Biology subjects

Morton, J. T.

Publications and source records attributed to Morton, J. T..

3 recordsLinked to original sources

bioRxiv2018

American Gut: an Open Platform for Citizen-Science Microbiome Research

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as compared to environmental samples, demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations, uncover new molecules and kinds of molecular communities in the human stool metabolome, and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness, and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.\n\nImportanceWe 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 effect of diverse plants in the diet which we confirm with untargeted metabolomics on hundreds of samples.

microbiology↗

bioRxiv2017

Phylofactorization - a graph partitioning algorithm to identify phylogenetic scales of ecological data

The problem of pattern and scale is a central challenge in ecology. The problem of scale is central to community ecology, where functional ecological groups are aggregated and treated as a unit underlying an ecological pattern, such as aggregation of \"nitrogen fixing trees\" into a total abundance of a trait underlying ecosystem physiology. With the emergence of massive community ecological datasets, from microbiomes to breeding bird surveys, there is a need to objectively identify the scales of organization pertaining to well-defined patterns in community ecological data.\n\nThe phylogeny is a scaffold for identifying key phylogenetic scales associated with macroscopic patterns. Phylofactorization was developed to objectively identify phylogenetic scales underlying patterns in relative abundance data. However, many ecological data, such as presence-absences and counts, are not relative abundances, yet it is still desireable and informative to identify phylogenetic scales underlying a pattern of interest. Here, we generalize phylofactorization beyond relative abundances to a graph-partitioning algorithm for any community ecological data.\n\nGeneralizing phylofactorization connects many tools from data analysis to phylogenetically-informe analysis of community ecological data. Two-sample tests identify three phylogenetic factors of mammalian body mass which arose during the K-Pg extinction event, consistent with other analyses of mammalian body mass evolution. Projection of data onto coordinates defined by the phylogeny yield a phylogenetic principal components analysis which refines our understanding of the major sources of variation in the human gut microbiome. These same coordinates allow generalized additive modeling of microbes in Central Park soils and confirm that a large clade of Acidobacteria thrive in neutral soils. Generalized linear and additive modeling of exponential family random variables can be performed by phylogenetically-constrained reduced-rank regression or stepwise factor contrasts. We finish with a discussion of how phylofac-torization produces an ecological species concept with a phylogenetic constraint. All of these tools can be implemented with a new R package available online.

ecology↗

bioRxiv2017

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

bioinformatics↗