scholarly journals Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 325 ◽  
Author(s):  
Jaswal ◽  
Pathak ◽  
III ◽  
III ◽  
Seaman ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Growth Conditions ◽  
Taxonomic Composition ◽  
Metagenomic Analysis ◽  
Whole Genome Sequence ◽  
Resistant Bacteria ◽  
Comparative Genomic ◽  
Soil Microbial Diversity ◽  
Penicillium Species ◽  
Isolation And Characterization

Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.

scholarly journals Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol

2015 ◽  
Vol 28 (3) ◽  
pp. 249-260 ◽  
Author(s):  
Claudia E. Calderón ◽  
Cayo Ramos ◽  
Antonio de Vicente ◽  
Francisco M. Cazorla
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Antifungal Compound ◽  
Antifungal Compounds ◽  
Pseudomonas Chlororaphis ◽  
Biosynthetic Genes ◽  
Biocontrol Activity

Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.

scholarly journals Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Prince Kumar ◽  
Mukesh K. Meghvansi ◽  
D. V. Kamboj
Keyword(s):  
Sequence Data ◽  
Burst Size ◽  
Genomic Analysis ◽  
Dna Helicase ◽  
Shigella Dysenteriae ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Parsimony Method

AbstractShigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.

Comparison of three species of Elizabethkingia genus by whole-genome sequence analysis

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Information Storage ◽  
Whole Genome Sequence ◽  
Neonatal Meningitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Significant Finding ◽  
Beta Lactams ◽  
Clusters Of Orthologous Groups

Abstract Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that ‘metabolism’ occupied the largest part in core genome, ‘information storage and processing’ was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.

scholarly journals Comparative genomic analysis and characterization of Staphylococcus sp. AOAB, isolated from a notoriously invasive Mnemiopsis leidyi gut revealed multiple antibiotic resistance determinants

2021 ◽  
Author(s):  
Richard M. Mariita ◽  
Mohammad J. Hossain ◽  
Anthony G. Moss
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Mnemiopsis Leidyi ◽  
Comparative Genomic ◽  
Marker Genes ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Isolation And Characterization ◽  
Taxonomic Approach

AbstractHere, we describe the isolation and characterization of a coagulase-negative, vancomycin and oxacillin-susceptible novel bacterium of the genus Staphylococcus. Staphylococcus sp. strain AOAB was isolated from the stomodeum (gut) of the Mnemiopsis leidyi from Mobile Bay, Alabama USA. A polyphasic taxonomic approach comprised of phenotypic, chemotaxonomic and genotypic characteristics was used for analysis. The dominant respiratory quinone detected was MK-7 (100%). Major cellular fatty acids were anteiso-C15:0 (40.52%), anteiso-C17:0 (13.04 %), C-18:0 (11.53%) and C-20:0 (10.45%). The polar lipid profile consisted of glycolipid, phospholipid, phosphatidylglycerol and diphosphatidylglycerol. Although strain AOAB had a 16SrRNA gene sequence similarity of 99% with S. warneri SG1, S. pasteuri, S. devriesei KS-SP_60, S. lugdunensis HKU09-01, S. epidermidis RP62A, S. haemolyticus JCSC1435 and S. hominis DM 122, it was be distinguished from those species based on Multi-Locus Sequence Analysis (MLSA) using 6 marker genes (16S rRNA, hsp60, rpoB, dnaJ, sodA and tuf). MLSA revealed strain AOAB to be closely related to S. warneri SG1 and S. pasteuri SP1 but distinct from two hitherto known species. These results were confirmed by Average Nucleotide Identity (closest ANI of 84.93% and 84.58% identity against S. warneri SG1 and S. pasteuri SP1 respectively). In-silico DNA-DNA hybridization was <70% (33.1 % and 32.8% against S. warneri SG1 and S. pasteuri SP1 respectively), which further confirmed that the strain was a potential novel Staphylococcus species.

scholarly journals Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

2019 ◽  
Vol 9 (10) ◽  
pp. 3057-3066 ◽  
Author(s):  
Eoin O’Connor ◽  
Jamie McGowan ◽  
Charley G. P. McCarthy ◽  
Aniça Amini ◽  
Helen Grogan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agaricus Bisporus ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Single Strain ◽  
Protein Coding Genes ◽  
Starting Point

