Ithin bacterial genomes, PHASTER, with default arguments [36]. A total of 150 prophage-like
Ithin bacterial genomes, PHASTER, with default arguments [36]. A total of 150 prophage-like components have been detected (Supplementary Table S1), of which 104 had been classified as intact, 39 as incomplete and 7 as questionable (Figure 1a, Supplementary Table S2). One strain was found to harbor only a single prophage, SBP-3264 Purity & Documentation whilst the remaining 39 strains (97.5 ) have at the very least two prophages, which indicates that prophages are abundant within the K. pneumoniae genome. The total number of prophages per strain ranged from 1 to 10, with an typical of three.7 prophages per strain, and most strains harbored either two (n = 13) or four (n = 11) prophages (Figure 1b).Figure 1. (A) Box plot displaying the total, intact, incomplete, questionable, and defective (incomplete questionable) prophages of Klebsiella pneumoniae. (B) Bars graph displaying the distribution of total prophages (intact, incomplete, and questionable) in K. pneumoniae strains.A considerably larger prevalence of incomplete and questionable prophages was expected due to the fact intact prophages are usually below strong selection or genetic degradation by bacteria for rapid deletion from bacterial genomes [53,54]. As an alternative, we discovered that 97.five in the K. pneumoniae strains include intact prophages. Strains isolated from sufferers 1, six, 21, 23, 24, 25 and 26 contained only intact prophages, whereas strains isolated from sufferers 2, 3, five, 9, 11, 14, 16, 17, 18 and 19 contained intact and incomplete prophages, and strains isolated from individuals four, 7, 8, 10, 13 and 15 contained intact, incomplete, and questionable prophages (Supplementary Table S2). Additionally, sufferers had been colonized with a single K. pneumoniae strain, except sufferers 1, 3, 15, 17, 19, 23 and 26, which have been colonized with 6, 2, 4, 5, 3, 2 and 2 strains, respectively. It really is significant to note that the genomes were divided into contigs, which implies that PHASTER might have underestimated the right quantity of intact prophages (some had been split into various contigs and identified as incomplete or questionable prophages). three.2. GSK2646264 MedChemExpress genome Qualities of K. pneumoniae Prophages The shortest (remnant) prophage sequence is eight.9 kbp, as well as the greatest is 60.eight kbp, using the coding sequences (CDS) number ranging from 12 to 75. The typical GC content material in all 150 prophages is 52.2 (min 45.1 , max 60.2 ), whilst the average bacterial GC content material isMicroorganisms 2021, 9,six of57.1 (min 54.9 , max 57.4 ) (Supplementary Table S1), which suggests horizontal gene transfer with the prophage region. Genomic evaluation of the upstream and downstream regions in the prophage insertion web-sites revealed that prophages are integrated among distinct coding regions: proteins involved in metabolic pathways (18.1 ), tRNA genes (16.1 ), transporters (11.1 ), recombinant proteins (5.four ), protein synthesis (five.4 ), transferases (four.7 ), transcriptional regulators (four.0 ), membrane proteins (2.0 ), ribosome biogenesis (1.three ) and sequences showing homology with other bacterial genes (eight.7 ). Within the case of some incomplete prophages, it was not probable to identify the insertion site (23.two ) (Supplementary Table S1). Moreover, related prophages from different K. pneumoniae strains had a conserved insertion web-site involving exactly the same two contiguous genes of K. pneumoniae reference genomes (GenBank Accession: CP003200.1 and NZ_CP040993.1). For the objective of our analysis, incomplete and questionable prophage sequences divided into unique contigs have been scaffolded as described in components and procedures. Immediately after this analysis.
