Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead

• Published in: International journal of molecular sciences 2021-04, Vol.22 (7), p.3780
• Main Authors: Gustaw, Klaudia, Koper, Piotr, Polak-Berecka, Magdalena, Rachwał, Kamila, Skrzypczak, Katarzyna, Waśko, Adam
• Format: Article
• Language: English
• Subjects: Alcohol; Alcoholic beverages; Arsenic; Bacteria; Carbohydrate metabolism; Carbohydrates; Chromosomes; CRISPR; Deoxyribonucleic acid; Detoxification; DNA; Environmental changes; Ethanol; Experimental research; Fructose; Genes; Genome, Bacterial; Genomes; Genomic analysis; Glucose; Honey; Honey - microbiology; Hybridization; Information processing; Lactobacillus - genetics; Lactobacillus - isolation & purification; Lactobacillus hilgardii; Microorganisms; Phylogenetics; Phylogeny; Plasmids; Proteins; Pseudogenes; Spoilage; Sugar; Surface layers; Whole Genome Sequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms22073780

The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the species. The genome of FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of FLUB. The core of the genome of is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins. Variants of MRS broth with ethanol (10-20%), glucose (2-25%), and fructose (2-24%) were prepared to test the strain's growth preferences using Bioscreen C and the PYTHON script. FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of FLUB to the mead environment.