Raad Gharaibeh

Raad Gharaibeh, Ph.D.

Program Director & Research Assistant Professor

Department: MD-GASTROENTEROLOGY
Business Phone: (352) 294-8777

Teaching Profile

Courses Taught
2021
GMS6232 Advanced Applications of Bioinformatics in Genetics
2022
GMS6014 Applications of Bioinformatics to Genetics

Research Profile

RESEARCH INTERESTS:

1) Understanding how alterations in the microbiome can lead to promotion of gastrointestinal ailments using computational approaches.

2) Integrative approaches that examine microbiome and host response.

3) Understanding the functional capacities of gut microbiota.

Areas of Interest
  • Bioinformatics
  • Genomics
  • Gut Microbiome
  • Metagenomics
  • Metagenomics Sequencing
  • Metatranscriptome
Open Researcher and Contributor ID (ORCID)

0000-0001-5484-8902

Publications

2022
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort.
Genome medicine. 14(1) [DOI] 10.1186/s13073-022-01037-7. [PMID] 35346337.
2022
MarZIC: A Marginal Mediation Model for Zero-Inflated Compositional Mediators with Applications to Microbiome Data.
Genes. 13(6) [DOI] 10.3390/genes13061049. [PMID] 35741811.
2022
The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Cancer Research Communications. 2(6):447-455 [DOI] 10.1158/2767-9764.crc-22-0075.
2021
Avenanthramide Metabotype from Whole-Grain Oat Intake is Influenced by Faecalibacterium prausnitzii in Healthy Adults.
The Journal of nutrition. 151(6):1426-1435 [DOI] 10.1093/jn/nxab006. [PMID] 33694368.
2021
Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis
Science. 374(6564):216-224 [DOI] 10.1126/science.abf8403.
2021
Gut Microbiota Dysbiosis Associated with Persistent Fatigue in Hematopoietic Cell Transplantation Survivors.
Transplantation and cellular therapy. 27(6):498.e1-498.e8 [DOI] 10.1016/j.jtct.2021.02.017. [PMID] 33775619.
2021
IFAA: Robust Association Identification and Inference for Absolute Abundance in Microbiome Analyses.
Journal of the American Statistical Association. 116(536):1595-1608 [DOI] 10.1080/01621459.2020.1860770. [PMID] 35241863.
2021
Increased ACE2 Levels and Mortality Risk of Patients With COVID-19 on Proton Pump Inhibitor Therapy.
The American journal of gastroenterology. 116(8):1638-1645 [DOI] 10.14309/ajg.0000000000001311. [PMID] 34047305.
2021
Microbiota phylogenic analysis revealed decreased abundance of Faecalibacterium prausnitzii, an anti-inflammatory commensal bacterium, in patients with chronic graft-versus-host disease.
Hematology/oncology and stem cell therapy. 14(3):263-265 [DOI] 10.1016/j.hemonc.2021.03.004. [PMID] 33785388.
2021
Nuclear βArrestin1 regulates androgen receptor function in castration resistant prostate cancer.
Oncogene. 40(14):2610-2620 [DOI] 10.1038/s41388-021-01730-8. [PMID] 33692468.
2021
Septic Stability? Gut Microbiota in Young Adult Mice Maintains Overall Stability After Sepsis Compared to Old Adult Mice.
Shock (Augusta, Ga.). 55(4):519-525 [DOI] 10.1097/SHK.0000000000001648. [PMID] 32826817.
2021
Small intestinal immunopathology and GI-associated antibody formation in hereditary alpha-tryptasemia.
The Journal of allergy and clinical immunology. 148(3):813-821.e7 [DOI] 10.1016/j.jaci.2021.04.004. [PMID] 33865872.
2021
Stress-related changes in the gut microbiome after trauma.
The journal of trauma and acute care surgery. 91(1):192-199 [DOI] 10.1097/TA.0000000000003209. [PMID] 34144563.
2021
The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort.
Gut microbes. 13(1):1-15 [DOI] 10.1080/19490976.2021.1926840. [PMID] 34100340.
2020
Alterations in mouse spinal cord and sciatic nerve microRNAs after the chronic constriction injury (CCI) model of neuropathic pain.
Neuroscience letters. 731 [DOI] 10.1016/j.neulet.2020.135029. [PMID] 32380144.
2020
Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer.
Nature cancer. 1(7):723-734 [DOI] 10.1038/s43018-020-0078-7. [PMID] 33768208.
2020
Baseline Gut Microbiota Composition Is Associated with Major Infections Early after Hematopoietic Cell Transplantation.
Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 26(11):2001-2010 [DOI] 10.1016/j.bbmt.2020.07.023. [PMID] 32717434.
2020
Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites.
BMC microbiology. 20(1) [DOI] 10.1186/s12866-020-01892-7. [PMID] 32652929.
2020
Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer.
mSystems. 5(1) [DOI] 10.1128/mSystems.00451-19. [PMID] 31937674.
2020
Oral therapy with colonization factor antigen I prevents development of type 1 diabetes in Non-obese Diabetic mice.
Scientific reports. 10(1) [DOI] 10.1038/s41598-020-62881-4. [PMID] 32273533.
2020
Seaweed natural products modify the host inflammatory response via Nrf2 signaling and alter colon microbiota composition and gene expression.
Free radical biology & medicine. 146:306-323 [DOI] 10.1016/j.freeradbiomed.2019.09.013. [PMID] 31536771.
2020
Structural Insights into Endobiotic Reactivation by Human Gut Microbiome-Encoded Sulfatases.
Biochemistry. 59(40):3939-3950 [DOI] 10.1021/acs.biochem.0c00711. [PMID] 32993284.
2020
Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy.
Proceedings of the National Academy of Sciences of the United States of America. 117(13):7374-7381 [DOI] 10.1073/pnas.1918095117. [PMID] 32170007.
2019
Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin.
Gut. 68(2):289-300 [DOI] 10.1136/gutjnl-2018-317200. [PMID] 30377189.
2019
Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic.
The Journal of clinical investigation. 129(4):1699-1712 [DOI] 10.1172/JCI124196. [PMID] 30855275.
