Abstract The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

INTRODUCTION

ABSTRACT: The time delays between point-like images in gravitational lens systems can be used to measure cosmological parameters as well as probe the dark matter (sub-)structure within the lens galaxy. The number of lenses with measuring time delays is growing rapidly due to dedicated efforts. In the near future, the upcoming _Large Synoptic Survey Telescope_ (LSST), will monitor ∼10³ lens systems consisting of a foreground elliptical galaxy producing multiple images of a background quasar. In an effort to assess the present capabilities of the community to accurately measure the time delays in strong gravitational lens systems, and to provide input to dedicated monitoring campaigns and future LSST cosmology feasibility studies, we pose a “Time Delay Challenge” (TDC). The challenge is organized as a set of “ladders,” each containing a group of simulated datasets to be analyzed blindly by participating independent analysis teams. Each rung on a ladder consists of a set of realistic mock observed lensed quasar light curves, with the rungs’ datasets increasing in complexity and realism to incorporate a variety of anticipated physical and experimental effects. The initial challenge described here has two ladders, TDC0 and TDC1. TDC0 has a small number of datasets, and is designed to be used as a practice set by the participating teams as they set up their analysis pipelines. The non mondatory deadline for completion of TDC0 will be December 1 2013. The teams that perform sufficiently well on TDC0 will then be able to participate in the much more demanding TDC1. TDC1 will consists of 10³ lightcurves, a sample designed to provide the statistical power to make meaningful statements about the sub-percent accuracy that will be required to provide competitive Dark Energy constraints in the LSST era. In this paper we describe the simulated datasets in general terms, lay out the structure of the challenge and define a minimal set of metrics that will be used to quantify the goodness-of-fit, efficiency, precision, and accuracy of the algorithms. The results for TDC1 from the participating teams will be presented in a companion paper to be submitted after the closing of TDC1, with all TDC1 participants as co-authors.

ABSTRACT

ABSTRACT Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: 1) the Average American (AMERICAN): focused on convenience foods, 2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at \(1.3 X 10^9\) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at \(6 X 10^6 \)and \(1.4 X 10^6\) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbial approaches beyond probiotics taken as supplements - _i.e._, ingested as foods - are important contributors to the composition, inter-individual variation, and function of our gut microbiota.

I started a Twitter account in 2010, during my first year of graduate school, because I was told I needed to. Not by my graduate program, but by the Society for Neuroscience (SfN). I had just been accepted to be an official “neuro-blogger” for the SfN conference – an annual gathering that draws over 30,000 attendees. The requirements for outreach were minimal: at least one blog post per day during the conference, preferably within our assigned “theme”. Additional postings were encouraged and Twitter accounts were mandatory. 

ABSTRACT Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration and colonization of the solar system come to fruition. Results: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for 1) the Wildlife of Our Homes project and 2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both Earth homes and data from the Human Microbiome Project. Conclusions: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1036-4294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

ABSTRACT Background: While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in these habitats have received less consideration. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on earth. Here we report results of sending 48 bacterial strains, collected from built environments on earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Results: Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on earth using a relative growth measurement adapted for microgravity. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain showed significantly different growth in space. _Bacillus safensis_ JPL-MERTA-8-2 grew 60% better in space than on earth. Conclusions: The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on _Bacillus safensis_ could lead to interesting insights on why this strain grew so much better in space.

In recent years, microbial ecology studies have increasingly focused on the "Built Environment", characterizing community assemblages across indoor habitats such as classrooms, homes, and hospitals. Human activity and manipulation of indoor spaces can impact both the microbial taxa present and changes in communities over time. In this study, we sought to characterize the spatial and temporal patterns of microbes in two saltwater aquariums at UC Davis; the goal of this project was to provide a substantial research experience for undergraduate students while examining the microbiology of the built environment. Aquariums are a common feature of homes and buildings, yet little is known about how environmental perturbations (water changes, addition of living rocks) can impact the succession of microbial communities. We monitored microbial succession as two "coral pond" aquaria were being established. Water and sediment samples were collected over a 3-month period from November 2012 to January 2013, in parallel with water chemistry data at each timepoint. Samples were subjected to DNA extraction and environmental amplification of the 16S rRNA gene, followed by sequencing on the Illumina MiSeq platform. High-throughput sequence data was processed and analyzed using the QIIME pipeline. Our results showed similar patterns of microbial community succession in both saltwater aquariums, in regard to the profiles of abundant taxa and the timing of successional changes. Furthermore, we observed a significant difference in microbial assemblages in sediment versus water samples, indicating strong heterogeneity and partitioning of microbial habitats within aquariums.

