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July 7, 2019

Complete genome sequence and comparative analysis of Staphylococcus condimenti DSM 11674, a potential starter culture isolated from soy sauce mash.

Coagulase-negative staphylococci (CNS) are key players in the majority of food fermentation ecosystems, which are commonly found in the production of fermented meat and milk products (Blaiotta et al., 2005; Resch et al., 2008). Strains of CNS have been implicated in exerting desirable effects as components of a fermentation flora, such as color formation, aroma development, and shelf-life enhancement, and may therefore have the potential for future application as starter cultures (Zell et al., 2008). Staphylococcus condimenti is one of the most prominent species and has the potential for use in starter cultures for the production of fermented sausage and cured ham (Zell et al., 2008). S. condimenti DSM 11674 was originally isolated from fermenting soy sauce mash and suggested to be a new species in 1998 (Probst et al., 1998). However, S. condimenti has been found in a few clinical samples (Argemi et al., 2015; Misawa et al., 2015). Therefore, some concerns have been raised with regard to the safety of this species for use in food production (Zell et al., 2008; Seitter et al., 2011a,b). To further understand the biochemical and genetic characteristics of DSM 11674 and advance the potential biotechnological applications of this strain, we constructed the complete genome sequence of S. condimenti DSM 11674.


July 7, 2019

Complete genome sequence of Bacillus velezensis GQJK49, a plant growth-promoting rhizobacterium with antifungal activity.

Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal activity, which was isolated from Lycium barbarum L. rhizosphere. Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene clusters related to its biosynthesis of secondary metabolites, including antifungal and antibacterial antibiotics, were predicted. Copyright © 2017 Ma et al.


July 7, 2019

Complete genome sequence of the pathogenic Vibrio vulnificus type strain ATCC 27562.

Vibrio vulnificus has the highest death rate and economic burden per case of any foodborne pathogen in the United States. A complete genome sequence of the type strain promotes comparative analyses with other clinical and environmental isolates, improving our understanding of this important human pathogen and successful environmental organism. Copyright © 2017 Rusch and Rowe-Magnus.


July 7, 2019

Complete genome sequence of Mesorhizobium ciceri bv. biserrulae WSM1497, an efficient nitrogen-fixing microsymbiont of the forage legume Biserrula pelecinus.

We report here the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1497, the efficient nitrogen-fixing microsymbiont and commercial inoculant in Australia of the forage legume Biserrula pelecinus The genome consists of 7.2 Mb distributed across a single chromosome (6.67 Mb) and a single plasmid (0.53 Mb). Copyright © 2017 Brewer et al.


July 7, 2019

Whole-genome sequence of Chlamydia abortus strain GN6 isolated from aborted yak fetus.

The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative agents of abortion and fetal loss in sheep, goats, and cattle in many countries. It also affects the reproductivity of yaks (Bos grunniens). This study reports the whole-genome sequence of Chlamydia abortus strain GN6, which was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China. Copyright © 2017 Li et al.


July 7, 2019

Whole-genome sequence of Streptococcus tigurinus strain osk_001, isolated from postmortem material.

Streptococcus tigurinus was recently described as a novel species, and some strains are highly virulent. We detected S. tigurinus in infected tissue sampled by necropsy. In order to characterize and confirm the virulence of this species, whole-genome sequencing of the pure cultured bacterium was performed. We found that the strain has specific and unique genetic elements contained in highly virulent strains of S. tigurinus. Copyright © 2017 Yoshizawa et al.


July 7, 2019

Rapid and affordable size-selected PacBio single-molecule real-time sequencing template library construction using the bead-beating DNA extraction method

This study demonstrated that bead-beating method facilitates a simple and rapid protocol for genomic DNA isolation for Pacific BioSciences (PacBio) sequencing with library construction of sufficient length. The protocol may also be beneficial for inactivating pathogens by simultaneous and instant DNA fragmentation, with no special equipment required to obtain large DNA fragments. This protocol was comparable in terms of quality to the standard protocol suggested by PacBioand represents an alternative, rapid shortcut for performing accurate PacBio sequencing.


