Understanding, deconstructing and rebuilding microbiomes to make a better world

Javier A. Izquierdo, Ph.D.
Associate Professor of Biology, Hofstra University

How I became a rainforest explorer: Ant genomes to microbiomes

Corrie S. Moreau, Ph.D.
Moser Professor of Biosystematics and Biodiversity and
Director & Curator of the Cornell University Insect Collection Cornell University

At a Glance:

20 participating teams
42 students from 13 high schools
20 scientists from 11 institutions

Taxonomic Group Studied:

• 45% Animals
• 40% Microbes
• 10% Plants
• 5% Other

Students collected 500+ samples, an average of 25 samples per team. Traditional DNA barcoding methods produced 520+ sequence reads, and next-generation sequencing methods generated more than 6.2 million sequence reads.

Wild Microbes

Claudia Wultsch, Ph.D.
Hunter College, City University of New York
Sackler Lab of Comparative Genomics, American Museum of Natural History
Jaguar Program, Panthera

Kristoff Misquitta, Rita Chen, Michelangelo Pagan, and Davida Smyth

Sequencing the Smoke: The Unseen Microbial Hazards of Vaping

Kristoff Misquitta, Michelangelo Pagan, and Rita Chen; Stuyvesant High School
Mentored by Davida Smyth, The New School.

E-cigarettes are rapidly rising in popularity among young adults. While the dangers of the aerosols produced by e-cigarerres are well-established, the risks posed by the cartridges themselves–shared among peers and infrequently cleaned–remain unexplored. Students analyzed the diversity and potential virulence of bacteria isolated from e-cigarette cartridges, users’ noses, and a control group of non-users’ noses. Bacteria present on cartridges and nasal swabs were isolated using selective and differential agar plates. The microbiome of each sample was also determined by 16S rRNA sequencing. While few colonies were isolated from the cartridges, several colonies were observed on agar plates from user and non-user noses. Bioinformatic analyses revealed that the nasal bacteria of users and non-users were similar to each other but distinct from the microbiomes of the cartridges, implying that e-cigarette surfaces may not contribute to bacterial transmission.

At a Glance:

20 participating teams
40 students from 26 high schools
20 scientists from 11 institutions

Taxonomic Group Studied:

• 55% Animals
• 25% Microbes
• 20% Plants

Students collected 500+ samples, an average of 25 samples per team. Traditional DNA barcoding methods produced 2500+ sequence reads, and next-generation sequencing methods generated more than 100 million sequence reads.

An Ecosystem in a Drop of Water: Molecular Approaches to Surveying Aquatic Biodiversity in Urban Habitats.

Elizabeth Alter, Ph.D.
Assistant Professor
Marine Evolutionary & Ecological Genetics
York College and The Graduate Center, CUNY

Elizabeth Argiro and Joshua Antony

Isolation, Identification, and Characterization of Novel Viral RNA Dependent RNA Polymerases for Use in Synthetic Biology

Joshua Antony, Regis High School, and Elizabeth Argiro, Hunter College High School. Mentored by Benajmin tenOever, Icahn School of Medicine at Mount Sinai.

In an effort to survey and isolate novel viruses, students sequenced RNA from a collection of arthropods found in the New York area. Students identified and named the novel Jiminy Cricket virus. The virus is composed of a positive-sense single-stranded RNA that encodes four putative open reading frames (ORF1-ORF4) and is related to members of the Negevirus group. RNA transfection of Jiminy Cricket virus into arthropod and mammalian cultures demonstrated limited replication only in arthropod cells, which is consistent with members of this virus group.

