metagenomics
Research Article | Applied and Environmental ScienceIntegrated Omic Analyses Provide Evidence that a “Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions“Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report...
Editor's Pick Research Article | Applied and Environmental ScienceMetatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic MicrobiomeMixed communities of microbes play important roles in health, the environment, agriculture, and biotechnology. While tapping the combined activities of organisms within microbiomes may allow the utilization of a wider range of substrates in preference to the use of pure cultures for biomanufacturing, harnessing the metabolism of these mixed cultures remains a major challenge. Here, we predicted metabolic functions of bacteria in a...
Methods and Protocols | Novel Systems Biology TechniquesEvaluating the Information Content of Shallow Shotgun MetagenomicsA common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S...
Editor's Pick Commentary | Applied and Environmental ScienceSizing Up the Uncultured Microbial MajorityPredicting the total number of microbial cells on Earth and exploring the full diversity of life are fundamental research concepts that have undergone paradigm shifts in the genomic era. In this issue, Lloyd and colleagues (K.
Editor's Pick Research Article | Ecological and Evolutionary ScienceSelection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome ResearchAncient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately...
Editor's Pick Research Article | Ecological and Evolutionary ScienceCharacterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic ResistomesAntibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the...
Methods and Protocols | Novel Systems Biology TechniquesSHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality ControlQuality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is...
Research Article | Novel Systems Biology TechniquesNonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence DiversityEstimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and...
Special Issue Perspective | Ecological and Evolutionary ScienceUsing Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path AheadAs troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge.
Special Issue Perspective | Host-Microbe BiologyExploring Linkages between Taxonomic and Functional Profiles of the Human MicrobiomeMicrobiome studies typically focus on characterizing the taxonomic and functional profiles of the microbes within a community. Functional profiling is generally thought to be superior to taxonomic profiling for investigating human-microbe interactions, but there are several limitations and challenges to existing approaches.