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

scholarly journals Isolation and Characterization of a Novel Phage for Controlling Multidrug-Resistant Klebsiella pneumoniae

2020 ◽  
Vol 8 (4) ◽  
pp. 542 ◽  
Author(s):  
Qin Peng ◽  
Meng Fang ◽  
Xushan Liu ◽  
Chunling Zhang ◽  
Yue Liu ◽  
...  
Keyword(s):  
Bacterial Pathogens ◽  
Physical Stability ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
High Antibacterial Activity ◽  
Isolation And Characterization ◽  
Hospital Sewage ◽  
Siphoviridae Family

The emergence of multidrug-resistant bacterial pathogens has severely threatened global health. A phage with the ability to efficiently and specifically lyse bacteria is considered an alternative for controlling multidrug-resistant bacterial pathogens. The discovery of novel agents for controlling the infections caused by K. pneumoniae is urgent due to the broad multidrug-resistance of K. pneumoniae. Only a few phage isolates have been reported to infect multidrug-resistant K. pneumoniae. In this study, by using the multidrug-resistant K. pneumoniae strain as an indicator, a novel phage called vB_KleS-HSE3, which maintains high antibacterial activity and high physical stability, was isolated from hospital sewage. This phage infected one of four tested multidrug-resistant K. pneumoniae strains. This phage belongs to the Siphoviridae family and a comparative genomic analysis showed that this phage is part of a novel phage lineage among the Siphoviridae family of phages that infect strains of Klebsiella. Based on its features, the vB_KleS-HSE3 phage has potential for controlling infections caused by multidrug-resistant K. pneumoniae.

scholarly journals 638. Comparative Genomics of Mycoplasma pneumoniae Isolated From Children with Pneumonia: South Korea, 2010–2016

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S295-S295
Author(s):  
Hoan J Lee ◽  
Joon Kee Lee ◽  
Yun Young Choi ◽  
Ji Young Park ◽  
Moon-Woo Seong ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome

Abstract Background This study applied high-throughput whole-genome sequencing (WGS) technologies to investigate the comparative genomics of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during two epidemics from 2010 to 2016 in comparison with a global collection of 48 Mycoplasma pneumoniae strains which includes seven countries ranging from 1944 to 2017. Methods A total number of 30 M. pneumoniae strains were selected for whole-genome sequence analysis from two epidemics, 2010–2012 and 2014–2016. Next-generation sequencing (NGS) of all M. pneumoniae strains was performed using the Illumina MiSeq desktop sequencer. Comparative genomic analysis was performed using BLAST Ring Image Generator (BRIG), MAUVE, MAFFT, CLC Phylogeny Module, SnpEff, and Pathosystems Resource Integration Center (PATRIC). Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to>99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea, formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusion The comparative genomics of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high. Disclosures All authors: No reported disclosures.

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 Phage Selective Pressure Reduces Virulence of Hypervirulent Klebsiella pneumoniae Through Mutation of the wzc Gene

2021 ◽  
Vol 12 ◽  
Author(s):  
Lingjie Song ◽  
Xianggui Yang ◽  
Jinwei Huang ◽  
Xiaokui Zhu ◽  
Guohui Han ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Analysis ◽  
Resistant Bacteria ◽  
Comparative Genomic ◽  
Wild Type ◽  
Bacteriophage Therapy ◽  
Deletion Mutations ◽  
Invasive Infections

Hypervirulent Klebsiella pneumoniae (hvKp), one of the major community-acquired pathogens, can cause invasive infections such as liver abscess. In recent years, bacteriophages have been used in the treatment of K. pneumoniae, but the characteristics of the phage-resistant bacteria produced in the process of phage therapy need to be evaluated. In this study, two Podoviridae phages, hvKpP1 and hvKpP2, were isolated and characterized. In vitro and in vivo experiments demonstrated that the virulence of the resistant bacteria was significantly reduced compared with that of the wild type. Comparative genomic analysis of monoclonal sequencing showed that nucleotide deletion mutations of wzc and wcaJ genes led to phage resistance, and the electron microscopy and mucoviscosity results showed that mutations led to the loss of the capsule. Meanwhile, animal assay indicated that loss of capsule reduced the virulence of hvKp. These findings contribute to a better understanding of bacteriophage therapy, which not only can kill bacteria directly but also can reduce the virulence of bacteria by phage screening.

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