 
REBASE version 901                                              refmgr.901
 
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    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2018.   All rights reserved.
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Rich Roberts                                                    Dec 28 2018
 
TY  - Type of reference.
AU  - Authors, listed one per line.
TI  - Title.
JO  - Journal.
PY  - Year.
SP  - Starting page.
EP  - Ending page.
VL  - Volume number.
AB  - Abstract.
ER  - End of Record.

TY  - JOUR
AU  - Alejo-Viderique A.
AU  - Contreras-Castro L.
AU  - Felix-Gastelum R.
AU  - Maldonado L.A.
AU  - Quintana E.T.
TI  - Draft Genome Sequence of a Streptomycete Isolated from Potato Common Scab Lesions in the State of Sinaloa, Mexico.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00827
EP  - e00818
VL  - 7
AB  - Streptomyces sp. strain V2 was isolated from potato scab lesions in the state of  Sinaloa,
AB  - Mexico, and appears to be responsible for outbreaks in the area. The
AB  - thaxtomin cluster was found in the approximately 10.2-Mb genome; this cluster is
AB  - associated with potato common scab disease in other potato pathogens.
ER  -

TY  - JOUR
AU  - Arai H.
AU  - Shomura Y.
AU  - Higuchi Y.
AU  - Ishii M.
TI  - Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus  thermoluteolus TH-1.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00857
EP  - e00818
VL  - 7
AB  - Hydrogenophilus spp., which are moderately thermophilic aerobic betaproteobacteria, are widely
AB  - distributed in geothermal environments. They fix
AB  - carbon dioxide via the Calvin-Benson-Bassham cycle and exhibit rapid autotrophic
AB  - growth using hydrogen as an energy source. Here, we report the complete genome
AB  - sequence of Hydrogenophilus thermoluteolus strain TH-1.
ER  -

TY  - JOUR
AU  - Atack J.M.
AU  - Weinert L.A.
AU  - Tucker A.W.
AU  - Husna A.U.
AU  - Wileman T.M.
AU  - Hadjirin N.F.
AU  - Hoa N.T.
AU  - Parkhill J.
AU  - Maskell D.J.
AU  - Blackall P.J.
AU  - Jennings M.P.
TI  - Streptococcus suis contains multiple phase-variable methyltransferases that show  a discrete lineage distribution.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 11466
EP  - 11476
VL  - 46
AB  - Streptococcus suis is a major pathogen of swine, responsible for a number of chronic and acute
AB  - infections, and is also emerging as a major zoonotic pathogen, particularly in South-East
AB  - Asia. Our study of a diverse population of S. suis shows that this organism contains both Type
AB  - I and Type III phase-variable methyltransferases. In all previous examples, phase-variation of
AB  - methyltransferases results in genome wide methylation differences, and results in differential
AB  - regulation of multiple genes, a system known as the phasevarion (phase-variable regulon). We
AB  - hypothesized that each variant in the Type I and Type III systems encoded a methyltransferase
AB  - with a unique specificity, and could therefore control a distinct phasevarion, either by
AB  - recombination-driven shuffling between different specificities (Type I) or by biphasic on-off
AB  - switching via simple sequence repeats (Type III). Here, we present the identification of the
AB  - target specificities for each Type III allelic variant from S. suis using single-molecule,
AB  - real-time methylome analysis. We demonstrate phase-variation is occurring in both Type I and
AB  - Type III methyltransferases, and show a distinct association between methyltransferase type
AB  - and presence, and population clades. In addition, we show that the phase-variable Type I
AB  - methyltransferase was likely acquired at the origin of a highly virulent zoonotic
AB  - sub-population.
ER  -

TY  - JOUR
AU  - Audisio M.C.
AU  - Albarracin L.
AU  - Torres M.J.
AU  - Saavedra L.
AU  - Hebert E.M.
AU  - Villena J.
TI  - Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis  mellifera L.).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00975
EP  - e00918
VL  - 7
AB  - This report describes the draft genome sequences of Lactobacillus salivarius A3iob and
AB  - Lactobacillus johnsonii CRL1647, probiotic strains isolated from the
AB  - gut of honeybee Apis mellifera workers. The reads were generated by a
AB  - whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were
AB  - assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the
AB  - A3iob and CRL1647 strains, respectively. The draft genome sequences of L.
AB  - salivarius A3iob and L. johnsonii CRL1647 will be useful for further studies of
AB  - the specific genetic features of these strains and for understanding the
AB  - mechanisms of their probiotic properties.
ER  -

TY  - JOUR
AU  - Aziz S.
AU  - Mast Y.
AU  - Wohlleben W.
AU  - Gross H.
TI  - Draft Genome Sequence of the Pristinamycin-Producing Strain Streptomyces sp. SW4, Isolated from Soil in Nusa Kambangan, Indonesia.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00912
EP  - e00918
VL  - 7
AB  - Streptomyces sp. strain SW4 exhibited broad-spectrum antibacterial activity toward
AB  - Gram-positive and Gram-negative pathogens. The 7.5-Mb draft genome
AB  - sequence gives insight into the complete secondary metabolite production capacity
AB  - and reveals genes putatively responsible for its antibacterial activity.
ER  -

TY  - JOUR
AU  - Baaziz H.
AU  - Lemaire O.N.
AU  - Jourlin-Castelli C.
AU  - Iobbi-Nivol C.
AU  - Mejean V.
AU  - Alatou R.
AU  - Fons M.
TI  - Draft Genome Sequence of Shewanella algidipiscicola H1, a Highly Chromate-Resistant Strain Isolated from Mediterranean Marine Sediments.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00905
EP  - e00918
VL  - 7
AB  - The ability of different Shewanella spp. to convert heavy metals and toxic substances into
AB  - less toxic products by using them as electron acceptors has led
AB  - to their use in environmental clean-up strategies. We present here the draft
AB  - genome sequence of Shewanella algidipiscicola H1, a strain resistant to high
AB  - concentrations of chromates.
ER  -

TY  - JOUR
AU  - Baek K.
AU  - Chung E.J.
AU  - Choi G.G.
AU  - Nam Y.H.
AU  - Choi A.
TI  - Draft Genome Sequence of Deinococcus koreensis SJW1-2(T), a Gamma Radiation-Resistant Bacterium Isolated from River Water.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00894
EP  - e00818
VL  - 7
AB  - Deinococcus koreensis SJW1-2(T) was isolated from river water and was observed to be highly
AB  - resistant to gamma radiation. In this study, we report a draft genome
AB  - sequence which revealed that SJW1-2(T) possesses genes involved in nucleotide
AB  - excision repair. The primary genomic information will aid in elucidating the DNA
AB  - repair mechanism during ionizing radiation.
ER  -

