Contact details +6469517743

Dr Abby Johnson

Associate Professor (Sustainable Nutrition Initiative)

Riddet Institute

Research Projects

Current Projects

Project Title: Kai anamata mō Aotearoa – exploring future food system scenarios and impacts

Creating the first computational model of Aotearoa-NZs food system that captures environmental, economic, social, and cultural aspects of wellbeing will enable policy and business to evaluate the holistic impacts of change. The model will be co-designed with national and regional policy-makers and food sector stakeholders to ensure it reflects stakeholder values and is relevant for end-users. In partnership with Wakatū, a hapu-based organisation, the model will be applied to support assessment of the food system in Te Tauihu; develop a pathway towards a regenerative food system; and test the scalability of indigenous species and practices in a culturally appropriate manner.
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Date Range: 2023 - 2028

Funding Bodies: MBIE: Endeavour Fund: Research Programme; Ministry of Business, Innovation and Employment

Project Team:

Research Outputs

Journal

O'Sullivan, E., Solano, O., Oliveira, JS., Johnson, AJ., Dhital, S., S Pillai, PK., . . . Teigen, L. (2026). The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.. Gut Microbes Rep. 3(1), 2671724
[Journal article]Authored by: Johnson, A.
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Adam, HS., Guan, W., Johnson, AJ., Sedaghat, S., Goh, C., Pankow, JS., . . . Demmer, RT. (2026). Salivary microbiota and clinical periodontal measures predicting cardiometabolic disease mortality: A nationwide survey. Journal of Periodontology. 97(3), 552-568
[Journal article]Authored by: Johnson, A.
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2
Johnson, AJ., O’Sullivan, EN., Valyasevi, P., Metras, B., Jang, S., Shields-Cutler, R., . . . Teigen, L. (2026). The potential for complex interplay between GLP-1 receptor agonists, gut microbiome, and obesity management. Canadian Journal of Physiology and Pharmacology. 104, 1-8
[Journal article]Authored by: Johnson, A.
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1
Kohn, J., Troester, A., Ziegert, Z., Frebault, J., Boatman, S., Martell, M., . . . Gaertner, WB. (2025). The Role of Surgical and Perioperative Factors in Shaping Gut Microbiome Recovery After Colorectal Surgery †. Antibiotics. 14(9)
[Journal article]Authored by: Johnson, A.
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5
Johnson, AJ., Alvear, A., Knights, D., Chow, LS., & Bantle, AE. (2025). A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes. Nutrients. 17(1)
[Journal article]Authored by: Johnson, A.
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2

