Research Area

The System Microbiology and Antimicrobial Resistance (SMART) lab headed by Dr. Tun uses conventional microbiology and molecular biology techniques as well as cutting-edge sequencing technologies, coupled with bioinformatics, statistical, and epidemiological approaches to 1) study the composition, function, and dynamics of human microbiomes in health and diseases, and 2) to monitor antimicrobial resistance (AMR) and the resistome in humans, animals, and the environment using a holistic One Health approach. Our goal is to contribute to improving the scientific understanding of the roles of microbiome and AMR in public health.

Team Description

Among several impactful projects at the SMART Lab, the team focuses on the often overlooked interplays between gut microbiota and vaccination. We hope to be able to bolster vaccine efficacy and durability, while reducing side effects, with microbiota-based adjuvants to reduce the necessity of frequent booster doses and lessen the burden on public vaccination initiatives. To that end, we have been investigating long-term associations between vaccination and microbiome composition, narrowing down exact species and metabolites that contribute to immunogenicity. We owe the progress we’ve made so far to the tight-knit nature of our group. Whether someone has a question about bioinformatics analysis, lab equipment, or biological mechanisms, there’s always a knowledgeable lab member happy and available to help. More information about our research foci and lab members can be found on our website:

Team Members

Dr. Ye Peng
Dr. Xi Zhang
Suisha Liang
Hogan Wai
Shilin Zhao
Juelei Yu
Zhu Jie
Xin Liu
Brian Ho
Daniel Zhen Ye Sin
Matthew Kwok Leong Wong
Ingrid Chan
Gary Chan
Vivian Chan
Guanwen Huang
Xueqi Wu
Manoj Chamlagain
Yuzhou Chen

Team Show


Year 2023

105. Richer LP, Tan Q, Butler MG, Avedzi HM, DeLorey DS, Peng Y, Tun HM, Sharma AM, Ainsley S, Orsso CE, Triador L, Freemark M, Haqq AM. (2023). Evaluation of automatic nervous system dysfunction in childhood obesity and Prader-Willi Syndrome. Int J Mol Sci. 24(9):8013.

104. Wong MCS, Zhang L, Ching JYL, Mak JWY, Huang J, Wang S, Mok CKP, Wong A, Chiu OL, Fung YT, Cheong PK, Tun HM, Ng SC, Chan FKL. (2023). Effects of gut microbiome modulation on reducing adverse health outcomes among elderly and diabetes patients during the COVID-19 pandemic: a randomized, double-blind, placebo-controlled trial (IMPACT Study). Nutrients. 15(8):1982.

103. Lin Y, Xu Z, Yeoh YK, Tun HM, Huang W, Jiang W, Chan FKL, Ng SC. (2023). Combing fecal microbial community data to identify consistent obesity-specific microbial signatures and shared metabolic pathways. iScience. 26(4):106476.

102. Fan M, Wong SC, Yu Q, Li PH, Wu P, Chang EWY, Wong ICK, Tun HM, Cowling BJ, Cheng VC, Chui CSL. (2023). Epidemiology and risk factors for Carbapenemase-poducing Enterbactericeae carriage in the hospital: a population-based nested case-control study. J Glob Antimicrob Resist. In press.

101. Yang X, Zhang M, Zhang Y, Wei H, Guan Q, Dong C, Deng S, Tun HM, Xia Y. (2023). Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia. NPJ Biofilms Microbiomes. 9(1):14.

100. Xu Z, Mak JWY, Lin Y, Yang K, Liu Q, Zhang F, Lau L, Tang W, Ching JY, Tun HM, Chan P, Chan FKL, Ng SC. (2023). Mixed-donor faecal microbiota transplantation was associated with increased butyrate-prducing bacteria for obesity. Gut. In press

99. Ariyawansa S, Gunawardana KN, Hapudeniya MM, Manelgamage NJ, Karunarathne CR, Madalagama RP, Ubeyratne KH, Wickramasinghe D, Tun HM, Wu P, Lam TTY, Chan OSK. (2023). One health surveillance of antimicrobial use and resistance: challenges and successes of implementing surveillance programs in Sri Lanka. Antibiotics. 12(3):446.

98. Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. (2023). Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep. 13(1):4488.

