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Research Article | Host-Microbe BiologyAmerican Gut: an Open Platform for Citizen Science Microbiome ResearchWe show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the...
Observation | Host-Microbe BiologyMigraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project CohortRecent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546–551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have...
Editor's Pick Research Article | Applied and Environmental ScienceA Phylogenetic and Functional Perspective on Volatile Organic Compound Production by ActinobacteriaSoil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain...
Editor's Pick Observation | Novel Systems Biology TechniquesDeblur Rapidly Resolves Single-Nucleotide Community Sequence PatternsDeblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.
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...
Editor's Pick Perspective | Host-Microbe BiologyThe Dimension of Time in Host-Microbiome InteractionsThe intestinal microbiota contains trillions of commensal microorganisms that shape multiple aspects of host physiology and disease. In contrast to the host’s genome, the microbiome is amenable to change over the course of an organism’s lifetime, providing an opportunity to therapeutically modulate the microbiome’s impact on human pathophysiology.
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...
Editor's Pick Research Article | Applied and Environmental SciencePhylogenetically Novel Uncultured Microbial Cells Dominate Earth MicrobiomesIn the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of...
Research Article | Host-Microbe BiologyLongitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight InfantsPreterm infants are at greater risk of microbial insult than full-term infants, including reduced exposure to maternal vaginal and enteric microbes, higher rates of formula feeding, invasive procedures, and administration of antibiotics and medications that alter gastrointestinal pH. This investigation of the VLBW infant microbiome over the course of the neonatal intensive care unit (NICU) stay, and at ages 2 and 4 years, showed that...
Methods and Protocols | Novel Systems Biology TechniquesMicrobiome Helper: a Custom and Streamlined Workflow for Microbiome ResearchAs the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results....