metagenomics
Research Article | Applied and Environmental ScienceRefSoil+: a Reference Database for Genes and Traits of Soil PlasmidsSoil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil...
Research Article | Host-Microbe BiologyEvaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's DiseaseA majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a...
Research Article | Ecological and Evolutionary ScienceA Novel Sparse Compositional Technique Reveals Microbial PerturbationsBy accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this...
Perspective | Ecological and Evolutionary ScienceBridging the Holistic-Reductionist Divide in Microbial EcologyMicrobial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace.
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...