97. Peng Y, Chiu A, Li VW, Zhang X, Yeung WL, Chan HSSC, Tun HM. (2023). The role of the gut-microbiome-brain axis in metabolic remodeling amongst children with cerebral palsy and epilepsy. Front Neurol. 14:1109469. (Accepted)

96. Buchholz V, Bridgman SL, Nielsen C, Gascon M, Tun HM, Simons E, Turvey SE, Subbarao P, Takaro T, Brook J, Scott JA, Mandhane PJ, Kozryskyj AL. (2023). Natural green spaces, sensitization to allergens and the role of gut microbiota during infancy. mSystems. (Online ahead of print).

95. Zhao X, Bridgman SL, Drall KM, Tun HM, Mandhane PJ, Moraes TJ, Simons E, Turvey SE, Subbarao P, Scott JA, Kozyrkyj AL. (2023). Infant vitamin D supplements, fecal microbiota and their metabolites at 3 months of age in the CHILD Study cohort. Biomolecules. 13(2):200.

94. Chen YY, Tun HM, Field CJ, Mandhane PJ, Moraes TJ, Simons E, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. (2023). Impact of cesarean delivery and breastfeeding on secretory immunoglobulin A in the infant gut is mediated by gut microbiota and metabolites. Metabolites. 13(2):148.

93. Su Q, Tun HM, Liu Q, Yeoh YK, Mak JWY, Chan FK, Ng Sc. (2023). Gut microbiome signatures reflect different subtupes of irritable bowel syndrome. Gut Microbes. 15(1):2157697.

Year 2022

92. Tun HM, Sanyal S. (2022). Proteomics-based approach for target disocovery in Zika virus infection: abridged secondary publication. Hong Kong Med J. 6(6):29-32.

91. Liang S, Sin ZY, Yu J, Zhao S, Xi Z, Bruzzone R, Tun HM. (2022). Multi-cohort analysis of depression-associated gut bacteria sheds insight on bacterial biomarkers across populations. Cell Mol Life Sci. 80(1):9.

90. Luo Y, Lv H, Zhao S, Sun Y, Liu C, Chen C, Liang W, Kwok KO, Teo QW, So RT, Lin Y, Deng Y, Li B, Dai Z, Zhu J, Zhang D, Fernando J, Wu NC, Tun HM. Bruzoone R, Mok CK, Mu X. (2022). Age-related seroprevalence trajectories of seasonal coronaviruses in children including neonates in Guangzhou, China. Int J Infect Dis. S1201-9712(22)00636.

89. Su Q, Liu Q, Lau RI, Zhang J, Xu Z, Yeoh YK, Leung TWH, Tang W, Zhang L, Liang JQY, Yau YK, Zheng J, Liu C, Zhang M, Cheung CP, Ching JYL, Tun HM, Yu J, Chan FKL, Ng SC. (2022). Fecal microbiome-based machine learning for multi-class disease disgnosis. Nat Commun. 13(1): 6818.

88. Liu Q, Su Q, Zhang F, Tun HM, Mak JWY, Lui GC, Ng SSS, Ching JYL, Li A, Lu W, Liu C, Cheung CP, Hui DSC, Chan PKS, Chan FKL, Ng Sc. (2022). Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome. Nat Commun. 13(1):6806.

87. Chan OSK, Lam WWT, Fukuda K, Tun HM, Ohmagari N, Littmann J, Zhou XD, Xiao Y, Liu P, Wernli D. (2022). Antimicrobial resistance policy protagonists and processes-A qualitative study of policy adovacy and implementation. Antibiotics. 11(10):1434.

86. Chan OSK, Baranger-Ete M, Lam WWT, Wu P, Yeung M, Lee E, Bond H, Swan O, Tun HM. (2022). A retrospective study of antimicrobial resistant bacteria associated with feline and canine urinary tract infection in Hong Kong SAR, China- A case study on implication of first-line antibiotics use. Antibiotics. 11(9):1140.

85. Xiao T, Zhang D, Tun HM, Shah NP. (2022). Cysteine protected cells from H2O2-induced damage and promoted long-chain fatty acids synthesis in vivo to improve -aminobutyric acid production in Levilactobacillus brevis. World J Microbiol Biotechnol. 38(11)185.

