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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
TLDR
There is incongruent taxonomic nomenclature among curators even at the phylum level, and environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
TLDR
An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
TLDR
A ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology is developed and used to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences.
STAMP: statistical analysis of taxonomic and functional profiles
TLDR
UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles and a user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
TLDR
This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
Our perspective on microbial diversity has improved enormously over the past few decades. In large part this has been due to molecular phylogenetic studies that objectively relate organisms.
Community structure and metabolism through reconstruction of microbial genomes from the environment
TLDR
Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
TLDR
Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.
Insights into the phylogeny and coding potential of microbial dark matter
TLDR
This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
Defining the core Arabidopsis thaliana root microbiome
TLDR
The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages.
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