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Publications

Journal articles

Prasad N, Trenholme AA, Huang QS, Thompson MG, Pierse N, Widdowson MA, Wood T, Seeds R, Taylor S, Grant CC, Newbern EC, team S. 2018. Interactive effects of age and respiratory virus on severe lower respiratory infection. Epidemiology and Infection doi:10.1017/S0950268818002017:1-9.

Waldron L. 2018. Data and statistical methods to analyze the human microbiome. mSystems 3.

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L: HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. (In Press, American Journal of Epidemiology).

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. 2018. bioBakery: a meta’omic analysis environment. Bioinformatics 34:1235–1237.

Leong, C., Taylor, R. W., Haszard, J. J., Fleming, E. A., Tannock, G. W., Szymlek-Gay, E., Cameron, S. L., Yu, R., Carter, H., Chee, L. K., Kennedy, L., Moore, R., Heath, A-L. M. 2018. Relative validity and reproducibility of a food frequency questionnaire to assess nutrients and food groups of relevance to the gut microbiota in young children. Nutrients doi:10.3390/nu10111627.

Bell, T., Draper, S., Centanni, M., Carnachan, S., Tannock, G., Sims, I. 2018. Characterisation of polysaccharides from feijoa fruits (Acca sellowiana Berg.) and their utilisation as growth substrates by gut commensal Bacteroides species. (In Press, Journal of Agricultural and Food Chemistry).

Dzuvor, C., J. Taylor, C. Acquah, S. Pan and D. Agyei (2018). Bioprocessing of Functional Ingredients from Flaxseed. Molecules 23(10): 2444. https://www.mdpi.com/1420-3049/23/10/2444

Lawley, B., Centanni, M., Watanabe, J., Sims, I., Carnachan, S., Broadbent, R., Lee, P. S., Wong, K. H., Tannock, G. W. 2018. Tuf gene sequence variation in Bifidobacterium longum subsp. infantis detected in the fecal microbiota of Chinese infants. Applied and Environmental Microbiology. doi: 10.1128/AEM.00336-18

Centanni, M., Lawley, B., Butts, C. A., Roy, N., Lee, J., Kelly, W. J., Tannock, G. W. 2018. Bifidobacterium pseudolongum has characteristics of a keystone species in bifidobacterial blooms in the ceca of rats fed Hi-Maize starch. Applied and Environmental Microbiology. doi: 10.1128/AEM.00547-18

Wilson, R., Willis, J., Gearry, R. B., Hughes, A., Lawley, B., Skidmore, P., Frampton, C., Fleming, E., Anderson, A., Jones, L., Tannock, G. W., Carr, A. C. 2018. SunGold kiwifruit supplementation of individuals with prediabetes alters gut microbiota and improves vitamin C status, anthropometric and clinical markers. Nutrients. doi: 10.3390/nu10070895

Leong, C., Haszard, J. J., Lawley, B., Otal, A., Taylor, R. W., Szymlek-Gay, E. A., Fleming, E. A., Danieals, L., Fangupo, L. J., Tannock, G. W., Heath, A. M. 2018. Mediation analysis as a means of identifying dietary components that affect the fecal microbiota of infants weaned by modified baby-led, compared to traditional, approaches. Applied and Environmental Microbiology. doi: 10.1128/AEM.00914-18

Taylor, R. W., Gray, A. R., Heath, A-L. M.,Galland, B. C., Lawrence, J., Sayers, R., Healey, D., Tannock. G. W., Meredith-Jones, K. A., Hanna, M., Hatch, B., Taylor, B. J. 2018. Sleep, nutrition, and physical activity interventions to prevent obesity in infancy: follow-up of the Prevention of Overweight in Infancy (POI) randomized controlled trial at ages 3.5 and 5 y. American Journal of Clinical Nutrition. 108:228–236

Blatchford P, Stoklosinski H, Eady S, Wallace A, Butts C, Gearry R, Gibson G, Ansell J. Consumption of kiwifruit capsules increases Faecalibacterium praunitzii abundance in functionally constipated individuals: a randomised controlled human trial. Journal of Nutritional Science. 2017;6(e52)

