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microbiology
8 downloads
44 views

Nitrogen (N) and Carbon (C) are popular indicators of soil fertility; however, they are not soil fertility itself. In fact, they may be seen as just two aspects of the one entity. Soil microbial biomass (SMB) is also one of soil fertility indicators; furthermore,...

["Agricultural Science","Microbiology","Soil Science"]
doi:10.7287/peerj.preprints.1217v2

A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages...

["Biodiversity","Ecology","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.1061

Background. It is widely assumed that the uterine cavity in non-pregnant women is a sterile body environment under physiological conditions. We have previously shown that some women with overt dysbiosis of the vaginal microbiome, present with a polymicrobial Gardnerella...

["Microbiology","Molecular Biology","Gynecology and Obstetrics","Women's Health"]
doi:10.7287/peerj.preprints.1269v1
11 downloads
62 views

Crude oil is still the dominant energy source in Brazil and that the consumption keeps rising since 2013, being responsible for 2.2% of the world’s energy consumption. The recent discovery of crude oil reservoirs at the Espirito Santo basin, Campos basin and Santos...

["Biodiversity","Biotechnology","Ecology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.1254v1
8 downloads
54 views

Quorum sensing (QS) is a mechanism that plays important roles in gene expression in response to an expanding bacterial population. In many Gram-negative bacteria, N-acyl homoserine lactone is mainly secreted as the diffusible signalling molecules. This QS system...

["Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1232v1
241 downloads
151 views

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial...

["Biodiversity","Bioinformatics","Environmental Sciences","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1222v2
287 downloads
804 views

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms.Results: We present three advances in our ability to assign and interpret taxonomic classifications of short...

["Bioinformatics","Computational Biology","Ecology","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.934v2
109 downloads
195 views

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids...

["Entomology","Evolutionary Studies","Microbiology","Plant Science"]
doi:10.7287/peerj.preprints.649v2
43 downloads
189 views

Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic...

["Biochemistry","Biophysics","Microbiology","Neuroscience"]
doi:10.7717/peerj.1065
1 citation
435 downloads
4,060 views

The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.1029
145 downloads
1,472 views

As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates....

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.1025
138 downloads
673 views

Associations between microorganisms occur extensively throughout Earth’s oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate...

["Computational Biology","Ecology","Genomics","Marine Biology","Microbiology"]
doi:10.7717/peerj.1008
66 downloads
424 views

Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral...

["Biodiversity","Bioinformatics","Microbiology","Virology"]
doi:10.7717/peerj.997
43 downloads
277 views

Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different...

["Biodiversity","Ecology","Environmental Sciences","Marine Biology","Microbiology"]
doi:10.7717/peerj.890
242 downloads
1,321 views

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains...

["Bioinformatics","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.985

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