Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian Probiotic Isolate of Human Gut Origin

Sunita Grover; Vineet K. Sharma; Rashmi H. Mallapa; Virender K. Batish

doi:10.1128/genomeA.00976-13

DOI: 10.1128/genomeA.00976-13

ABSTRACT

Lactobacillus plantarum is a highly versatile species among lactic acid bacteria that has been widely isolated from highly diversified ecological niches, including the gastrointestinal tract. Here, we report the first draft genome sequence of an Indian isolate of the probiotic strain L. plantarum Lp91, isolated from human gut.

GENOME ANNOUNCEMENT

Lactobacillus plantarum merits special attention in view of its multitude of bioactive metabolic functions beneficial for human health and its presence in many environmental niches, including dairy and meat products and a variety of vegetable fermentations, in addition to the human gastrointestinal (GI) tract (1). The complete 3.3-Mb genome sequence of L. plantarum WCFS1 (from saliva) has been determined (2) and resequenced and completely annotated recently by Siezen et al. (3). In addition, the complete genomes of three other L. plantarum strains have also been sequenced, viz. L. plantarum ST-III (4), L. plantarum JDM1 (5), and L. plantarum strain NC8 (CCUG 61730) (6).

L. plantarum strain Lp91 is an indigenous isolate of Indian gut origin and has been identified by 16S rRNA (GQ922598) sequencing as well as housekeeping genes, viz. pheS (KC509913.1), tkt4 (KC509921.1), pgm (KC509919.1), gyr (KC509917.1), and purK1 (KC509920.1). Lp91 has expressed several probiotic and functional attributes, such as high acid and bile tolerance, colonization potential, cholesterol assimilation, reduction in low-density lipoprotein (LDL)-cholesterol, and antibacterial, antioxidative, anti-inflammatory, and immunomodulatory potentials in both in vitro cell lines (THP-1 and HT-29) and in vivo animal models (7 –15). Since L. plantarum Lp91 serves as a candidate probiotic for developing probiotic fermented dairy products and powders and sachets, its whole-genome sequence was deciphered.

Genome sequencing was performed using an Illumina (HiScanSQ) genome analyzer. A total of 13,098,338 high-quality reads were obtained after filtering, with a Phred score of <20, and were used for alignment with L. plantarum WCFS1 (LpWCFS1), which was used as the reference genome. As much as 80.63% of the total reads were aligned with the reference genome, with 89.11% genome coverage and a total gap length of 0.36 Mb. A total of 15,820 single nucleotide polymorphisms (SNPs) were found by genomic comparison of Lp91 with LpWCFS1.

The draft genome of Lp91 was assembled into a single circular chromosome of 3,308,256 bp by use of the reference LpWCFS1genomic sequence and the Burrows-Wheeler Aligner (BWA) (16), by inserting “N” to fill the gaps. The G+C content of Lp91 was 45%, and 2,779 predicted protein-coding genes were identified by using Glimmer 3.02 (17) followed by manual curation. As many as 2,346 (84.4%) genes were annotated with known functions by use of BLASTP against NCBI nonreduntant (NR) and Clusters of Orthologous Groups (COG) databases (18). However, 433 (15.6%) genes were annotated as hypothetical, conserved hypothetical, or unnamed protein products. The Lp91 strain includes five rRNA gene operons and 65 tRNA genes in the genome. In addition, 1,586 genes were classified into 20 COG functional classes, of which the most abundant classes were transcription (16%) and carbohydrate transport and metabolism (13%).

Nucleotide sequence accession numbers.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AXDQ00000000. The version described in this paper is version AXDQ01000000.

ACKNOWLEDGMENTS

This work was funded by the Ministry of Food Processing Industries (MoFPI) (grant number 27/MFPI/R&D/2009), India, and the Indian Council of Medical Research (ICMR) (grant number 5/3/8/75/2009-RHN) for whole-genome sequencing, data analysis, and publication.

We also acknowledge M/s Sandor Proteomics Pvt. Ltd., Hyderabad, for performing the whole-genome sequencing.

FOOTNOTES

Address correspondence to Sunita Grover, sungro{at}gmail.com.
S.G. and V.K.S. contributed equally to this work.
Citation Grover S, Sharma VK, Mallapa RH, Batish VK. 2013. Draft genome sequence of Lactobacillus plantarum strain Lp91, a promising Indian probiotic isolate of human gut origin. Genome Announc. 1(6):e00976-13. doi:10.1128/genomeA.00976-13.

