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View Article and Find Full Text PDFThe current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 °C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction.
View Article and Find Full Text PDFSequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation.
View Article and Find Full Text PDFThe rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with antimicrobial activity. This brief report describes the genome sequence of threeBacillusspecies isolates from South African marine sponges, which produce compounds with antimicrobial activity. A search for secondary metabolite clusters revealed several secondary metabolite pathways in these genomes, which may hold promise as novel antibiotics.
View Article and Find Full Text PDFBackground: Next generation sequencing (NGS) allows the detection of minor variant HIV drug resistance mutations (DRMs). However data from new NGS platforms after Prevention-of-Mother-to-Child-Transmission (PMTCT) regimen failure are limited.
Objective: To compare major and minor variant HIV DRMs with Illumina MiSeq and Life Technologies Ion Personal Genome Machine (PGM) in infants infected despite a PMTCT regimen.
Antonie Van Leeuwenhoek
November 2011
Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA-DNA hybridization (DDH) for distinguishing closely related species was also assessed.
View Article and Find Full Text PDFGiven the advances in molecular biology, many microbial taxonomists feel that a sequencing based method should be developed that can replace DNA-DNA hybridisation for species delineation. The potential of the gyrB gene to be used for phylogenetic studies has been investigated within a number of actinobacterial genera, including Gordonia, Micromonospora and the whorl-forming Streptomyces species. This study aimed to determine whether the gyrB gene can discriminate between type strains of the genus Kribbella.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
June 2010
A novel actinomycete, strain TVU1(T), was isolated from leaves of the indigenous South African plant Tulbaghia violacea. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain TVU1(T) was most closely related to Micromonospora echinospora DSM 43816(T).
View Article and Find Full Text PDFDespite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as 'uncultured'. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study.
View Article and Find Full Text PDFTwo novel nocardioform actinomycetes, strains Q41T and HMC25T, were isolated from soil samples collected in the Western Cape province, South Africa. Rapid genus identification revealed that the isolates belonged to the genus Kribbella (based on single-digestion restriction analysis of the 16S rRNA gene sequences with MboI, VspI, SphI, SnaBI, SalI and AgeI). Both isolates had ll-diaminopimelic acid and glycine in their cell-wall peptidoglycan, and contained mannose and ribose as whole-cell sugars.
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