Doctor Thomas Jeffries

Doctor Thomas Jeffries

Senior Lecturer, Microbiology,
Life Sciences


Dr. Thomas Jeffries is a microbial ecologist with a wide expertise in microbiology, microbial biogeography, computational biology and ecogenomics.  His research seeks to determine the environmental factors and ecological principles which drive patterns in microbial diversity in habitats spanning the ocean, dryland soils, contaminated sites and the human microbiome.  

 He completed his PhD. In 2011 at Flinders University where he was an "early adopter" of metagenomics  to study the influence of salinity in structuring microbial communities in the Coorong Lagoon.  His postdoctoral fellowship at the University of Technology Sydney utilized ecogenomic tools to study coastal marine microbiomes and the response of microbes to local oceanographic patterns and contamination inputs in Sydney Harbour.  In 2014 Dr. Jeffries became a Research Fellow in the Hawkesbury Institute for the Environment at Western Sydney University.  His research here focused on applying metagenomics to soils and contributing to a global survey of dryland microbiomes and the response of soil microbiomes to aridification.   Dr. Jeffries subsequently has joined the INDIGOV Expedition citizen science project which utilizes ocean going yachts to sample the world’s ocean microbiomes on unprecedented scales ( . 

 He was recently appointed Lecturer in Microbiology at Western Sydney University and is establishing his own research group.  He has published over 35 peer reviewed articles, is the chair of Joint Academic Microbiology Seminars (JAMS, and is on the committee of the Australian Society for Microbiology. 

This information has been contributed by Doctor Jeffries.


  • PhD Flinders University of South Australia
  • BSc Flinders University of South Australia
  • BSc Flinders University of South Australia

Professional Memberships

  • Joint Academic Microbiology Seminars (2012 - 2018)
  • International Society for Microbial Ecology (2003 - 2018)
  • Australian Society for Microbiology (2015 - 2018)


  • bioinformatics
  • microbial ecology
  • microbiology
  • microbiomes

Organisational Unit (School / Division)