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Molinsky, RL., Johnson, AJ., Marotz, L., Roy, S., Bohn, B., Goh, CE., . . . Demmer, RT. (2025). Association Between Dietary Patterns and Subgingival Microbiota: Results From the Oral Infections, Glucose Intolerance, and Insulin Resistance Study (ORIGINS). Journal of Clinical Periodontology. 52(1), 2-15
[Journal article]Authored by: Johnson, A.
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7
Heisel, T., Gonia, S., Dillon, A., Hoops, SL., Al-Ghalith, GA., Gohl, D., . . . Gale, CA. (2025). Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches. Frontiers in Microbiology. 16
[Journal article]Authored by: Johnson, A.
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1
Teigen, LM., Hoeg, A., Zehra, H., Shah, P., Johnson, R., Hutchison, K., . . . Vaughn, BP. (2025). Nutritional optimization of fecal microbiota transplantation in humans: a scoping review. Gut Microbes. 17(1)
[Journal article]Authored by: Johnson, A.
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8
Johnson, AJ., Stevenson, J., Pettit, J., Jasthi, B., Byhre, T., & Harnack, L. (2025). Assessing the Nutrient Content of Plant-Based Milk Alternative Products Available in the United States. Journal of the Academy of Nutrition and Dietetics. 125(4), 515-527.e8
[Journal article]Authored by: Johnson, A.
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19
Dai, A., Adintori, PA., Funnell, T., Jogia, WP., Fei, T., Waters, NR., . . . Peled, J. (2024). Sugar-rich foods exacerbate antibiotic-induced microbiome injury.. bioRxiv.
[Journal article]Authored by: Johnson, A.
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Sadohara, R., Jacobs, D., Pereira, MA., & Johnson, AJ. (2024). Dietary pattern and diversity analysis using DietDiveR in R: a cross-sectional evaluation in the National Health and Nutrition Examination Survey. American Journal of Clinical Nutrition. 119(5), 1301-1308
[Journal article]Authored by: Johnson, A.
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11
Guse, K., Sharma, A., Weyenberg, E., Davison, S., Ma, Y., Choi, Y., . . . Gomez, A. (2023). Regular consumption of lacto-fermented vegetables has greater effects on the gut metabolome compared with the microbiome.. Gut Microbiome (Camb). 4, e11
[Journal article]Authored by: Johnson, A.
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Boatman, S., Kaiser, T., Nalluri-Butz, H., Khan, MH., Dietz, M., Kohn, J., . . . Jahansouz, C. (2023). Diet-induced shifts in the gut microbiota influence anastomotic healing in a murine model of colonic surgery. Gut Microbes. 15(2)
[Journal article]Authored by: Johnson, A.
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14
Johnson, AJ. (2023). Connecting the Healthy Eating Index With Microbiota Diversity. Journal of Nutrition. 153(7), 1846-1847
[Journal article]Authored by: Johnson, A.
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5
Gauglitz, JM., West, KA., Bittremieux, W., Williams, CL., Weldon, KC., Panitchpakdi, M., . . . Dorrestein, PC. (2023). Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation (Nature Biotechnology, (2022), 40, 12, (1774-1779), 10.1038/s41587-022-01368-1). Nature Biotechnology. 41(11), 1656
[Journal article]Authored by: Johnson, A.
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2
Johnson, AJ., & Mueller, NT. (2022). Can data-driven approaches for dietary pattern assessment improve microbiome epidemiology research?. American Journal of Clinical Nutrition. 115(2), 329-331
[Journal article]Authored by: Johnson, A.
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1
Choi, Y., Hoops, SL., Thoma, CJ., & Johnson, AJ. (2022). A Guide to Dietary Pattern-Microbiome Data Integration. Journal of Nutrition. 152(5), 1187-1199
[Journal article]Authored by: Johnson, A.
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32
Weber, C., Harnack, L., Johnson, A., Jasthi, B., Pettit, J., & Stevenson, J. (2022). Nutrient comparisons of margarine/margarine-like products, butter blend products and butter in the US marketplace in 2020 post-FDA ban on partially hydrogenated oils. Public Health Nutrition. 25(5), 1123-1130
[Journal article]Authored by: Johnson, A.
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14
Greathouse, KL., Wyatt, M., Johnson, AJ., Toy, EP., Khan, JM., Dunn, K., . . . Reddy, S. (2022). Diet-microbiome interactions in cancer treatment: Opportunities and challenges for precision nutrition in cancer. Neoplasia United States. 29