84. Peng Y, Sin DZY, Tun HM. (2022). International travel, gut microbiome and ESBL-E. coli carriage. Lancet Microbe. S2666-5247(22)00201.

83. Huang Y, Liu J, Tun HM, Stanton C, Chen T, El-Nezami H, Wei H, Wang M, Wu Q. (2022). Gut microbiota insights into human adaption to high-plateau diet. Imeta. 1(1):e6

82. Chan OS, Uchea C, Tun HM, Wu P, Fukuda K. (2022). What and where should the next antimicrobial resistance policies focus on? J Glob Antimicrob Resist 31:149-51.

81. Xiao T, Zhang D, Tun HM, Shah NP. (2022). Cysteine protected cells from H2O2-induced damage and promoted long-chain fatty acids synthesis in vivo to improve -aminobutyric acid production in Levilactobacillus brevis. World J Microbiol Biotechnol. 38(11):185.

80. Obiakor CV, Parks J, Takaro TK, Tun HM, Morales-Lizcano N, Anzad MB, Mandhane PJ, Moraes TJ, Simons E, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. (2022). Early life antimicrobial exposure: impact on Clostridioides difficile colonization in infants. Antibiotics. 11(7):981.

79. Chan CL, Wai HKF, Wu P, Lai SW, Chan OSK, Tun HM. (2022). A universal LC-MS/MS method for simultaneous detection of antibiotic residues in animal and environmental samples. Antibiotics. 11(7):845.

78. Zheng X, Li S, Deng Y, Xu X, Ding J, Lau FTK, In Yau C, Poon LLM, Tun HM, Zhang T. (2022). Quantification of SARS-CoV-2 RNA in wastewater treatment plants mirrors the pandemic trend in Hong Kong. Sci Total Environ. 844:157121.

77. Chan OSK, Wernli D, Liu P, Tun HM, Fukuda K, Lam W, Xiao YH, Zhou X, Grepin KA. (2022). Unpacking multi-level governance of antimicrobial resistance policies: the case of Guangdong, China. Health Policy Plan. 37(9)1148-1157.

76. Xu X, Deng Y, Zheng X, Li S, Ding J, Yang Y, On HY, Yang R, Chui HK, Yau CI, Tun HM, Chin AWH, Poon LLM, Peiris M, Leung GM, Zhang T. (2022). Evaluation of RT-qPCR primer-probe sets to inform public health interventions based on COVID-19 sewage tests. Environ Sci Technol. 56(12)8875-8884.

75. Ng SC*, Peng Y*, Zhang L*, Mok CKP, Zhao S, Li A, Ching JYL, Liu Y, Yan S, Chan DLS, Zhu J, Chen C, Fung ACH, Wong KKY, Hui DS, Chan FKL#, Tun HM#. (2022). Gut microbiota composition modulates SARS-CoV-2 vaccine immunogenicity and vaccine-related adverse events. Gut. 71(6):1106-1116.

74. Zheng X, Deng Y, Xu X, Li S, Zhang Y, Ding J, On HY, Lai JCC, Yau CI, Chin AWH, Poon LLM, Tun HM, Zhang T. (2022). Comparison of virus concentration methods for SARS-CoV-2 sewage surveillance. Sci Total Environ, 824:153687.

73. Zhang S, Tun HM, Zhang D, Chou H, Huang F, Kwok H, Wong DK, Mak L, Yuen M, Seto WK. (2022). Alleviation of Hepatic Steatosis: Dithizone-related gut microbiome restoration during Paneth Cell Dysfunction. Front Microbiol. 13:813783.

72. Deng Y, Zheng X, Xu X, Chui HK, Lai WK, Li S, Tun HM, Poon LM, Ding J, Peiris M, Leung GM, Zhang T. Use of sewage surveillance for COVID-19: a large-scale evidence-based program in Hong Kong. Environ Health Perspect. 130(5):57008.

Year 2021

71. Peng Y, Zhang D, Chen T, Xia Y, Wu P, Seto WK, Kozyrskyj AL, Cowling BJ, Zhao J, Tun HM. (2021). Gut microbiome and resistome changes during the first wave of the COVID-19 pandemic in comparison with pre-pandemic travel-related changes. J Travel Med, 28(7):taab067.

