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Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

ABSTRACT: Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.

SUBMITTER: Sun Z

PROVIDER: S-EPMC4667430 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Sun Zhihong Z Harris Hugh M B HM McCann Angela A Guo Chenyi C Argimón Silvia S Zhang Wenyi W Yang Xianwei X Jeffery Ian B IB Cooney Jakki C JC Kagawa Todd F TF Liu Wenjun W Song Yuqin Y Salvetti Elisa E Wrobel Agnieszka A Rasinkangas Pia P Parkhill Julian J Rea Mary C MC O'Sullivan Orla O Ritari Jarmo J Douillard François P FP Paul Ross R R Yang Ruifu R Briner Alexandra E AE Felis Giovanna E GE de Vos Willem M WM Barrangou Rodolphe R Klaenhammer Todd R TR Caufield Page W PW Cui Yujun Y Zhang Heping H O'Toole Paul W PW

Nature communications 20150929

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapp ...[more]

PMID: 26415554

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Project description:BackgroundOenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group "C" has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses.ResultsSequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group "C" consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group "D" exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades.ConclusionsThe obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.

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Dataset Information

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Publications

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

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