Biology subjects

Green, J. L.

Publications and source records attributed to Green, J. L..

4 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

The geometry of the distance-decay of similarity in ecological communities

Understanding beta-diversity has strong implications for evaluating the extent of biodiversity and formulating effective conservation policy. Here, we show that the distance-decay relationship, an important measure of beta-diversity, follows a universal form which we call the piecewise quadratic model. To derive the piecewise quadratic model, we develop a new conceptual framework which is based on geometric probability and several key insights about the roles of study design (e.g., plot dimensions and spatial distributions). We fit the piecewise quadratic model to six empirical distance-decay relationships, spanning a range of taxa and spatial scales, including surveys of tropical vegetation, mammals, and amphibians. We find that the model predicts the functional form of the relationships extremely well, with coefficients of determination in excess of 0.95. Moreover, the model predicts a phase transition at distance scales where sample plots are overlapping, which we confirm empirically. Our framework and model provide a fundamental, quantitative link between distance-decay relationships and the shapes of ranges of taxa.

ecology↗

bioRxiv2016

Cleanliness in context: reconciling hygiene with a modern microbial perspective

The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with that of sterilization. Recent research on microbial ecology is demonstrating that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota). Human skin is home to a diverse, skin habitat specific community of microorganisms; this includes members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host, and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease. To examine the implications of this definition, we review the literature related to hand drying as an aspect of hand hygienic practice. Research on hand drying generally focuses on hygienic efficacy, a concept not typically defined explicitly, but nearly always including alterations to bulk microbial load. The corresponding literature is differentiable into two divisions: research supporting the use of forced air dryers, which typically includes effectiveness of drying as an aspect of hygienic efficacy; and research supporting the use of paper towels, which typically includes risk of aerosolized spread of microbes from hands as an aspect of hygienic efficacy. Utilizing a definition of hygiene that explicitly relies on reduction in disease spread rather than alterations to bulk microbial load would address concerns raised on both sides of the debate. Future research should take advantage of cultivation-independent techniques, working to bridge the gap between the two existing divisions of research by using health outcomes (such as the spread of disease) as dependent variables, taking into account the microbial community context of the skin microbiota, and focusing on understanding the relative contribution of bioaerosols and residual moisture to the risk of disease transmission.

microbiology↗

bioRxiv2016

Global-scale structure of the eelgrass microbiome

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial plant species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of their surrounding seawater and sediment communities, we uncovered the structure, composition and variability of microbial communities associated with Z. marina. We also investigated hypotheses about the mechanisms driving assembly of the eelgrass microbiome using a whole-genomic metabolic modeling approach. Our results reveal aboveground leaf communities displaying high variability and spatial turnover, that strongly mirror their adjacent coastal seawater microbiomes. In contrast, roots showed relatively low spatial turnover and were compositionally distinct from surrounding sediment communities -- a result largely driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Metabolic modeling of enriched taxa was consistent with an assembly process whereby similarity in resource use drives taxonomic co-occurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core Z. marina root microbiome with putative functional roles and highlights potentially disparate processes influencing microbiome assembly on different plant compartments.

microbiology↗