Nature Science Proceedings of the National Academy of Sciences Nature Communications Nature Physics Physical Review Letters Applied Physics Letters Nature Chemistry Journal of American Chemistry Society Analytical Chemistry Nature Materials Advanced Materials Advanced Functional Materials Nature Nanotechnology Nano Letters ACS Nano Lab on a Chip Physics of Fluids Journal of Fluid Mechanics

ABSTRACT Background: While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, much less has focused on the non-pathogenic microbes in these habitats. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on earth. Here we report results of sending 48 bacterial strains, collected from built environments on earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Results: Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on earth. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain that avoided contamination showed significantly different growth in space. _Bacillus safensis_ JPL-MERTA-8-2 grew 60% better in space than on earth. Conclusions: The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on _Bacillus safensis_ could lead to interesting insights on why this bacteria grew so much better in space.

Target? http://www.nature.com/nature/careers/

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

EDUCATION University of California, Davis - Ph.D. Microbiology (2012) Dissertation Title: Exploring Microbial Community Composition and Genome Evolution Using Environmental and Comparative Genomics ##University of Texas, Arlington - M.S. Quantitative Biology (2001) Thesis Title: Worldwide Phylogeny of the Damselfly Genus Ischnura Based on Mitochondrial Cytochrome Oxidase II and Cytochrome B Sequence Data ##University of New Orleans - B.S. Biology (1995)

INTRODUCTION [Probably start with modeling] A fundamental goal of biochemistry is understanding the intricate relationship between a protein sequence, its structure, and its function. Atomic-level knowledge of enzymes in particular has proven immensely challenging. Because we don't understand how enzymes work, the field of synthetic biology is unable to harness the catalytic power of enzymes for arbitrary chemical reactions. Previous efforts to computationally model the relationship between the thermal stability of enzymes and point mutations in enzyme systems have relied on the addition of evolutionary information (Thompson) and, see CASP, have had success in creating models of proteins to an accuracy of X previously-believed to be impossible to model accurately. People have tried to model the biophysical constraints on protein evolution but there is rarely any actual mutational data to draw from (only the "fossil record" of known holomologues sequences and the evolutionary history of the organisms that we see a snapshot of) Here, we measure the thermal denaturation temperature of 117 mutants of a family 1 glycoside hydrolase, BlgB. After generating models of each mutant, we combine the experimental data with 45 features (e.g., total system energy, ligand energy). A machine learning algorithm trained on the data is used to make a prediction for the thermal stability of 15 point mutants evenly sampled from the single nucleotide polymorphism--accessible space and 15 point mutants evenly sampled from the elastic net model. The predictive model achieved a Pearson correlation coefficient of [...] in our tests, showing that [...] Bagel uses residues E164, E353, and Y295 as catalytic residues [Bagel enzyme in general, represents a common fold and evolutionary conserved function and diverse sequences that all fold the same way and have the same function, just residing in different organisms] Evolutionary constraints limit protein evolvability in the sense that only certain mutations are physically possible (SNP-accessible, not divert folding trajectory)

