Dynamics of antibiotic resistance genes in plasmids and bacteriophages.

This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.

New alkali tolerant ß-galactosidase from Paracoccus marcusii KGP - A promising biocatalyst for the synthesis of oligosaccharides derived from lactulose (OsLu), the new generation prebiotics.

The enzyme ß-galactosidase can synthesise novel prebiotics such as oligosaccharides derived from lactulose (OsLu) which can be added as a supplement in infant food formula. In this study, the intracellular ß-galactosidase produced by the alkaliphilic bacterium Paracoccus marcusii was extracted and purified to homogeneity using hydrophobic and metal affinity chromatography. The purification resulted in 18 U/mg specific activity, with a yield of 8.86% and an 18-fold increase in purity. The purified enzyme was a monomer with an 86 kDa molecular weight as determined by SDS PAGE and Q-TOF-LC/MS. ß-Galactosidase was highly active at 50 °C and pH 6-8. The enzyme displayed an alkali tolerant nature by maintaining more than 90% of its initial activity over a pH range of 5-9 after 3 h of incubation. Furthermore, the enzyme activity was enhanced by 37% in the presence of 5 M NaCl and 3 M KCl, indicating its halophilic nature. The effects of metal ions, solvents, and other chemicals on enzyme activity were also studied. The kinetic parameters KM and Vmax of ß-galactosidase were 1 mM and 8.56 µmoles/ml/min and 72.72 mM and 11.81 µmoles/ml/min on using oNPG and lactose as substrates. P. marcusii ß-galactosidase efficiently catalysed the transgalactosylation reaction and synthesised 57 g/L OsLu from 300 g/L lactulose at 40 °C. Thus, in this study we identified a new ß-galactosidase from P. marcusii that can be used for the industrial production of prebiotic oligosaccharides.

Draft Genome Sequence of a Highly Pigmented Bacterium Paracoccus marcusii KGP Capable of Producing Galacto-oligosaccharides Synthesising Enzyme.

The genome of Paracoccus marcusii KGP, isolated from the marine sediment collected from the coast of the Bay of Bengal, was sequenced using Oxford Nanopore sequencing technology. The assembled genome sequence consists of seven contigs and has a 4,085,678 bp circular chromosome with 1647 coding genes and a G+C content of 66.7%. Besides, the genome of P. marcusii KGP contains three copies of the rrn operon. The genes coding for the industrially relevant enzymes and secondary metabolites such as ß-galactosidase, protease, amylase, ß-glucosidase, ectoine, indigoidine, and carotenoid biosynthesis clusters were also identified in the genome. When the ß-galactosidase extracted from P. marcusii KGP was mixed with a high concentration of lactose, galacto-oligosaccharides were produced, which revealed the transgalactosylation property of the enzyme. The genome sequence of P. marcusii KGP was found to have an average nucleotide identity value of 96.16 and a digital DNA-DNA hybridisation value of 73.90% with the genome sequence of P. marcusii CGMCC. Furthermore, by comparing the genome sequences of both strains, it was found that the size of the KGP genome was large, indicating the possibility of strain-specific genes in addition to core genes.

Metagenomic Analysis of the Faecal Microbiome of Rats with 1, 2-Dimethylhydrazine Induced Colon Cancer and Prophylactic Whole-Cell Carotenoid Intervention.

Rapidly evolving sequencing technologies have enabled efficient sequencing of complex genomes and metagenomes. Here, we have presented our metagenomic analysis of rat faeces isolated DNA, sequenced using long-read sequencing technology. The microbiome changes in the rat faeces after sixteen weeks of prolonged administration of subcutaneous 1,2 dimethylhydrazine to induce colon carcinogenesis and oral carotenoid-rich whole-cell lyophilised Dunaliella salina supplement. The faecal pellets were aseptically collected, and DNA was isolated and sequenced subsequently. The post-sequencing analysis revealed that the rat gut microbiome is highly complex and diverse. There was a significant difference between the microbiome of rats that received Dunaliella salina supplement in comparison with rats treated with 1,2 dimethylhydrazine and control rats. We observed the dominance of Bacteroidetes over Firmicutes in both cases of administration. The dominance was notably contributed by individuals like B. vulgatus, B. dorei, B. fragilis, P. ruminicola, and P. copri. The presence of protozoans like Trypanosoma, Trichomonas, and Leishmania was also identified among other commensal eukaryotes. Moreover, there was an abundant presence of bacteriophages targeting probiotic organisms like Lactobacillus among the identified DNA viruses.

Comparative data analsysis of two multi-drug resistant homoserine lactone and rhamnolipid producing Pseudomonas aeruginosa from diabetic foot infected patient.

Pseudomonas aeruginosa generally forms strong biofilm during chronic condition of wound. The whole mechanism of biofilm formation works in tandem with quorum sensing circuit of the organism in order to produce virulence. Here we report the draft genome sequence of two diabetic foot ulcer Pseudomonas aeruginosa isolates (VIT PC 7 and VIT PC 9) displaying homoserine lactone, rhamnolipid producing, biofilm phenotype and antibiotic resistance genes related to carbapenem, aminoglycoside, beta- lactamase and tetracycline resistance. The whole genome sequencing library was prepared according to the Oxford Nanopore's SQK-LSK108 kit protocol on Oxford Nanopore's Minion platform. The 7.1 Mb and 6.3-Mb draft genome sequence with GC content of 65.8% and 66.4% respectively provides insight into their resistance mechanism and virulence factors.