Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies
Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in
microbial ecology studies. This has led to the rapid expansion of research in the field and …
microbial ecology studies. This has led to the rapid expansion of research in the field and …
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …
monitoring biodiversity in ecology. However, taxa identifications produced through …
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable
diversity estimates are difficult to achieve and validate. Here we present and validate a …
diversity estimates are difficult to achieve and validate. Here we present and validate a …
Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity …
Advances in the analysis of amplicon sequence datasets have introduced a methodological
shift in how research teams investigate microbial biodiversity, away from sequence identity …
shift in how research teams investigate microbial biodiversity, away from sequence identity …
[PDF][PDF] Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
Rapid development of high-throughput (HTS) molecular identification methods has
revolutionized our knowledge about taxonomic diversity and ecology of fungi. However …
revolutionized our knowledge about taxonomic diversity and ecology of fungi. However …
The development of terrestrial ecosystems emerging after glacier retreat
The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes,
with new ecosystems develo** from apparently barren substrates,,–. The study of these …
with new ecosystems develo** from apparently barren substrates,,–. The study of these …
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
L Tedersoo, A Tooming‐Klunderud… - New Phytologist, 2018 - Wiley Online Library
Second‐generation, high‐throughput sequencing methods have greatly improved our
understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) …
understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) …
Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline
Fungal communities associated with plants and soil influence plant fitness and ecosystem
functioning. They are frequently studied by metabarcoding approaches targeting the …
functioning. They are frequently studied by metabarcoding approaches targeting the …
Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management
Network models of soil and plant microbiomes provide new opportunities for enhancing
disease management, but also challenges for interpretation. We present a framework for …
disease management, but also challenges for interpretation. We present a framework for …
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
Background Understanding the genetic and environmental factors that structure plant
microbiomes is necessary for leveraging these interactions to address critical needs in …
microbiomes is necessary for leveraging these interactions to address critical needs in …