Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus

Abstract

BackgroundThe genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococcus species/subspecies were sequenced to assess their genomic characteristics, metabolic diversity, and phylogenetic relationships.ResultsThe total genome sizes varied between 1.99 (Lactococcus plantarum) and 2.46 megabases (Mb; L. lactis subsp. lactis), and the G + C content ranged from 34.81 (L. lactis subsp. hordniae) to 39.67% (L. raffinolactis) with an average value of 37.02%. Analysis of genome dynamics indicated that the genus Lactococcus has an open pan-genome, while the core genome size decreased with sequential addition at the genus and species group levels. A phylogenetic dendrogram based on the concatenated amino acid sequences of 643 core genes was largely consistent with the phylogenetic tree obtained by 16S ribosomal RNA (rRNA) genes, but it provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis.ConclusionsComparative genomics indicated that species in the genus Lactococcus had high degrees of diversity in genome size, gene content, and carbohydrate metabolism. This may be important for the specific adaptations that allow different Lactococcus species to survive in different environments. These results provide a quantitative basis for understanding the genomic and metabolic diversity within the genus Lactococcus, laying the foundation for future studies on taxonomy and functional genomics.Electronic supplementary materialThe online version of this article (10.1186/s12866-017-1120-5) contains supplementary material, which is available to authorized users.

Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

“…rhamnosus, the carbohydrate-utilization related genes were predicted using the CAZY database, which contained GH, GT, PL, CE, CBM and AA (Lugli et al, 2017 (Hammes and Hertel, 2015). Invertase (EC 3.2.1.26), also known as sucrase or fructofuranosidase, is an important enzyme for the irreversible hydrolysis of sucrose to glucose and fructose (Yu et al, 2017). This enzyme and the corresponding PTS system were present in all the strains indicating that all of them could utilize sucrose.…”

Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

“…Carbohydrate metabolism plays a key role in the growth of Lactococcus species. On average, 12.5% of genes are associated with carbohydrate metabolism and involved in glycolysis/gluconeogenesis and the pentose phosphate pathway (PPP) [53]. Four L. lactis phenotypic groups were obtained: (A) for isolates L1 to L6, L10 to L13 and L15 to L17 (n = 13); (B) for isolates L7 and L8 (n = 2); (C) for isolates L14 and L18 (n = 2) and (D) for isolate L9 (n = 1) ( Table 6).…”

“…Phenotypic characteristics of UMSC Lactococcus isolates. Phenotypic characteristics of two strain types, ATCC 19,435 and ATCC 19,257; data were extracted from Buron-Moles et al and Yu et al [14,53]. Phenotypic data of the type strain IL1403 was extracted from Siezen et al [54].…”

Evaluasi Kandungan Nutrien dan Antinutrien Tepung Daun Kelor Terfermentasi sebagai Bahan Baku Pakan Ikan

“…L. raffinolactis merupakan bakteri dari genus Lactococcus yang hidup pada kisaran suhu 10-40°C. Bakteri tersebut berkembang dengan baik pada pH 4,5-7,0 dan akan berhenti tumbuh pada pH di bawah 4,5 (Yu et al, 2017). L. raffinolactis merupakan bakteri asam laktat yang dapat dijadikan agen probiotik karena mampu mengubah karbohidrat (glukosa) menjadi asam laktat serta menurunkan pH (Putri et al, 2014).…”