Lopez RN, Evans HM, Appleton L, Bishop J, Chin S, Mouat S, Gearry RB, Day AS. Prospective incidence of paediatric inflammatory bowel disease in New Zealand in 2015: results from the PINZ study. J Paediatr Gastroenterol Nutr. 2017

Willington A, Taylor G, White J, Gearry RB. Gastrointestinal: Ulcerative colitis-associated duodenitis. J Gastroenterol Hepatol. 2017

Asl Baakhtari S, McCombie A, Ten Bokkel Huinink S, Irving P, Siegel CA, Mulder R, Mulder CJ, Gearry RB. Observational study of perspectives of inflammatory bowel disease patients concerning the use of corticosteroids. Digestive Diseases. 2017

Wallace A, Eady S, Drummond L, Hedderley D, Ansell J, Gearry R. A Pilot Randomized Cross-Over Trial to Examine the Effect of Kiwifruit on Satiety and Measures of Gastric Comfort in Healthy Adult Males. Nutrients. 2017 Jun 22;9(7). pii: E639

Julsgaard M, Hvas CL, Gearry RB, Vestergaard T, Fallingborg J, Svenningsen L, Kjeldsen J, Sparrow MP, Wildt S, Kelsen J, Bell SJ. Fecal Calprotectin Is Not Affected by Pregnancy: Clinical Implications for the Management of Pregnant Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 Jul;23(7):1240-1246

Lamba MJ, Tharayil VS, Gearry RB. Editorial: inflammatory bowel disease risk reduction after migration - are early life events important? Aliment Pharmacol Ther. 2017 May;45(10):1367-1368

Rayen J, Currie T, Gearry RB, Frizelle F, Eglinton T. The long-term outcome of anti-TNF alpha therapy in perianal Crohn's disease. Tech Coloproctol. 2017 Feb;21(2):119-124

Lee JC, Biasci D, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L, Anderson CA, UKIBD Genetics Consortium, Trherne JA, Lyons PA, Parkes M, Smith KGC. Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn’s disease. Nature Genetics. 2017;49(2):262-268

Parkar SG, Jobsis CMH, Herath TD, Stoklosinski H, van Klink JW, Sansom CE, Sims IM, Hedderley D. 2017. Metabolic and microbial responses to the complexation of manuka honey with α-cyclodextrin after simulated gastrointestinal digestion and fermentation. Journal of Functional Foods, 31: 266–273

Kim CC, Kelly WJ, Patchett ML, Tannock GW, Jordens Z, Stoklosinski HM, Taylor JW, Sims IM, Bell TJ and Rosendale DI. 2017. Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces. Int J Syst Evol Microbiol 67: 4992-4998

McIver, L. J., Abu-Ali, G., Franzosa, E. A., Schwager, R., Morgan, X. C., Waldron, L., Segata, N., Huttenhower, C. (2017). bioBakery: A meta'omic analysis environment. Bioinformatics (Oxford, England)

Pasolli, E.*, Schiffer, L.*, Manghi, P.*, Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., Huttenhower, C., Morgan, M., Segata, N.*, Waldron, L.* (2017). Accessible, curated metagenomic data through ExperimentHub. Nature methods, 14(11), 1023-1024. *equal contribution

Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol 18, 1 (2017). IF 11.9, 1 citation

Osborne AJ, Jose BR, Perry J, Smeele Z, Aitken J, Gardner PP, Slow S. Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates. Genome Announc. 2017 Jun 1;5(22). pii: e00436-17. doi: 10.1128/genomeA.00436-17. PubMed PMID: 28572318; PubMed Central PMCID: PMC5454201

Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP, MacKichan JK. Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts. mSystems. 2017 Nov 14;2(6). pii: e00127-17. doi: 10.1128/mSystems.00127-17. eCollection 2017 Nov-Dec. PubMed PMID: 29152586; PubMed Central PMCID: PMC5686521

Centanni, M., Hutchinson, J. C., Carnachan, S. M., Daines, A. M., Kelly, W. J., Tannock, G. W., Sims, I. M. 2017. Differential growth of bowel commensal Bacteroides species on plant xylans of differing structural complexity. Carbohydrate Polymers 157:1374-1382. Doi.org/10.1016/j.carpol.2016.11.017