2019
Microbiota and cancer immunotherapy: in search of microbial signals.
Gut. 68(3):385-388 [DOI] 10.1136/gutjnl-2018-317220. [PMID] 30530851.
2019
Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure.
mSystems. 4(4) [DOI] 10.1128/mSystems.00452-19. [PMID] 31455640.
2019
Yersiniabactin-Producing Adherent/Invasive Escherichia coli Promotes Inflammation-Associated Fibrosis in Gnotobiotic Il10-/- Mice.
Infection and immunity. 87(11) [DOI] 10.1128/IAI.00587-19. [PMID] 31481410.
2018
Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma.
Nature communications. 9(1) [DOI] 10.1038/s41467-018-04111-0. [PMID] 29700302.
2018
Impact of vitamin D depletion during development on mouse sperm DNA methylation.
Epigenetics. 13(9):959-974 [DOI] 10.1080/15592294.2018.1526027. [PMID] 30239288.
2018
Interactions Between Stress and Sex in Microbial Responses Within the Microbiota-Gut-Brain Axis in a Mouse Model.
Psychosomatic medicine. 80(4):361-369 [DOI] 10.1097/PSY.0000000000000572. [PMID] 29533327.
2018
Intestinal microbiota enhances pancreatic carcinogenesis in preclinical models.
Carcinogenesis. 39(8):1068-1078 [DOI] 10.1093/carcin/bgy073. [PMID] 29846515.
2018
Microbiota-Derived Metabolic Factors Reduce Campylobacteriosis in Mice.
Gastroenterology. 154(6):1751-1763.e2 [DOI] 10.1053/j.gastro.2018.01.042. [PMID] 29408609.
2018
Publisher Correction: Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma.
Nature communications. 9(1) [DOI] 10.1038/s41467-018-05360-9. [PMID] 30026604.
2017
An Atlas of β-Glucuronidases in the Human Intestinal Microbiome.
Structure (London, England : 1993). 25(7):967-977.e5 [DOI] 10.1016/j.str.2017.05.003. [PMID] 28578872.
2017
Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes.
Microbiome. 5(1) [DOI] 10.1186/s40168-017-0338-7. [PMID] 28915922.
2017
Reduced Intestinal Motility, Mucosal Barrier Function, and Inflammation in Aged Monkeys.
The journal of nutrition, health & aging. 21(4):354-361 [DOI] 10.1007/s12603-016-0725-y. [PMID] 28346561.
2015
Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period.
Journal of clinical microbiology. 53(1):237-47 [DOI] 10.1128/JCM.02555-14. [PMID] 25392361.
2015
Gut Microbial Dysbiosis Due to Helicobacter Drives an Increase in Marginal Zone B Cells in the Absence of IL-10 Signaling in Macrophages.
Journal of immunology (Baltimore, Md. : 1950). 195(7):3071-85 [DOI] 10.4049/jimmunol.1500153. [PMID] 26324769.
2014
Comparison of culture and molecular techniques for microbial community characterization in infected necrotizing pancreatitis.
The Journal of surgical research. 191(2):362-9 [DOI] 10.1016/j.jss.2014.05.003. [PMID] 24952411.
2014
Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer.
Nature communications. 5 [DOI] 10.1038/ncomms5724. [PMID] 25182170.
2014
Reply to KN Litwak and S Levin.
The American journal of clinical nutrition. 99(1) [DOI] 10.3945/ajcn.113.074633. [PMID] 24363257.
2013
Dietary fructose induces endotoxemia and hepatic injury in calorically controlled primates.
The American journal of clinical nutrition. 98(2):349-57 [DOI] 10.3945/ajcn.112.057331. [PMID] 23783298.
2013
Rapid emergence of a ceftazidime-resistant Burkholderia multivorans strain in a cystic fibrosis patient.
Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society. 12(6):812-6 [DOI] 10.1016/j.jcf.2013.01.009. [PMID] 23478130.
2013
Reply to JS White.
The American journal of clinical nutrition. 98(5) [DOI] 10.3945/ajcn.113.072264. [PMID] 24142242.
2013
Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model.
The ISME journal. 7(11):2116-25 [DOI] 10.1038/ismej.2013.106. [PMID] 23823492.
2013
The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.
BMC research notes. 6 [DOI] 10.1186/1756-0500-6-72. [PMID] 23445545.
2013
VSL#3 probiotic modifies mucosal microbial composition but does not reduce colitis-associated colorectal cancer.
Scientific reports. 3 [DOI] 10.1038/srep02868. [PMID] 24100376.
2010
Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.
PloS one. 5(12) [DOI] 10.1371/journal.pone.0014464. [PMID] 21209932.
2010
Application of equilibrium models of solution hybridization to microarray design and analysis.
PloS one. 5(6) [DOI] 10.1371/journal.pone.0011048. [PMID] 20548788.
2010
Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies.
Genome biology. 11(10) [DOI] 10.1186/gb-2010-11-10-r101. [PMID] 20950453.
2008
Background correction using dinucleotide affinities improves the performance of GCRMA.
BMC bioinformatics. 9 [DOI] 10.1186/1471-2105-9-452. [PMID] 18947404.
2008
Usefulness of strb1 and 16S rDNA-targeted PCR for detection of Streptomyces spp. in environmental samples.
Polish journal of microbiology. 57(1):81-4 [PMID] 18610660.
2007
Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.
Computational biology and chemistry. 31(2):92-8 [PMID] 17387043.
2003
Evaluation of combined 16S rDNA and strb1 gene targeted PCR to identify and detect streptomycin-producing Streptomyces.
Journal of basic microbiology. 43(4):301-11 [PMID] 12872311.
2003
Genotypic and phenotypic characteristics of antibiotic-producing soil Streptomyces investigated by RAPD-PCR.
Journal of basic microbiology. 43(1):18-27 [PMID] 12596238.
2003
Multiplex PCR for the direct detection of Salmonella enterica from chicken, lamb and beef food products.
Journal of basic microbiology. 43(4):328-36 [PMID] 12872313.
Vaginal microbiome is associated with endometrial cancer grade and histology
. [DOI] 10.1101/2022.01.31.22270189.

