Comparative genomics of the Komagataeibacter strains—Efficient bionanocellulose producers

Abstract

Komagataeibacter species are well‐recognized bionanocellulose ( BNC ) producers. This bacterial genus, formerly assigned to Gluconacetobacter , is known for its phenotypic diversity manifested by strain‐dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K . xylinus and the K. hansenii . We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c‐di‐ GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi‐genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.

Genomic and metabolic analysis of Komagataeibacter xylinus DSM 2325 producing bacterial cellulose nanofiber

“…It seems that the same Komagataeibacter species are not necessarily grouped together, as observed in this study. Consistently, in a recent study, K. xylinus NBRC 13693 was grouped with Komagataeibacter oboediens 174Bp2 rather than another same species K. xylinus E25, K. xylinus E26, and K. xylinus BCRC 12334 according to a clustering analysis of 868 orthologous proteins shared by 20 Komagataeibacter species (Ryngajłło, Kubiak, Jędrzejczak‐Krzepkowska, Jacek, & Bielecki, ). When the name Komagataeibacter was recently suggested as a new genus (Yamada et al, ), 16S rRNA gene sequence‐based phylogenetic and phenotypic characteristics were considered that could differentiate the Komagataeibacter species from other Gluconacetobacter species, but they were probably not specific enough to differentiate species within the Komagataeibacter genus.…”

Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488

“…() and Ryngajłło et al . (). This fact suggests that these strains could be taxonomically assigned to the Komagataeibacter genus instead of the Gluconacetobacter .…”

“…In this sense, the diversity in the regulatory network of cellulose biosynthesis has been discussed by Ryngajllo et al . for Komagataiebacter strains (Ryngajłło et al ., ), and we cannot exclude that these operons might be active under other environmental growth conditions.…”

“…Recently, the complete genome sequence of several Komagataeibacter species has been reported (Ogino et al ., ; Kubiak et al ., ; Florea et al ., ; Zhang et al ., ; Ryngajłło et al ., ). The genomic data analyses of these cellulose‐producing bacteria showed a great diversity in bcs operons.…”

Molecular aspects of bacterial nanocellulose biosynthesis

“…In recent years, comparative genomic and transcriptomic analyses are gaining attention in the scientific community. Recently, it has been shown that high complexity of regulatory mechanisms, directly or indirectly involved in the cellulose biosynthesis in Komagataeibacter strains, could be predicted by comparative genomic analysis (Ryngajłło et al ., ). Transcriptome analysis‐based RNA‐seq is an important technique to identify differentially expressed genes under distinct experimental conditions in bacteria.…”