Schulich School of Medicine and Dentistry
Department of Biochemistry
B.Sc. (Hons) (University of Western Ontario): 1983
Ph.D. (Univeristy of Western Ontario): 1988
Post-Doctoral (University of Wisconsin-Madison): 1990
Look here for microbiota analysis using the Illumina multiplex method or the Ion Torrent method.This service is offered through the London Regional Genomics Centre
The Vaginal Microbiome
I am examining the vaginal microbiome in a long-term collaboration with Gregor Reid from the Lawson Health Research Institute. The number and type of bacteria in the vagina have a profound effect on women's health and their risk of contracting or transmitting STDs. We are using the Illumina, 454 and ABI-Solid high-throughput sequencing methods to determine which organisms are associated with health and disease, what genes they are using in each state and to determine the genome sequences of various lactobacilli that are of use as probiotics. The set of shell, perl and C programs to extract the information from paired-end Illumina sequencing reactions is here.
Protein Sequence Coevolution
We are using variations on mutual information to identify protein active sites. We have found that active sites (binding sites, catalytic sites, domain interfaces) are unexpectedly rich in mutual information. This suggests that the pairs of residues in these interfaces evolve coordinately. We have refined and extended the methodology and can now reliably detect three times as many coevolving positions as our first method. In concert with Andrew Fernandes and Lindi Wahl, we are working on next-generation methods of detecting covariation.
We are now directly testing the hypothesis that coevolving positions are important for structure and function using mutagensis. Positions that coevolve in candidate genes are being mutated and then assayed biochemically and genetically to assess their function.
We believe that the ability to accurately identify coevolving positions in proteins will have broad clinical and fundamental applications, on par with our current abilities to identify and use conserved positions in protein families.
Recent Publications and Manuscripts:
1. Julia M Di Bella, Yige Bao, Gregory B Gloor, Jeremy P Burton, and Gregor Reid. , "High throughput sequencing methods and analysis for microbiome research.", J Microbiol Methods, 95, 3, [401-14], (2014).
2. RussellJDicksonandGregoryBGloor , "Bioinformatics identification of coevolving residues", Methods Mol Biol, 1123, [223-43], (2014).
3. Mariana Rosenthal, Allison E Aiello, Carol Chenoweth, Deborah Goldberg, Elaine Larson, Gregory Gloor, and Betsy Foxman , "Impact of technical sources of variation on the hand microbiome dynamics of healthcare workers", PLoS One, 9, 2, [e88999], (2014).
4. Xiaohong Tracey Gan, Grace Ettinger, Cathy X Huang, Jeremy P Burton, James V Haist, Venkatesh Rajapurohitam, James E Sidaway, Glynn Martin, Gregory B Gloor, Jonathan R Swann, Gregor Reid, and Morris Karmazyn , "Probiotic administration attenuates myocardial hypertrophy and heart failure following myocardial infarction in the rat.", Circ Heart Fail, 7, 3, [491-9], (2014).
5. S Rahat-Rozenbloom, J Fernandes, G B Gloor, and T M S Wolever , "Evidence for greater production of colonic short chain fatty acids in overweight than lean humans.", Int J Obes (Lond), Accepted: 2014-03-19
6. CamillaUrbaniak,JoanneCummins,MurielBrackstone,JeanMMacklaim,GregoryBGloor,Chwan- row K Baban, Leslie Scott, Deidre M O’Hanlon, Jeremy P Burton, Kevin P Francis, Mark Tangney, and Gregor Reid , "Microbiota of human breast tissue", Appl Environ Microbiol, 80, 10, [3007-14], (2014).
7. Andrew D Fernandes, Jennifer Reid, Jean M Macklaim, Thomas A McMurrough, David R Edgel, and Gregory B Gloor , "Unifying the analysis of high-throughput sequencing datasets: characterizing RNA- seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis", Microbiome, 2, 1, , (2014).
8. Thomas A McMurrough, Russell J Dickson, Stephanie M. F. Thibert, Gregory B Gloor, and David R Edgell , "Control of catalytic efficiency by a co-evolving network of catalytic and non-catalytic residues", PNAS (USA), Accepted: 2014-05-08
9. Kernohan KD , Vernimmen D , Gloor GB , Bérubé NG. , " Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping", Nucleic Acids Research, Accepted: 2014-02-17
10. Urbaniak C, McMillan A, Angelini M, Gloor GB, Sumarah M, Burton JP, Reid G. , "Effect of chemotherapy on the microbiota and metabolome of human milk, a case report.", Microbiome, 2, , (2014).
11. Bisanz JE, Seney S, McMillan A, Vongsa R, Koenig D, Wong L, Dvoracek B, Gloor GB, Sumarah M, Ford B, Herman D, Burton JP, Reid G. , "A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women.", PLoS One, 9, 8, [e104511], (2014).
12. Bisanz JE, Enos MK, Mwanga JR, Changalucha J, Burton JP, Gloor GB, Reid G. , "Randomized open-label pilot study of the influence of probiotics and the gut microbiome on toxic metal levels in tanzanian pregnant women and school children", MBio, 7, 5, [e1580], (2014).
13. Reid G, Nduti N, Sybesma W, Kort R, Kollmann TR, Adam R, Boga H, Brown EM, Einerhand A, El-Nezami H, Gloor GB, Kavere II, Lindahl J, Manges A, Mamo W, Martin R, McMillan A, Obiero J, Ochieng\' PA, Onyango A, Rulisa S, Salminen E, Salminen S, Sije A, Swann JR, van Treuren W, Waweru D, Kemp SJ. , "Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop", Microbiome, 2, , (2014).
14. Macphee R, Miller WL, Gloor G, McCormick JK, Burton J, Reid G. , "Influence of vaginal microbiota on toxic shock syndrome toxin-1 production by Staphylococcus aureus.", Appl Environ Microbiol., Accepted: 2013-01-11
15. Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, Brown EM, Schroeter K , Allen-Veroce EA , "Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut", Microbiome, Accepted: 2013-01-09
KEYWORDS: Computational Biology, Protein Evolution, Coevolution, Molecular Biology, High throughput sequencing, Genomics,
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Department of Biochemistry
Rm #: C8
Telephone: 661-2111 x83526