(WGS) Whole Genome Sequencing Customer Publications

seudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425–CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA–DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.

Plant growth promoting bacteria with dual activity, 1-aminocyclopropane-1-carboxylic-acid deaminase (ACCD) and nitrogenase, is more effective in supporting plant growth under stress condition. Previously, we were obtained several endophytic bacterial strains that exhibited dual activity, one of which was Raoultella terrigena PCM8. This study aimed to characterize the ACCD and nitrogenase genes of PCM8 strain. The acdS gene was obtained from the results of Whole Genomic Sequencing analyis, while the nifH gene was obtained by PCR. The characterization of both of the genes was carried out by means of in-silico analysis. WGS annotation analysis, showed that the acdS gene of PCM8 was located at the locus 19090 of genomic DNA and contains 978 nucleotides. In silico analysis of both acdS and nifH gene products showed that the ACCD enzyme of PCM8 had 325 amino acids, with molecular weight of 34.95 kDa, while nitrogenase as represented by nifH subunit product consist of 96 amino acids with molecular weight of 93.98 kDa, respectively.  The ACCD had pI value of 5.06, and catalytic residues of Lys51, Ser78, Tyr287, and Thr288, while nifH gene product had the pI value of 11.77. The results suggested that R. terrigena PCM8 potentially produce double activity of ACCD and nitrogenase and therefore it can be a good candidate as plant growth promoting under stress condition.

Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia’s North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an “open” pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.

Lactiplantibacillus plantarumis commonly analyzed as a potential probiotic. We herebyinvestigated two strains isolated from chicken crop (Lpb. plantarumF75) and human breast milk (Lpb.plantarumSU–KC1a). Ability to withstand osmotic stress (1.5%, 2.5% or 3.5% of NaCl) and phenol compounds (0.2% or 0.5%), ability to survive gastric juices for a maximum of 120 minutes and bile salt for a maximum 3 hours, as well as susceptibility to 25antibiotic discs,were compared between both strains. Whole genomes of both strains were sequenced and analyzed in silicoto determine the availability of antibiotic–resistancegenes as well as the presence of mobile genetic elements and plasmid. Both strainswere sensitive to increased concentrations of NaCl and phenol as well as to prolonged exposure to gastric juices. In contrast, both strains could withstand a prolonged exposure of 0.3% of bile salt. Both isolates had similar genome sizes and were susceptible to many tested antibiotics. The detected resistance genes were observed within the chromosomal genomes but no mobile genetic element nor plasmid was found. In conclusion, both strains of Lpb. plantarumdisplayed several characteristics of beneficial bacteria and could be used as probiotic candidates for poultry and human beings, respectively

Plant growth promoting bacteria with dual activity, 1-aminocyclopropane-1-carboxylic-acid deaminase (ACCD) and nitrogenase, is more effective in supporting plant growth under stress condition. Previously, we were obtained several endophytic bacterial strains that exhibited dual activity, one of which was Raoultella terrigena PCM8. This study aimed to characterize the ACCD and nitrogenase genes of PCM8 strain. The acdS gene was obtained from the results of Whole Genomic Sequencing analyis, while the nifH gene was obtained by PCR. The characterization of both of the genes was carried out by means of in-silico analysis. WGS annotation analysis, showed that the acdS gene of PCM8 was located at the locus 19090 of genomic DNA and contains 978 nucleotides. In silico analysis of both acdS and nifH gene products showed that the ACCD enzyme of PCM8 had 325 amino acids, with molecular weight of 34.95 kDa, while nitrogenase as represented by nifH subunit product consist of 96 amino acids with molecular weight of 93.98 kDa, respectively.  The ACCD had pI value of 5.06, and catalytic residues of Lys51, Ser78, Tyr287, and Thr288, while nifH gene product had the pI value of 11.77. The results suggested that R. terrigena PCM8 potentially produce double activity of ACCD and nitrogenase and therefore it can be a good candidate as plant growth promoting under stress condition.