70. Tun HM*#, Peng Y*, Chen B, Konya TB, Morales-Lizcano NP, Chari R, Field CJ, Guttman DS, Becker AB, Mandhane PJ, Moares TJ, Sears, MR, Turvey SE, Subbarao P, Simons E, Scott JA, Kozyrskyj AL#. (2021). Ethnicity associations with food sensitization are mediated by gut microbiota development in the first year of life. Gastroenterology, 161(1):94-106. Selected by Editors from Journal of Allergy and Clinical Immunology to feature in their journal (

69. Peng Y*, Liang S*, Poonsuk K*, On H, Li SW, Maurin M, Chan CH, Chan CL, Sin ZY, Tun HM. 2021. Role of gut microbiota in travel-related acquisition of extended spectrum β-lactamase producing Enterobacteriaceae. J Travel Med, 28(3):taab022.

68. Tamana SK*, Tun HM*, Konya T, Chari R, Field CJ, Guttman DS, Becker AB, Moraes TJ, Turvey SE, Subbarao P, Sears MR, Pei J, Scott JA, Mandhane PJ, Kozyrskyj AL. (2021). Bacteroides-dominant gut microbiome of late infancy is associated with enhanced neurodevelopment. Gut Microbes, 13(1):1-17.

67. Li Y*, Hou G*, Zhou H*, Wang Y*, Tun HM*, Zhu A, Zhao J, Xiao F, Lin S, Liu D, Zhou D, Mai L, Zhang L, Zhang Z, Kuang L, Guan J, Chen Q, Wen L, Zhang Y, Zhuo J, Li F, Zhuang Z, Chen Z, Luo L, Liu D, Chen C, Gan M, Zhong N, Zhao J, Ren Y, Xu Y. (2021). Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery. Signal Transduct Target Ther, 6(1):155.

66. Peng Y, Zhao J, Tun HM. (2021). The new foe and old friends: are we ready for microbiota-based therapeutics in treating COVID-19 patients? Gastroenterology, 160(6)2192-2193.

65. Vu K, Lou W, Tun HM, Konya TB, Morales-Lizcano N, Chari RS, Field CJ, Guttman DS, Mandal R, Wishart DS, Azad MB, Becker AB, Mandhane PJ, Moraes TJ, Lefebvre DL, Sears MR, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. (2020). From birth to overweight and atopic disease: multiple and common pathways of the infant gut microbiome. Gastroenterology, 160(1)128-144.e10.

64. Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J, Zhao J. (2021) . Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients. Cell Discov, 7(1):23.

63. Xu X, Zheng X, Li S, Lam NS, Wang Y, Chu DKW, Poon LL, Tun HM, Peiris M, Deng Y, Leung GM, Zhang T. (2021). The first case study of wastewater-based epidemiology of COVID-19 in Hong Kong. Sci Total Environ, 790:148000.

62. Chen T, Qin Y, Chen M, Zhang Y, Wang X, Dong T, Chen G, Sun X, Lu T, White RA, Ye P, Tun HM, Xia Y. (2021). Gestational diabetes mellitus reprograms the neonatal gut microbiome and metabolome. BMC Medicine, 19(1):120. [

61. Chen YY, Zhao X, Moeder W, Tun HM, Simons E, Mandhane PJ, Moraes TJ, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. (2021). Impact of maternal intrapartum antibiotics, and caesarean section with and without labour on Bifidobacterium and other infant gut microbiota. Microorganisms, 9(9):1847.

60. Chan OSK, Naing T, Tun HM. (2021). Upholding veterinary services as a pillar of one health in Myanmar. One Health, 13: 100329.

59. Chan OSK, Bradley KCF, Grioni A, Lau SKP, Li WT, Magouras I, Naing T, Padula A, To EMW, Tun HM, Tutt C, Woo PCY, Bloch R, Mauroo NF. (2021). Veterinary experiences can inform one health strategies for animal coronaviruses. Ecohealth, 20:1-24.

58. Zhang D, Peng Y, Chan CL, On H, Wai H, Shekhawat S, Gupta AB, Varsheney A, Chuanchuen R, Zhou X, Xia Y, Lian, S, Fukuda K, Mohan MK, Tun HM. (2021). Metagenomic survey reveals more diverse and abundant antibiotic resistance genes in municipal wastewater than hospital wastewater. Front Microbiol, 12:712843.