[Journal article]Authored by: Johnson, A.
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48
Heisel, T., Johnson, AJ., Gonia, S., Dillon, A., Skalla, E., Haapala, J., . . . Gale, CA. (2022). Bacterial, fungal, and interkingdom microbiome features of exclusively breastfeeding dyads are associated with infant age, antibiotic exposure, and birth mode. Frontiers in Microbiology. 13
[Journal article]Authored by: Johnson, A.
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15
Taylor, JC., Allman-Farinelli, M., Chen, J., Gauglitz, JM., Hamideh, D., Jankowska, MM., . . . Hekler, E. (2022). Perspective: A Framework for Addressing Dynamic Food Consumption Processes. Advances in Nutrition. 13(4), 992-1008
[Journal article]Authored by: Johnson, A.
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14
Leeming, ER., Mompeo, O., Turk, P., Bowyer, RCE., Louca, P., Johnson, AJ., . . . Gibson, R. (2022). Characterisation, procedures and heritability of acute dietary intake in the Twins UK cohort: an observational study. Nutrition Journal. 21(1)
[Journal article]Authored by: Johnson, A.
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8
Harnack, LJ., Reese, MM., & Johnson, AJ. (2022). Are Plant-Based Meat Alternative Products Healthier Than the Animal Meats They Mimic?. Nutrition Today. 57(4), 195-199
[Journal article]Authored by: Johnson, A.
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12
Gauglitz, JM., West, KA., Bittremieux, W., Williams, CL., Weldon, KC., Panitchpakdi, M., . . . Dorrestein, PC. (2022). Enhancing untargeted metabolomics using metadata-based source annotation. Nature Biotechnology. 40(12), 1774-1779
[Journal article]Authored by: Johnson, A.
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59
Mihindukulasuriya, KA., Mars, RAT., Johnson, AJ., Ward, T., Priya, S., Lekatz, HR., . . . Kashyap, PC. (2021). Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology. 161(4), 1194-1207.e8
[Journal article]Authored by: Johnson, A.
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55
Greathouse, KL., & Johnson, AJ. (2021). Does caloric restriction prime the microbiome for pathogenic bacteria?. Cell Host and Microbe. 29(8), 1209-1211
[Journal article]Authored by: Johnson, A.
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5
Johnson, AJ., Zhou, S., Hoops, SL., Hillmann, B., Schomaker, M., Kincaid, R., . . . Nelson, AC. (2021). Saliva Testing Is Accurate for Early-Stage and Presymptomatic COVID-19. Microbiology Spectrum. 9(1), 1-11
[Journal article]Authored by: Johnson, A.
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17
Johnson, AJ., & Howell, BR. (2021). Dietary diversity contributes to microbiome associations in autism. Cell Metabolism. 33(12), 2311-2313
[Journal article]Authored by: Johnson, A.
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5
Teigen, LM., Johnson, AJ., Shmidt, E., & Vaughn, BP. (2020). Use of exclusive enteral formula diet as adjunctive therapy for treatment of a Crohn's disease flare. Crohn S and Colitis 360. 2(1)
[Journal article]Authored by: Johnson, A.
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1
Johnson, AJ., Zheng, JJ., Kang, JW., Saboe, A., Knights, D., & Zivkovic, AM. (2020). A Guide to Diet-Microbiome Study Design. Frontiers in Nutrition. 7
[Journal article]Authored by: Johnson, A.
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119
Mars, RAT., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, HR., . . . Kashyap, PC. (2020). Erratum: Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome (Cell (2020) 182(6) (1460–1473.e17), (S0092867420309983), (10.1016/j.cell.2020.08.007)). Cell. 183(4), 1137-1140
[Journal article]Authored by: Johnson, A.
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50
Sidiropoulos, DN., Al-Ghalith, GA., Shields-Cutler, RR., Ward, TL., Johnson, AJ., Vangay, P., . . . Clayton, JB. (2020). Wild primate microbiomes prevent weight gain in germ-free mice. Animal Microbiome. 2(1)
[Journal article]Authored by: Johnson, A.
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11
Mars, RAT., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, HR., . . . Kashyap, PC. (2020). Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell. 182(6), 1460-1473.e17
[Journal article]Authored by: Johnson, A.
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333
Leeming, ER., Johnson, AJ., Spector, TD., & Roy, CIL. (2019). Effect of diet on the gut microbiota: Rethinking intervention duration. Nutrients. 11(12)
[Journal article]Authored by: Johnson, A.
