Note: †corresponding author; co-corresponding authors; * co-first authors. 

73.  Beninger C, Naqvi SA, Naushad S, Orsel K, Luby C, Derakhshani H, Khafipour E, and De Buck J2018. Associations between digital dermatitis lesion grades in dairy cattle and the quantities of four Treponema species. Vet. Res. 49:111. doi: 10.1186/s13567-018-0605-z.

72. Derakhshani H, Plaizier JC, De Buck J, Barkema HW, and Khafipour E†2018. Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation. Microbiome. 6:203. doi: 10.1186/s40168-018-0586-1.

71.  MacKay DS*, Mollard RC*, Granger M, Bruce S, Blewett H, Carlberg J, Duhamel T, Eck PK, Khafipour E, Lix L, McMillan D, Myrie S, Ravandi A, Tangri N, Azad MB, and Jones PJ2018. The Manitoba Personalized Lifestyle Research (TMPLR) study protocol: a dual-center observational cohort study and healthcare utilization surveys investigating the interactions between lifestyle and health in Manitoba, Canada. BMJ Open. Accepted.

70.  Arrazuria R, Pérez V, Molina E, GarridoJM, Juste RA, Khafipour E, and Elguezabal N2018. Diet induced changes in the microbiota and cell composition of rabbit gut associated lymphoid tissue (GALT). Sci. Rep. 8:14103. doi: 10.1038/s41598-018-32484-1.

69.  Derakhshani H, Fehr KB, Sepehri S, Francoz D, De Buck J, Barkema HW, Plaizier JC, and Khafipour E†2018. Invited Review: Microbiota of the bovine udder: contributing factors and potential implications for udder health and mastitis susceptibility. J. Dairy Sci. 101:10605–10625. doi: 10.3168/jds.2018-14860.

68.  Derakhshani H, Plaizier JC, De Buck J, Barkema HW, and Khafipour E†2018. Composition of teat canal and intramammary microbiota of dairy cows subjected to antimicrobial dry cow therapy and internal teat sealant. J. Dairy Sci. 101:10191–10205. doi: 10.3168/jds.2018-14858.

67.  Hosseini SM, Danesh Mesgaran M, Vakili AR, Naserian AA, and Khafipour E2018. Altering uNDF through additives applied in corn, whole barley crop and alfalfa silages and its effect on milk yield and composition of Holstein lactating dairy cows. Asian-Australas. J. Anim. Sci. doi: 10.5713/ajas.18.0314.

66.  Zhang Z, Tun HM, Li R, Montenegro Gonzalez BJ, Keenes HC, Nyachoti CM, Kiarie E, and Khafipour E†2018. The impact of xylanases on gut microbiota of growing pigs fed with corn- or wheat-based diets. Anim. Nutr. doi: 10.1016/j.aninu.2018.06.007

65.  PlaizierJC, Derakhshani H, Golder H, Khafipour E, Kleen J, Lean I, Loor J, Mesgaran MD, Penner G, Zebeli Q. 2018. Invited Review: Enhancing gut health in dairy cows. Animal. doi: 10.1017/S1751731118001921

64.  Govia RNM, Birse KD, Sepehri S, Khafipour E, MenticoglouSM, Burgener AD, and Poliquin V2018. Amniotic fluid proteomic signatures of cervical insufficiency and their association with length of latency. Am. J. Reprod. Immunol. 80:e13030. doi: 10.1111/aji.13030

63.  Moossavi S, Miliku K, Sepehri S, Khafipour E, and Azad MB2018. The prebiotic and probiotic properties of human milk: implications for infant immune development and pediatric asthma. Front. Pediatr. 6:197. doi: 10.3389/fped.2018.00197.

62.  Ackerman J, Khafipour E and Cicek N. 2018. Sustainable re-use of dairy cow manure as bedding and compost: nutrients and self-heating potential. Can. Biosyst. Eng. 60:6.1-6.7. doi: 10.7451/CBE.2018.60.6.1.

61.  Levesque CL, Akhtar N, Huynh E, Walk C, Wilcock P, Zhang Z, Dyce PW, de Lange CFM, Khafipour E, and Li J. 2018. The impact of epidermal growth factor supernatant on pig performance and ileal microbiota. Trans. Anim. Sci. doi: 10.1093/tas/txy019.

60.  Ndou SP, Tun HM, Kiarie E, Walsh MC, Khafipour E, and Nyachoti CM. 2018. Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs. Sci. Rep. 8: 5880. doi: 10.1038/s41598-018-24043-5

59.  Kiros TG*, Derakhshani H*, Pinloche E, D’Inca R, Marshall J, Auclair E, Khafipour E‡, and Van Kessel A. 2018. Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs. Sci. Rep. 8:5315. doi: 10.1038/s41598-018-23373-8.

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: 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 O K. 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 E‡2017. 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 Khafipour†2016. 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 E‡2016. 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 E‡2016Mycobacterium 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 E†2016. 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 E†2016. 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 E†2016. 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 E†2016. 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 E‡2016. 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.