metagenomics
Special Issue Perspective | Host-Microbe BiologyMetaproteomics: Much More than Measuring Gene Expression in Microbial CommunitiesMetaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.
Editor's Pick Research Article | Clinical Science and EpidemiologyMicrofluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway MetagenomicsThe airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community—the metagenome. Here, we describe a protocol for airway sample preparation which couples a...
Special Issue Perspective | Ecological and Evolutionary ScienceA Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection.
Research Article | Host-Microbe BiologyA Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut MicrobiomeThe composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with...
Special Issue Perspective | Host-Microbe BiologyBovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle SystemsThe mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and...
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...