Metagenomic analysis to identify gene clusters associated with IgA production

Project Title: Metagenomic analysis to identify gene clusters associated with IgA production
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/177/BM_plasmacells.png
Tags:
bioinformatics (277), biology (515), genomics (537), python (69), r (32), research-facilitation (442)

Status: Finishing Up
Project Leader
--------------
Project Leader:
Joel Wilmore

Email: wilmorej@upstate.edu
Mobile Phone: {Empty}
Work Phone: 315-464-5729

Project Personnel
-----------------
Mentor(s):
Joel Wilmore (1365), Neil McGlohon (471)

Student-facilitator(s):
Eren Ada (1781)

Mentee(s):
{Empty}


Project Information
-------------------
Project Description:
The development of systemic IgA responses is highly dependent on the composition of the intestinal microbiome. We performed shotgun metagenomics on fecal bacteria based on the binding of serum IgA (IgA+ vs IgA-). Our goal is to identify genes or functional clusters of genes that are highly associated with serum IgA binding. We will then be able to target specific pathways, rather than specific species or classes of microbes. Identification of these pathways will provide the basis for improved mucosal vaccine design or inflammatory bowel disease treatments. 

Project Information Subsection
------------------------------
Project Deliverables:
Analysis of existing shotgun metagenomics data (potentially some 16S data) to identify genes or clusters associated with IgA. Additional analysis of the microbiome will depend on the results. Some standard microbiome analyses will be likely as well (diversity, relative abundance, etc).

Deliverables will include:

    A MIDAS database other researchers can use to analyze mouse gut microbiome data, either by itself or with phylogenize.
    A tree that includes both mouse MAGs and reference genomes.
    Evidence that this does (or does not) increase coverage.
    Genes associated with IgA binding (via phylogenize).

Project Deliverables:
{Empty}

Student Research Computing Facilitator Profile:
The ability to analyze genomic data and learn to use new programs based on publications in the field. 

Mentee Research Computing Profile:
{Empty}

Student Facilitator Programming Skill Level: Need help identifying
Mentee Programming Skill Level: {Empty}
Project Institution: SUNY Upstate Medical University
Project Address:
Syracuse , New York

Anchor Institution: CR-Rensselaer Polytechnic Institute
Preferred Start Date: {Empty}
Start as soon as possible.: Yes
Project Urgency: Already behind2Start date is flexible
Expected Project Duration (in months): 6
Launch Presentation: {Empty}
Launch Presentation Date: 05/11/2022
Wrap Presentation: {Empty}
Wrap Presentation Date: {Empty}
Project Milestones:
- Milestone Title: Annotating Mouse Metagenome Assembled Genome (MAGs)
  Milestone Description: Downloading mouse MAGs and annotating them with a common, comprehensive set of protein families
- Milestone Title: Create mouse-focused MIDAS Database
  Milestone Description: Creating a mouse-focused MIDAS database (using tools available in the MIDAS software package)
- Milestone Title: Mouse MAGs Clustering
  Milestone Description: Clustering mouse MAGs together with other reference genomes into species-level clusters, using core genes.
- Milestone Title: Pangenome Definitions
  Milestone Description: Defining the pangenomes of each species-level cluster
- Milestone Title: Phylogenetic preparation
  Milestone Description: Constructing a new phylogenetic tree based on a concatenated alignment of core genes.
- Milestone Title: MIDAS application
  Milestone Description: Applying MIDAS to existing data (also: benchmarking whether, with this new database, species coverage 1. increases and 2. matches better to the phylogenetic diversity seen using 16S).
- Milestone Title: Phylogenetic analysis
  Milestone Description: Applying phylogenize to the MIDAS output to find genes associated with IgA binding

Github Contributions: {Empty}
Planned Portal Contributions (if any):
Deliverables will include:

    A MIDAS database other researchers can use to analyze mouse gut microbiome data, either by itself or with phylogenize.
    A tree that includes both mouse MAGs and reference genomes.
    Evidence that this does (or does not) increase coverage.
    Genes associated with IgA binding (via phylogenize).



Planned Publications (if any):
{Empty}

What will the student learn?:
{Empty}

What will the mentee learn?:
{Empty}

What will the Cyberteam program learn from this project?:
{Empty}

HPC resources needed to complete this project?:
{Empty}

Notes:
{Empty}



Final Report
------------
What is the impact on the development of the principal discipline(s) of the project?:
{Empty}

What is the impact on other disciplines?:
{Empty}

Is there an impact physical resources that form infrastructure?:
{Empty}

Is there an impact on the development of human resources for research computing?:
{Empty}

Is there an impact on institutional resources that form infrastructure?:
{Empty}

Is there an impact on information resources that form infrastructure?:
{Empty}

Is there an impact on technology transfer?:
{Empty}

Is there an impact on society beyond science and technology?:
{Empty}

Lessons Learned:
{Empty}

Overall results:
{Empty}