corresponding author; co-corresponding authors; * co-first authors. 


Accepted Manuscripts



58.  Aluko KR, Velayudhan DE, Khafipour E, Li A, Yin Y, and Nyachoti CM. 2017. Combined effects of chitosan and microencapsulated Enterococcus faecalis CG1.0007 probiotic supplementation on performance and diarrhea incidences in enterotoxigenic Escherichia coli K88+ challenged piglets. Anim. Nutr. 3:366-371. doi.org/10.1016/j.aninu.2017.09.003.

57.  Azad E, Derakhshani H, Wang Y, Narvaez N, Alazzeh AY, McAllister TA, and Khafipour E†. 2017. Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet. Benef. Microbes. 8:785-799. doi: 10.3920/bm2016.0145

56.  Rabbi MF, Eissa N, Munyaka PM, Kermarrec L, Elgazzar O, Khafipour E, Bernstein CN and Ghia JE. 2017. Reactivation of intestinal inflammation is suppressed by Catestatin in a murine model of colitis via M1 macrophages and not the gut microbiota. Front. Immunol. 8:985. doi: 10.3389/fimmu.2017.00985.

55.  McCann JC, Segers JR, Derakhshani H, Felix TL, Khafipour E, and Shike DW. 2017. Increasing corn distillers solubles alters the liquid fraction of the ruminal microbiome. J. Anim. Sci. 95:3540-3551. doi: 10.2527/jas2016.1361.

54.  Aluko KR, Velayudhan DE, Khafipour E, Fang L, and Nyachoti CM. 2017. Effect of chicken egg anti-F4 antibodies on performance and diarrhea incidences in enterotoxigenic Escherichia coli K88+-challenged piglets. Anim Nutr. 3:353-358. doi: 10.1016/j.aninu.2017.06.006.

53.  Li R* , Tun HM*, Jahan M*, Zhang Z, Kumar A, Fernando DW, Farenhorst A‡ and Khafipour E‡. 2017. Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water. Sci. Rep.  7: 5752. doi: 10.1038/s41598-017-02516-3.

52.  Zhao Q, Harbour SN, Kolde R, Latorre I, Tun HM, Schoeb TR, Turner H, Moon JJ, Khafipour E, Xavier RJ, Weaver CT, and Elson CO. 2017. Selective induction of homeostatic Th17 cells in the murine intestine by cholera toxin interacting with the microbiota. J. Immunol. 1700171. doi: 10.4049/jimmunol.1700171.

51.  Shang Y, Khafipour E, Derakhshani H, Sarna LK, Woo CO, Siow YL and Karmin O. 2017. Impact of short-term dietary fat intervention on gut mucosa-associated microbiota in a mouse model. Lipids. 52: 499-511. doi: 10.1007/s11745-017-4253-2.

50.  Meale SJ, Li SC, Azevedo P, Derakhshani H, DeVries TJ, Plaizier JC, Steele MA‡, and Khafipour E‡. 2017. Weaning age influences the severity of gastrointestinal microbiome shifts in dairy calves. Sci. Rep. 7: 198. doi: 10.1038/s41598-017-00223-7.

49.  Qasem W, Azad MB, Hossain Z, Azad E, Jorgensen S, San Juan SC, Cai C, Khafipour E, Beta T, Roberts II LJ, and Friel J. 2017. Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial. BMC Pediatr. 17:54. doi: 10.1186/s12887-017-0805-0.

48.  Plaizier JC, Li S, Danscher AM, Derakshani H, Andersen PH, and Khafipour E. 2017. Changes in microbiota in rumen digesta and feces due to a grain-based subacute ruminal acidosis (SARA) challenge. Microbiol. Ecol. 74:485-495. doi: 10.1007/s00248-017-0940-z.

47.  Wu Q, Tun HM, Yang X, Law YS, Khafipour E, and Shah NP2017. Common distribution of gad operon in Lactobacillus brevis and its GadA contributes to efficient GABA synthesis towards cytosolic near-neutral pH. Front. Microbiol. 8:206. doi: 10.3389/fmicb.2017.00206.