TY  - JOUR
AU  - Bajpai A.
AU  - Shende K.K.
AU  - Meena N.
AU  - Suravajhala P.
AU  - Medicherla K.M.
AU  - Johri B.N.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas protegens Strain BNJ-SS-45, Isolated from Rhizosphere Soil of Wheat (Triticum  aestivum).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00926
EP  - e00918
VL  - 7
AB  - Here, we present the draft genome sequence of Pseudomonas protegens strain BNJ-SS-45, which
AB  - was isolated from wheat rhizosphere. The genome is assembled
AB  - with 7,116,445 bp with a GC content of 63.34% consisting of 32 scaffolds. The
AB  - genome is useful in prediction of secondary metabolites, particularly rhizoxin,
AB  - pyoverdine, and bacteriocin.
ER  -

TY  - JOUR
AU  - Bangera S.R.
AU  - Umakanth S.
AU  - Mukhopadhyay A.K.
AU  - Leekitcharoenphon P.
AU  - Chowdhury G.
AU  - Hendriksen R.S.
AU  - Ballal M.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00990
EP  - e00918
VL  - 7
AB  - Salmonella enterica subsp. enterica serotype Typhimurium sequence type 313 (ST313) is most
AB  - commonly associated with invasive nontyphoidal Salmonella disease
AB  - in Africa among patients with HIV infection and malignancy. Here, we report a
AB  - draft genome sequence of S. Typhimurium ST313, isolated from an elderly
AB  - immunosuppressed patient from India with non-Hodgkins lymphoma.
ER  -

TY  - JOUR
AU  - Boyd D.A.
AU  - Mataseje L.F.
AU  - Pelude L.
AU  - Mitchell R.
AU  - Bryce E.
AU  - Roscoe D.
AU  - Embree J.
AU  - Katz K.
AU  - Kibsey P.
AU  - Lavallee C.
AU  - Simor A.E.
AU  - Taylor G.
AU  - Turgeon N.
AU  - Langley J.M.
AU  - Amaratunga K.
AU  - Mulvey M.R.
TI  - Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16.
JO  - J. Antimicrob. Chemother.
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - Objectives: Globally there is an increased prevalence of carbapenem-resistant
AB  - Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs)
AB  - in the hospital setting. This increase prompted the Canadian Nosocomial Infection
AB  - Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and
AB  - infections identified from patients in CNISP-participating hospitals between 2010
AB  - and 2016. Methods: Participating acute care facilities across Canada submitted
AB  - CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from
AB  - medical records using a standardized questionnaire. WGS was conducted on all CRAs
AB  - and data underwent single nucleotide variant analysis, resistance gene detection
AB  - and MLST. Results: The 7 year incidence rate of CRA was 0.02 per 10 000 patient
AB  - days and 0.015 per 1000 admissions, with no significant increase observed over
AB  - the surveillance period (P > 0.73). Ninety-four CRA isolates were collected from
AB  - 58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%)
AB  - was the most common due to two separate clusters, followed by the OXA-23 group
AB  - (41.9%). Patients with a travel history were associated with 38.8% of CRA cases.
AB  - The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA
AB  - cases. Colistin was the most active antimicrobial agent (95.8% susceptibility).
AB  - Conclusions: CRA remains uncommon in Canadian hospitals and the incidence did not
AB  - increase from 2010 to 2016. Almost half of the cases were from two clusters
AB  - harbouring OXA-235-group enzymes. Previous medical treatment during travel
AB  - outside of Canada was common.
ER  -

TY  - JOUR
AU  - De Leon M.P.
AU  - Park A.Y.
AU  - Montecillo A.D.
AU  - Siringan M.A.T.
AU  - Rosana A.R.R.
AU  - Kim S.G.
TI  - Near-Complete Genome Sequences of Streptomyces sp. Strains AC1-42T and AC1-42W, Isolated from Bat Guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00904
EP  - e00918
VL  - 7
AB  - Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave,
AB  - Mabini, Pangasinan, Philippines, are active against Bacillus
AB  - subtilis subsp. subtilis KCTC 3135(T). The near-complete genome sequences
AB  - reported here represent a possible source of ribosomally synthesized,
AB  - posttranslationally modified peptides, such as lantipeptides, bacteriocins,
AB  - linaridin, and a lasso peptide.
ER  -

TY  - JOUR
AU  - Denny A.L.
AU  - Arruda S.E.
TI  - Draft Genome Sequences of Escherichia coli Strains FP2 and FP3, Isolated from the Canada Goose (Branta canadensis).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01079
EP  - e01018
VL  - 7
AB  - Draft genomes of two strains of Escherichia coli, FP2 and FP3, isolated from the  feces of the
AB  - Canada goose (Branta canadensis), were sequenced. Genome sizes were
AB  - 5.26 Mb with a predicted G+C content of 50.54% (FP2) and 5.07 Mb with a predicted
AB  - G+C content of 50.41% (FP3).
ER  -

TY  - JOUR
AU  - Dumigan C.R.
AU  - Perry G.E.
AU  - Pauls K.P.
AU  - Raizada M.N.
TI  - Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00846
EP  - e00818
VL  - 7
AB  - Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte
AB  - solubilizes rock phosphate and was isolated from Zea
AB  - nicaraguensis. The genome contains 4,579,108 bp in 264 contigs.
ER  -

TY  - JOUR
AU  - Estes A.M.
AU  - Hearn D.J.
AU  - Nadendla S.
AU  - Pierson E.A.
AU  - Dunning H.J.C.
TI  - Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01068
EP  - e01018
VL  - 7
AB  - Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive
AB  - fruit fly Bactrocera oleae. The 5.07-kbp genome sequence of
AB  - Enterobacter sp. strain OLF encodes metabolic pathways that allow the bacterium
AB  - to partially supplement the diet of the olive fly when its dominant endosymbiont,
AB  - Erwinia dacicola, is absent.
ER  -

