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).

INTRODUCTION

ABSTRACT

INTRODUCTION

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.

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.

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.

ABSTRACT A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain Coronado(T) falls within the _Erythrobacteraceae_ family based on 16S rRNA phylogenetic analysis, but is both phylogenetically and physiologically distinct from existing genera in the family. A phylogenetic tree inferred from 16S rRNA gene sequences shows a highly supported clade containing Coronado(T), _Porphyrobacter_, _Erythromicrobium_, and _Erythrobacter_. While 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 distinct. Coronado(T) contains predominatly 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, the latter of which is unusual for the other genera present in the same clade. Coronado(T) 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 Coronado(T) represents a novel species in a new genus in the family _Erythrobacteraceae_ for which the name _Kirrobacter mercurialis_ gen. nov., sp. nov. is proposed; the type strain is Coronado(T) (=DSMZ 29971, =LMG 28700).

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.

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.

There were flies in space. We looked at their gut microbes. Because, why not?

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.

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.

ABSTRACT

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.