Peer-reviewed Articles - Biology

63 downloads
629 views

Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors...

["Bioinformatics","Ecology","Marine Biology","Microbiology","Taxonomy"]
doi:10.7717/peerj.5248
108 downloads
514 views

Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed...

["Bioinformatics","Ecology","Entomology"]
doi:10.7717/peerj.5126
88 downloads
570 views

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer...

["Bioinformatics","Ecology","Genomics","Microbiology","Population Biology"]
doi:10.7717/peerj.5098
81 downloads
528 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
144 downloads
1,395 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
1 citation
243 downloads
1,471 views

Confirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome...

["Bioinformatics","Ecology","Evolutionary Studies","Zoology","Statistics"]
doi:10.7717/peerj.4718
259 downloads
1,170 views

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood....

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4395
2 citations
504 downloads
2,216 views

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4303
2 citations
783 downloads
4,225 views

Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.4320
168 downloads
782 views

Accurate taxonomic resolution in light microscopy analyses of microalgae is essential to achieve high quality, comparable results in both floristic analyses and biomonitoring studies. A number of closely related diatom taxa have been detected to date co-occurring...

["Bioinformatics","Ecology","Marine Biology","Taxonomy","Freshwater Biology"]
doi:10.7717/peerj.4159
3 citations
687 downloads
9,698 views

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4029
281 downloads
1,436 views

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors...

["Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.3944
148 downloads
1,525 views

Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has...

["Animal Behavior","Bioinformatics","Ecology","Entomology","Zoology"]
doi:10.7717/peerj.3821
317 downloads
1,927 views

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
6 citations
555 downloads
1,970 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

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