Purpose and Research Focus:
The mission of the PennCHOP Microbiome Program is to facilitate research across campus focused on understanding the microbiome and altering its composition and activity to improve health. Pilot/Feasibility grants are designed to bring together microbiome investigators and to stimulate other researchers to enter the field and investigate the influence of the microbiome in their subject areas. The Pilot/Feasibility Projects can focus on the microbiota at any body site of the human or animal hosts. Projects can focus on composition and/or function of bacterial, fungal, archaeal, or viral communities as well as their physiological and pathological effects on their hosts.
The CHOP Microbiome Center
The CHOP Microbiome Center supports planning microbiome projects, DNA purification, library preparation, high throughput sequence analysis, and bioinformatic analysis of the output.
Analytics Core
The Analytical Core provides expertise in large-scale bioinformatics analysis of microbiome datasets. Core services start with a thorough quality check and review of sequencing results. This includes removal of host genomic sequences and other DNA added during the sequencing protocol. Automated pipelines assess the bacterial, fungal, and viral taxa found in each sample. Alignments to genes of known function are summarized, and the data are queried against a curated collection of full genomes for microbes of interest.
High-Throughput Screening Core
The High-throughput Screening (HTS) core provides the Perelman School of Medicine community with professional HTS screening services to identify genes or organic small molecule modulators of signaling pathways, cellular phenotypes, and protein function in models of human disease.
Microbial Culture and Metabolomics Core
Many trillions of microbes—too small to be seen by the naked eye–live in our guts and elsewhere on our bodies. These microbes contribute to health by helping with digestion, guiding growth of our immune systems, and shouldering out invading pathogens. People differ greatly in the composition of their microbiota, influencing us each in unique ways.
High-Throughput Sequencing Core
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples. Services include sample aliquoting, DNA extraction, quantitative PCR, library preparation, and sequencing. All protocols and workflows are optimized for individual sample types.
Proteomics Core
The Quantitative Proteomics Resource Core (QPRC) provides investigators access to the most advanced high resolution mass-spectrometry-based proteomics technologies. These approaches are implemented with a broad variety of mass-spectrometry-based experiments to characterize and quantify proteins from complex biological samples.
Acute Care Biobanking Core
The goals of the Acute Care Biobanking Core are to encourage and facilitate microbiome- focused research in the pathogenesis, diagnosis and treatment of patients with critical illness. Many patients who are critically ill are subject to processes and complications with microbially-driven or infectious mechanisms.
Microbiome Human Intervention Core
The Human Intervention Core offers a wide array of services to assist with the design and implementation of microbiome studies. The core can assist with longitudinal studies as well as pilot studies. Pilot studies can be rapidly implemented with human intervention core staff, project managers and research coordinators, to conduct these studies.
Gnotobiotic Mouse Core
Some 100 trillion beneficial microorganisms populate your body inside and out. Various species are healthy, and aid in processes like digestion, and strengthening the immune system. However, what would happen if humans did not have this symbiotic relationship with commensal bacteria? The University of Pennsylvania has launched The Penn Gnotobiotic Mouse Facility (PGMF) in order to aid new research in this area, and provide investigators with germ-free mice.
Announcements
Date:
Friday, January 18, 2019
The Metabolism, Nutrition and Development Research Affinity Group is hosting:
Katherine Gregory, PhD, RN, FAAN
Executive Director Women’s and Newborn Health Brigham and Women’s Hospital
Assistant Professor – Harvard Medical School
Neonatal Editor – Journal of Perinatal and Neonatal Nursing
“Microbiome and Gut Inflammation in the Preterm Infant”
January 17, 2019 12:00pm
Children’s Hospital of Philadelphia
Colket Translational Research Building
Room 1100A
Please RSVP to courtwrigs [at] email.chop.edu
Date:
Thursday, January 17, 2019
The PennCHOP Microbiome Program, along with its matching partners in the School of Veterinary Medicine and the Center for AIDS Research, is proud to announce the next call for projects as a part of the Microbiome Pilot & Feasibility Program.
Application Deadline: 3/16/18
Date:
Monday, January 1, 2018
In the second lecture of our spring series, Kyle Bittinger PhD discussed the diversity of bacterial communities. Diversity can mean the number of species observed in each sample (alpha diversity) or the number of species shared between samples (beta diversity). The way diversity is used to analyze bacterial communities was discussed, as well as special topics such as UniFrac distance and principal coordinates analysis.
Date:
Thursday, April 27, 2017
We would like to congratulate those selected for 2017 Pilot & Feasibility Project funding, and thank all those who applied.
Please click here to see a full project listing.
Date:
Tuesday, April 18, 2017