microbiome
Research Article | Host-Microbe BiologyTime Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial PathogensThe microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across...
Research Article | Host-Microbe BiologyInterpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance SelectionHigh-throughput sequencing provides an easy and cost-effective way to measure the relative abundance of bacteria in any environmental or biological sample. When these samples come from humans, the microbiome signatures can act as biomarkers for disease prediction. However, because bacterial abundance is measured as a composition, the data have unique properties that make conventional analyses inappropriate. To overcome this, analysts...
Editor's Pick Research Article | Host-Microbe BiologyShotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic DegradationThe study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive...
Research Article | Host-Microbe BiologyConsumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and MetabolomePublic interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented...
Research Article | Novel Systems Biology TechniquesMultiple-Disease Detection and Classification across Cohorts via Microbiome SearchHere, we present a search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares them to databases of samples from patients. This approach enables the identification of microbiome states associated with disease even in the presence of different cohorts, multiple sequencing platforms, or significant...
Research Article | Host-Microbe BiologyMetabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive CheetahsMetabolome-informed analyses can enhance omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate here the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an...
Research Article | Host-Microbe BiologyCorrelations between the Composition of the Bovine Microbiota and Vitamin B12 AbundanceIn this paper, we examined the microbiome of the bovine rumen, feces, and milk and attempted to understand how the bacterial communities at each site affected the production and movement of vitamin B12 around the animal’s body. It was determined that the composition of the bovine rumen microbiome correlates well with vitamin B12 concentration, indicating that the rumen microbiota may be a good target for...
Research Article | Host-Microbe BiologyImproving Characterization of Understudied Human Microbiomes Using Targeted PhylogeneticsThe human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited...
Methods and Protocols | Novel Systems Biology Techniquesmanta: a Clustering Algorithm for Weighted Ecological Networksmanta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.
Research Article | Host-Microbe BiologyComparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream FermentersRice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in...