Publications by authors named "Joshua Ladau"

22 Publications

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Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.

mSystems 2021 02 23;6(1). Epub 2021 Feb 23.

Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.
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http://dx.doi.org/10.1128/mSystems.01194-20DOI Listing
February 2021

A genomic catalog of Earth's microbiomes.

Nat Biotechnol 2021 04 9;39(4):499-509. Epub 2020 Nov 9.

DOE Joint Genome Institute, Berkeley, CA, USA.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
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http://dx.doi.org/10.1038/s41587-020-0718-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041624PMC
April 2021

A meta-analysis of global fungal distribution reveals climate-driven patterns.

Nat Commun 2019 11 13;10(1):5142. Epub 2019 Nov 13.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.
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http://dx.doi.org/10.1038/s41467-019-13164-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853883PMC
November 2019

Global ecotypes in the ubiquitous marine clade SAR86.

ISME J 2020 01 14;14(1):178-188. Epub 2019 Oct 14.

Gladstone Institutes, San Francisco, CA, USA.

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.
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http://dx.doi.org/10.1038/s41396-019-0516-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908720PMC
January 2020

Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology.

Trends Microbiol 2019 08 15;27(8):662-669. Epub 2019 Apr 15.

Joint Genome Institute, Walnut Creek, CA, USA. Electronic address:

Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.
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http://dx.doi.org/10.1016/j.tim.2019.03.003DOI Listing
August 2019

Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage.

Anim Microbiome 2019 Feb 12;1(1). Epub 2019 Feb 12.

Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA, 95616, USA.

Background: Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH) production from beef cattle by up to ~ 99% when added to Rhodes grass hay; a common feed in the Australian beef industry. These experiments have shown significant reductions in CH without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California, the largest milk producing state in the US.

Results: Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome consistent with the Anna Karenina hypothesis, with increased β-diversity, over time scales of approximately 3 days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of CH in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed.

Conclusions: The methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy for dairy cattle. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.
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http://dx.doi.org/10.1186/s42523-019-0004-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7803124PMC
February 2019

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Oct 23.

State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.

Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems. There have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the contrary in Tibet and North America. These findings could significantly improve understanding of climate impacts on soil microbial communities.
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http://dx.doi.org/10.1128/mSystems.00167-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199470PMC
October 2018

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Sep 25.

Joint Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, USA.

To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 × 10 (81%) and 2.2 × 10 (25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems. In 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 microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions. : An author video summary of this article is available.
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http://dx.doi.org/10.1128/mSystems.00055-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156271PMC
September 2018

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

mSystems 2018 May-Jun;3(3). Epub 2018 May 15.

Human Food Project, Terlingua, Texas, USA.

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 United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes 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. We 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 = 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.
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http://dx.doi.org/10.1128/mSystems.00031-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954204PMC
May 2018

A communal catalogue reveals Earth's multiscale microbial diversity.

Nature 2017 11 1;551(7681):457-463. Epub 2017 Nov 1.

Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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http://dx.doi.org/10.1038/nature24621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192678PMC
November 2017

Urban greenness influences airborne bacterial community composition.

Sci Total Environ 2016 Nov 11;571:680-7. Epub 2016 Jul 11.

Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States.

Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing neighborhoods and open space systems that foster better human health.
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http://dx.doi.org/10.1016/j.scitotenv.2016.07.037DOI Listing
November 2016

Marked seasonal variation in the wild mouse gut microbiota.

ISME J 2015 Nov 29;9(11):2423-34. Epub 2015 May 29.

FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.
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http://dx.doi.org/10.1038/ismej.2015.53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611506PMC
November 2015

Continental-scale distributions of dust-associated bacteria and fungi.

Proc Natl Acad Sci U S A 2015 May 20;112(18):5756-61. Epub 2015 Apr 20.

Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309;

It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans.
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http://dx.doi.org/10.1073/pnas.1420815112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426398PMC
May 2015

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.

Science 2013 Nov;342(6158):621-4

Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.

Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.
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http://dx.doi.org/10.1126/science.1243768DOI Listing
November 2013

Global marine bacterial diversity peaks at high latitudes in winter.

ISME J 2013 Sep 21;7(9):1669-77. Epub 2013 Mar 21.

The Gladstone Institutes, University of California, San Francisco, CA 94158, USA.

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms.
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http://dx.doi.org/10.1038/ismej.2013.37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749493PMC
September 2013

Predicting microbial distributions in space and time.

Nat Methods 2012 May 30;9(6):549-51. Epub 2012 May 30.

Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA.

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http://dx.doi.org/10.1038/nmeth.2041DOI Listing
May 2012

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

PLoS Comput Biol 2011 Jan 20;7(1):e1001061. Epub 2011 Jan 20.

The J. David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
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http://dx.doi.org/10.1371/journal.pcbi.1001061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024254PMC
January 2011

Robust hypothesis tests for independence in community assembly.

J Math Biol 2008 Oct 17;57(4):537-55. Epub 2008 Apr 17.

Santa Fe Institute, Santa Fe, NM 87501, USA.

The extent to which competition affects the distributions of species at large spatial scales is unclear. To evaluate this question, hypothesis tests that do not depend on parametric assumptions are needed. Here, we develop a broadly applicable test that requires only one parametric assumption. Letting i and j denote the ith and jth colonists to arrive at a site, respectively, and [i j] the event that i and j belong to the same "unit" (e.g., functional group, genus), we show how colonists will be partitioned into units if for all i and j, [i j] is independent of whether i and j share unit membership with the other colonists, conditional on other information about shared units. Our distribution of partitions is useful for inferring competitive effects, because these effects predict that for at least one i and j, P ([i j]) will be less when i and j share unit membership than when they do not.
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http://dx.doi.org/10.1007/s00285-008-0176-0DOI Listing
October 2008

Plant-derived pyrrolizidine alkaloid protects eggs of a moth (Utetheisa ornatrix) against a parasitoid wasp (Trichogramma ostriniae).

Proc Natl Acad Sci U S A 2004 Jun 1;101(24):9029-32. Epub 2004 Jun 1.

Department of Neurobiology, Cornell University, Ithaca, NY 14853, USA.

Pyrrolizidine alkaloid (PA), sequestered by the moth Utetheisa ornatrix from its larval food plant, is transmitted by both males and females to the eggs. Males confer PA on the female by seminal infusion, and females pass this gift, together with PA that they themselves procured as larvae, to the eggs. Here we show that PA protects the eggs against parasitization by the chalcidoid wasp, Trichogramma ostriniae. Eggs laid subsequent to a first mating of an Utetheisa female receive most of their PA from the female. The amount they receive from the male is insufficient to provide for full protection. However, female Utetheisa are promiscuous and therefore likely to receive PA on a cumulative basis from their male partners.
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http://dx.doi.org/10.1073/pnas.0402480101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC428467PMC
June 2004