Lawley, B., Munro, K., Hughes, A., Hodgkinson, A. J., Prosser, C. G., Lowry, D., Zhou, S. J., Makrides, M., Gibson, R. A., Lay, C., Chew, C., Lee, P. S., Womg, K. H., Tannock, G. W. 2017. Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets. PeerJ 5:e3375. DOI:10.7717/peerj.3375

Kristin L. Wickens, Christine A. Barthow, Rinki Murphy, Peter R. Abels, Robyn M. Maude, Peter R. Stone, Edwin A. Mitchell, Thorsten V. Stanley, Gordon L. Purdie, Janice M. Kang, Fiona E. Hood, Judy L. Rowden, Phillipa K. Barnes, Penny F. Fitzharris and Julian Crane. Early pregnancy probiotic supplementation with Lactobacillus rhamnosus HN001 may reduce the prevalence of gestational diabetes mellitus: a randomised controlled trial. British Journal of Nutrition. DOI:10.1017/S0007114517000289

Review articles

Lawley, B., and Tannock, G. W. (2017). Analysis of 16S rRNA gene amplicon sequences using the QIIME software package. Methods in Molecular Biology 1537:153-163.

Books

Tannock, G. W. Understanding the gut microbiota. John Wiley & Sons Inc, Hoboken, USA, (2017) 174 p. [ISBN 9781118801420

Conference presentations

Waldron, L., New York City R/Bioconductor for Genomics, "Microbiome Data Analysis," Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, United States. (December 15, 2017).

Waldron, L., Epidemiology and Population Health Summer Institute at Columbia University, "Functional meta’omic analyses for microbial communities," New York, NY, United States. (June 30, 2017).

Waldron, L., BioC 2017, "Microbiome data analysis," Boston, MA, United States. (June 27, 2017).

Waldron, L., 5th Annual Bioinformatics Short Course, "Analysis of microbiome data," Iowa Institute of Human Genetics, Iowa City, United States. (May 22, 2017).

Waldron, L., Microbiome & Health Symposium, "Accessible, curated metagenomic data through ExperimentHub and Bioconductor. Microbiome & Health Symposium.," Vidarium Research Center, Medellin, Colombia. (March 11, 2017).

Yason JA, Tan KSW. New Insights on Blastocystis-Microbiota Interactions. Poster presented at EMBO 6th International Conference on Anaerobic Protists (ICAP) - Integrating Parasitology with Mucosal Microbiota and Immunology, 31st August-3rd September 2017, Newcastle University, Newcastle Upon Tyne, United Kingdom. (EMBO Cell Press Best Poster Award).

Tan KSW. New Insights in Blastocystis-Host Interactions: New Tools, Animal Models and Implications for Microbiome Studies. Paper presented at EMBO 6th International Conference on Anaerobic Protists (ICAP) - Integrating Parasitology with Mucosal Microbiota and Immunology, 31st August-3rd September 2017, Newcastle University, Newcastle Upon Tyne, United Kingdom. (Invited Paper).

Morgan, XM. “Comparative genomics and antibiotic resistance in poultry and clinical VRE isolates from the post-avoparcin era”. New Zealand Microbiological Society, Auckland, NZ.

Morgan, XM. “Quantifying the effects of probiotic and other early life exposures on the gut microbiota of NZ children”. Queenstown Research Week, Queenstown, NZ.

Morgan, XM. “Gut microbiota acquisition in New Zealand children in relation to early life exposures including probiotic”. Keystone Symposium – Microbiome in Health and Disease. Keystone, CO, USA.

Tannock, GW. Developing complexity of the human gut microbiota in childhood. Symposium on human microbiome interactions. Liggins Institute, University of Auckland. Invited paper.

Tannock GW. Sustaining the bowel microbiota of children. Otago Spotlight Series “Child Health Research”. University of Otago, Wellington. Invited paper.

Tannock GW. Sustaining the bowel microbiota of infants. NZ Microbiological Society annual meeting. Auckland. Invited paper.