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Spring 2021 Microbiome Informatics Webinar Series

OSU's Microbiome Informatics Webinar Series

 

Welcome to the Spring 2021 Microbiome Informatics Webinar Series!

 

Meet your instructors

Throughout the course of the webinar series, each topic will be covered by experts in their fields:

 

Faculty organizer

Matthew B. Sullivan

Matthew Sullivan

Dr. Matthew B. Sullivan is a Professor of Microbiology and Civil, Environmental and Geodetic Engineering, founding Director of OSU’s Center of Microbiome Science and co-founder of the UA Ecosystem Genomics Institute.

He is recognized for his work as a co-director of OSU’s Infectious Disease Institute Microbial Communities Program, a Gordon and Betty Moore Foundation Investigator, a Kavli Fellow, a Beckman Mentor, and a senior editor at Nature Publishing Group’s ISME Journal.

His laboratory focuses on viruses that infect microbes in their natural settings, using an experimental and informatic toolkit his team pioneered, and now applies it to the oceans, soils, humans, and extreme environments.

Specifically, the Sullivan Lab pioneered viral ecogenomics as a means to study viruses in complex communities via quantitative viral metagenomic sample-to-sequence pipelines, new approaches to link viruses and hosts, and developing iVirus, a community-available analytical platform.

Sullivan has taught a Microbiome Informatics course since 2012, and these years of experience have translated into the development of the current Microbiome Informatics Webinar Series.


Instructors

Ben Bolduc

Ben Bolduc

Dr. Ben Bolduc is a Research Scientist in Matthew Sullivan’s lab at the Ohio State University


Mikayla Borton

Mikayla Borton

Dr. Mikayla Borton is a postdoctoral research associate at Pacific Northwest National Laboratory.

Her research focuses on understanding how microbial metabolism contributes to ecosystem processes, with a specific focus on river ecosystems.

She co-developed DRAM, a tool that automates the profiling of microbial metabolism across thousands of genomes.


Dylan Cronin

Dylan Cronin

Dylan Cronin is currently a graduate student at The Ohio State University under the labs of Virginia Rich and Matthew Sullivan.

He received dual B.S. degrees in computer science and biology from Bowling Green State University, and his research currently centers around leveraging -omics data to understand the ecology of microbes and viruses in the context of climate change.


Shareef M. Dabdoub

Shareef Dabdoub

Dr. Shareef M. Dabdoub is an Assistant Professor at the Ohio State University College of Dentistry.

He is a Bioinformatician with interest in data visualization and microbial ecology of the oral environment. In particular, profiling the peri-implant microbiome in health, mucositis, and implantitis, host-microbial interactions, as well as resistance and resilience of the microbiome to environmental perturbations such as nicotine and electronic cigarettes.

He is also the developer of multiple bioinformatic software packages including PhyloToAST, kraken-biom, FIND, and ProkaryMetrics.


Webinar Q&A Liaison

Jiarong Guo

Jiarong Guo

Dr. Jiarong Guo earned his PhD at Michigan State University, where he majored in microbial ecology and data science.

His research interest center around understanding microbiome diversity and global nutrient cycling dynamics.

Currently, he is involved in the development of novel virus ecogenomics tools. Most recently, he led the development and release of the next-generation of a virus identification tool, VirSorter2.


Donovan Parks

Donovan Parks

Dr. Donovan Parks holds a PhD in computer science from Dalhousie University and has developed a number of bioinformatic programs including GTDB-Tk, CheckM, STAMP, and GenGIS.

He has expertise in microbial ecology, phylogenetics, and metagenome-assembled  genomes.

He is a bioinformatic consultant with the Australian Centre for Ecogenomics at the University of Queensland where he helps develop and maintain the Genome Taxonomy Database, an initiative to establish a standardized bacterial and archaeal taxonomy based on genome phylogeny.


Mike Shaffer

Mike Shaffer

Dr. Mike Shaffer is a postdoctoral Fellow in the Wrighton lab at Colorado State University.

His research focuses on bioinformatics associated with metabolic interactions among microbes within communities.

This has resulted in the release of DRAM, a tool that enables a user-friendly and deep analysis of metagenomics data.

He also does applied research of microbial communities with a focus on the gut microbiome of humans and mouse model systems.


Olivier Zablocki

Oliver Zablocki

Dr. Olivier Zablocki is a Research Scientist & Coordinator in Matthew Sullivan’s lab at the Ohio State University.

His interests include soil virus ecology and long-read metagenomics.

During the webinar series, he will be presenting his research on how to generate and leverage long-read sequencing (with Oxford Nanopore) to analyze virus community data.


Ahmed A. Zayed

Ahmed Zayed

Dr. Zayed is a Postdoctoral Scholar in Dr Matthew Sullivan’s lab at the Ohio State University.

His research spans environmental, medical, and pharmaceutical microbiology, and aims at understanding the interactions happening between microbes and their environments across different ecosystems.

Employing cutting-edge bioinformatic and high-throughput tools, his research led to the discovery of hundreds of thousands of DNA/RNA viral sequences and thousands of microbes in the global ocean, human/animal bodies, and carbon-rich soils.

Dr. Zayed is also part of the leadership team of the EMERGE Biology Integration Insititute which aims at understanding microbial acclimation, assembly, and adaptation processes in complex, dynamic ecosystems.

What can you find here?