57. Rodriguez, N, Tun HM, Field CJ, Mandhane PJ, Scott JA, Kozyrskyj AL. (2021). Prenatal Depression, Breastfeeding, and Infant Gut Microbiota. Front Microbiol, 12:664257.

56. Orsso CE*, Peng Y*, Deehan EC, Tan Q, Field CJ, Madsen KL, Walter J, Prado CM, Tun HM#, Haqq AM#. (2021). Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance. Microorganisms, 9(7):1490.

55. Tan Q, Orsso CE, Deehan EC, Kung JY, Tun HM, Wine E, Madsen KL, Zwaigenbaum L, Haqq AM. (2021). Probiotics, prebiotics, synbiotics, and fecal microbiota transplantation in the treatment of behavioral symptoms of autism spectrum disorder: A systematic review. Autism Res, 14(9):1820-1836.

54. Suwannarong K, Janetanakit T, Kanthawee P, Suwannarong K, Theamboonlers A, Poovorawan Y, Tun HM, Chanabun S, Amonsin A. (2021). Coronavirus seroprevalence among villagers exposed to bats in Thailand. Zoonoses Public Health, 2021 Aug; 68(5): 464-473.

53. Deehan EC, Colin-Ramirez E, Triador L, Madsen KL, Prado CM, Field CJ, Ball G, Tan Q, Orsso C, Dinu I, Pakseresht M, Rubin D, Sharma AM, Tun H, Walter J, Newgard CB, Freemark m, Wine E, Haqq AM. (2021). Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance: study protocol for a double-blind randomized controlled trial. Trials, 22(1): 148.

Year 2020

52. Nielsen CC, Gascon M, Osornio-Vargas AR, Shier, Guttman DS, Becker AB, Azad MB, Sears MR, Lefebvre DL, Moares TJ, Turvey SE, Subbarao P, Takaro TK, Brook JR, Scott JA, Mandhane PJ, Tun HM#, Koyzrskyj AL#. (2020). Natural environments in the urban context and gut microbiota in infants. Environ Int, 142:105881.

51. Zhang M, Wang X, Yang X, Dong T, Hu W, Guan Q, Tun HM, Chen Y, Chen R, Sun Z, Cheng T, Xia Y. (2020). Increased risk of gestational diabetes mellitus in women with higher prepregnancy ambient PM2.5 exposure. Sci Total Environ, 730:138982.

50. Drall KM, Field CJ, Haqq AM, de Souza RJ, Tun HM, Morales-Lizcano NP, Konya TB, Guttman DS, Azad MB, Becker AB, Lefebvre DL, Mandhane PJ, Moraes TJ, Sears MR, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. (2020). Vitamin D supplementation in pregnancy and early infancy in relation to gut microbiota composition and C. difficile colonization: implications for viral respiratory infections. Gut Microbes, 12(1):1799734.

49. Sobko T, Liang S, Cheng WHG, Tun HM. (2020). Impact of outdoor nature-related activities on gut microbiota, fecal serotonin, and perceived stress in preschool children: the Play&Grow randomized controlled trial. Sci Rep, 10(1):21993.

48. Peng Y, Tan Q, Afhami S, Deehan EC, Liang S, Gantz M, Triador L, Madsen KL, Walter J, Tun HM#, Haqq AM#. (2020). The gut microbiota profile in children with Prader-Willi syndrome. Genes (Basel), 11(8):904.

47. Tun HM, Li S, Yoon I, Meale SJ, Azevedo PA, Khafipour E, Plaizier JC. (2020). Saccharomyces cerevisiae fermentation prdocuts (SCFP) stabilize the ruminal microbiota of lactating dairy cows during preiods of a depressed rumen pH. BMC Vet Res, 16(1):237.

Year 2019

46. Tun HM and Bruzzone R. (2019). Early-life antibiotic exposure, gut microbiome, and colonization resistance. J Health Sci Altern Med, 1(3):1-5. Invited Editorial

45. Drall KM, Tun HM, Morales-lizcano N, Konya TB, Guttman DS, Field CJ, Mandal R, Wishart DS, Becker AB, Azad MB, Lefebvre DL, Mandhane PJ, Moraes TJ, Sears MR, Turvey SE, Subbarao P, Scott JA, Kozyrskyj A. (2019). Clostrdioides difficile colonization is differentially associated with gut microbiome profiles by infant feeding modality at 3 months of age. Front Immunol, 10:2866.