July 7, 2019

Genomics of Helicobacter pylori

As Helicobacter pylori infects half the world’s population and displays an extensive intraspecies diversity, genomics is a powerful tool to understand evolution and disease, to identify factors that confer higher risk of severe sequelae, and to find new approaches for therapy both among bacterial and host targets. In line with these objectives, this review article summarizes the major findings in Helicobacter genomics in papers published between April 2016 and March 2017.


July 7, 2019

Novel multiresistance cfr plasmids in linezolid-resistant methicillin-resistant Staphylococcus epidermidis and vancomycin-resistant Enterococcus faecium (VRE) from a hospital outbreak: co-location of cfr and optrA in VRE.

Linezolid is often the drug of last resort to treat infections caused by Gram-positive cocci. Linezolid resistance can be mutational (23S rRNA or L-protein) or, less commonly, acquired [predominantly cfr, conferring resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogramin A compounds (PhLOPSA) or optrA, encoding oxazolidinone and phenicol resistance].To investigate the clonality and genetic basis of linezolid resistance in 13 linezolid-resistant (LZDR) methicillin-resistant Staphylococcus epidermidis (MRSE) isolates recovered during a 2013/14 outbreak in an ICU in an Irish hospital and an LZDR vancomycin-resistant Enterococcus faecium (VRE) isolate from an LZDR-MRSE-positive patient.All isolates underwent PhLOPSA susceptibility testing, 23S rRNA sequencing, DNA microarray profiling and WGS.All isolates exhibited the PhLOPSA phenotype. The VRE harboured cfr and optrA on a novel 73?kb plasmid (pEF12-0805) also encoding erm(A), erm(B), lnu(B), lnu(E), aphA3 and aadE. One MRSE (M13/0451, from the same patient as the VRE) harboured cfr on a novel 8.5?kb plasmid (pSEM13-0451). The remaining 12 MRSE lacked cfr but exhibited linezolid resistance-associated mutations and were closely related to (1-52 SNPs) but distinct from M13/0451 (202-223 SNPs).Using WGS, novel and distinct cfr and cfr/optrA plasmids were identified in an MRSE and VRE isolate, respectively, as well as a cfr-negative LZDR-MRSE ICU outbreak and a distinct cfr-positive LZDR-MRSE from the same ICU. To our knowledge, this is the first report of cfr and optrA on a single VRE plasmid. Ongoing surveillance of linezolid resistance is essential to maintain its therapeutic efficacy.© The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.


July 7, 2019

Complete genome analysis of Lactobacillus fermentum SK152 from kimchi reveals genes associated with its antimicrobial activity.

Research findings on probiotics highlight their importance in repressing harmful bacteria, leading to more extensive research on their potential applications. We analysed the genome of Lactobacillus fermentum SK152, which was isolated from the Korean traditional fermented vegetable dish kimchi, to determine the genetic makeup and genetic factors responsible for the antimicrobial activity of L. fermentum SK152 and performed a comparative genome analysis with other L. fermentum strains. The genome of L. fermentum SK152 was found to comprise a complete circular chromosome of 2092 273 bp, with an estimated GC content of 51.9% and 2184 open reading frames. It consisted of 2038 protein-coding genes and 73 RNA-coding genes. Moreover, a gene encoding a putative endolysin was found. A comparative genome analysis with other L. fermentum strains showed that SK152 is closely related to L. fermentum 3872 and F-6. An evolutionary analysis identified five positively selected genes that encode proteins associated with transport, survival and stress resistance. These positively selected genes may be essential for L. fermentum to colonise and survive in the stringent environment of the human gut and exert its beneficial effects. Our findings highlight the potential benefits of SK152.© FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.


July 7, 2019

Complete mitochondrial genome sequence of Aspergillus oryzae RIB 127 and its comparative analysis with related species

Here, we determined the complete sequence and annotation of the mitochondrial genome of A. oryzae (strain RIB 127). The complete mitochondrial genome is 29,202 base pairs (bp), with low GC content of 26.2%. Conserved genes identified include 26 transfer RNAs, the small and large ribosomal RNA subunits, and 14 protein-coding genes. Phylogenetic analysis based on the complete mitochondrial genome revealed that RIB 127 formed a single clade with two other A. oryzae species.


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