Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea

Abstract

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.

GENOME ANNOUNCEMENT

Komagataeibacter intermedius AF2, previously known as Gluconacetobacter intermedius, is a Gram-negative rod isolated from Kombucha tea. Briefly, for the isolation of K. intermedius AF2, 1 ml of Kombucha tea was subjected to serial 10-fold dilutions in 0.85% sterile NaCl solution. Aliquots of each dilution were plated on petri dishes containing Hestrin and Schramm (HS) medium. The plates were incubated aerobically at 30°C for 5 days. Suspected colonies were seeded in HS medium and incubated again as described above. After the incubation period, the colonies were transferred to test tubes (20 × 150 mm) containing HS broth and incubated aerobically at 30°C for five to seven days, in order to evaluate the production of cellulose, which can be easily observed on the surface of the culture medium. The AF2 isolate produced 1.41 g/L of cellulose, whereas K. rhaeticus strain AF1, isolated at the same time form the same environment, produced cellulose at higher levels (1).

Here, we present the genome sequence of K. intermedius strain AF2. This genome was sequenced on the Illumina HiSeq2000 system, generating 45,480,010 paired-end reads of 100 bp (insert size, 250 bp). The reads were preprocessed with Trimmomatic (2), resulting in 34,345,171 paired-end reads. Digital normalization was carried using Khmer (3), resulting in 482,978 reads, which were used to assemble contigs with SPAdes (4), using the best k-mer size chosen using KmerGenie (5). The post-assembly genome-improvement toolkit (PAGIT) was used to close gaps and correct substitution and insertion/deletion errors (6). An additional scaffolding step was carried out in SSPACE (7), followed by gap filling with GapFiller (8). The final assembly has a total length of 4,465,062 bp and an N₅₀ of 70,565 bp, represented by 268 scaffolds. The average G+C content of the genome is 61.35%, which is similar to related species: K. rhaeticus AF1 (GC: 62.44%) (1); K. xylinus NBRC 3288 (GC: 60.92%) (9); K. hansenii (GC: 59.0%) (10); K. europaeus 5P3 (GC: 61.2%); K. oboediens 174Bp2 (GC: 61.3%) (11); and Gluconacetobacter diazotrophicus PaI 5 (GC: 66.19%) (12). Gene prediction was carried out with the Prokka Pipeline (13) using a nonredundant database of proteins in Acetobacteriaceae as the first annotation source. A total of 4,232 genes were identified, including 4,145 protein-encoding genes, 11 rRNA genes, 64 tRNA genes, 303 signal peptide genes, 1 tmRNA gene, and 11 ncRNA genes. Gene content is similar to related species: K. rhaeticus (3,460 genes), K. xylinus (3,195), K. hansenii (3,308), K. medellinensis (3,195), K. europaeus 5P3 (3,586), K. oboediens 174Bp2 (3,601), and G. diazotrophicus (3,864). A search against the UniProt database revealed 3,641 protein-encoding genes with strong sequence similarity hits to proteins in that database. The current genome assembly provides a preliminary landscape of the genomic and metabolic capabilities of K. intermedius strain AF2 and will provide insights about the molecular mechanisms involved in high and low cellulose production in this genus.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JUFX00000000. The version described in this paper is the second version, JUFX02000000.