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July 7, 2019

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii.

Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. Copyright © 2015 Elsevier Inc. All rights reserved.

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July 7, 2019

Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment.

We sequenced the genomes of five new Methylophilaceae strains isolated from Lake Washington sediment. We used the new sequences to sort these new strains into specific Methylophilaceae ecotypes, including one novel ecotype. The new genomes expand the known diversity of Methylophilaceae and provide new models for studying the ecology of methylotrophy. Copyright © 2015 McTaggart et al.

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July 7, 2019

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.

The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an outbreak mediated by an endemic plasmid. We describe the interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from a single institution over 5 years following the introduction of blaKPC in August 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16 distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp was imported into the institution on numerous occasions, with other blaKPC plasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and spread locally, making it a future candidate for clinical persistence and dissemination. Copyright © 2015, Mathers et al.

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July 7, 2019

Complete genome sequence of Sphingobacterium sp. strain ML3W, isolated from wings of Myotis lucifugus infected with white nose syndrome.

Sphingobacterium sp. strain ML3W was isolated from the wing of a bat infected with white nose syndrome. We report the complete 5.33-Mb genome sequence of Sphingobacterium sp. strain ML3W, obtained using Pacific Biosciences technology. Being the second complete Sphingobacterium sequence, this will increase knowledge of the genus. Copyright © 2015 Smith et al.

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July 7, 2019

Complete genome sequence of the Clostridium difficile laboratory strain 630¿ erm reveals differences from strain 630, including translocation of the mobile element CTn 5.

Background Clostridium difficile strain 630¿erm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.ResultsIn addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.ConclusionsTogether, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.

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July 7, 2019

Complete genome sequence of Yersinia ruckeri strain CSF007-82, etiologic agent of red mouth disease in salmonid fish.

We present the complete, closed, and finished chromosomal and extrachromosomal genome sequences of Yersinia ruckeri strain CSF007-82, the etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted coding sequences (CDS), 7 ribosomal operons, and 80 tRNAs. Copyright © 2015 Nelson et al.

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July 7, 2019

Complete genome sequence of the unclassified iron-oxidizing, chemolithoautotrophic Burkholderiales bacterium GJ-E10, isolated from an acidic river.

Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan, is an unclassified, iron-oxidizing chemolithoautotrophic bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced by using three types of next-generation sequencers and the sequences were then confirmed by PCR-based Sanger sequencing. Copyright © 2015 Fukushima et al.

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July 7, 2019

Complete genome sequence of BS49 and draft genome sequence of BS34A, Bacillus subtilis strains carrying Tn916.

Bacillus subtilis strains BS49 and BS34A, both derived from a common ancestor, carry one or more copies of Tn916, an extremely common mobile genetic element capable of transfer to and from a broad range of microorganisms. Here, we report the complete genome sequence of BS49 and the draft genome sequence of BS34A, which have repeatedly been used as donors to transfer Tn916, Tn916 derivatives or oriTTn916-containing plasmids to clinically important pathogens. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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July 7, 2019

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and rainbow trout fry mortality syndrome in salmonid fishes and is associated with significant losses in the aquaculture industry. The virulence factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly understood. Moreover, at the present time, there are no effective vaccines and control using antimicrobial agents is problematic due to growing antimicrobial resistance and the fact that sick fish don’t eat. In the hopes of identifying vaccine and therapeutic targets, we sequenced the genome of the type strain ATCC 49418 which was isolated from the kidney of a Coho salmon (Oncorhychus kisutch) in Washington State (U.S.A.) in 1989. The genome is 2,715,909 bp with a G+C content of 32.75%. It contains 6 rRNA operons, 49 tRNA genes, and is predicted to encode 2,329 proteins.

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July 7, 2019

Complete genome sequence of Bifidobacterium adolesentis BBMN23, a probiotic strain from healthy centenarian.

Bifidobacterium adolesentis BBMN23 (CGMCC No. 2264) was a probiotic strain originated from the feces of a centenarian. It is an excellent model for the study of the adaptation of genus bifidobacteria to adult human gut, which is a key factor in bifidobacterial strains that allows them to persist in gut and become useful in the food and medical industries. In the present study the complete genome sequence of BBMN23 is presented to provide insight into this strain. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

A17, the first sequenced strain of Lactococcus lactis subsp. cremoris with potential immunomodulatory functions.

Lactococcus lactis subsp. cremoris A17, isolated from Taiwan fermented cabbage, is the first sequenced strain of L. lactis subsp. cremoris with immunomodulatory activity and antiallergic functions. The resulting A17 draft genome contains 2,679,936 bp and indicates that A17 is a potential exopolysaccharide-producing strain without any known virulence gene. Copyright © 2015 Yang et al.

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July 7, 2019

Draft genome of Janthinobacterium sp. RA13 isolated from Lake Washington sediment.

Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is announced. From the genome content, a versatile life-style is predicted, but not bona fide methylotrophy. With the availability of its genomic sequence, Janthinobacterium sp. RA13 presents a prospective model for studying microbial communities in lake sediments. Copyright © 2015 McTaggart et al.

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July 7, 2019

Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.

Base J (ß-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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