Session 1: Current Paradigm in Metagenomics

“The Built Environment Microbiome: Health and Disease” – Jack Gilbert, University of Chicago, USA

Little is known about how microbial (e.g. bacteria, Archaea and fungi) organisms are transmitted around built infrastructure. Here we will discuss our continued exploration of the home and hospital microbiome. The Home Microbiome Project has identified forensic level capabilities for tracking microbial and host interaction in the building space. The Hospital Microbiome Project is characterizing the microbial taxonomic and functional composition of surface, air, water, and human associated communities to monitor changes in community structure following the introduction of patients and hospital staff. The goal of the hospital study is to determine the influence of numerous factors on the rate and nature of microbial community succession in these hospitals including: human population demographics, how these demographics interface with a space, and the building materials, environmental conditions, and building operational characteristics used to create and maintain that space. A total of 10,000 samples were collected using sterile swabs from patients, staff, rooms, common areas, water, and air filters over 365 time points prior to and following the official opening of the hospital. Absolute microbial abundance (plate counts and qPCR) and building environmental measurements (ventilation rates, temperature, relative humidity, light intensity, and human occupancy) were combined with relative taxonomic and functional gene abundance via amplicon sequencing (16S/ITS) and shotgun metagenomics. The microbial assemblage trends towards increased diversity with the introduction of patients and staff, and an increased human microbiome presence. A total of 70,000 bacterial taxa that call the hospital home are exploiting novel transmission routes that may influence building design and operation.

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“Air Microbiome of Hong Kong’s Subways” – Patrick Lee, City University of Hong Kong, China

This presentation described the Hong Kong’s subways, one of the busiest in the world. We have previously investigated the air microbiome of the subway network of Hong Kong. Our sampling methodology and some of the results were highlighted. Potential future works to be conducted are discussed.

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“PathoMap: City-Scale Metagenomics” – Christopher E. Mason, Weill Cornell Medicine, USA

Technological advances in next-generation sequencing (NGS) have created an opportunity for rapid genetic studies of microbes and their hosts, giving scientists and clinicians a new molecular view of humans and their microbiomes and metagenomes. However, a metagenome profile has never been created for an entire city, which is an essential baseline for contextualizing the microbial changes within a person. Here, we have created a “pathogen map,” or “PathoMap,” of the entire New York City (NYC) subway system and several above-ground areas, which is currently being used to track the microbiotic population and genetic dynamics of the system over time. We built a mobile app for real-time data entry, GPS-tagging, and timestamp marking; this was implemented for 1,435 samples that catalogued all 468 subway stations in NYC, creating a molecular catalog of over 600 species identified from shotgun (125x125bp) sequencing. Yet, our data show 48% of the DNA does not match any known species, indicating a wealth of discovery left in metagenomics and genome assembly projects. Strikingly, a “molecular echo” can be seen from marine-related bacteria in a subway station flooded by Hurricane Sandy, distinct from the Gowanus Canal in Brooklyn, showing the persistence of some bacteria from flooding events. We also demonstrated how “public genomes” can predict human ancestry from human DNA left on surfaces, and they also showed a high correlation to the U.S. Census data demographics (black, white, Hispanic, Asian). Finally, we show that metagenomics profiling can reveal the likely source of antibiotic (tetracycline) resistance, and that both shotgun and rDNA sequence data reveal widespread eukaryotic diversity across the stations, including high levels of insect, human, and rat DNA, which themselves contribute to the metagenome. These data provide the first baseline molecular map of an entire city, and the station – specific microbiome and DNA profiles implicate these methods as a forensic tool for tracking individuals as they move through a city.

