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Article
Open AccessLow-abundance populations distinguish microbiome performance in plant cell wall deconstruction
Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological...
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Article
Open AccessCharacterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery
The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of a...
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Article
Open AccessMetagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera
Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a...
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Article
Open AccessezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
Inferring phylogenetic trees for newly recovered genomes from metagenomic samples is very useful in determining the identities of uncultivated microorganisms. Even though 16S ribosomal RNA small subunit genes ...
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Article
Open AccessMetabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or bet...
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Article
Open AccessMaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these ...
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Article
Open AccessEditing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes
Sequence analysis of organelle genomes and comprehensive analysis of C-to-U editing sites from flowering and non-flowering plants have provided extensive sequence information from diverse taxa. This study incl...