The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1

Abstract Background Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear. Results In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC. Conclusions This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400563 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3057-3066 ◽

Cited By ~ 2

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.

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Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria monocytogenes

Journal of Bacteriology ◽

10.1128/jb.00758-06 ◽

2006 ◽

Vol 188 (21) ◽

pp. 7405-7415 ◽

Cited By ~ 74

Author(s):

Torsten Hain ◽

Christiane Steinweg ◽

Carsten Tobias Kuenne ◽

André Billion ◽

Rohit Ghai ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Genome Sequence ◽

Genomic Analysis ◽

Open Reading Frames ◽

Listeria Innocua ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Circular Chromosome ◽

Evolutionary Paths ◽

Listeria Welshimeri

ABSTRACT We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an FoF1 ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of “fitness” genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.

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Biology and Genome Sequence of Streptococcus mutans Phage M102AD

Applied and Environmental Microbiology ◽

10.1128/aem.07726-11 ◽

2012 ◽

Vol 78 (7) ◽

pp. 2264-2271 ◽

Cited By ~ 12

Author(s):

Allan L. Delisle ◽

Ming Guo ◽

Natalia I. Chalmers ◽

Gerard J. Barcak ◽

Geneviève M. Rousseau ◽

...

Keyword(s):

Streptococcus Mutans ◽

Genome Sequence ◽

Gc Content ◽

Genomic Analysis ◽

Streptococcus Thermophilus ◽

Open Reading Frames ◽

Comparative Genomic ◽

Content Type ◽

Close Relationship ◽

Virion Structure

ABSTRACTM102AD is the new designation for aStreptococcus mutansphage described in 1993 as phage M102. This change was necessitated by the genome analysis of anotherS. mutansphage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed thatS. mutansphage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains ofS. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3′-overhangcossite that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship betweenS. mutansphages M102AD and M102 as well as withStreptococcus thermophilusphages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.

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

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-14-0326-fi ◽

2015 ◽

Vol 28 (3) ◽

pp. 249-260 ◽

Cited By ~ 21

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.

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Insights from the Complete Genome Sequence of Bacillus circulans GN03, a Plant Growth-Promoting Bacterium Isolated from Pak Choi Cabbage (Brassica chinensis L.) Root Surface

Microbiology Resource Announcements ◽

10.1128/mra.00581-20 ◽

2020 ◽

Vol 9 (34) ◽

Author(s):

Lijun Qin ◽

Xingyong Yang ◽

Hong Shen

Keyword(s):

Plant Growth ◽

Genome Sequence ◽

Gc Content ◽

Root Surface ◽

Bacillus Circulans ◽

Whole Genome Sequence ◽

Circular Chromosome ◽

Pak Choi ◽

Plant Growth Promoting ◽

Growth Promoting

ABSTRACT A plant growth-promoting rhizobacterium, Bacillus circulans GN03, was isolated from the root surface of pak choi cabbage. Here, we report the whole-genome sequence of the GN03 strain, which includes a circular chromosome (5,217,129 bp; GC content, 35.64%) and a plasmid (181,705 bp; GC content, 31.62%).

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Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

Microbiology Resource Announcements ◽

10.1128/mra.01011-21 ◽

2021 ◽

Vol 10 (50) ◽

Author(s):

Asha Santhi ◽

Venkatesh Subramanian ◽

Krishnaveni Muthan

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Gc Content ◽

Draft Genome Sequence ◽

Whole Genome Sequence ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Content Type ◽

Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

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

FEMS Microbiology Letters ◽

10.1093/femsle/fnab018 ◽

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.

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Whole-Genome Sequence of Mycobacterium ulcerans CSURP7741, a French Guianan Clinical Isolate

Microbiology Resource Announcements ◽

10.1128/mra.00215-19 ◽

2019 ◽

Vol 8 (29) ◽

Cited By ~ 1

Author(s):

Jamal Saad ◽

Marine Combe ◽

Nassim Hammoudi ◽

Pierre Couppié ◽

Romain Blaizot ◽

...

Keyword(s):

Clinical Isolate ◽

Genome Sequence ◽

Buruli Ulcer ◽

Gc Content ◽

Mycobacterium Ulcerans ◽

Whole Genome Sequence ◽

Whole Genome ◽

Protein Coding ◽

Content Type ◽

Rna Genes

Combined Nanopore and Illumina whole-genome sequencing of a French Guianan Mycobacterium ulcerans (Buruli ulcer agent) clinical isolate yielded a 5.12-Mbp genome with a 65.5% GC content, 5,215 protein-coding genes, and 51 predicted RNA genes. This publicly available M. ulcerans whole-genome sequence from a strain isolated in South America is closely related to M. ulcerans subsp. liflandii.

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Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil

Genome Announcements ◽

10.1128/genomea.00416-16 ◽

2016 ◽

Vol 4 (3) ◽

Cited By ~ 3

Author(s):

Fábio Faria da Mota ◽

Renata Estebanez Vollú ◽

Diogo Jurelevicius ◽

Lucy Seldin

Keyword(s):

Soil Sample ◽

Genome Sequence ◽

Noncoding Rnas ◽

Whole Genome Sequence ◽

Trna Genes ◽

Whole Genome ◽

Antarctic Soil ◽

Circular Chromosome ◽

Protein Coding ◽

Protein Coding Genes

The whole genome of Rummeliibacillus stabekisii PP9, isolated from a soil sample from Antarctica, consists of a circular chromosome of 3,412,092 bp and a circular plasmid of 8,647 bp, with 3,244 protein-coding genes, 12 copies of the 16S-23S-5S rRNA operon, 101 tRNA genes, and 6 noncoding RNAs (ncRNAs).

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

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.706 ◽

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.

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