Received 20 October 2013.
Accepted 22 October 2013.
Published 21 November 2013.

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

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1. Kumar R,
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Cited By...

[1] 1.↵
de Vries MC,
Vaughan EE,
Kleerebezem M,
de Vos WM
. 2006. Lactobacillus plantarum survival, functional and potential probiotic properties in the human intestinal tract. Int. Dairy J. 16:1018–1028.
OpenUrl CrossRef Web of Science

[2] de Vries MC,

[3] Vaughan EE,

[4] Kleerebezem M,

[5] de Vos WM

[6] 2.↵
Kleerebezem M,
Boekhorst J,
Van Kranenburg R,
Molenaar D,
Kuipers OP,
Leer R,
Tarchini R,
Peters SA,
Sandbrink HM,
Fiers MW,
Stiekema W,
Lankhorst RM,
Bron PA,
Hoffer SM,
Groot MN,
Kerkhoven R,
de Vries M,
Ursing B,
De Vos WM,
Siezen RJ
. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U. S. A. 100:1990–1995.
OpenUrl Abstract/FREE Full Text

[7] Kleerebezem M,

[8] Boekhorst J,

[9] Van Kranenburg R,

[10] Molenaar D,

[11] Kuipers OP,

[12] Leer R,

[13] Tarchini R,

[14] Peters SA,

[15] Sandbrink HM,

[16] Fiers MW,

[17] Stiekema W,

[18] Lankhorst RM,

[19] Bron PA,

[20] Hoffer SM,

[21] Groot MN,

[22] Kerkhoven R,

[23] de Vries M,

[24] Ursing B,

[25] De Vos WM,

[26] Siezen RJ

[27] 3.↵
Siezen RJ,
Francke C,
Renckens B,
Boekhorst J,
Wels M,
Kleerebezem M,
van Hijum SA
. 2012. Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 Genome. J. Bacteriol. 194:195–196.
OpenUrl Abstract/FREE Full Text

[28] Siezen RJ,

[29] Francke C,

[30] Renckens B,

[31] Boekhorst J,

[32] Wels M,

[33] Kleerebezem M,

[34] van Hijum SA

[35] 4.↵
Wang Y,
Chen C,
Ai L,
Zhou F,
Zhou Z,
Wang L,
Zhang H,
Chen W,
Guo B
. 2011. Complete genome sequence of the probiotic Lactobacillus plantarum ST-III. J. Bacteriol. 193:313–314.
OpenUrl Abstract/FREE Full Text

[36] Wang Y,

[37] Chen C,

[38] Ai L,

[39] Zhou F,

[40] Zhou Z,

[41] Wang L,

[42] Zhang H,

[43] Chen W,

[44] Guo B

[45] 5.↵
Zhang ZY,
Liu C,
Zhu YZ,
Wei YX,
Tian F,
Zhao GP,
Guo XK
. 2012. Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome. Int. J. Food Microbiol. 153:166–170.
OpenUrl CrossRef PubMed

[46] Zhang ZY,

[47] Liu C,

[48] Zhu YZ,

[49] Wei YX,

[50] Tian F,

[51] Zhao GP,

[52] Guo XK

[53] 6.↵
Axelsson L,
Rud I,
Naterstad K,
Blom H,
Renckens B,
Boekhorst J,
Kleerebezem M,
van Hijum S,
Siezen RJ
. 2012. Genome sequence of the naturally Plasmid-free Lactobacillus plantarum Strain NC8 (CCUG 61730). J. Bacteriol. 194:2391–2392.
OpenUrl Abstract/FREE Full Text

[54] Axelsson L,

[55] Rud I,

[56] Naterstad K,

[57] Blom H,

[58] Renckens B,

[59] Boekhorst J,

[60] Kleerebezem M,

[61] van Hijum S,

[62] Siezen RJ

[63] 7.↵
Duary RK,
Batish VK,
Grover S
. 2010. Expression of the atpD gene in putative indigenous probiotic Lactobacillus plantarum strains under in vitro acidic conditions using RT-qPCR. Res. Microbiol. 161:399–405.
OpenUrl PubMed

