Metagenomic Sequencing and Microbiome Analysis

The metagenomics and bioinformatics core was established to provide technical and research support to study microbial communities' structure and function form variety of sample types belonging to human, animal, plants and environmental origin. The primary goal of the microbiome core is to facilitate microbiome studies for researchers at university of south Florida (USF). The facility is a centralized and cost-effective resource for processing and storing biological specimens, and sequencing and analysis of microbial communities for various research studies, including basic science, clinical, translational, and epidemiological projects. We also provide bioinformatics analytic support services to investigators interested in basic, pre-clinical, clinical and epidemiological transplant studies. We provide consultation on all aspects of study design and sample collection. The core receives, processes, and stores coded samples as needed. We provide DNA and RNA extraction and prepare and sequence samples with the Illumina Nextseq 1000 /2000 platform. We also perform bioinformatics analyses on sequencing data.

Services

1. Sample collection, microbial genomic DNA extraction.
2. DNA, RNA, Protein quantification using Nanodrop, Qubit 3 fluorometer.
3. Provide study design input like number of samples required to provide a sufficient statistical power, selection of appropriate sequencing method (16S amplicon profiling or metagenome sequencing)
4. Total bacteria quantitation by 16S rRNA quantitative PCR
5. 16R amplicon, ITS amplicon, transcriptome sequencing, miRNA sequencing, shotgun metagenomic sequencing.
6. Microbiome analysis.
7. Pathway analyses.

All requests for services are processed through Dr. Hariom Yadav (hyadav@usf.edu)

Preclinical studies and testing of anti-aging therapeutics

The aging preclinical studies core provides state-of-art models for the study of age associated physiological changes and restoring the adverse changes by therapeutic interventions. We have mice models for Aging, Alzheimer’s disease, (all other models) etc. The experimental animal facility comprised of two central facilities including Comparative Medicine facility for Research & Innovation at university of south Florida and Byrd Alzheimer’s Institute at university of south Florida. The animal includes (detailed names of the models) B6, APPS, Vilcre, F2, F3, 3XTG-AD etc. The core has developed standard operating procedures for all behavioral testing that is approved by the University’s Institutional Animal Care and Use Committee.

We perform the following behavioral testing on the animals. The testing apparatuses are located in eight individual sound-proof testing suites, including:

• SENSORY & MOTOR TESTS:  Rotarod, Grip strength-motor test, Balance beam, Hanging wire test, Mouse staircase test, Olfactory avoidance test, Adhesive removal test.
• LEARNING & MEMORY TESTS: Morris water maze, Y-maze, Conditioned place preference, Object recognition task
• SOCIAL/EMOTIONAL/STRESS RESPONSE TESTS: Elevated plus maze, elevated zero maze, Marble burying test, Sociability 3-chamber test, Automated tail suspension test, Sucrose preference test

Services

1. Aging modeling.
2. Animal Functional & Pharmacological Studies.
3. Cell & Tissue-based Studies.
4. Drug & Compound Delivery.
5. Prebiotics, Probiotics and humanized FMTs delivery.
6. Breeding of specialized mouse strains.
7. In vivo therapeutics efficacy & safety testing.
8. Hematopoietic & immune cell analysis.

All requests for services are processed through Dr. Hariom Yadav (hyadav@usf.edu)