  1. Links to the full set of recorded webinar videos as a playlist on our YouTube channel
  2. Software/tools relevant to each webinar topic
     

Past webinar recordings (redirects to YouTube)

  • March 2, 2021 | Introduction to microbiome science and why OSU?
  • March 9, 2021 | Introduction to high-performance computing (HPC)
  • March 16, 2021 | Introduction to QIIME, Mothur and ecological statistics for microbiomes
  • March 23, 2021 | VirION2 – hybrid short-/long-read virus metagenomics
  • March 30, 2021 | Front-end metagenome processing to MAGs (QC, assemble, read map, binning)
  • April 6, 2021 | DRAM and genome-resolved inference
    • Kayla Borton & Mike Shaffer (Colorado State University)
  • April 13, 2021 | Genome-based taxonomy and phylogenomics
    • Donovan Parks (Australian Centre for Ecogenomics)
  • April 20, 2021 | Viromics 1 – iVirus, KBase and IMG/VR overview of ‘virus’ tools available
  • April 27, 2021 | Viromics 2 – the viral ecogenomic pipeline
  • May 4, 2021 | Advanced ecological statistics for microbiomes

 

Software/tools for each webinar session

  • March 16, 2021 | Introduction to QIIME, Mothur and ecological statistics for microbiome:
  • March 23, 2021 | VirION2 – hybrid short-/long-read virus metagenomics
  • April 6, 2021 | DRAM and genome-resolved inference
  • April 13, 2021 | Genome-based taxonomy and phylogenomics | Donovan Parks (Australian Centre for Ecogenomics
    • Background reading and literature cited during the webinar:
      • Genomics and the bacterial species problem Link
      • Polyphasic taxonomy, a consensus approach to bacterial systematics Link
      • A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Link
      • A complete domain-to-species taxonomy for Bacteria and Archaea Link
      • Genome sequences as the type material for taxonomic descriptions of prokaryotes Link
      • Roadmap for naming uncultivated Archaea and Bacteria Link
      • International Code of Nomenclature of Prokaryotes Link
         
    • Nomenclatural resources:
      • LPSN
        • List of Prokaryotic names with Standing in Nomenclature Link
      • Bergey’s Manual of Systematic of Archaea and Bacteria
      • NamesForLife
    • Taxonomic resources:
      • GTDB
        • Genome Taxonomy Database Link
      • NCBI
      • SILVA
        • High-quality ribosomal RNA databases Link
           
    • Bioinformatic tools:
      • GTDB-Tk
        • Genome Taxonomy Database Toolkit
          • Delineates species using ANI and higher rank using RED Link
      • MiGA
        • Microbial Genome Atlas
          • Delineates taxa using AAI and ANI Link
      • TYGS
        • Type Strain Genome Server
          • Delineates taxa using Genome BLAST Distance Phylogeny Link
      • FastANI
  • April 20/April 27, 2021 | Viromics – the viral ecogenomic pipelin
  • May 4, 2021 | Advanced ecological statistics for microbiomes
    • Ahmed Zayed (OSU)
       
      • Materials needed for this webinar can be found here
  • Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L.^, & Sullivan, M.B.^ 2017. iVirus: facilitating new insights into viral ecology with software and community datasets imbedded in a cyberinfrastructure. ISMEJ. 11:7-14.   (^ denotes co-corresponding authors)  
  • Parks, D.H., Chuvochina, M., Waite, D.W., Rinke, C., Skarshewski, A., Chaumeil, P-A. & Hugenholtz, P. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology. 36: 996-1004. 
  • Jang, H.B., Bolduc, B., Zablocki, O., Kuhn, J., Roux, S., Adriaenssens, E.M., Brister, J.R., Kropinski, A.M., Krupovic, M., Lavigne, R., Turner, D., & Sullivan, M.B. 2019. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. 37:632–639. († denotes co-first authors)  
  • Parks, D.H., Chuvochina, M., Chaumeil, P-A., Rinke, C., Mussig, A.J. & Hugenholtz, P. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology. 38: 1079-1086.
  • Shaffer M., Borton, M.A., McGivern, B.B., Zayed, A.A., La Rosa, S.L., Solden, L.M., Liu, P, Narrowe, A.B., Rodríguez-Ramos, J., Bolduc, B., Gazitua, M.C., Daly, R.A., Smith, G.J., Vik, D.R., Pope, P.B., Sullivan, M.B., Roux, S., Wrighton, K.C. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research. 48:8883-8900.

Spring 2021 Agenda Overview

Tuesdays 1-3 EST

  • March 2, 2021 | Introduction to microbiome science and why OSU?
    • Matt Sullivan (OSU)
       
  • March 9, 2021 | Introduction to high-performance computing (HPC)
    • Shareef Dabdoub (OSU)
       
  • March 16, 2021 | Introduction to QIIME, Mothur and ecological statistics for microbiomes
    • Shareef Dabdoub (OSU)
       
  • March 23, 2021 | VirION2 – hybrid short-/long-read virus metagenomics
    • Olivier Zablocki (OSU)
       
  • March 30, 2021 | Front-end metagenome processing to MAGs (QC, assemble, read map, binning)
    • Dylan Cronin (OSU)
       
  • April 6, 2021 | DRAM and genome-resolved inference
    • Kayla Borton & Mike Shaffer (Colorado State University)
       
  • April 13, 2021 | Genome-based taxonomy and phylogenomics
    • Donovan Parks (Australian Centre for Ecogenomics)
       
  • April 20, 2021 | Viromics 1 – iVirus, KBase and IMG/VR overview of ‘virus’ tools available
    • Ben Bolduc (OSU)
       
  • April 27, 2021 | Viromics 2 – the viral ecogenomic pipeline
    • Ben Bolduc (OSU)
       
  • May 4, 2021 | Advanced ecological statistics for microbiomes
    • Ahmed Zayed (OSU)