  • Life Sciences


Phone: (02) 4570 1917
(02) 4570 1794
Location: L9.G.29

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Previous Teaching Areas

  • 300833 Microbiology 1, 2018
  • 300896 Microbiology 2, 2018


Journal Articles

  • Maisnam, P., Jeffries, T., Szejgis, J., Bristol, D., Singh, B., Eldridge, D., Horn, S., Chieppa, J. and Nielsen, U. (2023), '[In Press] Severe prolonged drought favours stress-tolerant microbes in Australian drylands', Microbial Ecology, .
  • Schupfer, E., Ooi, S., Jeffries, T., Wang, S., Micalos, P. and Pak, S. (2023), 'Changes in the human gut microbiome during dietary supplementation with modified rice bran arabinoxylan compound', Molecules, vol 28, no 14 .
  • Ajani, P., Savela, H., Kahlke, T., Harrison, D., Jeffries, T., Kohli, G., Verma, A., Laczka, O., Doblin, M., Seymour, J., Larsson, M., Potts, J., Scanes, P., Gribben, P., Harrison, L. and Murray, S. (2023), 'Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary', Water Research, vol 243 .
  • Hirekodathakal Jayaramaiah, R., Egidi, E., Macdonald, C., Wang, J., Jeffries, T., Megharaj, M. and Singh, B. (2022), 'Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation', Microbial Biotechnology, vol 15, no 1 , pp 318 - 336.
  • Hill, R., Wong-Bajracharya, J., Anwar, S., Coles, D., Wang, M., Lipzen, A., Ng, V., Grigoriev, I., Martin, F., Anderson, I., Cazzonelli, C., Jeffries, T., Plett, K. and Plett, J. (2022), 'Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus', New Phytologist, vol 233, no 2 , pp 966 - 982.
  • Radzieta, M., Sadeghpour-Heravi, F., Peters, T., Hu, H., Vickery, K., Jeffries, T., Dickson, H., Schwarzer, S., Jensen, S. and Malone, M. (2021), 'A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections : a pilot study', NPJ Biofilms and Microbiomes, vol 7 .
  • Trevathan-Tackett, S., Jeffries, T., Macreadie, P., Manojlovic, B. and Ralph, P. (2020), 'Long-term decomposition captures key steps in microbial breakdown of seagrass litter', Science of the Total Environment, vol 705 .
  • O'Carroll, D., Jeffries, T., Lee, M., Le, S., Yeung, A., Wallace, S., Battye, N., Patch, D., Manefield, M. and Weber, K. (2020), 'Developing a roadmap to determine per- and polyfluoroalkyl substances-microbial population interactions', Science of the Total Environment, vol 712 .
  • Ooi, S., Pak, S., Micalos, P., Schupfer, E., Zielinski, R., Jeffries, T., Harris, G., Golombick, T. and McKinnon, D. (2020), 'Rice bran arabinoxylan compound and quality of life of cancer patients (RBAC-QoL) : study protocol for a randomized pilot feasibility trial', Contemporary Clinical Trials Communications, vol 19 .
  • Delgado Baquerizo, M., Doulcier, G., Eldridge, D., Stouffer, D., Maestre, F., Wang, J., Powell, J., Jeffries, T. and Singh, B. (2020), 'Increases in aridity lead to drastic shifts in the assembly of dryland complex microbial networks', Land Degradation and Development, vol 31, no 3 , pp 346 - 355.
  • Brice, K., Trivedi, P., Jeffries, T., Blyton, M., Mitchell, C., Singh, B. and Moore, B. (2019), 'The koala (Phascolarctos cinereus) faecal microbiome differs with diet in a wild population', PeerJ, vol 7 .
  • Rinke, C., Rubino, F., Messer, L., Youssef, N., Parks, D., Chuvochina, M., Brown, M., Jeffries, T., Tyson, G., Seymour, J. and Hugenholtz, P. (2019), 'A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)', The ISME Journal, vol 13, no 3 , pp 663 - 675.
  • Tang, F., Jeffries, T., Vervoort, R., Conoley, C., Coleman, N. and Maggi, F. (2019), 'Microcosm experiments and kinetic modeling of glyphosate biodegradation in soils and sediments', Science of the Total Environment, vol 658 , pp 105 - 115.
  • Hurtado-McCormick, V., Kahlke, T., Petrou, K., Jeffries, T., Ralph, P. and Seymour, J. (2019), 'Regional and microenvironmental scale characterization of the Zostera muelleri seagrass microbiome', Frontiers in Microbiology, vol 10 .
  • Simoniello, C., Jencks, J., Lauro, F., Loftis, J., Weslawski, J., Deja, K., Forrest, D., Gossett, S., Jeffries, T., Jensen, R., Kobara, S., Nolan, L., Ostrowski, M., Pounds, D., Roseman, G., Basco, O., Gosselin, S., Reed, A., Wills, P. and Wyatt, D. (2019), 'Citizen-science for the future : advisory case studies rrom around the globe', Frontiers in Marine Science, vol 6 .
  • Edwards, R., Vega, A., Norman, H., Ohaeri, M., Levi, K., Dinsdale, E., Cinek, O., Aziz, R., McNair, K., Barr, J., Bibby, K., Brouns, S., Cazares, A., de Jonge, P., Desnues, C., Diaz Munoz, S., Fineran, P., Kurilshikov, A., Kurilshikov, R., Mazankova, K., McCarthy, D., Nobrega, F., Reyes Munoz, A., Tapia, G., Trefault, N., Tyakht, A., Vinuesa, P., Wagemans, J., Zhernakova, A., Aarestrup, F., Ahmadov, G., Alassaf, A., Anton, J., Asangba, A., Billings, E., Cantu, V., Carlton, J., Cazares, D., Cho, G., Condeff, T., Cortes, P., Cranfield, M., Cuevas, D., Iglesia, R., Decewicz, P., Doane, M., Dominy, N., Dziewit, L., Elwasila, B., Eren, A., Franz, C., Fu, J., Garcia-Aljaro, C., Ghedin, E., Gulino, K., Haggerty, J., Head, S., Hendriksen, R., Hill, C., Hyoty, H., Ilina, E., Irwin, M., Jeffries, T. and et al, .. (2019), 'Global phylogeography and ancient evolution of the widespread human gut virus crAssphage', Nature Microbiology, vol 4, no 10 , pp 1727 - 1736.
