Peer-reviewed Articles

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7717/peerj.3812

Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed...

["Ecology","Genomics","Microbiology","Virology","Freshwater Biology"]
doi:10.7717/peerj.3810
1 download
2 views

Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years,...

["Ecology","Entomology","Microbiology","Veterinary Medicine","Zoology"]
doi:10.7717/peerj.3816

Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains...

["Microbiology"]
doi:10.7717/peerj.3796
16 downloads
228 views

Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in...

["Genetics","Microbiology"]
doi:10.7717/peerj.3830
35 downloads
338 views

Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3817
37 downloads
379 views

Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis...

["Biodiversity","Genomics","Microbiology"]
doi:10.7717/peerj.3837
25 downloads
258 views

Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for...

["Bioinformatics","Computational Biology","Microbiology","Pharmacology"]
doi:10.7717/peerj.3765
60 downloads
255 views

Background Dengue viral infection is an acute infection that has the potential to have severe complications as its major sequela. Currently, there is no routine laboratory biomarker with which to predict the severity of dengue infection or monitor the effectiveness...

["Microbiology","Virology","Epidemiology","Immunology","Infectious Diseases"]
doi:10.7717/peerj.3589
57 downloads
283 views

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3729
60 downloads
206 views

Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role...

["Genomics","Microbiology"]
doi:10.7717/peerj.3698
51 downloads
507 views

Background Chlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms...

["Microbiology","Veterinary Medicine","Public Health"]
doi:10.7717/peerj.3799
67 downloads
722 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3788
41 downloads
171 views

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms...

["Microbiology","Soil Science"]
doi:10.7717/peerj.3777
43 downloads
508 views

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides...

["Ecology","Microbiology","Soil Science"]
doi:10.7717/peerj.3773

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