scholarly journals Characterization of prodiginine compounds produced by a Vibrio species isolated from salt flat sediment along the Florida Gulf Coast

Fine Focus ◽  
2017 ◽  
Vol 3 (1) ◽  
pp. 33-51 ◽  
Author(s):  
Stephanie Morgan ◽  
Matthew J. Thomas ◽  
Katherine M. Walstrom ◽  
Eric C. Warrick ◽  
Brittany J. Gasper
Keyword(s):  
Gulf Coast ◽  
Bacterial Species ◽  
Whole Genome ◽  
Medicinal Uses ◽  
Salt Flat ◽  
Florida Gulf Coast ◽  
Flash Column Chromatography ◽  
Vibrio Genus ◽  
Pink Pigment

Prodiginines are secondary metabolites produced by several known species of bacteria. These metabolites are known for their bright pigmentation and their potential medicinal uses. Biosynthesis of prodiginine compounds, including the well-studied prodigiosin, has been well characterized in Serratia marcescens and other bacterial species, including several marine bacteria. In an effort to isolate and identify natural products from marine organisms, an environmental sample was taken from a salt flat along the Florida Gulf Coast and cultured for bacterial growth. A bacterial species that produces a vibrant pink pigment was isolated and identified as a member of the Vibrio genus and was named MI-2. Whole genome sequencing identified a 13-gene operon with homology to the S. marcescens prodigiosin biosynthetic operon. The pigment produced by MI-2 was hypothesized to be composed of prodigiosin or related prodiginine compounds and was purified by flash column chromatography and identified by mass spectrometry.

scholarly journals Occurrence and Molecular Characterization of Abundant tet(X) Variants Among Diverse Bacterial Species of Chicken Origin in Jiangsu, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingshan Li ◽  
Kai Peng ◽  
Yi Yin ◽  
Xinran Sun ◽  
Wenhui Zhang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Bioinformatics Analysis ◽  
Bacterial Species ◽  
Whole Genome ◽  
Poultry Farms ◽  
High Level ◽  
Level Resistance

Many novel tigecycline-inactivating enzymes encoded by tet(X) variants from different bacteria were discovered since the plasmid-mediated tet(X3) and tet(X4) genes conferring high-level resistance to tigecycline in Enterobacterales and Acinetobacter were reported. However, there have been no comprehensive studies of the prevalence of different tet(X) variants in poultry farms. In this study, we collected 45 chicken fecal samples, isolated tet(X)-positive strains, and performed antimicrobial susceptibility testing, conjugation assay, whole-genome sequencing, and bioinformatics analysis. A total of 15 tet(X)-bearing strains were isolated from 13 samples. Species identification and tet(X) subtyping analysis found that the 15 strains belonged to eight different species and harbored four different tet(X) variants. Genomic investigation showed that transmission of tet(X) variants was associated with various mobile genetic elements, and tet(X4) was the most prevalent variant transferred by conjugative plasmids. Meanwhile, we characterized a plasmid co-harboring tet(X6) and blaOXA–58 in Acinetobacter baumannii. In summary, we demonstrated that different tet(X) variants were widely disseminated in the chicken farming environment and dominated by tet(X4). This finding expands the understanding of the prevalence of tet(X) among different animal sources, and it was advocated to reduce the usage of antibiotics to limit the emergence and transmission of novel tet(X) variants in the poultry industry.

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

scholarly journals A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathy E. Raven ◽  
Sophia T. Girgis ◽  
Asha Akram ◽  
Beth Blane ◽  
Danielle Leek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Dna Extraction ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Bacterial Species ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Library Preparation ◽  
Simultaneous Processing ◽  
Antimicrobial Resistance Gene

AbstractWhole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.

scholarly journals Characterization of the SOS response of Pseudomonas fluorescens strain DC206 using whole-genome transcript analysis

2007 ◽  
Vol 269 (2) ◽  
pp. 256-264 ◽  
Author(s):  
Hongfan Jin ◽  
Diane M. Retallack ◽  
Steven J. Stelman ◽  
C. Douglas Hershberger ◽  
Tom Ramseier
Keyword(s):  
Pseudomonas Fluorescens ◽  
Sos Response ◽  
Whole Genome ◽  
Transcript Analysis
Sign in / Sign up

Export Citation Format

Share Document