Description of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis

Abstract

A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94–97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter . The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95–96 and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T)

Pufferfish (Tetraodon cutcutia) Sampled from a Freshwater River Serves as an Intermediate Reservoir of a Sucrose Nonfermenting Variant of Vibrio cholerae PS-4

“…The bacteria from the cotton swabs were suspended in PBS by vigorous vortexing. The suspension was used as a master mix ( 37 ) for the isolation of bacteria. An aliquot (100 μL) of master mix sample was serially diluted using PBS and plated onto nutrient agar (BD, Difco).…”

“…Growth and reaction to ferment sucrose were tested on TCBS agar medium (BD, Difco). Utilization of sugars was tested separately by adding 0.5% concentration of glucose or fructose in Luria-Bertani agar medium (BD, Difco) containing bromothymol blue (2.0 mg/L) as a pH indicator at 37°C for 48 h. To ascertain hemolytic activity, strain PS-4 was streaked on Columbia blood agar base supplemented with 5% (vol/vol) defibrinated sheep blood followed by incubation at 37°C for 48 h ( 37 ). Preparation of O antisera and slide agglutination were performed as previously described ( 38 ).…”

“…A combination of both short-read Illumina and long-read Oxford Nanopore sequencing platforms was used to generate the high-quality complete genome sequence of V. cholerae strain PS-4. Illumina short-read DNA sequencing was carried out as described earlier ( 37 ). For long-read Nanopore sequencing, a genomic library was prepared using the Nanopore ligation sequencing kit (SQK-LSK109; Oxford Nanopore, Oxford, UK).…”

The genome wide analysis deciphered virulence factors and secondary metabolites of Chryseobacterium and description of Chryseobacterium indicum sp. nov

“…Bacterial strain and growth medium. Chryseobacterium strain PS-8 was isolated from the skin of freshwater pufferfish as described earlier (Das et al 2021). A colony with yellowish-orange colour designated strain PS-8 was selected for further analyses.…”

Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus

“…A BlastP search was performed with an e-value cutoff of 1.0 e-15 among the genomes of 74 type strains downloaded from the NCBI database to construct single-copy core gene families. The hits were selected with ≥50% and ≥70% of alignment coverage, as previously described in Staphylococcus and Acinetobacter genus [22, 23]. The recombinant genes were removed from the core gene families with the help of PhiTest feature implemented in PhiPack program [24].…”