Edward Myers, Nicole Kanzler, and Henry Kates

Sidewinders in Southwest America

Henry Kates, Trinity School, and Nicole Kanzler, Baruch College Campus High School. Mentored by Edward Myers, American Museum of Natural History

Crotalus cerastes is a species of rattlesnake native to the southwestern United States and northern Mexico. Three subspecies have been described, Crotalus cerastes cerastes, Crotalus cerastes cercobombus, and Crotalus cerastes laterorepens. However, subspecies are often classified based on color pattern and other superficial traits that may not represent the evolutionary history of the species. By obtaining DNA from samples of Crotalus cerastes and barcoding them, the students determined the genetic diversity of populations at varying levels of genetic and geographic interconnectedness. The findings suggested that both within the same subspecies and within the same general geographical area, there were significant enough genetic differences that distinct genetic groups could be identified. This implies that the way organisms are grouped into subspecies based on morphology may not be indicative of evolutionary history.

At a Glance:

19 participating teams
39 students from 26 high schools
18 scientists from 15 institutions

Taxonomic Group Studied:

• 53% Animals
• 32% Microbes
• 5% Algae
• 5% Fungi
• 5% Plants

Students collected 600+ samples—an average 32 samples per team. Traditional DNA barcoding methods produced 1000+ sequence reads, and next-generation sequencing methods generated more than a million sequence reads.

Some Adventures in Urban Barcoding

Jesse H. Ausubel
Director, Program for the Human Environment
The Rockefeller University

Jessica Fong Ng and Lina Liu mentored by Nathan Morris, Sam Chew Chin, and Elizabeth Alter.

Building a System of DNA Barcodes for Aquatic Species in the Bronx River

This project focused on building a system of DNA barcodes for the fish species in the Bronx River for further environmental research. We collected 11 samples and used two specific primer sets to target two mitochondrial loci, one on the COI gene and one in the 12S locus to amplify the DNA of our samples. 10 out of 11 samples were sent to sequence. However, only 6 samples had high quality DNA sequences that can be used for identification. This project can benefit scientists interested in exploring the fish species or the biodiversity in the Bronx River. Our follow-up project focuses on completing the DNA barcode data for the all fishes in the Bronx River and reporting new DNA sequences to the NCBI database.

At a Glance:

20 participating teams
42 students from 24 high schools
19 scientists from 13 institutions

Taxonomic Group Studied:

• 35% Animals
• 30% Plants
• 20% Algae
• 15% Microbes

Students submitted 700+ samples for sequencing —an average 35 samples/team. Traditional DNA barcoding methods produced 1000+ sequence reads, and next-generation sequencing methods generated 1 million+ sequence reads.

Pamela Stavrakos and Katherine Lamattina mentored by Eugenia Naro-Maciel, Seth Wollney, and John Davis

Ground Thruthing Environmental DNA Arthropod Profiles Through Single Species Barcoding

The major aims of this study are to 1) characterize aquatic invertebrate biodiversity in NYC, and 2) to compare and contrast DNA barcoding and eDNA metabarcoding approaches for revealing an ecosystem’s taxonomic profile. Additionally, we hope to 3) build a library of local genetic variants for Staten Island.

Amani Fawaz and Chepeara Curry mentored by Richard Li

Using DNA Barcoding Assays to Identify Diatoms in New York City Waterways

Diatoms have been used in forensic investigations to determine if someone died from drowning. Our aim is to find out the most abundant diatoms at one location of New York City waterways. The results of this study can be potentially helpful in drowning investigations by law enforcement agencies.

At a Glance:

20 participating teams
39 students from 21 high schools
17 scientists from 10 institutions

Taxonomic Group Studied:

• 55% Animals
• 20% Microorganisms
• 20% Plants
• 5% Fungi

Students submitted 600+ samples for sequencing – an average 30 samples/team. Traditional DNA barcoding methods produced 800+ sequence reads, and next-generation sequencing methods generated 1 million+ sequence reads.

Welcome & Student Presentation Part I

Student Presentation Part II

20 participating teams
40 students from 17 high schools
16 public and 1 private
19 scientists from 12 institutions

Taxonomic Group Studied:

• 65% Animals
• 20% Microorganisms
• 15% Plants

Students submitted 500+ samples for sequencing – an average 27 samples/team. Traditional DNA barcoding methods produced 800+ sequence reads, and next-generation sequencing methods generated 600,000+ sequence reads.

Welcome & Student Presentation Part I

Student Presentation PartII