TY  - JOUR
AU  - Fan X.
AU  - Tang J.
AU  - Nie L.
AU  - Huang J.
AU  - Wang G.
TI  - High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30(T).
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 34
EP  - 34
VL  - 13
AB  - Mucilaginibacter pedocola TBZ30(T) (= CCTCC AB 2015301(T) = KCTC 42833(T)) is a Gram-
AB  - negative, rod-shaped, non-motile and non-spore-forming bacterium isolated
AB  - from a heavy metal contaminated paddy field. It shows resistance to multiple
AB  - heavy metals and can adsorb/remove Zn(2+) and Cd(2+) during cultivation. In
AB  - addition, strain TBZ30(T) produces exopolysaccharides (EPS). These features make
AB  - it a great potential to bioremediate heavy metal contamination and biotechnical
AB  - application. Here we describe the genome sequence and annotation of strain
AB  - TBZ30(T). The genome size is 7,035,113 bp, contains 3132 protein-coding genes
AB  - (2736 with predicted functions), 50 tRNA encoding genes and 14 rRNA encoding
AB  - genes. Putative heavy metal resistant genes and EPS associated genes are found in
AB  - the genome.
ER  -

TY  - JOUR
AU  - Gan H.M.
AU  - Lee M.V.J.
AU  - Savka M.A.
TI  - High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01045
EP  - e01018
VL  - 7
AB  - Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of
AB  - Allorhizobium vitis K309(T) (= ATCC 49767(T), = NCPPB 3554(T)), a
AB  - phytopathogenic strain isolated from a grapevine in Australia. The hybrid
AB  - approach generated 50% fewer contigs and a 3-fold increase in the N 50 value
AB  - compared with the previous Illumina-only assembly.
ER  -

TY  - JOUR
AU  - Goen A.E.
AU  - Silverwood T.
AU  - Underriner A.
AU  - Trachtenberg A.M.
AU  - Kelley C.
AU  - MacLea K.S.
TI  - Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154(T).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00841
EP  - e00818
VL  - 7
AB  - The aerobic, Gram-positive, psychrotolerant bacterium Kurthia sibirica was first  isolated
AB  - from the stomach and intestinal contents of the Magadan mammoth
AB  - recovered from the permafrost in eastern Siberia in 1977. K. sibirica was
AB  - sequenced, and the predicted genome size is 3,496,665 bp, with 36.42% G+C
AB  - content.
ER  -

TY  - JOUR
AU  - Gonzalez-Escalona N.
AU  - Haendiges J.
AU  - Miller J.D.
AU  - Sharma S.K.
TI  - Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01075
EP  - e01018
VL  - 7
AB  - Here we report the genome sequences of two toxin-producing Clostridium botulinum  strains, one
AB  - environmental sample (83F) and one clinical sample (CDC51232). The
AB  - genomes were closed by a combination of long-read and short-read sequencing. The
AB  - strains belong to C. botulinum sequence type 4 (ST4) and ST7, respectively.
ER  -

TY  - JOUR
AU  - Grinkevich P.
AU  - Sinha D.
AU  - Iermak I.
AU  - Guzanova A.
AU  - Weiserova M.
AU  - Ludwig J.
AU  - Mesters J.R.
AU  - Ettrich R.H.
TI  - Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.
JO  - J. Biol. Chem.
PY  - 2018
SP  - 15043
EP  - 15054
VL  - 293
AB  - Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it
AB  - still presents many challenges to detailed analyses because of its
AB  - structural and functional complexity and missing structural information. In all
AB  - available structures of its motor subunit HsdR, responsible for DNA translocation
AB  - and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal
AB  - structure of the C terminus of HsdR, obtained with a crystallization chaperone in
AB  - the form of pHluorin fusion and refined to 2.45 A, revealed that this part of the
AB  - protein forms an independent domain with its own hydrophobic core and displays a
AB  - unique alpha-helical fold. The full-length HsdR model, based on the WT structure
AB  - and the C-terminal domain determined here, disclosed a proposed DNA-binding
AB  - groove lined by positively charged residues. In vivo and in vitro assays with a
AB  - C-terminal deletion mutant of HsdR supported the idea that this domain is
AB  - involved in complex assembly and DNA binding. Conserved residues identified
AB  - through sequence analysis of the C-terminal domain may play a key role in
AB  - protein-protein and protein-DNA interactions. We conclude that the motor subunit
AB  - of EcoR124 comprises five structural and functional domains, with the fifth, the
AB  - C-terminal domain, revealing a unique fold characterized by four conserved motifs
AB  - in the IC subfamily of Type I restriction-modification systems. In summary, the
AB  - structural and biochemical results reported here support a model in which the
AB  - C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is
AB  - involved in complex assembly and DNA binding.
ER  -

TY  - JOUR
AU  - Hynes R.K.
AU  - Dumonceaux T.J.
AU  - Kangsopa J.
AU  - Town J.R.
TI  - Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Pseudomonas sp. Strain 31-12.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00947
EP  - e00918
VL  - 7
AB  - We present here a draft genome sequence of Pseudomonas sp. strain 31-12, a plant
AB  - growth-promoting rhizobacterium of several crop plants that was isolated from the
AB  - rhizosphere of corn in southern Ontario, Canada.
ER  -

TY  - JOUR
AU  - Iglesias N.G.
AU  - Valdes La.H.D.
AU  - Olguin N.T.
AU  - Bravo-Ferrada B.M.
AU  - Brizuela N.S.
AU  - Tymczyszyn E.E.
AU  - Bibiloni H.
AU  - Caballero A.C.
AU  - Delfederico L.
AU  - Semorile L.
TI  - Genome Sequence of Oenococcus oeni UNQOe19, the First Fully Assembled Genome Sequence of a Patagonian Psychrotrophic Oenological Strain.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00889
EP  - e00818
VL  - 7
AB  - Oenococcus oeni UNQOe19 is a native strain isolated from a Patagonian pinot noir  wine
AB  - undergoing spontaneous malolactic fermentation. Here, we present the 1.83-Mb
AB  - genome sequence of O. oeni UNQOe19, the first fully assembled genome sequence of
AB  - a psychrotrophic strain from an Argentinean wine.
ER  -

TY  - JOUR
AU  - Inaba T.
AU  - Sato Y.
AU  - Koike H.
AU  - Hori T.
AU  - Kanno M.
AU  - Kimura N.
AU  - Kirimura K.
AU  - Habe H.
TI  - Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00906
EP  - e00918
VL  - 7
AB  - Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass
AB  - hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This
AB  - study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The
AB  - draft genome sequence will aid the study of the LA catabolic pathway, which will
AB  - allow for more applications of LA-utilizing bacteria.
ER  -

