Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Hubert Szczerba,Adam Waśko,Adam Kuzdraliński,Mariusz Krawczyk,Zdzisław Targoński,Anna Nowak,Karolina Dudziak,Elwira Komoń-Janczara

doi:10.1038/s41598-020-58929-0

Abstract

Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION single-molecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals.

Highlights

Enterobacter aerogenes LU2 is a gram-negative, wild bacterium that was isolated from cow rumen as a part of environmental screening for succinic acid-producing bacteria identification
E. aerogenes has a complete reductive branch of the tricarboxylic acid cycle (TCA) cycle as well as the glyoxylate pathway, which may result in higher succinic acid production efficiency[23]
The presence of many genes involved in uptake and degradation pathways for a wide range of sugars is probably related to their presence in the rumen where the strain LU2 was isolated from

Summary

Introduction

Enterobacter aerogenes LU2 is a gram-negative, wild bacterium that was isolated from cow rumen as a part of environmental screening for succinic acid-producing bacteria identification. Among the most frequently described bacterial species that have been recognized as natural succinic acid producers are Basfia succiniciproducens, Mannheimia succiniciproducens, Actinobacillus succinogenes and Anaerobiospirillum succiniciproducens[9,10,11,12]. These microorganisms are well characterized both physiologically and biochemically. The novelty and attractiveness of this new strain is that it is the first wild strain from the species Enterobacter aerogenes that is capable of efficiently producing SA by utilizing whey permeate with high lactose content derived from the whey industry. To better understand the unique properties of this strain, in this study, a complete genome was obtained, and genetic characterization was performed

Methods

Results

Conclusion