Grants

May 2022 ACTIVE
Bacteriophage-mediated microbiota modification to prevent colorectal cancer development
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Dec 2021 ACTIVE
Bacteriophages as Modulators of Bacterial Colonization
Role: Other
Funding: NATL INST OF HLTH NIAID
Jul 2021 ACTIVE
McJunkin Family Foundation – UFHCC
Role: Faculty
Funding: UF FOUNDATION via MCJUNKIN FAMILY FOUNDATION
Jun 2021 ACTIVE
Modulation of microbiome function by host-derived noncoding small RNA
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Jul 2018 ACTIVE
Role of Bacteria in Colitis-Associated Colon Cancer
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDDK
Jan 2018 ACTIVE
The role of the microbiome on pancreatic carcinogenesis in a murine model
Role: Project Manager
Funding: AMER CANCER SOC
Jul 2017 – Jun 2019
Transcriptional control of genes implicated in suppression function of Treg cells
Role: Project Manager
Funding: NATL INST OF HLTH NIAID
Feb 2015 ACTIVE
UF Health Cancer Center Pilot Project Grants funded through the Florida Consortium of National Cancer Institute Centers Program
Role: Project Manager
Funding: UF HEALTH SHANDS HOSPITAL

Education

PhD
2009 · University of North Carolina at Charlotte
MSc
2001 · Jordan University of Science and Technology

Contact Details

Phones:
Business:
(352) 294-8777
Addresses:
Business Mailing:
CGRC-455
2033 MOWRY RD
GAINESVILLE FL 326100001