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“Identifying Protists in NYC Subway Samples” – Julia Maritz, New York University, USA

Microbial eukaryotes (protists) are important components of terrestrial, and aquatic environments as well as animal and human microbiomes. Their relationships with metazoa range from mutualistic to parasitic zoonoses (i.e., transmissible between humans and animals). Despite their ecological and economic importance little is known about protist diversity, incidence or emergence in urban environments. I conducted a pilot project to develop wet-lab protocols and bioinformatic pipelines for detecting protists in environmental samples using DNA from four subway samples collected in July 2013 by the Mason lab (Weill Cornell Medical College). Amplicon sequencing of the V9 region of the18S rRNA marker gene revealed a diverse protist community and several zoonotic taxa present across the samples, including Blastocystis hominis, Toxoplasma gondii and multiple Trichomonads. These results establish effective methods to detect microbial eukaryotes in environmental samples and pave the way forward for investigation into the population dynamics and genetic diversity of zoonotic protists in New York City.

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“The Gowanus Canal” – Ellen Jorgensen, Genspace, USA

The Gowanus Canal has been an integral part of the Brooklyn community and the economy of New York City since its creation in 1849. The Environmental Protection Agency (EPA) declared the canal a Superfund site in 2009 and it is considered to be one of the most polluted waterways in the United States. It is lined with several feet of toxic sediment, the result of decades of industrial waste from nearby factories and sewage from surrounding residences. It remains open to the East River and thus experiences daily shifts in water level and salinity due to the tides. This unique set of industrial and environmental inputs at the canal makes it an attractive target for microbiome and metagenomics analysis, and we selected 14 sites for a longitudinal study. These sites are distributed over the length of the canal and were chosen to be representative of the varying conditions in depth, turbidity, sewer overflow, light and salinity. Bottom sediment samples were collected summer and winter of 2014, spring of 2015, and are ongoing seasonally. DNA was extracted, purified, and sequenced using next generation shotgun sequencing (NGS), and these data were used to identify taxa present in each sample, as well as for functional dynamics analyses. Preliminary results from the summer 2014 dataset show a unique “molecular signature” associated with the Gowanus Canal, found nowhere else in our New York City metagenomic samples. Most notably, archaea including methanogens and sulfur-degrading bacteria were identified, a testament to the aquatic environment, stench and adaptation to toxicity, respectively.
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“The Extreme Microbiome Project (XMP)” – Scott Tighe, University of Vermont, USA

The Extreme Microbiome Project (XMP) is a subgroup within the Association of Biomolecular Research Facilities metagenomic research group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extremophilic and unique environments. Samples from several sites are underway including Lake Hillier in Western Australia, the “Door to Hell” crater in Turkmenistan, deep ocean brine lakes, and deep ocean sediments from Greenland, permafrost tunnels in Alaska, and acidic saline lakes of Australia, as well as the fecal microbiomes of Penguin and Hummingbird. The goals of the XMP are multifaceted: to refine techniques for the detection and characterization of novel microbes, evaluate nucleic acid techniques for extremophilic samples, and to identify the appropriate bioinformatic pipelines needed for these types of samples. The XMP is supported by the ABRF, Illumina, BioO, New England Biolabs, ATCC, Sterlitech, and Omega BioTek, as well as the labs and technicians of the participating team members.

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“Space Microbes” – Russell Neches, University of California Davis, USA

Project MERCURRI was one of the winning ISS Research Competition proposals. It was a collaboration between
microBE.net in the laboratory of Jonathan Eisen at UC Davis, Science Cheerleader, and Scistarter.com, and had three goals. First, we aimed to raise public awareness of microbiology and research on board the International Space Station (ISS). Second, we examined how a number of non-pathogenic, built environment associated microbes would grow on board the ISS compared to on earth. Third, we used culture-independent methods to examine the microbial communities of fifteen surfaces aboard the ISS, and compared these results to those of similar studies of ground-based built-environment sites.

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“An Overview of Promega’s Science and Business” – Tom Livelli, Promega Corporation, USA

Promega founded in 1978 is an innovative and responsive global Life Sciences Research technologies and tools
company. Promega’s scientific capabilities span Genomics, Cell Biology, Biochemistry, Organic Chemistry,
Microbiology, Proteomics, and Automation. Promega is the market leader in bioluminescence assays for research
and discovery, and in ATP detection in the applied markets. We have robust chemistries in nucleic acid purification
along with enzymes for amplification that are key components of molecular diagnostics, and molecular assays used
in the agricultural, food and environmental industries.