Peer-reviewed Articles - Biology

60 downloads
699 views

Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation...

["Biodiversity","Bioinformatics","Microbiology"]
doi:10.7717/peerj.5299
82 downloads
532 views

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical...

["Agricultural Science","Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4991
2 citations
145 downloads
1,400 views

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Mycology"]
doi:10.7717/peerj.4925
125 downloads
1,341 views

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial...

["Biodiversity","Bioinformatics","Genomics","Microbiology","Veterinary Medicine"]
doi:10.7717/peerj.4827
1 citation
140 downloads
864 views

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response...

["Biodiversity","Biogeography","Bioinformatics","Microbiology"]
doi:10.7717/peerj.3827
3 citations
294 downloads
1,485 views

Background The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the...

["Biodiversity","Bioinformatics","Microbiology"]
doi:10.7717/peerj.3254
288 downloads
1,945 views

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported...

["Biochemistry","Biodiversity","Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3162
287 citations
1,894 downloads
10,848 views

Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010)...

["Biodiversity","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.2584
7 citations
371 downloads
1,899 views

Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine...

["Biodiversity","Bioinformatics","Environmental Sciences","Microbiology","Molecular Biology"]
doi:10.7717/peerj.1692
58 citations
673 downloads
3,609 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:10.7717/peerj.1420
11 citations
374 downloads
2,229 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
145 citations
1,790 downloads
12,580 views

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Molecular Biology"]
doi:10.7717/peerj.593
13 citations
896 downloads
5,022 views

In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Statistics"]
doi:10.7717/peerj.157

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