Research Interests:
My research focus is on understanding the composition and function of gut microbiome, its interaction with the environment and its role in human and animal health and diseases. Most of my projects involve multidisciplinary research teams. Collaborators include animal scientists, soil scientists, food scientists, plant scientists, human nutritionists, medical microbiologists and gastroenterologists. Examples of current projects include: studying the microbial etiology of inflammatory bowel disease (IBD) in humans; understanding the role of gut microbes in the development of autoimmune diseases including multiple sclerosis (MS) and rheumatoid arthritis (RA); comparing water microbiome composition among geographical areas with high and low incidence rate of IBD; finding novel microbial based diagnostics for Johne’s disease in cattle; new markers for subacute ruminal acidosis (SARA) in cattle; assessing the effect of antibiotic alternatives on health and productivity of young pigs; evaluating the role of environmental stressors in gut microbial dysfunction and gut inflammation in young pigs, and cattle; assessing the role of canola and flax oils on gut microbiome and gastrointestinal metabolism; and evaluating the effect of organic and conventional farming systems on beneficial bacterial communities in soil that influence plant health.    

My new CFI-funded Gut Microbiome Laboratory offers cutting-edge sequencing technologies and metagenomics coupled with bioinformatics, and advanced statistical and mathematical approaches to examine the gut microbiome composition and function to relate the variation in this ecosystem to health and disease status, or productivity of the host in various species and environments.

The complementory Large Animal Biosecurity Laboratory includes level II containment infrastructures and animal rooms that facilitate micobiome research. All animal research in this facility are conducted in accordance to the guidelines of Canadian Council on Animal Care and are overseen by the University of Manitoba Senate Committee on Animal Care and Animal Care Protocol Management and Review Committee.

Publications: (Book Chapters)

1. Plaizier JC, Khafipour E, Hendriks RAM, Brand A. 2012. Monitoring Bovine Ruminal Acidosis. In Hendriks RAM, Brand A. (ed.), Metabolic Diseases of Dairy Cattle.,st  ed. 

2. Krause DO, and Khafipour E. 2010. The Fecal Environment-The Gut, p. 1-21. In M. Sadowsky, R. Whitman (ed.), The Fecal Indicator Bacteria.,st  ed. ASM Press. Washington, D.C.

(Manuscripts)

1. Khafipour E, Berard NC, Little AC, Tkachuk VL, Dowd SE, Plaizier JC, and Krause DO. Microbiome changes during subacute ruminal acidosis using high-throughput pyrosequencing and statistical evaluation of sequence data. Appl. Environ. Microbiol. (under review) 


    

2. Berard NC, Ominski KH, Tkachuk VL, Khafipour E, and Krause DO. Heterogeneity of the rumen and hindgut microbial ecosystem. ISME J. (under review)

3. Mariangeli CP, Khafipour E, Jones PJ, and Krause DO. Effects of whole and fractionated yellow pea flours on indices of cardiovascular disease, diabetes, and gastrointestinal microbiome. Am. J. Clin. Nutr. (under review)

4. Li R, Khafipour E, Krause DO, Entz MH, de Kievit TR, Fernando WGD. Pyrosequencing reveals the influence of organic and conventional farming systems on soil bacterial communities. PLoS One. (under review)

5. Li S, Khafipour E, Krause DO, Rodriguez-Lecompte JC, Kroeker AD, Gozho GN, and Plaizier JC.  2012. Effects of subacute ruminal acidosis challenges on fermentation and endotoxins in the rumen, cecum and peripheral blood of dairy cows. J. Dairy Sci. 95: 294-303.

6. Plaizier JC, Khafipour E, Li S, Gozho GN, and Krause DO. 2012. Review: Subacute rumen acidosis (SARA), endotoxins and health consequences. Anim. Feed. Sci. Tech. 172: 9-21.

7. Sepehri S, Khafipour E, Bernstein CN, Coombes BK, Karmali M, Ziebell K, and Krause DO. 2011. Virulence characterization of the Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease. Inflamm. Bowel Dis. 17: 1451-1463.

8. Li S, Khafipour E, Krause DO, Gonzalez LA, and Plaizier JC. 2011. Effects of grain-pellet and alfalfa-pellet subacute ruminal acidosis (SARA) challenges on feeding behaviour of lactating dairy cows. Can. J. Anim. Sci. 91: 323-330.