46.  Plaizier JC, Li SC, Tun HM, and Khafipour E. 2017. Nutritional models of experimentally-induced subacute ruminal acidosis (SARA) differ in their impact on rumen and hindgut microbiota in dairy cows. Front. Microbiol. 7:2128. doi: 10.3389/fmicb.2016.02128.

45.  Rabbi MF, Munyaka PM, Eissa N, Metz-Boutigue MH, Khafipour E, and Ghia JE2017. Human catestatin alters gut microbiota composition in mice. Front. Microbiol. 7:2151. doi: 10.3389/fmicb.2016.02151.

44.  Derakhshani H, Tun HM, Cardoso FC, Plaizier JC, Khafipour E‡, and Loor. JJ2017. Linking peripartal dynamics of rumen microbiota to dietary changes and production parameters. Front. Microbiol. 7:2143. doi: 10.3389/fmicb.2016.02143.

43.  Farenhorst A, Li R, Jahan M, Tun HM, Mi R, Mudiyansel IA, Kumar A, and Khafipour E2017. Bacteria in drinking water sources of a First Nation reserve in Canada. Sci. Total Environ. 575: 813-819. doi: 10.1016/j.scitotenv.2016.09.138.

42.  Pu S, Jones PJ, Khazanehei HR, and Ehsan Khafipour2016. Dietary monounsaturated and polyunsaturated oils on human gut microbiome profiles in the canola oil multicenter intervention trial (COMIT). Front. Microbiol. 7:1612. doi: 10.3389/fmicb.2016.01612.

41.  Haroun BM, Nakhla G, Hafez H, Velayutham P, Levin DB, Derakhshani H, Khafipour E, and Nasr FA2016. Significance of acclimatization for biohydrogen production from synthetic lignocellulose hydrolysate in continuous-flow systems. Int. J. Hydro. En. 41:14003-14014. doi: 10.1016/j.ijhydene.2016.05.289.

40.  Fernando D, Tun HM, Poole J, Patidar R, Li R, Mi R, Amarawansha G, Fernando DW, Khafipour E, Farenhorst A, and Kumar A2016. Detection of antibiotic resistance genes in source and drinking water samples from a First Nation community in Canada. Appl. Environ. Microbiol. 82:4767-4775. doi: 10.1128/AEM.00798-16.

39.  Munyaka PM*, Rabbi MFA*, Khafipour E‡, and Ghia JE. 2016. Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice. J. Basic Microbiol. 56:1-13. doi: 10.1002/jobm.201500726.

38.  McCann JC, Luan S, Cardoso FC, Derakhshani H, Khafipour E, and Loor JJ2016. Induction of subacute ruminal acidosis affects the ruminal microbiome and epithelium. Front. Microbiol. 7:701. doi: 10.3389/fmicb.2016.00701.

37.   Meale SJ*, Li S*, Azevedo P, Derakhshani H, Plaizier JC, Khafipour E‡, Steele M2016. Development of ruminal and fecal microbiomes are affected by weaning but not weaning strategy in dairy calves. Front. Microbiol. 7:582. doi: 10.3389/fmicb.2016.00582.

36.  Khafipour E, Li S, Tun HM, Derakhshani H, Moossavi S, and Plaizier JC2016. Effects of grain feeding on microbiota in the digestive tract of cattle. Animal Frontiers. 6:13-19. doi: 10.2527/af.2016-0018.

35.  Munyaka PM, Sepehri S, Ghia JE and Khafipour E2016. Carrageenan gum and adherent invasive Escherichia coli in a piglet model of inflammatory bowel disease: impact on intestinal mucosa-associated microbiota. Front. Microbiol. 7:462. doi: 10.3389/fmicb.2016.00462.

34.  Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, and Khafipour E2016Mycobacterium avium subspecies paratuberculosis infection modifies gut microbiota under different dietary conditions in a rabbit model. Front. Microbiol. 7:446. doi: 10.3389/fmicb.2016.00446.

33.  Derakhshani H, De Buck J, Mortier R, Barkema HW, Krause DO, and Khafipour E2016. The features of fecal and ileal mucosa-associated microbiota in dairy calves during early infection with Mycobacterium avium subspecies paratuberculosis. Front. Microbiol. 7:426. doi: 10.3389/fmicb.2016.00426.

