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Of bees and buzz: towards validated NGS-based methods in honey authentication
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Read PDFBenchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis
Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic …
Read PDFWater kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food
Water Kefir is a plant-based fermented beverage, traditionally produced on a small scale by fermenting a sucrose solution with fresh or dried fruits, using water kefir grains as inoculum. The grains are relatively simple communities …
Read PDFBorrelia turicatae in Ticks from Animals in a Public Park, Aguascalientes, Mexico
We obtained 5 isolates of Borrelia turicatae from ticks captured in a public park in Aguascalientes, Mexico. A serologic survey in resident fauna showed antibodies against B. turicatae. Relapsing fever borrelias are present in Ornithodoros …
Read PDFA polyvalent phage shapes bacterial dynamics
Bacteria and the viruses that infect them (known as bacteriophages or phages) are important microbial ecosystem members. Antagonistic interactions between different bacteria or between bacteria and phages can profoundly impact population dynamics. Lytic phages are …
Read PDFStaphylococcus aureus sequence type 71 is a chimera that emerged twice
BACKGROUND: Staphylococcus aureus is a Gram-positive coccus that colonises or infects humans and a wide range of domestic and wild animals. Various lineages of S. aureus are adapted to ruminants, including cattle, where they commonly …
Read PDFComplete genome sequence of the type strain <i>Piscinibacterium candidicorallinum</i> LMG 29480
<i>Piscinibacterium candidicorallinum</i> LMG 29480 is a motile gram-stain-negative bacterium able to reduce nitrate and accumulate poly-β-hydroxybutyrate storage granules. Here, we report the complete genome sequence (3,829,664 bp, 65.16 mol% G+C content), which may prove useful …
Read PDFGallium in liquid state shows nuclease-mimicking activity
Replicating biological systems using non-living materials, from the foundational molecular level to complex tissue structures, is central to abiotic mimicry. Enzymes play a vital role in these systems; however, replicating their enzymatic power with minimal …
Read PDFDraft genome of <i>Streptomyces globosus</i> OSY-MM, a broad-spectrum antimicrobial producer isolated from a cave in South Central Kentucky
<i>Streptomyces globosus</i> OSY-MM was originally isolated from a soil sample collected from a cave in South Central Kentucky and was found to display strong, broad-spectrum antimicrobial activity. <i>S. globosus</i> OSY-MM has a 7,277,920 bp genome …
Read PDFDraft genome sequence of a kombucha isolate of <i>Pichia kudriavzevii</i>
<i>Pichia kudriavzevii</i> (syn. <i>Candida krusei</i>) is a fermentative yeast of importance to both the food and biotechnology industries, as well as being of significant clinical concern. Here, we report the draft genome sequence of <i>P. …
Read PDFComplete genome sequence of <i>Bacillus altitudinis</i> NBTC-002, isolated from agricultural ecological ditches
We presented the complete genome of <i>Bacillus altitudinis</i> NBTC-002 isolated from soil samples from ecological ditches on farmland, of which the total length is 3,799,862 bp and possesses 3,817 protein-coding sequences (CDS).
Read PDF<i>In vivo</i> evolution of resistance to contemporary β-lactam/β-lactamase inhibitor combinations during treatment of a KPC-producing <i>Serratia marcescens</i> infection
<i>Klebsiella pneumoniae</i> carbapenemases (KPCs) are a family of serine β-lactamases that confer broad antibiotic resistance by hydrolyzing virtually all β-lactam (BL) agents. Contemporary β-lactamase inhibitors (BLIs) such as avibactam were developed to neutralize the activity …
Read PDFComplete genome sequence of <i>Streptococcus suis</i> isolated from an aborted bovine fetus and placenta in British Columbia, Canada
We present the complete genome of <i>Streptococcus suis</i> KKAHC02 isolated from an aborted bovine fetus and placenta in British Columbia, Canada. The genome consists of a circular chromosome of 2,340,488 bp long and five circular …
Read PDFA Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia
Norovirus is a leading cause of acute gastroenteritis, with genogroup II (NoV-GII) being predominant. This study presents a novel genotyping system for norovirus GII, combining long-range PCR to amplify the complete ~3.2 kb RdRp-VP1 region …
Read PDFGenome sequences of nicotine-degrading <i>Pseudomonas</i> and <i>Stutzerimonas</i> strains isolated from nicotine-enriched activated sludge
We have isolated seven novel nicotine-degrading <i>Pseudomonas</i> and <i>Stutzerimonas</i> strains from activated sludge enrichment cultures. These strains were obtained through successive passages of activated sludge microbial communities in M9 minimal media containing nicotine as the …
Read PDFFull-length transcriptome of <i>Camellia perpetua</i> reveals candidate <i>SCPL</i>1<i>A</i> gene family members involved in galloylated catechins biosynthesis
Catechins includ galloylated catechins and non-galloylated catechins, among which galloylated catechins exhibit stronger antioxidant, anti-inflammatory and anti-cancer activities. Section <i>Chrysantha</i> Chang, the only group of yellow <i>Camellia</i> with rich catechins in their flowers, is a …
Read PDFGenome sequence of <i>Stenotrophomonas geniculata</i> AS50Mn isolated from sand filters used to treat manganese-containing alkaline mine water
<i>Stenotrophomonas geniculata</i> AS50Mn was isolated from sand filters used to treat manganese-containing mine water under alkaline conditions. Here, we report the complete genome sequence of this bacterium, which comprises a 4,478,846 bp circular chromosome. The …
Read PDFViruses Infecting Cuban Honey Bees and Evolution of Deformed-Wing-Virus Variants
Cuba is in a unique situation in which it has a large (220,000 managed colonies) and isolated honey bee population due to a 60+ year ban on the importation of bees. Despite this, the ectoparasitic …
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