44. Tan Q, Orsso CE, Deehan EC, Triador L, Field CJ, Tun HM, Han JC, Muller TD, Haqq AM. (2019). Current and emerging therapies for managing hyperphagia and obesity in Prader-Willi syndrome: A narrative review. Obes Reviews, 21(5):e12992.

Year 2018

43. Drall KM, Tun HM, Kozyrskyj AL. (2018). Commentary: The influence of proton pump inhibitors on the fecal microbiome of infants with gastroesophageal reflux-a prospective longitudinal interventional study. Front Cell Infect Microbiol, 8:430.

42. Tun MH, Tun HM, Mahoney JJ, Konya TB, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Brook JR, Lou W, Takaro TK, Scott JA, Kozyrskyj AL, CHILD Study Investigators. (2018). Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children. CMAJ, 190(37):E1097-E1107. Featured in CNN, USA Today etc. Most popular paper in 2018 by CMAJ with an Altmetric score of 1224. Editors’ choice for Podcast.

41. Zhang Z, Tun HM, Li R, Gonzalez BJM, Keenes HC, Nyachoti CM, Kiarie E, Khafipour E. (2018). Impact of xylanases on gut microbiota of growing pigs fed corn- or wheat-based diets. Anim Nutr, 4(4):339-350.

40. Obiakor VC, Tun HM, Bridgman SL, Arrieta M, Kozyrskyj AL. (2018). The association between early life antibiotic use and allergic disease in young children: recent insights and their implications. Expert Rev Clin Immunol, 14(10):841-855.

39. Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompon AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM, Kuhn L. (2018). Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations. Nat Commun, 9(1):4169.

38. Forbes JD, Azad MB, Vehling L, Tun HM, Konya TB, Guttman DS, Field CJ, Lefebvre D, Sears MR, Becker AB, Mandhane PJ, Turvey SE, Moraes TJ, Subbarao P, Scott JA, Kozyrskyj AL. (2018). Association of Exposure to Formula in hospital and subsequent infant feeding practices with gut microbiota and overweight risk in the first year of life. JAMA Pediatr, 172(7):e181161. Featured in CNN, Physician’s Briefing etc. Editors’ choice for iTune Podcast- July 2018. Highly Cited Paper in the field of Clinical Medicine.

37. Ndou SP, Tun HM, Kiarie E, Walsh MC, Khafipour E, 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(1):5880.

36. Tun HM, Bridgman SL, Chari R, Field CJ, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA, Kozyrskyj AL, the CHILD study investigators. (2018). Roles of birth mode and infant gut microbiota in intergenerational transmission of overweight and obesity from mother to offspring. JAMA Pediatr, 172(4):368-377. Featured in New York Time, Science Daily, Physician’s Briefing etc. Editor’s choice for iTune Podcast- April 2018. One of the top 5 news stories of the year 2018, FoMD, U of Alberta. Highly Cited Paper in the field of Clinical Medicine.

35. Liu S*, Tun HM*, Leung FC, Bennett DC, Zhang H, Cheng KM. (2018). Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet. Sci Rep, 8(1):2381.

Year 2017

34. Koleva PT, Tun HM, Shestopaloff K, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, CHILD Study Investigators, Scott JA, Kozyrskyj AL. (2017). Sex-specific impact of asthma during pregnancy on infant gut microbiota. Eur Respir J, 50(5):1700280.

33. Yasmin F, Tun HM, Dinu I, Azad MB, Konya T, Guttman DS, Field CJ, Chari RS, Sears MR, Subbarao P, Mandhane PJ, Turvey SE, Becker AB, Scott JA, Kozyrskyj AL and the CHILD Study Investigators. (2017). Caesarean section, formula feeding, and infant antibiotic exposure: separate and combined impacts on gut microbial changes in later infancy. Front Pediatr, 5:200.

32. Tun HM, Matenchuk BA, Kozyrskyj AL. (2017). Gut microbial-induced inflammation: normal aging or lifestyle changes? J Lab Precis Med, 2:48. Invited Editorial.

