Unveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses

Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses

“…The quality of the genome sequence was predicted according to the GC% of strain DNA. A good-quality sequence is ensured by its GC%, and at least 40–70% of GC% is accepted in research ( Abdullah-Al-Mamun et al, 2022 ). The strain investigated in this study exhibited 55.1% GC% after fast QC analysis, and the sequence quality was confirmed to be excellent.…”

“…Biochemical tests, including methyl red, Voges–Proskauer, catalase, KOH string, oxidase, triple sugar iron, citrate utilization, motility indole urease, and urease, and individual sugar fermentation tests such as dextrose, lactose, maltose, and sucrose utilization ( Adedayo et al, 2004 ; Das et al, 2022 ), were performed to facilitate the identification of the bacterium. In addition, the activities of extracellular cellulase, amylase, protease, and xylanase were determined as described elsewhere ( Abdullah-Al-Mamun et al, 2022 ; Das et al, 2022 ).…”

“…The preparation of the genomic library of Enterobacter sp. HSTU-ASh6 and the sequencing of the complete genome were performed using the Illumina MiniSeq System (Illumina, Inc., San Diego, CA, USA), as described previously ( Abdullah-Al-Mamun et al, 2022 ; Das et al, 2022 ). After complete genome sequencing, the quality test was conducted using the fast QC analysis and Illumina Base Space sequence analysis Hub.…”

“…Average nucleotide identity (ANI) and digital DNA–DNA hybridization (DDH) analyses were performed using the JSpecies WS, Type Strain Genome Server (TYGS) and GGDC web server, respectively ( Abdullah-Al-Mamun et al, 2022 ). A total of 15 types of nearest homolog complete genome sequences were utilized for the ANI analysis.…”

Fate of heavy metals in Swarna rice after traditional cooking and submerged fermentation linked to bacterial interactions

“…A set of purified isolates was stored in 80% glycerol for further analysis. The isolates were biochemically characterized according to the results of oxidase, catalase, methyl red (MR), Voges-Proskauer (VP), triple sugar iron (TSI), citrate utilization (CU), indole, motility indole urease (MIU), and carbohydrates (lactose, maltose, sucrose and dextrose) fermentation tests in aseptic condition (Abdullah-Al-Mamun et al, 2022;Haque et al, 2015a). The activities of the extracellular amylase, pectinase, xylanase, and protease of the isolates were conducted by spreading the bacterial samples with a sterile loop in starch, pectin, xylan, and casein medium that served as the sole carbon source in an aseptic condition as described (Das et al, 2022;Haque et al, 2021).…”