9. Khafipour E, Plaizier JC, Aikman PC, and Krause DO. 2011. Molecular population analysis of rumen Escherichia coli associated with subacute ruminal acidosis in dairy cattle. J. Dairy Sci. 94: 351-360.

10. Li S, Khafipour E, Krause DO, Rodriguez-Lecompte JC, and Plaizier JC. 2010. Free endotoxins in the feces of lactating dairy cows. Can. J. Anim. Sci. 90:  591-594.

11. Khafipour E, Li S, Plaizier JC, and Krause DO. 2009. Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Appl. Environ. Microbiol. 75: 7115-7124.

12. Khafipour E, Krause DO, and Plaizier JC. 2009. Alfalfa pellet-induced subacute ruminal acidosis in dairy cows increases bacterial endotoxin in the rumen without causing inflammation. J. Dairy Sci. 92: 1712-1724.

13. Khafipour E, Krause DO, and Plaizier JC. 2009. A grain-based subacute ruminal acidosis challenge causes translocation of lipopolysaccharide and triggers inflammation. J. Dairy Sci. 92: 1060-1070.

Manuscripts in Preparation:


1. Bouchard JJ, Tkachuk VL, Li S, Ominski KH, Wittenberg KM, Khafipour E, and Krause DO. Rumen microbial community analysis and methanogenesis during adaptation to monensin. Target Journal: Appl. Environ. Microbiol.

2. Khafipour E, Zhu F, Romero-Perez GA, Li S, Ominski KH, McAllister TA, and Krause DO. Use of tannin-containing forages as bedding material for feedlot cattle reduces survival of Escherichia coli in the manure. Target Journal: Appl. Environ. Microbiol.

3. Gakhar N, Li S, Khafipour E, Krause DO, Ominski KH, and Plaizier JC. Short communication: Effects of an in vitro model of subacute ruminal acidosis on rumen lipopolysaccharide and fermentation characteristics. Target Journal: Can. J. Anim. Sci.

4. Forbes JD, Van Domselaar G, Bernstein CN, Krause DO, and Khafipour E. Metagenomic analysis of water supply in geographically defined areas of low and high incidence rates of inflammatory bowel disease in Manitoba, Canada. Target Journal: Inflamm. Bowel Dis.

5. Khafipour E, Krause DO, and Gulden RH. Generalized linear mixed approach for detecting differentially abundant features in high throughput pyrosequenced samples. Target Journal: PLoS Comp. Biol.

6. Khafipour E, Tang W, Sepehri S, Dowd SE, Bernstein CN, and Krause DO. Gut microbiome analysis along an inflammatory gradient in patients with Crohn’s disease and ulcerative colitis. Target Journal: Inflamm. Bowel Dis.

7. Li S, Plaizier JC, Dowd SE, Krause DO, Khafipour E. Microbiome analysis of the rumen, cecum, and feces of dairy cows with subacute ruminal acidosis. Target Journal: Appl. Environ. Microbiol.

8. Khafipour E, Rodriguez-Lecompte JC, Christuck K, Meshkibaf S, and Krause DO. Impact of crowding and social stress on gut microbiome and function in an Escherichia coli K88 challenged model for young pigs. Target Journal: PLoS One.


9. Khafipour E, Forbes JD, Hendric SH, De Buck J, Barkem HW, Van Domselaar G, Krause DO. Gut microbiome analysis and novel microbial based diagnostics for Johne’s disease in cattle. Target Journal: ISME J.


10. Khafipour E, Forbes JD, De Buck J, Barkem HW, Hendric SH, Van Domselaar G, Krause DO. Gut microbiome analysis of infected calves with low or high doses of Mycobacterium avium subspecies paratuberculosis (MAP) at different ages identifies specific bacteria associated with the outcome. Target Journal: ISME J.

11. Sepehri S., Kotlowski R, Bernstein CN, Krause, DO, and Khafipour E. Global gene expression of eukaryotic cells in response to adherence and invasion by Escherichia coli. Target Journal: Gastroenterology.


Looking For Graduate Students (Masters, PhD, Post-Docs) Within the Next Year

Post-doc with expertise in functional metagenomics, metatrascriptomics, metaprotomics

Lab Members