31. Liu R*, Tun HM*, Jahan M, Farenhorst A, Kumar A, Fernando DW, 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.

30. Zhao Q, Harbour SN, Kolde R, Latorre I, Tun HM, Schoeb TR, Moon J, Khafipour E, Xavier RJ, Weaver CT, Elson CO. (2017). Selective induction of homeostatic Th17 cells in the murine intestine by cholera toxin interacting with the microbiota. J Immunol, 199(1):312-322. This paper is featured by the “In This Issue” section of the journal, which highlights articles considered to be among the top 10% of articles published in the journal.

29. Tun HM, Konya T, Takaro TK, Brook JR, Chari R, Field CJ, Guttman D, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA, Kozyrskyj AL and the CHILD Study Investigators. (2017). Exposure to household furry pets influences the gut microbiota of infant at 3-4 months following various birth scenarios. Microbiome, 5(1):40. The most popular microbiome paper of the year 2017 (by BMC and Microbiome Digest) with an Altmetric score of 931. Featured in TIME, Reuters, Reader’s Digest, USA Today, Science Daily etc. The paper was also highlighted in BMJ’s Veterinary Record. One of the top 5 news stories of the year 2017, FoMD, U of Alberta.

28. Wu Q, Tun HM, Law Y, Khafipour E, Shah NP. (2017). 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.

27. Farenhorst A, Li R, Jahan M, Tun HM, Mi R, Mudiyansel IA, Kumar A, Khafipour E. (2017). Bacteria in drinking water sources of a first nation reserve in Canada. Sci Total Environ, 575:813-819.

26. Plaizier JC, Li S, Tun HM, Khafipour E. (2017). Nutritional models of experimentally induced subacute ruminal acidosis (SARA) differ in their impact on rumen and hindgut bacterial communities in dairy cows. Front Microbiol, 7:2128.

Year 2016

25. Derakhshani H, Tun HM, Alqarni S, Cardoso FC, Plaizier JC, Khafipour E, Loor JJ. (2016). Linking peripartal dynamics of ruminal microbiota to dietary changes and production parameters. Front Microbiol, 7:2143.

24. Fernando D, Tun HM, Poole J, Patidar R, Li R, Mi R, Amarwansha G, Fernando D, Khafipour E, Farenhorst A, Kumar A. (2016). Detection of antibiotic resistance genes in source and drinking water samples from a first nation community in Canada. Applied Environ Microbiol, 82(15):4767-4775.

23. Khafipour E, Li S, Tun HM, Derakhshani H, Moosavi S, Plaizier JC. (2016). Effects of grain feeding on microbiota in the digestive tract of cattle. Animal Frontiers, 6(2): 13-19.

22. Zhang W, Hartmann R, Tun HM, Elson CO, Khafipour E, Garvey WT. (2016). Deletion of the Toll-like receptor 5 gene in mice does not determine the gut microbiome profile that induces metabolic syndrome: environment trumps genotype. PloS One, 11(3):e0150943.

21. Tun HM, Cai Z, Khafipour E. (2016). Monitoring the survivability and infectivity of porcine epidemic diarrhoea virus (PEDv) in infected on-farm earthen manure storages (EMS). Front Microbiol, 7:265.

20. Wang Y, Ames NP, Tun HM, Jones PJ, Khafipour E. (2016). High molecular weight β-glucan alters gut microbiota towards reduced cardiovascular disease risk. Front Microbiol, 7:129.

Year 2015

19. Ng J, Chan Y, Tun HM, Leung FC, Shin PKS, Chiu JMY. (2015). Pyrosequencing of the coral Platygyra carnosus reveals shift in bacterial community composition associated with skeletal tissue growth anomalies. Front Microbiol, 6:1142.

18. Liu S, Bennett DC, Tun HM, Kim J, Zhang H, Leung FC, Cheng KM. (2015). The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet. Front Microbiol, 6:1092.

17. Derakhshani H, Tun HM, Khafipour E. (2015). The impacts of extended single-indexing multiplexed 16S rRNA sequencing on taxonomic identification and diversity analysis. J Basic Microbiol, 56:321-326.

