Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia , and Genomic Insights into 4-Aminobenzenesulfonate, p -Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga

• Published in: Frontiers in microbiology Vol. 8; p. 1880
• Main Authors: Gan, Han M, Lee, Yin P, Austin, Christopher M
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 04-10-2017
• Subjects: comparative genomics; hydrogen metabolism; Hydrogenophaga; Microbiology; Nanopore; phylogeny; Hydrogenophaga; phylogeny; hydrogen metabolism; Nanopore; comparative genomics
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2017.01880

We improved upon the previously reported draft genome of
strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in
, the
operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various
strains. The absence of
gene in the complete genome of
PBC is consistent with its
-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14
genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several
strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of
as "hydrogen eating bacteria."