Metagenomic analysis to identify gene clusters associated with IgA production

Submission information

Submission Number: 103

Submission ID: 177

Submission UUID: 5a593c8d-3c9e-48b0-bff9-fffb022c2293

Submission URI: /form/project

Created: Wed, 07/14/2021 - 11:25

Completed: Wed, 07/14/2021 - 11:25

Changed: Tue, 01/10/2023 - 13:43

Remote IP address: 139.127.179.209

Submitted by: Joel Wilmore

Language: English

Is draft: No

Webform: Project

Project Title Metagenomic analysis to identify gene clusters associated with IgA production

Program CAREERS

Project Image

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, Neil McGlohon

Student-facilitator(s) Eren Ada

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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).

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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

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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

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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

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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).

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Notes {Empty}

Final Report

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

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