TY  - JOUR
AU  - Jaiswal D.
AU  - Sengupta A.
AU  - Sohoni S.
AU  - Sengupta S.
AU  - Phadnavis A.G.
AU  - Pakrasi H.B.
AU  - Wangikar P.P.
TI  - Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India.
JO  - Sci. Rep.
PY  - 2018
SP  - 16632
EP  - 16632
VL  - 8
AB  - Cyanobacteria provide an interesting platform for biotechnological applications
AB  - due to their efficient photoautotrophic growth, amenability to genetic
AB  - engineering and the ability to grow on non-arable land. An ideal industrial
AB  - strain of cyanobacteria would need to be fast growing and tolerant to high levels
AB  - of temperature, light, carbon dioxide, salt and be naturally transformable. In
AB  - this study, we report Synechococcus elongatus PCC 11801, a strain isolated from
AB  - India that fulfills these requirements. The physiological and biochemical
AB  - characteristics of PCC 11801 under carbon and light-limiting conditions were
AB  - investigated. PCC 11801 shows a doubling time of 2.3 h, that is the fastest
AB  - growth for any cyanobacteria reported so far under ambient CO2 conditions. Genome
AB  - sequence of PCC 11801 shows genome identity of ~83% with its closest neighbors
AB  - Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973. The
AB  - unique attributes of PCC 11801 genome are discussed in light of the physiological
AB  - characteristics that are needed in an industrial strain. The genome of PCC 11801
AB  - shows several genes that do not have homologs in neighbor strains PCC 7942 and
AB  - UTEX 2973, some of which may be responsible for adaptation to various abiotic
AB  - stresses. The remarkably fast growth rate of PCC 11801 coupled with its
AB  - robustness and ease of genetic transformation makes it an ideal candidate for the
AB  - photosynthetic production of fuels and chemicals.
ER  -

TY  - JOUR
AU  - Jang H. et al.
TI  - Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 35
EP  - 35
VL  - 13
AB  - Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening
AB  - infantile infections, such as meningitis, septicemia, and necrotizing
AB  - enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound
AB  - infections in adults. Here, we report 26 draft genome sequences of C. sakazakii,
AB  - which were obtained from dried spices from the USA, the Middle East, China, and
AB  - the Republic of Korea. The average genome size of the C. sakazakii genomes was
AB  - 4393 kb, with an average of 4055 protein coding genes, and an average genome G +
AB  - C content of 56.9%. The genomes contained genes related to carbohydrate transport
AB  - and metabolism, amino acid transport and metabolism, and cell wall/membrane
AB  - biogenesis. In addition, we identified genes encoding proteins involved in
AB  - osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as
AB  - virulence-related and heat shock-related proteins. Interestingly, a metabolic
AB  - island comprised of a variably-sized xylose utilization operon was found within
AB  - the spice-associated C. sakazakii genomes, which supports the hypothesis that
AB  - plants may serve as transmission vectors or alternative hosts for Cronobacter
AB  - species. The presence of the genes identified in this study can support the
AB  - remarkable phenotypic traits of C. sakazakii such as the organism's capabilities
AB  - of adaptation and survival in response to adverse growth environmental conditions
AB  - (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses
AB  - provided insights into many aspects of physiology and evolutionary history of
AB  - this important foodborne pathogen.
ER  -

TY  - JOUR
AU  - Jaomanjaka F.
AU  - Claisse O.
AU  - Philippe C.
AU  - Le Marrec C.
TI  - Complete Genome Sequence of Lytic Oenococcus oeni Bacteriophage OE33PA.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00818
EP  - e00818
VL  - 7
AB  - Oenococcus oeni is the most common species of lactic acid bacteria associated with malolactic
AB  - fermentation in wine. Here, we report the genome sequence of the
AB  - lytic phage OE33PA (vB_OeS_OE33PA). It has a morphotype similar to that of
AB  - members of the Siphoviridae family, a linear 39,866-bp double-stranded genome
AB  - with cohesive ends, and 57 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Jin H.
AU  - Nishizawa T.
AU  - Guo Y.
AU  - Nishizawa A.
AU  - Park H.D.
AU  - Kato H.
AU  - Tsuji K.
AU  - Harada K.I.
TI  - Complete Genome Sequence of a Microcystin-Degrading Bacterium, Sphingosinicella microcystinivorans Strain B-9.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00898
EP  - e00818
VL  - 7
AB  - Sphingosinicella microcystinivorans strain B-9 has the ability to degrade cyanobacterial
AB  - hepatotoxic cyclic peptides, microcystins, and nodularins. This is
AB  - the first report of the complete genome sequence of the microcystin-degrading
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Kelly S.A.
AU  - Megaw J.
AU  - Gilmore B.F.
TI  - Draft Genome Sequence of Salinisphaera sp. Strain KSM-18, an Obligately Halophilic Bacterium Isolated from a Triassic Salt Mine.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00897
EP  - e00818
VL  - 7
AB  - Here, we report the draft genome sequence of Salinisphaera sp. strain KSM-18. This obligately
AB  - halophilic bacterium was isolated from a brine sample obtained
AB  - from a Triassic salt mine.
ER  -

TY  - JOUR
AU  - Kim S.J.
AU  - Park S.J.
AU  - Kim J.G.
AU  - Jung M.Y.
AU  - Gwak J.H.
AU  - Rhee S.K.
TI  - Draft Genome Sequence of 'Candidatus Izimaplasma sp.' Strain ZiA1, Obtained from  a Toluene-Degrading and Iron-Reducing Enrichment Culture.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00861
EP  - e00818
VL  - 7
AB  - Here, we report the draft genome sequence of 'Candidatus Izimaplasma sp.' strain  ZiA1 (1.88
AB  - Mb and 29.6% G+C content). Strain ZiA1 was cocultured with
AB  - iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal
AB  - flat sediment. Like the genomes of other strains of 'Ca. Izimaplasma,' the ZiA1
AB  - genome contained genes required for anaerobic fermentation.
ER  -

