phosphotransferase system and a strong proteolytic system so that it is adaptable to different foods [26]. In another study, the genomic changes in the probiotic Lb. plantarum P8 was studied in humans and rats. Experiments with the oral ingestion of P8 were carried out. During the experiment, the dynamics of P8 frequency in feces was monitored by qPCR. The amount of P8 in the feces was high during the period of use and decreased when the use was stopped. However, after a few days in both human and rat experiments, a slight increase or stable level of P8 in the fecal sample was observed, indicating that P8 may be temporarily widespread in the human and rat gastrointestinal tract [27]. A large-scale comparative genomic study of 455 Lb. plantarum genomes were conducted. Animal and dairy isolates showed significant deviations in phylogenetic distribution. The research revealed that dairy as well animal isolates have a number of environment-specific genes [28].

3. Gene Sequencing for Lactiplantibacillus plantarum

Around 560 Lb. plantarum genomes are available in the NCBI repository, 135 of which have been completed [29]. As per the past studies, the genome of Lb. plantarum strains is one of the largest genomes within the Lactobacillus group, with a GC content of approximately 44%. In addition, the number of coding sequences (CDS) is in the range of 1964 to 3526 for Lb. plantarum WHE92 and Lb. plantarum SRCM101258, respectively [30]. The foremost Lb. plantarum strain (WCFS1) was fully sequenced in 2003 and isolated from the saliva of human beings [31]. Extensive genome sequencing of the WCFS1 strain has provided the research fraternity with a deeper knowledge of this Lb. plantarum species. It has been the standard for additional in-silico research based on its gene prediction/annotation as a primary approach in predicting the phenotype [30]. Lb. plantarum is commonly observed in Indian fermented foods, for example, idli, dosa, and fermented sorghum-based products [32][33][34]. Nevertheless, it was not until 2009 that the strains obtained from fermented foodstuffs were sequenced [30].
The Lb. plantarum strain of food origin encodes genes for several stress-related proteins. The presence of the OpuC (osmoregulatory system), the chaperones groESgroEL and the hcrAdnaKdnaJGrpE operon, NADH oxidase, and peroxidase or thiol and manganese transporters confers an advantage on strains that allow them to survive under extreme gastrointestinal conditions [21][35]. In the context of the presence of the CRISPR-Cas system, the maximum Lb. plantarum stain shows the magnificence of the CRISPR-Cas system (Type II) with four genes, i.e., cas9, cas1, cas2, and csn2 [36].
Lb. plantarum has a lifestyle adaptation zone or lifestyle island in its genome. Areas are specific to Lb. plantarum mainly consists of sugar transport and utilization and performs extracellular functions that encode genes. This region seems to play a key role in the effective adaptation of Lb. plantarum to the environment [21]. The ability to ferment multiple sugars is one of the major properties of Lb. plantarum strains that have received special consideration. Their effective transport systems lead to high adaptability and the ability to live in diverse ecological conditions. The comparative study of the genome of Lb. plantarum isolates from different sources showed that most of the genes encoded in the “lifestyle adaptation zone” were not preserved among strains and encode genes predictive of plantaricin and exopolysaccharide biosynthesis. These results confirm the excellent plasticity of the Lb. plantarum genome, coupled with an effective metabolism, makes it a nomadic as well as a versatile species [30].
A group of researchers isolated Lb. plantarum from different sources and studied its genome sequencing. Recently, the genomic description of Lb. plantarum obtained from dahi and kinema showed the production of putative bacteriocin and probiotics [14]. In addition, Lb. plantarum Lp91 isolated from the human intestine [37] and JDARSH isolated from sheep milk were also sequenced for studying the genome [38]. Recently, Lb. plantarum ST was isolated from De’ang pickled tea. The strain ST genome was fully sequenced and examined through the PacBio RS II sequencing arrangement. Lb. plantarum ST is a potent probiotic strain and is highly tolerated in the simulated artificial gastrointestinal tract. It also exhibited robust antibacterial activity in antagonism tests. Hence, it can be used as a livestock probiotic. The Lb. plantarum ST genome consisted of one circular chromosome and seven plasmids. The complete genome is 3,320,817 bp, the size of the ring chromosome is 3,058,984 bp, guanine + cytosine (G±C) content is 44.76%, and contains 2945 protein-coding sequences (CDS) [39].

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Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Birsen Yılmaz
,
Sneh Punia
,
Noemí Echegaray
,
Shweta Suri
,
Igor Tomasevic
,
Jose Manuel Lorenzo
,
Ebru Melekoglu
,
João Miguel Ferreira Rocha
,
Fatih OZOGUL
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Update Date: 05 May 2022
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