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666
Johnson, AJ., Vangay, P., Al-Ghalith, GA., Hillmann, BM., Ward, TL., Shields-Cutler, RR., . . . Knights, D. (2019). Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans. Cell Host and Microbe. 25(6), 789-802.e5
[Journal article]Authored by: Johnson, A.
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563
Shikany, JM., Demmer, RT., Johnson, AJ., Fino, NF., Meyer, K., Ensrud, KE., . . . Langsetmo, L. (2019). Association of dietary patterns with the gut microbiota in older, community-dwelling men. American Journal of Clinical Nutrition. 110(4), 1003-1014
[Journal article]Authored by: Johnson, A.
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58
Langsetmo, L., Johnson, A., Demmer, RT., Fino, N., Orwoll, ES., Ensrud, KE., . . . Shikany, JM. (2019). The Association between Objectively Measured Physical Activity and the Gut Microbiome among Older Community Dwelling Men. Journal of Nutrition Health and Aging. 23(6), 538-546
[Journal article]Authored by: Johnson, A.
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45
Vangay, P., Johnson, AJ., Ward, TL., Al-Ghalith, GA., Shields-Cutler, RR., Hillmann, BM., . . . Knights, D. (2018). US Immigration Westernizes the Human Gut Microbiome. Cell. 175(4), 962-972.e10
[Journal article]Authored by: Johnson, A.
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630
Kuchnia, A., Earthman, C., Teigen, L., Cole, A., Mourtzakis, M., Paris, M., . . . Heyland, DK. (2017). Evaluation of Bioelectrical Impedance Analysis in Critically Ill Patients: Results of a Multicenter Prospective Study. Journal of Parenteral and Enteral Nutrition. 41(7), 1131-1138
[Journal article]Authored by: Johnson, A.
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71
Kuchnia, AJ., Teigen, LM., Cole, AJ., Mulasi, U., Gonzalez, MC., Heymsfield, SB., . . . Earthman, CP. (2017). Phase Angle and Impedance Ratio: Reference Cut-Points From the United States National Health and Nutrition Examination Survey 1999–2004 From Bioimpedance Spectroscopy Data. Journal of Parenteral and Enteral Nutrition. 41(8), 1310-1315
[Journal article]Authored by: Johnson, A.
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65
Heisel, T., Montassier, E., Johnson, A., Al-Ghalith, G., Lin, YW., Wei, LN., . . . Gale, CA. (2017). High-fat diet changes fungal microbiomes and interkingdom relationships in the murine gut. Msphere. 2(5)
[Journal article]Authored by: Johnson, A.
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126
Cole, AJ., Kuchnia, AJ., Beckman, LM., Jahansouz, C., Mager, JR., Sibley, SD., . . . Earthman, CP. (2017). Long-Term Body Composition Changes in Women Following Roux-en-Y Gastric Bypass Surgery. Journal of Parenteral and Enteral Nutrition. 41(4), 583-591
[Journal article]Authored by: Johnson, A.
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24
Jahansouz, C., Xu, H., Hertzel, AV., Serrot, FJ., Kvalheim, N., Cole, A., . . . Ikramuddin, S. (2016). Bile acids increase independently from hypocaloric restriction after bariatric surgery. Annals of Surgery. 264(6), 1022-1028
[Journal article]Authored by: Johnson, A.
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70
Mulasi, U., Kuchnia, AJ., Cole, AJ., & Earthman, CP. (2015). Erratum: Bioimpedance at the bedside: Current applications, limitations, and opportunities (Nutrition in Clinical Practice (2015) 30 (180-193) (DOI:10.1177/0884533614568155)). Nutrition in Clinical Practice. 30(4), 589
[Journal article]Authored by: Johnson, A.
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1
Mulasi, U., Kuchnia, AJ., Cole, AJ., & Earthman, CP. (2015). Bioimpedance at the bedside: Current applications, limitations, and opportunities. Nutrition in Clinical Practice. 30(2), 180-193
[Journal article]Authored by: Johnson, A.
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294
Cole, AJ., Teigen, LM., Jahansouz, C., Earthman, CP., & Sibley, SD. (2015). The Influence of Bariatric Surgery on Serum Bile Acids in Humans and Potential Metabolic and Hormonal Implications: a Systematic Review. Current Obesity Reports. 4(4), 441-450
[Journal article]Authored by: Johnson, A.
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30
Cole, AJ., Beckman, LM., & Earthman, CP. (2014). Vitamin D status following bariatric surgery: Implications and recommendations. Nutrition in Clinical Practice. 29(6), 751-758
[Journal article]Authored by: Johnson, A.
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