TY  - JOUR
AU  - Kisiala M.
AU  - Copelas A.
AU  - Czapinska H.
AU  - Xu S.Y.
AU  - Bochtler M.
TI  - Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 10489
EP  - 10503
VL  - 46
AB  - TagI belongs to the recently characterized SRA-HNH family of modification-dependent
AB  - restriction endonucleases (REases) that also includes
AB  - ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of
AB  - dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease
AB  - domains, and separate binding sites for modified DNA bases in the two protomers.
AB  - The nuclease domains have characteristic features of HNH/betabetaalpha-Me REases,
AB  - and catalyze nicks or double strand breaks, with preference for /RY and RYN/RY
AB  - sites, respectively. The SRA domains have the canonical fold. Their pockets for
AB  - the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or
AB  - 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).
AB  - Such preference is in agreement with the biochemical determination of the TagI
AB  - modification dependence and the results of phage restriction assays. The ability
AB  - of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or
AB  - M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to
AB  - different sequence contexts of the modified base.
ER  -

TY  - JOUR
AU  - Lazarte J.N.
AU  - Lopez R.P.
AU  - Ghiringhelli P.D.
AU  - Beron C.M.
TI  - Bacillus wiedmannii biovar thuringiensis: A Specialized Mosquitocidal Pathogen with Plasmids from Diverse Origins.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 2823
EP  - 2833
VL  - 10
AB  - Bacillus cereus sensu lato also known as B. cereus group is composed of an
AB  - ecologically diverse bacterial group with an increasing number of related
AB  - species, some of which are medically or agriculturally important. Numerous e ff
AB  - orts have been undertaken to allow presumptive di ff erentiation of B. cereus
AB  - group species from one another. FCC41 is a Bacillus sp. strain toxic against
AB  - mosquito species like Aedes aegypti, Aedes (Ochlerotatus) albifasciatus, Culex
AB  - pipiens, Culex quinquefasciatus, and Culex apicinus, some of them responsible for
AB  - the transmission of vector-borne diseases. Here, we report the complete genome
AB  - sequence of FCC41 strain, which consists of one circular chromosome and eight
AB  - circular plasmids ranging in size from 8 to 490 kb. This strain harbors six
AB  - crystal protein genes, including cry24Ca, two cry4-like and two cry52-like, a
AB  - cry41-like parasporin gene and multiple virulence factors. The phylogenetic
AB  - analysis of the whole-genome sequence of this strain with molecular approaches
AB  - places this strain into the Bacillus wiedmannii cluster. However, according with
AB  - phenotypical characteristics such as the mosquitocidal activity due to the
AB  - presence of Cry proteins found in the parasporal body and cry genes encoded in
AB  - plasmids of different sizes, indicate that this strain could be renamed as B.
AB  - wiedmannii biovar thuringiensis strain FCC41.
ER  -

TY  - JOUR
AU  - Le Guern R.
AU  - Grandjean T.
AU  - Faure K.
AU  - Bauduin M.
AU  - Kipnis E.
AU  - Dessein R.
TI  - Draft Genome Sequences of Two Carbapenemase-Producing Klebsiella pneumoniae Strains Isolated from Blood Cultures.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01057
EP  - e01018
VL  - 7
AB  - Carbapenemase-producing Klebsiella pneumoniae represents an emerging public health issue.
AB  - Here, we present the draft whole-genome sequences of K. pneumoniae
AB  - clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase).
AB  - These genome sequences should help in investigating pathophysiological mechanisms
AB  - of digestive colonization or infection with these highly resistant bacteria.
ER  -

TY  - JOUR
AU  - Li Y.
AU  - Guo X.H.
AU  - Dang Y.R.
AU  - Sun L.L.
AU  - Zhang X.Y.
AU  - Chen X.L.
AU  - Qin Q.L.
AU  - Wang P.
TI  - Complete genome sequence of Arcticibacterium luteifluviistationis SM1504(T), a cytophagaceae bacterium isolated from Arctic surface seawater.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 33
EP  - 33
VL  - 13
AB  - Arcticibacterium luteifluviistationis SM1504(T) was isolated from Arctic surface  seawater and
AB  - classified as a novel genus of the phylum Bacteroides. To date, no
AB  - Arcticibacterium genomes have been reported, their genomic compositions and
AB  - metabolic features are still unknown. Here, we reported the complete genome
AB  - sequence of A. luteifluviistationis SM1504(T), which comprises 5,379,839 bp with
AB  - an average GC content of 37.20%. Genes related to various stress (such as
AB  - radiation, osmosis and antibiotics) resistance and gene clusters coding for
AB  - carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the
AB  - genome contained a 245-kb genomic island and a 15-kb incomplete prophage region.
AB  - A great percentage of proteins belonging to carbohydrate metabolism especially in
AB  - regard to polysaccharides utilization were found. These related genes and
AB  - metabolic characteristics revealed genetic basis for adapting to the diverse
AB  - extreme Arctic environments. The genome sequence of A. luteifluviistationis
AB  - SM1504(T) also implied that the genus Arcticibacterium may act as a vital organic
AB  - carbon matter decomposer in the Arctic seawater ecosystem.
ER  -

TY  - JOUR
AU  - Liang J.
AU  - Hoffrichter A.
AU  - Brachmann A.
AU  - Marin M.
TI  - Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 36
EP  - 36
VL  - 13
AB  - Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic  interaction
AB  - with legume plants in which a bidirectional nutrient exchange takes
AB  - place. Occasionally, this interaction is suboptimal resulting in the formation of
AB  - ineffective nodules in which little or no atmospheric nitrogen fixation occurs.
AB  - Rhizobium leguminosarum Norway induces ineffective nodules in a wide range of
AB  - Lotus hosts. To investigate the basis of this phenotype, we sequenced the
AB  - complete genome of Rl Norway and compared it to the genome of the closely related
AB  - strain R. leguminosarum bv. viciae 3841. The genome comprises 7,788,085 bp,
AB  - distributed on a circular chromosome containing 63% of the genomic information
AB  - and five large circular plasmids. The functionally classified bacterial gene set
AB  - is distributed evenly among all replicons. All symbiotic genes (nod, fix, nif)
AB  - are located on the pRLN3 plasmid. Whole genome comparisons revealed differences
AB  - in the metabolic repertoire and in protein secretion systems, but not in
AB  - classical symbiotic genes.
ER  -

TY  - JOUR
AU  - Loy J.D.
AU  - Dickey A.M.
AU  - Clawson M.L.
TI  - Complete Genome Sequence of Moraxella bovis Strain Epp-63 (300), an Etiologic Agent of Infectious Bovine Keratoconjunctivitis.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01004
EP  - e01018
VL  - 7
AB  - We report here the complete closed genome sequence of Moraxella bovis strain Epp-63 (300)
AB  - (Epp63). This strain was isolated from an infectious bovine
AB  - keratoconjunctivitis (IBK) case in 1963. Since then, Epp63 has been used
AB  - extensively for IBK research. Consequently, the genome sequence of Epp63 should
AB  - help elucidate IBK host-pathogen interactions.
ER  -