32.  Tun HM, Cai Z, and Khafipour E2016. Monitoring survivability and infectivity of porcine epidemic diarrhea virus (PEDv) in the infected on-farm earthen manure storages (EMS). Front. Microbiol. 7:265.  doi: 10.3389/fmicb.2016.00265.

31.  Zhang W*, Hartmann RJ*, Tun HM, Elson CO, Khafipour E and Garvey WT2016. Deletion of the Toll-like receptor 5 gene per se does not determine the gut microbiome profile that induces metabolic syndrome: environment trumps genotype. PLoS One. 11:e0150943. doi: 10.1371/journal.pone.0150943. 

30.  Munyaka PM, Nandha NK, Nyachoti CM, Kiarie E, and Khafipour E2016. Impact of combined β-glucanase and xylanase enzymes on growth performance, nutrients utilization and gut microbiota in broiler chickens fed corn or wheat-based diets. Poultry Sci. 95:528-540. doi: 10.3382/ps/pev333.

29.  Derakhshani H, Tun HM, and Khafipour E2016. An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq Illumina platforms. J. Basic Microbiol. 56:321-326. doi: 10.1002/jobm.201500420.

28.  Wang Y, Ames NP, Tun HM, Jones PJ, and Khafipour E2016. High molecular weight barley β-glucan promotes a favorable human gut microbiota associated with reduced cardiovascular disease risk. Front. Microbiol. 7:129. doi: 10.3389/fmicb.2016.00129.

27.  De Nardi R, Marchesini G, Li S, Khafipour E, Plaizier JC, Gianesella M, Ricci R, Andrighetto I, and
Segato S2016. Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols. BMC Vet. Res. 12:29. doi: 10.1186/s12917-016-0653-4.

26.  Li S, Yoon I, Scott M, Khafipour E, and Plaizier JC. 2016. Impact of Saccharomyces cerevisiae fermentation product and subacute ruminal acidosis on production, inflammation, and fermentation in the rumen and hindgut of dairy cows. Anim. Feed Sci. Technol. 211:50-60. doi: 10.1016/j.anifeedsci.2015.10.010.

25.  Munyaka PM, Bernstein CN, Eissa N, Khafipour E, and Ghia JE. 2015. Antepartum antibiotic treatment increases offspring susceptibility to experimental colitis: a role of the gut microbiota. PLOS One 10:e0142536. doi: 10.1371/journal. pone.0142536. 

24.  Khazanehei H, Khafipour E, and Plaizier JC. 2015. Effects of dry period management and parity on rumen fermentation, blood metabolites, and liver triacylglyceride (TAG) in dairy cows. Can. J. Anim. Sci. 93:445-453. doi: 10.4141/CJAS-2014-157.

23.  Khazanehei H, Khafipour E, and Plaizier JC. 2015. Effects of dry period management on milk production, dry matter intake, and energy balance of dairy cows. Can. J. Anim. Sci. 93:433-444. doi: 10.4141/CJAS-2014-058.

22.  Nasr N, Velayutham P, Elbeshbishy E , Nakhla G, El Naggar MH, Khafipour E, Derakhshani H , Levin DB, and Hafez H. 2015. Effect of headspace carbon dioxide sequestration on microbial biohydrogen communities. Int. J. Hydro. En. 40:9966-9976. doi: 10.1016/j.ijhydene.2015.06.077.

21.  Danscher AM, Li SC, Andersen PH, Khafipour E, Kristensen NB and Plaizier JC. 2015. Indicators of induced subacute ruminal acidosis (SARA) in Danish Holstein dairy cows. Acta Vet. Scand. 57:39. doi: 10.1186/s13028-015-0128-9. 

20.  Bouchard K, Wittenberg KM, Legesse G, Krause DO, Khafipour E, Buckley KE, and Ominski KH. 2015. Comparison of feed intake, body weight gain, enteric methane emission and relative abundance of rumen microbes in steers fed sainfoin and Lucerne silages under Western Canadian conditions. Grass Forage Sci. 70:116–129. doi: 10.1111/gfs.12105. 

