scholarly journals Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

2009 ◽  
Vol 191 (15) ◽  
pp. 4854-4862 ◽  
Author(s):  
Patricia Romero ◽  
Nicholas J. Croucher ◽  
N. Luisa Hiller ◽  
Fen Z. Hu ◽  
Garth D. Ehrlich ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Major Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Bioinformatic Tools ◽  
Dichelobacter Nodosus ◽  
First Time

ABSTRACT Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage φSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.

scholarly journals Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa

2021 ◽  
Vol 9 (9) ◽  
pp. 1928
Author(s):  
Tawanda E. Maguvu ◽  
Cornelius C. Bezuidenhout
Keyword(s):  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Taxonomic Classification ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Pathogens ◽  
Wastewater Treatment Process ◽  
North West

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

scholarly journals Complete genome sequence analysis of a lytic Shigella flexneri vB_SflS-ISF001 bacteriophage

2019 ◽  
pp. 99-112 ◽  
Author(s):  
Khashayar SHAHIN ◽  
Majid BOUZARI ◽  
Ran WANG
Keyword(s):  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Shigella Flexneri ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Shigella Spp ◽  
Enteric Infections

Shigellosis is one of the most important acute enteric infections caused by different species of Shigella, such as Shigella flexneri. Despite the use of antibiotic therapy to reduce disease duration, this approach is becoming less effective due to the emergence of antibiotic resistance among Shigella spp. Bacteriophages have been introduced as an alternative for controlling shigellosis. However, the bacteriophages must be without any lysogenic or virulence factors, toxin coding, or antibiotic-resistant genes. In this study, the whole genome sequence of vB_SflS-ISF001, a virulent Siphoviridae bacteriophage specific for Shigella flexneri, was obtained, and a comparative genomic analysis was carried out to identify its properties and safety. vB_SflS-ISF001 genomic DNA was measured at 50,552 bp with 78 deduced open reading frames (ORFs), with 24 ORFs (30.77%) sharing similarities with proteins from the genomes of homologous phages that had been reported earlier. Genetic analysis classifies it under the genus T1virus of the subfamily Tunavirinae. Moreover, comparative genomic analysis revealed no undesirable genes in the genome of vB_SflS-ISF001, such as antibiotic resistance, virulence, lysogeny, or toxin-coding genes. The results of this investigation indicate that vB_SflS-ISF001 is a new species, and confirm its safety for the biocontrol of S. flexneri.

scholarly journals Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success ◽  
First Time

Abstract Background Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of these structures is highly energy intensive and as such flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report for the first time on the occurrence of two peritrichous flagellar loci in some enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.

scholarly journals Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment

2017 ◽  
Vol 83 (15) ◽  
Author(s):  
Kimiho Omae ◽  
Yasuko Yoneda ◽  
Yuto Fukuyama ◽  
Takashi Yoshida ◽  
Yoshihiko Sako
Keyword(s):  
Electron Donor ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
High Energy ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Composition Analysis ◽  
Co Dehydrogenase ◽  
Content Type ◽  
Energy Converting

ABSTRACT Calderihabitans maritimus KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the de novo sequencing and feature analysis of the C. maritimus KKC1 genome. Genome-based phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore, C. maritimus KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Our analysis revealed that three cooS genes formed known gene clusters in other microorganisms, i.e., cooS-acetyl coenzyme A (acetyl-CoA) synthase (which contained a frameshift mutation), cooS–energy-converting hydrogenase, and cooF-cooS-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that these cooS genes likely evolved from a common ancestor. Collectively, these data suggest that C. maritimus KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which show adaptation at a thermodynamic limit. IMPORTANCE Calderihabitans maritimus KKC1 and members of the genus Moorella are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H2 production, whereas the latter include acetogenic bacteria that grow on H2 plus CO2 with acetate production. Both species may require reduced ferredoxin as an actual “energy equivalent,” but ferredoxin is a low-potential electron carrier and requires a high-energy substrate as an electron donor for reduction. Comparative genomic analysis revealed that C. maritimus KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike Moorella species. This suggests that C. maritimus KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic Moorella, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.

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