TY  - JOUR
AU  - Macey M.C.
AU  - Pratscher J.
AU  - Crombie A.
AU  - Murrell J.C.
TI  - Draft Genome Sequences of Obligate Methylotrophs Methylovorus sp. Strain MM2 and  Methylobacillus sp. Strain MM3, Isolated from Grassland Soil.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00824
EP  - e00818
VL  - 7
AB  - Methylotrophs of the family Methylophilaceae were isolated from grassland soil. Here, we
AB  - report the draft genome sequences of two obligate methylotrophs,
AB  - Methylovorus sp. strain MM2 and Methylobacillus sp. strain MM3. These genome
AB  - sequences provide further insights into the genetic and metabolic diversity of
AB  - the Methylophilaceae.
ER  -

TY  - JOUR
AU  - McClure J.A.
AU  - Shideler S.M.
AU  - Zhang K.
TI  - Complete Genome Sequences of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Strains CMRSA3 and CMRSA6.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00892
EP  - e00818
VL  - 7
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 8 (CC8) sequence type 239
AB  - (ST239) represents a predominant hospital-associated MRSA
AB  - sublineage present worldwide. The Canadian epidemic MRSA strains CMRSA3 and
AB  - CMRSA6 are moderately virulent members of this group but are closely related to
AB  - the highly virulent strain TW20. Whole-genome sequencing of CMRSA3 and CMRSA6 was
AB  - conducted to identify genetic determinants associated with their virulence.
ER  -

TY  - JOUR
AU  - Miyauchi T.
AU  - Kouzuma A.
AU  - Abe T.
AU  - Watanabe K.
TI  - Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01028
EP  - e01018
VL  - 7
AB  - Acidithiobacillus ferridurans is an acidophilic chemolithotrophic bacterium that  can grow in
AB  - the presence of high concentrations of ferrous iron. Here, we present
AB  - the complete 2,921,399-bp genome sequence of the strain A. ferridurans JCM
AB  - 18981(T), isolated from uranium mine drainage water.
ER  -

TY  - JOUR
AU  - Montecillo A.D.
AU  - Raymundo A.K.
AU  - Papa I.A.
AU  - Aquino G.M.B.
AU  - Rosana A.R.R.
TI  - Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00903
EP  - e00918
VL  - 7
AB  - Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna,
AB  - Philippines. The 7.07-Mb complete genome comprises three replicons, one
AB  - chromosome, and two plasmids, with a G+C content of 59.4% and 6,720
AB  - protein-coding genes. The genome encodes gene clusters supporting rhizosphere
AB  - processes, plant symbiosis, and secondary bioactive metabolites.
ER  -

TY  - JOUR
AU  - Nirwan N.
AU  - Singh P.
AU  - Mishra G.G.
AU  - Johnson C.M.
AU  - Szczelkun M.D.
AU  - Inoue K.
AU  - Vinothkumar K.R.
AU  - Saikrishnan K.
TI  - Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity.
JO  - Nucleic Acids Res.
PY  - 2018
AB  - McrBC is one of the three modification-dependent restriction enzymes encoded by the
AB  - Escherichia coli K12 chromosome. Amongst restriction enzymes, McrBC and its
AB  - close homologues are unique in employing the AAA+ domain for GTP
AB  - hydrolysis-dependent activation of DNA cleavage. The GTPase activity of McrB is
AB  - stimulated by the endonuclease subunit McrC. It had been reported previously that
AB  - McrB and McrC subunits oligomerise together into a high molecular weight species.
AB  - Here we conclusively demonstrate using size exclusion chromatography coupled
AB  - multi-angle light scattering (SEC-MALS) and images obtained by electron
AB  - cryomicroscopy that McrB exists as a hexamer in solution. Furthermore, based on
AB  - SEC-MALS and SAXS analyses of McrBC and the structure of McrB, we propose that
AB  - McrBC is a complex of two McrB hexamers bridged by two subunits of McrC, and that
AB  - the complete assembly of this complex is integral to its enzymatic activity. We
AB  - show that the nucleotide-dependent oligomerisation of McrB precedes GTP
AB  - hydrolysis. Mutational studies show that, unlike other AAA+ proteins, the
AB  - catalytic Walker B aspartate is required for oligomerisation.
ER  -

TY  - JOUR
AU  - Nishikawa S.
AU  - Ogawa Y.
AU  - Eguchi M.
AU  - Rambukkana A.
AU  - Shimoji Y.
TI  - Draft Genome Sequences of Lawsonia intracellularis Swine Strains Causing Proliferative Enteropathy in Japan.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01021
EP  - e01018
VL  - 7
AB  - The draft genome sequences of three strains of Lawsonia intracellularis, an obligate
AB  - intracellular animal pathogen responsible for causing proliferative
AB  - enteropathy, obtained from swine in different prefectures in Japan revealed the
AB  - absence of a genomic island previously reported to be linked to host adaptation
AB  - and to high genomic diversity, despite geographical proximity.
ER  -

TY  - JOUR
AU  - Permala R.R.
AU  - Glady-Croue J.
AU  - Watkin E.L.J.
AU  - Ramsay J.P.
AU  - Croue J.P.
TI  - Complete Genome Sequence of Stenotrophomonas maltophilia AB550, an Environmental  Solar Radiation- and Multidrug-Resistant Strain Isolated in Western Australia.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00914
EP  - e00918
VL  - 7
AB  - We report here the complete genome sequence of Stenotrophomonas maltophilia AB550, a
AB  - multidrug- and solar radiation-resistant strain isolated from the
AB  - effluents of an urban wastewater treatment plant in Western Australia. The genome
AB  - consists of a single 4.9-Mb chromosome.
ER  -