16. Lu WH*, Tun HM*, Sun BL, Mo JY, Zhou QF, Deng YX, Xie QM, Bi YZ, Leung FC, Ma JY. (2015). Re-emerging of porcine respiratory and reproductive syndrome virus (lineage 3) and increased pathogenicity after genomic recombination with vaccine variant. Vet Microbiol, 175(2-4):332-240.

Year 2014

15. Ahad A, Thornton RN, Rabbani M, Yaqub T, Younus M, Muhammad K, Mahmood A, Shabbir MZ, Kashem MA, Islam MZ, Mangtani P, Dhand NK, Burgess GW, Tun HM, Hoque MA. (2014). Risk factors for H7 infection in commercial poultry farm workers in provinces within Pakistan. Prev Vet Med, 117(3-4):610-614.

14. Jiang J*, Tun HM*, Yuen CS, Leung FC. 2014. Complete Genome sequence of Klebsiella oxytoca HKOP isolated from Giant Panda Feces. BMC Res Notes, 7:827.

13. Hoque MA, Hassan MM, Haque ME, Shaikat AH, Khan SA, Alim A, Skerratt LF, Islam A, Tun HM, Dissanayake R, Day TK, Debnath NC, Yamage M. (2014). A survey on gastro-intestinal parasites in domestic and wild birds in different areas of Chittagong and Greater Sylhet, Bangladesh. Prev Vet Med, 117(1):305-312.

12. Tun HM, Wisedchanwet T, Wongphatcharachai M, Nonthabenjawan N, Chaiyawong S, Theamboonlers A, Poovorawan Y, Amonsin A. (2014). Development of one-step reverse transcription loop-mediated isothermal amplification (LAMP) as a screening tool for influenza A viruses. TJVM, 44(4):427-434.

11. Ma AP, Jing J, Tun HM, Mauroo NF, Yuen CS, Leung FC. (2014). Complete genome sequence of Staphylococcus xylosus HKUOPL8, a potential opportunistic pathogen of mammals. Genome Announc, 2(4):e00653-14.

10. Wu Q, Tun HM, Leung FC, Shah N. (2014). Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophiles ASCC 1275. Sci Rep, 4:4794.

9. Park T, Ding W, Cheng S, Brar MS, Ma APY, Tun HM, Leung FC. (2014). Microbial community in microbial fuel cell (MFC) medium and effluent enriched with purple photosynthetic bacterium (Rhodopseudomonas sp.). AMB Express, 4:22.

8. Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FC. (2014). Microbial diversity and evidence of novel homoacetogens in the gut of giant panda (Ailuropoda melanoleuca). PloS One, 9(1):e79902.

Year 2013

7. Hoque MA*, Tun HM*, Hassan MM, Khan SA, Islam MN, Giasuddin M, Osmani MG, Islam MA, Thornton RN, Burgess GW, Skerratt LF, Selleck P, Burn E, Debnath NC, Leung FC. (2013). Molecular epidemiology of Influenza A (H5N1) viruses, Bangladesh, 2007-2011. Prev Vet Med, 111:314-318.

6. Bennett DC*, Tun HM*, Kim JE, Leung FC, Cheng KM. (2013). Characterization of cecal microbiota of the Emu (Dromaius novaehollandiae). Vet Microbiol, 166:304-310.

5. Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park T, Chen Y, Leung FC. (2013). Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment. Biotechnol Biofuels, 6:38.

Year 2012

4. Islam SK, Alauddin M, Hassan MM, Khan SA, Alam MR, Hossain MB, Ahasan AS, Saifuddin AK, Sultana S, Tun HM, Shaikat AH, Debnath NC, Hoque MA. (2012). Biochemical analysis on blood and crop contents of household chickens along with their production and health status in Bangladesh. Pakistan Vet J, 32(4):575-578.

3. Lam TT, Hon CC, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC, Leung FC. (2012). Phylodynamics of H5N1 avian influenza virus in Indonesia. Mol Ecol, 21(12):3062-77.

2. Tun HM, Brar MS, Khin N, Jun L, Hui RK, Dowd SE, Leung FC. (2012). Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. J Microbiol Methods, 88(3):369-76.

Year 2011

1. Tun HM, Shi M, Wong CL, Ayudhya SN, Amonsin A, Thanawongnuwech R, Leung FC. (2011). Genetic diversity and multiple introductions of porcine reproductive and respiratory syndrome viruses in Thailand. Virol J, 8:164.