[64] Duary RK,

[65] Batish VK,

[66] Grover S

[67] 8.↵
Duary RK,
Rajput YS,
Batish VK,
Grover S
. 2011. Assessing the adhesion of putative indigenous probiotic lactobacilli to human colonic epithelial cells. Indian J. Med. Res. 134:664–671.
OpenUrl CrossRef PubMed

[68] Duary RK,

[69] Rajput YS,

[70] Batish VK,

[71] Grover S

[72] 9.↵
Kumar R,
Grover S,
Batish VK
. 2011. Hypocholesterolaemic effect of dietary inclusion of two putative probiotic bile salt hydrolase-producing Lactobacillus plantarum strains in Sprague-Dawley rats. Br. J. Nutr. 105:561–573.
OpenUrl CrossRef PubMed

[73] Kumar R,

[74] Grover S,

[75] Batish VK

[76] 10.↵
Kumar R,
Grover S,
Batish VK
. 2011. Molecular identification and typing of putative probiotic indigenous Lactobacillus plantarum strain Lp91 of human origin by specific primed-PCR assays. Probiotics Antimicrob. Proteins 3:186–193.
OpenUrl CrossRef

[77] Kumar R,

[78] Grover S,

[79] Batish VK

[80] 11.↵
Duary RK,
Batish VK,
Grover S
. 2012. Relative gene expression of bile salt hydrolase and surface proteins in two putative indigenous Lactobacillus plantarum strains under in vitro gut conditions. Mol. Biol. Rep. 39:2541–2552.
OpenUrl CrossRef PubMed

[81] Duary RK,

[82] Batish VK,

[83] Grover S

[84] 12.↵
Duary RK,
Bhausaheb MA,
Batish VK,
Grover S
. 2012. Anti-inflammatory and immunomodulatory efficacy of indigenous probiotic Lactobacillus plantarum Lp91 in colitis mouse model. Mol. Biol. Rep. 39:4765–4775.
OpenUrl CrossRef PubMed

[85] Duary RK,

[86] Bhausaheb MA,

[87] Batish VK,

[88] Grover S

[89] 13.↵
Kumar R,
Grover S,
Batish VK
. 2012. Bile salt hydrolase (Bsh) activity screening of lactobacilli: in vitro selection of indigenous Lactobacillus strains with potential bile salt hydrolysing and cholesterol-lowering ability. Probiotics Antimicrob. Prot. 4:162–172.
OpenUrl CrossRef

[90] Kumar R,

[91] Grover S,

[92] Batish VK

[93] 14.↵
Achuthan AA,
Duary RK,
Mathadil A,
Panwar H,
Kumar H,
Batish VK,
Grover S
. 2012. Antioxidative potential of lactobacilli isolated from the gut of Indian people. Mol. Biol. Rep. 39:7887–7897.
OpenUrl CrossRef PubMed

[94] Achuthan AA,

[95] Duary RK,

[96] Mathadil A,

[97] Panwar H,

[98] Kumar H,

[99] Batish VK,

[100] Grover S

[101] 15.↵
Aparna Sudhakaran AV,
Panwar H,
Chauhan R,
Duary RK,
Rathore RK,
Batish VK,
Grover S
. 2013. Modulation of anti-inflammatory response in lipopolysaccharide stimulated human THP-1 cell line and mouse model at gene expression level with indigenous putative probiotic lactobacilli. Genes Nutr. 8:1–12.
OpenUrl CrossRef PubMed

[102] Aparna Sudhakaran AV,

[103] Panwar H,

[104] Chauhan R,

[105] Duary RK,

[106] Rathore RK,

[107] Batish VK,

[108] Grover S

[109] 16.↵
Li H,
Durbin R
. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
OpenUrl CrossRef PubMed Web of Science

[110] Li H,

[111] Durbin R

[112] 17.↵
Salzberg SL,
Delcher AL,
Kasif S,
White O
. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544–548.
OpenUrl CrossRef PubMed Web of Science

[113] Salzberg SL,

[114] Delcher AL,

[115] Kasif S,

[116] White O

[117] 18.↵
Benson DA,
Karsch-Mizrachi I,
Clark K,
Lipman DJ,
Ostell J,
Sayers EW
. 2012. GenBank. Nucleic Acids Res. 40:D48–D53.
OpenUrl CrossRef PubMed Web of Science

[118] Benson DA,

[119] Karsch-Mizrachi I,

[120] Clark K,

[121] Lipman DJ,

[122] Ostell J,

[123] Sayers EW

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