TY  - JOUR
AU  - Pitt M.E.
AU  - Elliott A.G.
AU  - Cao M.D.
AU  - Ganesamoorthy D.
AU  - Karaiskos I.
AU  - Giamarellou H.
AU  - Abboud C.S.
AU  - Blaskovich M.A.
AU  - Cooper M.A.
AU  - Coin L.J.
TI  - Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae.
JO  - Microbial Genomics
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high
AB  - mortality and are disseminating globally. Identifying the genetic basis
AB  - underpinning resistance allows for rapid diagnosis and treatment. XDR isolates
AB  - sourced from Greece and Brazil, including 19 polymyxin-resistant and five
AB  - polymyxin-susceptible strains, were subjected to whole genome sequencing.
AB  - Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or
AB  - within mgrB. The most common mutation identified was an insertion at nucleotide
AB  - position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13
AB  - in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and
AB  - another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations
AB  - (C28STOP, Q30STOP) or a missense mutation (D29E) affecting mgrB. Complementation
AB  - assays revealed all mgrB perturbations contributed to resistance. Missense
AB  - mutations in phoQ (T281M, G385C) were also found to facilitate resistance.
AB  - Several variants in phoPQ co-segregating with the ISKpn26-like insertion were
AB  - identified as potential partial suppressor mutations. Three ST258 samples were
AB  - found to contain subpopulations with different resistance-conferring mutations,
AB  - including the ISKpn26-like insertion colonizing with a novel mutation in pmrB
AB  - (P158R), both confirmed via complementation assays. These findings highlight the
AB  - broad spectrum of chromosomal modifications which can facilitate and regulate
AB  - resistance against polymyxins in K. pneumoniae.
ER  -

TY  - JOUR
AU  - Proust L.
AU  - Loux V.
AU  - Martin V.
AU  - Magnabosco C.
AU  - Pedersen M.
AU  - Monnet V.
AU  - Juillard V.
TI  - Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01029
EP  - e01018
VL  - 7
AB  - Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt
AB  - and cheese. We report here the complete genome sequence of
AB  - the industrial strain S. thermophilus N4L, which is used in dairy technology for
AB  - its fast-acidifying phenotype.
ER  -

TY  - JOUR
AU  - Quesada J.M.
AU  - Aguilar I.
AU  - de la Torre J.
AU  - Wittich R.M.
AU  - van Dillewijn P.
TI  - Draft Genome Sequences of Isolates from Sediments of the River Elbe That Are Highly Tolerant to Diclofenac.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00849
EP  - e00818
VL  - 7
AB  - Here, we report the genome sequences of one Achromobacter and four Pseudomonas strains
AB  - isolated from sediments of the River Elbe which are highly tolerant
AB  - toward the xenobiotic target compound diclofenac, a nonsteroidal
AB  - anti-inflammatory drug (NSAID) and emerging contaminant.
ER  -

TY  - JOUR
AU  - Quiroz-Castaneda R.E.
AU  - Martinez-Ocampo F.
AU  - Dantan-Gonzalez E.
TI  - Draft Genome Sequence of Mycoplasma wenyonii, a Second Hemotropic Mycoplasma Species Identified in Mexican Bovine Cattle.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00875
EP  - e00818
VL  - 7
AB  - The hemotropic mycoplasma (hemoplasma) Mycoplasma wenyonii is an animal pathogen  that affects
AB  - bovine cattle health. Here, we present the draft genome sequence of
AB  - the hemoplasma M. wenyonii strain INIFAP02 found in cattle from Mexico.
ER  -

TY  - JOUR
AU  - Rayyan A.A.
AU  - Meyer T.E.
AU  - Kyndt J.A.
TI  - Draft Genome Sequence and Brief History of Rhodovulum sp. Strain BSW8.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00983
EP  - e00918
VL  - 7
AB  - Rhodovulum is a marine Gram-negative purple photosynthetic bacterial genus that is a member of
AB  - the Alphaproteobacteria. Strain BSW8 is a variant that does not
AB  - appear to make a polysaccharide slime capsule, and its genome sequence further
AB  - contributes to the diversity of sequenced genomes belonging to this genus.
ER  -

TY  - JOUR
AU  - Saad J.
AU  - Levasseur A.
AU  - Drancourt M.
TI  - Draft Genome Sequence of Mycobacterium parafortuitum Strain P7335.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00950
EP  - e00918
VL  - 7
AB  - Mycobacterium parafortuitum is a rapidly growing nontuberculous mycobacterium, initially
AB  - isolated from soil in Japan. The 6,175,772-bp draft genome sequence of
AB  - M. parafortuitum strain P7335 exhibits a G+C content of 68.4%, 5,783
AB  - protein-coding genes, and 66 predicted RNA genes, including 59 tRNA genes, 6 rRNA
AB  - operons, and 1 transfer-messenger RNA.
ER  -

TY  - JOUR
AU  - Sakamoto M.
AU  - Ikeyama N.
AU  - Yuki M.
AU  - Ohkuma M.
TI  - Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01091
EP  - e01018
VL  - 7
AB  - Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896(T), an
AB  - acetate-producing bacterium isolated from human feces. The genomic
AB  - analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate
AB  - the study of the role of this strain in the human gut.
ER  -

TY  - JOUR
AU  - Sakoula D.
AU  - Nowka B.
AU  - Spieck E.
AU  - Daims H.
AU  - Lucker S.
TI  - The draft genome sequence of 'Nitrospira lenta' strain BS10, a nitrite oxidizing  bacterium isolated from activated sludge.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 32
EP  - 32
VL  - 13
AB  - The genus Nitrospira is considered to be the most widespread and abundant group of
AB  - nitrite-oxidizing bacteria in many natural and man-made ecosystems. However,
AB  - the ecophysiological versatility within this phylogenetic group remains highly
AB  - understudied, mainly due to the lack of pure cultures and genomic data. To
AB  - further expand our understanding of this biotechnologically important genus, we
AB  - analyzed the high quality draft genome of 'Nitrospira lenta' strain BS10, a
AB  - sublineage II Nitrospira that was isolated from a municipal wastewater treatment
AB  - plant in Hamburg, Germany. The genome of 'N. lenta' has a size of 3,756,190 bp
AB  - and contains 3968 genomic objects, of which 3907 are predicted protein-coding
AB  - sequences. Thorough genome annotation allowed the reconstruction of the 'N.
AB  - lenta' core metabolism for energy conservation and carbon fixation. Comparative
AB  - analyses indicated that most metabolic features are shared with N. moscoviensis
AB  - and 'N. defluvii', despite their ecological niche differentiation and
AB  - phylogenetic distance. In conclusion, the genome of 'N. lenta' provides important
AB  - insights into the genomic diversity of the genus Nitrospira and provides a
AB  - foundation for future comparative genomic studies that will generate a better
AB  - understanding of the nitrification process.
ER  -