19.  De Nardi R, Marchesini G, Plaizier JC, Li S, Khafipour E, Ricci R, Andrighetto I, and Segato S. 2014. Use of dicarboxylic acids and polyphenols to attenuate reticular pH drop and acute phase response in dairy heifers fed a high grain diet. BMC Vet. Res. 10:277. doi: 10.1186/s12917-014-0277-5.

18.  Gupta M, Velayutham P, Elbeshbishy E, Hafez H, Khafipoure E, Derakhshani H, El Naggar H, Levin DB. 2014. Co-fermentation of glucose, starch, and cellulose for mesophilic biohydrogen production. Int. J. Hydro. En. 39:20958-20967. doi: 10.1016/j.ijhydene.2014.10.079.

17.  Munyaka P, Khafipour E, and Ghia JE. 2014. External influence of early childhood establishment of gut microbiota and subsequent health implications. Front. Pediatr. 2:109. doi: 10.3389/fped.2014.00109. 

16.  Munyaka P*, Rabbi MF*, Pavlov VA, Tracey KJ, Khafipour E, and Ghia JE. 2014. Central muscarinic cholinergic activation alters interaction between splenic dendritic cell and CD4+CD25- T Cells in experimental colitis. PLoS One. 9:e109272. doi: 10.1371/journal.pone.0109272. 

15.  Khafipour E, Munyaka PM, Nyachoti CM, Krause DO, and Rodriguez-Lecompte JC. 2014. Effect of crowding stress and Escherichia coli K88 challenge in nursery pigs supplemented with anti- Escherichia coli K88 probiotics. J. Anim. Sci. 92:2017-2029. doi: 10.2527/jas.2013-7043.

14.  Wolf KJ, Daft JG, Tanner SM, Hartmann R, Khafipour E, and Lorenz RG. 2014. Consumption of acidic water alters the gut microbiome and decreases the risk of diabetes in NOD mice. J. Histochem. Cytochem. 62:237-250.  doi: 10.1369/0022155413519650.

13.  Khafipour E, and Ghia JE. 2013. Mode of delivery and inflammatory disorders. J. Immunol. Clin. Res. 1:1004. 

12.  Colman E, Khafipour E, Vlaeminck B, De Baets B, Plaizier JC, and Fievez V. 2013. Grain-based versus alfalfa-based subacute ruminal acidosis induction experiments: Similarities and differences between changes in milk fatty acids. J. Dairy Sci. 96:4100-4111. doi: 10.3168/jds.2012-6109.

11.  Li R, Khafipour E, Krause DO, Entz MH, de Kievit TR, and Fernando WGD. 2012. Pyrosequencing reveals the influence of organic and conventional farming systems on soil bacterial communities. PLoS One. 7:e51897. doi: 10.1371/journal.pone.0051897.  

10.  Li S, Gozho GN, Gakhar N, Khafipour E, Krause DO, and Plaizier JC2012. Evaluation of diagnostic measures for subacute ruminal acidosis in dairy cows. Can. J. Anim. Sci. 92:353-364. doi: 10.4141/CJAS2012-004.

9.  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. doi: 10.1016/j.anifeedsci.2011.12.004.

8.  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 and hindgut of dairy cows. J. Dairy Sci. 95:294-303. doi: 10.3168/jds.2011-4447.

7.  Sepehri S, Khafipour E, Bernstein CN, Coombes BK, Karmali M, Ziebell K, and Krause DO. 2011. Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease. Inflamm. Bowel Dis. 17:1451-1463. doi: 10.1002/ibd.21509.

6.  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.  doi: 10.4141/cjas10090.

5.  Khafipour E, Plaizier JC, Aikman PC, and Krause DO. 2011. Population structure of rumen Escherichia coli associated with subacute ruminal acidosis (SARA) in dairy cattle. J. Dairy Sci. 94:351-360. doi: 10.3168/jds.2010-3435.

4.  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. doi: 10.4141/CJAS10017.

3.  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. doi: 10.1128/AEM.00739-09.

2.  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. doi: 10.3168/jds.2008-1656.

1.  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. doi: 10.3168/jds.2008-1389.