Genome Sequence of
            <i>Lactobacillus amylovorus</i>
            GRL1112

Kant, Ravi; Paulín, Lars; Alatalo, Edward; Vos, Willem M. de; Palva, Airi

doi:10.1128/jb.01365-10

Cited by 18 publications

(14 citation statements)

References 15 publications

(11 reference statements)

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“…It requires a number of vitamins for growth. L. amylovorus does not exhibit oxidase-, catalase-, or nitrate-reducing activities (16) and is a member of the L. acidophilus group (8).…”

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confidence: 99%

Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum

et al. 2011

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“…It requires a number of vitamins for growth. L. amylovorus does not exhibit oxidase-, catalase-, or nitrate-reducing activities (16) and is a member of the L. acidophilus group (8).…”

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confidence: 99%

Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum

et al. 2011

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“…These include the genome sequences of Lactobacillus amylovorus 33,36 , Lactobacillus ruminis 37 31 .…”

Section: Genomic Technologies In Probiotic Researchmentioning

confidence: 99%

“…In most cases, genome assembly was done using different versions of Newbler assembler 33,39 except in a few cases where gsAssembler 36,37 or CLC Genomics Workbench 37 Phred-Phrap-Consed software package 41 . Genome annotation was done using the Rapid Assembly using Subsystems Technology (RAST) server 38 -40 , often combined with Glimmer 38 , tRNAscan-SE 38 , RNAmmer 38 , EDGAR 36 , PEDANT 41 , GeneMark 41 , and NCBI Prokaryotic Genome Automated Annotation Pipeline (PGAAP) analysis 33,36 .…”

Section: Genomic Technologies In Probiotic Researchmentioning

confidence: 99%

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2018

IJPSR

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Probiotics are live microorganisms that confer many health benefits to the host when administered in adequate quantities. These health benefits have garnered much attention towards Probiotics and have given an impetus to their use as dietary supplements for the improvement of general health and as adjuvant therapies for certain diseases. The increased demand for probiotic products in the recent times has provided the thrust for probiotic research applied to several areas of human biology. The advances in genomic technologies have further facilitated the sequencing of the genomes of such probiotic bacteria and their genomic analyses to identify the genes that endow the beneficial effects they are known to exert. This work reviews the application of genomic strategies on probiotic bacteria, while providing the details about the probiotic strains whose genome sequences are available. It also consolidates the Genomic tools used for the sequencing, assembly and annotation of the probiotic genes and how it has helped in comparative genomic analyses.

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“…Two circular plasmids that have not been reported were also identified: pRKC30SC1 (7,197 bp) and pRKC30SC2 (12,568 bp), with GC content values of 35.1% and 36.6%, respectively. The full annotation was performed by a RAST server (1) and NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov /genomes/static/Pipeline.html).…”

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Complete Genome Sequencing of Lactobacillus acidophilus 30SC, Isolated from Swine Intestine

Roh

et al. 2011

J Bacteriol

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Lactobacillus acidophilus 30SC has been isolated from swine intestines and considered a probiotic strain for dairy products because of its ability to assimilate cholesterol and produce bacteriocins. Here, we report the complete genome sequence of Lactobacillus acidophilus 30SC (2,078,001 bp) exhibiting strong acid resistance and enhanced bile tolerance.Lactobacillus acidophilus 30SC is an intestinal isolate from swine and known to assimilate cholesterol and produce a thermostable and pH-stable bacteriocin (9). This bacteriocin may have a potential application in food systems controlling food spoilage microorganisms and food-borne pathogens (3, 9). In addition, L. acidophilus 30SC showed excellent acid resistance and enhanced bile tolerance compared to commercial probiotic strains that are presently used in dairy products (9). These properties are advantageous characteristics to a probiotic strain by providing a greater chance of survival during passage through the stomach and intestinal tract. In order to understand these unique properties on the genomic level, we attempted whole-genome sequencing.The genome of L. acidophilus 30SC was sequenced by Roche 454 GS FLX (454 GS FLX) platforms. The initial draft assembly was prepared from two separate libraries of 158,188 and 235,924 paired-end reads containing 3-kb inserts and yielded 15 scaffolds (21 contigs) by the Newbler gsAssembler 2.3 (454 Life Sciences, Branford, CT). The actual order of scaffolds was checked by a series of PCRs based on a permutation table. The genome sequence was finished by filling gaps with gapResolution (Cliff Han, unpublished data; provided by the Joint Genome Institute) and sequencing by ABI system (Applied Biosystems, CA) followed by primer walking PCR between contigs.The complete genome sequence of L. acidophilus 30SC revealed one circular chromosome of 2,078,001 bp with a GC content of 38.1%. Two circular plasmids that have not been reported were also identified: pRKC30SC1 (7,197 bp) and pRKC30SC2 (12,568 bp), with GC content values of 35.1% and 36.6%, respectively. The full annotation was performed by a RAST server (1) and NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov /genomes/static/Pipeline.html). Both annotations were scrutinized with manual inspection. The chromosome has 2,138 coding sequences (CDS), 63 tRNA genes, and 12 rRNA genes. The pRKC30SC1 and pRKC30SC2 plasmids have 7 CDS and 16 CDS, respectively.The genome sequencing revealed genes known to be implicated in bile acid tolerance, such as choloylglycine hydrolase, known as bile salt hydrolase and bile acid-inducible operon protein (4, 10). As in Lactobacillus amylovorus, which has recently been sequenced (7), we found two kinds of S-layer proteins, mucus-and fibronectin-binding proteins participating in adhesion to intestinal cells (2, 6) and five genes encoding bacteriocins, such as amylovorin (5) and helveticin (11), that can inhibit the growth of pathogenic bacteria (8), suggesting its potential as a probiotic bacterium.Nucl...

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Genome Sequence of Lactobacillus amylovorus GRL1112

Cited by 18 publications

References 15 publications

Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum

Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum

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Complete Genome Sequencing of Lactobacillus acidophilus 30SC, Isolated from Swine Intestine

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