TY  - JOUR
AU  - Sarker M.S.A.
AU  - Rahman M.T.
AU  - Mahmud M.M.
AU  - Tagliamonte M.S.
AU  - Chowdhury S.M.Z.H.
AU  - Islam M.R.
AU  - Rahman M.B.
AU  - El Zowalaty M.E.
AU  - Nazir K.H.M.N.H.
TI  - First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00901
EP  - e00918
VL  - 7
AB  - Here, we report the first genome sequence of Pasteurella multocida BAUTB2 isolated from a
AB  - buffalo that died from hemorrhagic septicemia in Rajshahi,
AB  - Bangladesh. Using Illumina HiSeq technology, the BAUTB2 genome length was
AB  - determined to be 2,439,149 bp, with 40.8% GC content, 2,307 coding sequences
AB  - (CDS), 6 rRNAs, 51 tRNAs, and 4 noncoding RNAs (ncRNAs).
ER  -

TY  - JOUR
AU  - Sevigny J.L.
AU  - LaJoie J.
AU  - Shehata S.
AU  - Christensen E.
AU  - Cornfield S.
AU  - Koziol L.
TI  - Whole-Genome Sequences of Two Pseudomonas fluorescens Strains Isolated from Roots of Tomato and Cucumber Plants.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00974
EP  - e00918
VL  - 7
AB  - Pseudomonas fluorescens strain EC1 was isolated from Cucumis sativus (cucumber) roots, and P.
AB  - fluorescens SC1 was isolated from Solanum lycopersicum (tomato)
AB  - roots. The P. fluorescens SC1 genome has a total sequence length of 6,157,842 bp,
AB  - and the P. fluorescens EC1 genome has a total sequence length of 6,125,428 bp.
ER  -

TY  - JOUR
AU  - Shankar M.
AU  - Mageswari A.
AU  - Suganthi C.
AU  - Gunasekaran P.
AU  - Gothandam K.M.
AU  - Karthikeyan S.
TI  - Genome Sequence of a Moderately Halophilic Bacillus cereus Strain, TS2, Isolated  from Saltern Sediments.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00873
EP  - e00818
VL  - 7
AB  - We report the 5.3-Mbp genome sequence of Bacillus cereus strain TS2, which was isolated from
AB  - the sediments of a solar saltern in southern India. Genome analysis
AB  - of B. cereus TS2, a salt-resistant strain, will improve our understanding of how
AB  - B. cereus, a food pathogen, responds to hyperosmotic stress.
ER  -

TY  - JOUR
AU  - Vejarano F.
AU  - Suzuki-Minakuchi C.
AU  - Ohtsubo Y.
AU  - Tsuda M.
AU  - Okada K.
AU  - Nojiri H.
TI  - Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00935
EP  - e00918
VL  - 7
AB  - We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium
AB  - isolated from Tokyo Bay and capable of degrading carbazole. The genome
AB  - consists of a 3.3-Mb circular chromosome that carries the gene clusters involved
AB  - in carbazole degradation and biosynthesis of the photosynthetic apparatus of
AB  - aerobic anoxygenic phototrophic bacteria.
ER  -

TY  - JOUR
AU  - Veseli I.A.
AU  - Mascarenhas D.S.A.C.
AU  - Juarez O.
AU  - Stark B.C.
AU  - Pombert J.F.
TI  - Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00922
EP  - e00918
VL  - 7
AB  - Vitreoscilla sp. strain C1 is of historical importance as the source of the first prokaryotic
AB  - hemoglobin identified. Vitreoscilla spp. rely on their hemoglobin and
AB  - cytochrome oxidase to grow in microaerobic environments despite their aerobic
AB  - nature. To help characterize this historically relevant strain, we sequenced the
AB  - complete Vitreoscilla sp. strain C1 genome.
ER  -

TY  - JOUR
AU  - Victoria A.J.
AU  - Cao E.
AU  - Salmaso N.
AU  - Segata N.
AU  - Donati C.
TI  - Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00876
EP  - e00818
VL  - 7
AB  - Here, we report the genome of strain JJU2, a cyanobacterium of the family Hapalosiphonaceae
AB  - known to be resistant to high cadmium levels, assembled from a
AB  - nonaxenic, unialgal culture from Marinduque, Philippines. The draft genome is 7.1
AB  - Mb long with a GC content of 40.05% and contains 5,625 protein-coding genes.
ER  -

TY  - JOUR
AU  - Wang S.
AU  - Dong L.
AU  - Zhao B.
AU  - Xu S.
AU  - Wu K.
AU  - Wang H.
TI  - Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00882
EP  - e00818
VL  - 7
AB  - The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt
AB  - lake. It grows optimally at 8% (wt/vol) NaCl (pH 9.0). The draft
AB  - genome is composed of 4,006 predicted genes. Genomic analysis showed that various
AB  - genes are potentially involved in the adaptation mechanisms for osmotic stress
AB  - and pH homeostasis.
ER  -

TY  - JOUR
AU  - Xu A.
AU  - Tilman S.
AU  - Wisser-Parker K.
AU  - Scullen O.J.
AU  - Sommers C.H.
TI  - Draft Genomic Sequences of Nine Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Skin.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00859
EP  - e00818
VL  - 7
AB  - Extraintestinal pathogenic Escherichia coli strains were isolated from retail chicken skin.
AB  - Here, we report the draft genomic sequences for these nine E. coli
AB  - isolates, which are currently being used in agricultural and food safety
AB  - research.
ER  -

TY  - JOUR
AU  - Zagorskaite E.
AU  - Manakova E.
AU  - Sasnauskas G.
TI  - Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
JO  - FEBS Lett.
PY  - 2018
SP  - 3335
EP  - 3345
VL  - 592
AB  - Cytosine modifications expand the information content of genomic DNA in both eukaryotes and
AB  - prokaryotes, providing means for epigenetic regulation and self
AB  - versus nonself discrimination. For example, the methyl-directed restriction
AB  - endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing
AB  - 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine
AB  - (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal
AB  - structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine
AB  - (5fC), and 4mC, and characterize the relative affinity of McrB-N to various
AB  - cytosine variants. We find that McrB-N flips out modified bases into a protein
AB  - pocket and binds cytosine derivatives in the order of descending affinity: 4mC >
AB  - 5mC > 5hmC >> 5fC. We also show that pocket mutations alter the relative
AB  - preference of McrB-N to 5mC, 5hmC, and 4mC.
ER  -

