Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt

Iartchouk, Oleg; Kozyavkin, Sergei A.; Karamychev, Valeri N.; Slesarev, Alexei I.

doi:10.1128/genomea.00166-15

Cited by 9 publications

(3 citation statements)

References 14 publications

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“…Prokaryotic organisms usually have a very well organized single circular chromosome, which minimizes the content of intergenic nucleotide sequences. Generally L. acidophilus strains contain a small number of pseudogenes [ 22 – 25 ]. The higher number of pseudogenes in L. amylovorus JBD401 suggests that this strain might be in an active stage of evolution.…”

Section: Discussionmentioning

confidence: 99%

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

Singh

Chung

Lee³

et al. 2018

BMC Genomics

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BackgroundRecent experimental evidence showed that lactobacilli could be used as potential therapeutic agents for hyperammonemia. However, lack of understanding on how lactobacilli reduce blood ammonia levels limits application of lactobacilli to treat hyperammonemia.ResultsWe report the finished and annotated genome sequence of L. amylovorus JBD401 (GenBank accession no. CP012389). L. amylovorus JBD401 reducing blood ammonia levels dramatically was identified by high-throughput screening of several thousand probiotic strains both within and across Lactobacillus species in vitro. Administration of L. amylovorus JBD401 to hyperammonemia-induced mice reduced the blood ammonia levels of the mice to the normal range. Genome sequencing showed that L. amylovorus JBD401 had a circular chromosome of 1,946,267 bp with an average GC content of 38.13%. Comparative analysis of the L. amylovorus JBD401 genome with L. acidophilus and L. amylovorus strains showed that L. amylovorus JBD401 possessed genes for ammonia assimilation into various amino acids and polyamines Interestingly, the genome of L. amylovorus JBD401 contained unusually large number of various pseudogenes suggesting an active stage of evolution.ConclusionsL. amylovorus JBD401 has genes for assimilation of free ammonia into various amino acids and polyamines which results in removal of free ammonia in intestinal lumen to reduce the blood ammonia levels in the host. This work explains the mechanism of how probiotics reduce blood ammonia levels.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4672-3) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

Singh

Chung

Lee³

et al. 2018

BMC Genomics

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“…LA14, FSI4, ATCC53544, LA1,and DSM20079) from NCBI (Table 1) [21][22][23][24][25][26]. In this study, complete genome sequences of other strains in the NCBI database were used for comparative genome analysis of C5, which were isolated from different hosts, and none were isolated from dogs as in previous studies [27,28].…”

Section: Discussionmentioning

confidence: 99%

Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics

Son¹,

Lee²,

Park³

et al. 2021

J Anim Sci Technol

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Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host’s evolutionary adaptation process.

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“…Ramachandran et al [ 11 ] reported that the MLST scheme using seven conserved housekeeping genes ( fusA , gpmA , gyrA , gyrB , lepA , pyrG , and recA ) could be used as an intraspecies subtyping technique for the Lactobacillus complex ( L. acidophilus , L. amylovorus , L. crispatus , L. gallinarum , L. gasseri , and L. johnsonii ); however, two allelic profiles from five L. acidophilus strains were observed only in the gyrA gene. L. acidophilus strains have been considered to have little genome sequence variation [ 20 , 21 , 22 , 23 ], and they are regarded as a monophyletic taxon [ 10 ]. Therefore, higher-resolution strain-level differentiation methods must be developed for L. acidophilus strains.…”

Section: Introductionmentioning

confidence: 99%

Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain

et al. 2020

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Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products.

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Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt

Cited by 9 publications

References 14 publications

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics

Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain

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