PROJECT SUMMARY (1 PAGE) Due: January 25, 2016 at 5 PM (local time) DEB - Biodiversity: Discovery & Analysis Cluster Solicitation: http://www.nsf.gov/pubs/2015/nsf15609/nsf15609.htm Cluster description: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503666&org=DEB&from=home Overview The broad goal with this proposal is to increase the overall knowledge of the true diversity of microbial eukaryotes by identifying and culturing microeukaryotes from seagrass beds. Microorganisms, and specifically marine microbial eukaryotes, represent an underexplored area of diversity. Microbial eukaryotes are known to be important on a number of trophic levels in the marine system CITE, and microbial eukaryotes found in seagrass beds likely contribute to their tremendous biodiversity and roles as important players in nutrient cycling and carbon sequestration in the oceans. We will use a combination of sequencing and culturing techniques to (1) characterize microeukaryotes in a global census of the seagrass _Zostera marina_, (2) Explore microbial eukaryotic diversity across the Order Alismatales, including the 3 separate lineages of seagrasses and their freshwater and brackish relatives, and (3) Create a publicly available culture collection of microbial eukaryotes from _Zostera marina_ samples from Bodega Bay, CA. Intellectual Merit Microorganisms comprise the majority of diversity on Earth. Traditionally classified using morphological approaches, the advent of sequence data has dramatically altered our views of microbial evolution and diversity. Specifically, high throughput sequencing technologies have enabled us to explore multiple genes and genomes from microorganisms, giving us insight into genome complexity and function in these unseen organisms. As a result microbial ecologists are finding themselves in uncharted territory as they analyze large data sets full of "unclassified" organisms, and it now clear that microorganisms are much more diverse than previously thought. Although certain pathogenic microeukaryotes have been studied in great detail (ex. _giardia_, see ) for review, environmental microeukaryotes, specifically marine microeukatyores, are grossly uncharacterized despite their important functional roles in their ecosystems . Novel marine microeukaryotic lineages have previously been found at all phylogenetic scales ; however, many of these novel organisms are still a mystery to us as they have yet to be cultured. It is estimated that the total diversity of microbial eukaryotes is much higher than what we currently have in culture . Seagrasses are a unique system in which to explore marine microbial eukaryotic diversity. These important marine angiosperms provide habitat and food to many rare and endemic species, and contain tremendous levels of biodiversity that has currently only been characterized at the macrobe level . Seagrasses are known to be important contributors to biogeochemical processes within the ocean and are one of the largest carbon sinks on earth, sequestering carbon 35X faster than Tropical Rainforests . Given their importance in the complex marine food web and their contributions to nutrient cycling within the oceans, we hypothesize that seagrass-associated marine microbial eukaryotes are important to both the high levels of macrobe biodiversity within seagrass beds and to their role in nutrient cycling and carbon sequestration in the ocean ecosystem. We propose to perform a global census of microbial eukaryotes found in association with the leaves, roots, and sediment of the seagrass _Zostera marina_. We will then expand our investigation to census the microbial eukaryotes found in association with plants across the Order Alismatales, which includes three independent lineages of seagrasses. Concurrently with the afformentioned censuses, we will establish a culture collection of microbial eukaryotes found associated with _Zostera marina_ from Bodega Bay, California. We are uniquely positioned to be successful at the proposed research; using funds provided by the Gordon and Betty Moore Foundation, we have already established a program to explore bacterial diversity within seagrass beds, and have completed the majority of field work and formed ongoing collaborations with other seagrass researchers from both the Zostera Experimental Network (ZEN) and other research institutions. Broader Impacts The project we propose here is a global interdisciplinary collaboration that will result in increased knowledge of the biodiversity of an understudied group of organisms from an important marine ecosystem. The preposed project is the first to explore seagrass-associated microbial eukaryotes using both sequence and culture based methods, and will generate large amounts of publicly available sequence data and numerous new entries of novel marine organisms to culture collections. The project we are proposing will include a large outreach component both at the local level (undergraduate researchers, high school students) and the global level (website, collaborators). Undergraduates and local high school students will be intimately involved in creating the culture collection and our progress will be transparently available on our lab website.

ABSTRACT Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and very public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station. This sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 samples swabbed from surfaces onboard the International Space Station. This sampling is a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS) - a collaborative effort of the "microbiology of the Built Environment network" (microBE.net) project, Science Cheerleaders, NanoRacks, Space Florida, and Scistarter.com. Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration and colonization of the solar system come to fruition. Results Sterile swabs were used to sample 15 surfaces onboard the International Space Station. The sites sampled were designed to be analogous to samples collected for 1) the Wildlife of Our Homes project and 2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rRNA genes amplified from DNA extracted from each swab was used to produce a "census" of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both the Earth homes and the Human Microbiome Project. Conclusions While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the International Space Station was more similar to home surfaces than to the human microbiome samples. The International Space Station surfaces are species-rich with 1036-4294 operational taxonomic units per sample. There was no discernible biogeography of microbes on the 15 surfaces, although this may be a reflection of the small sample size we were able to obtain.

ABSTRACT A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain CoronadoT falls within the _Erythrobacteraceae_ family and the genus _Porphyrobacter_ based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other _Porphyrobacter_, however CoronadoT contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other _Erythrobacteraceae_. This strain is catalase-positive and oxidase-negative, can grow from 4-28 °C, at NaCl concentrations 0.1-1.5%, and at pH 6.0-8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain CoronadoT represents a novel species in the _Porphyrobacter_ genus for which the name _Porphyrobacter mercurialis_ sp. nov. is proposed; the type strain is CoronadoT (=DSMZ 29971, =LMG 28700).