A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Szczerba, Hubert; Dudziak, Karolina; Krawczyk, Mariusz; Targoński, Zdzisław

doi:10.3390/ijms21144835

Cited by 3 publications

(1 citation statement)

References 70 publications

(140 reference statements)

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“…The gap ratio (0%) in the sequence, both on the chromosome and the plasmids, confirms the good selection of the sequencing techniques. Hybrid long-read sequencing by MinION together with Illumina short-read are increasingly being used to avoid incomplete constructions that hinder complete genome assembly [ 23 , 24 , 25 ]. The GC content in the sequences ranges from 35.6 to 41.5%, and is 40.1% for the whole genome.…”

Section: Resultsmentioning

confidence: 99%

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

Gustaw

Koper

Polak-Berecka

et al. 2021

IJMS

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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, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii 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 L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii 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 L. hilgardii FLUB. The core of the genome of L. hilgardii 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. L. hilgardii 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. L. hilgardii 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 L. hilgardii FLUB to the mead environment.

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Section: Resultsmentioning

confidence: 99%

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

Gustaw

Koper

Polak-Berecka

et al. 2021

IJMS

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Genome-based characterization of the deep-sea psychrotolerant bacterium Bacillus altitudinis SORB11 isolated from the Indian Sector of the Southern Ocean

Halder,

Biswas,

Shaw

et al. 2023

Polar Biol

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Biosynthesis pathways of expanding carbon chains for producing advanced biofuels

Lin

2023

Biotechnol Biofuels

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Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.

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A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Cited by 3 publications

References 70 publications

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

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

Genome-based characterization of the deep-sea psychrotolerant bacterium Bacillus altitudinis SORB11 isolated from the Indian Sector of the Southern Ocean

Biosynthesis pathways of expanding carbon chains for producing advanced biofuels

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