  • Malone, M., Fritz, B., Vickery, K., Schwarzer, S., Sharma, V., Biggs, N., Radzieta, M., Jeffries, T., Dickson, H., Jensen, S. and Bjarnsholt, T. (2019), 'Analysis of proximal bone margins in diabetic foot osteomyelitis by conventional culture, DNA sequencing and microscopy', APMIS: Journal of Pathology, Microbiology and Immunology, vol 127, no 10 , pp 660 - 670.
  • Malone, M., Schwarzer, S., Radzieta, M., Jeffries, T., Walsh, A., Dickson, H., Micali, G. and Jensen, S. (2019), 'Effect on total microbial load and community composition with two vs six-week topical Cadexomer Iodine for treating chronic biofilm infections in diabetic foot ulcers', International Wound Journal, vol 16, no 6 , pp 1477 - 1486.
  • Aghajani, M., Cooper, A., McGuire, H., Jeffries, T., Saab, J., Ismail, K., Souza, P., Bray, V., De Saint Groth, F., Niles, N. and Roberts, T. (2019), 'Pembrolizumab for anaplastic thyroid cancer : a case study', Cancer Immunology, Immunotherapy, vol 68 , pp 1921 - 1934.
  • Ochoa-Hueso, R., Eldridge, D., Delgado-Baquerizo, M., Soliveres, S., Bowker, M., Gross, N., Le Bagousse-Pinguet, Y., Quero, J., Garcia-Gomez, M., Valencia, E., Arredondo, T., Beinticinco, L., Bran, D., Cea, A., Coaguila, D., Dougill, A., Espinosa, C., Gaitan, J., Guuroh, R., Guzman, E., Gutierrez, J., Hernandez, R., Huber-Sannwald, E., Jeffries, T., Linstadter, A., Mau, R., Monerris, J., Prina, A., Pucheta, E., Stavi, I., Thomas, A., Zaady, E., Singh, B. and Maestre, F. (2018), 'Soil fungal abundance and plant functional traits drive fertile island formation in global drylands', Journal of Ecology, vol 106, no 1 , pp 242 - 253.
  • Jeffries, T., Rayu, S., Nielsen, U., Lai, K., Ijaz, A., Nazaries, L. and Singh, B. (2018), 'Metagenomic functional potential predicts degradation rates of a model organophosphorus xenobiotic in pesticide contaminated soils', Frontiers in Microbiology, vol 9 .
  • Delgado Baquerizo, M., Maestre, F., Eldridge, D., Bowker, M., Jeffries, T. and Singh, B. (2018), 'Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands : observational evidence from three continents', New Phytologist, vol 220, no 3 , pp 824 - 835.
  • Brown, M., Van de Kamp, J., Ostrowski, M., Seymour, J., Ingleton, T., Messer, L., Jeffries, T., Siboni, N., Laverock, B., Bibiloni-Isaksson, J., Nelson, T., Coman, F., Davies, C., Frampton, D., Rayner, M., Goossen, K., Robert, S., Holmes, B., Abell, G., Craw, P., Kahlke, T., Sow, S., McAllister, K., Windsor, J., Skuza, M., Crossing, R., Patten, N., Malthouse, P., Van Ruth, P., Paulsen, I., Fuhrman, J., Richardson, A., Koval, J., Bissett, A., Fitzgerald, A., Moltmann, T. and Bodrossy, L. (2018), 'Data descriptor : systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative', Scientific Data, vol 5 .
  • Li, J., Lin, J., Pei, C., Lai, K., Jeffries, T. and Tang, G. (2018), 'Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation', PeerJ, vol 6 .
  • Varkey, D., Mazard, S., Jeffries, T., Hughes, D., Seymour, J., Paulsen, I. and Ostrowski, M. (2018), 'Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary', PLoS One, vol 13, no 12 .
  • Newton, K., Jeffries, T., Smith, R., Seymour, J., Seuront, L. and Mitchell, J. (2018), 'Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs', Journal of Oceanology and Limnology, vol 36, no 6 , pp 2033 - 2049.
  • Dann, L., Smith, R., Jeffries, T., McKerral, J., Fairweather, P., Oliver, R. and Mitchell, J. (2017), 'Persistence, loss and appearance of bacteria upstream and downstream of a river system', Marine and Freshwater Research, vol 68, no 5 , pp 851 - 862.
  • Trivedi, P., Delgado Baquerizo, M., Jeffries, T., Trivedi, C., Anderson, I., Lai, K., McNee, M., Flower, K., Singh, B., Minkey, D. and Singh, B. (2017), 'Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content', Environmental Microbiology, vol 19, no 8 , pp 3070 - 3086.
  • Travathan-Tackett, S., Seymour, J., Nielsen, D., Macreadie, P., Jeffries, T., Sanderman, J., Baldock, J., Howes, J., Steven, A. and Ralph, P. (2017), 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions', FEMS Microbiology Ecology, vol 93, no 6 .
  • Drigo, B., Nielsen, U., Jeffries, T., Curlevski, N., Singh, B., Duursma, R. and Anderson, I. (2017), 'Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities', Environmental Microbiology, vol 19, no 8 , pp 3175 - 3185.
  • Ijaz, A., Jeffries, T., Ijaz, U., Hamonts, K. and Singh, B. (2017), 'Extending SEQenv : a taxa-centric approach to environmental annotations of 16S rDNA sequences', PeerJ, vol 5 .
  • Delgado Baquerizo, M., Trivedi, P., Trivedi, C., Eldridge, D., Reich, P., Jeffries, T. and Singh, B. (2017), 'Microbial richness and composition independently drive soil multifunctionality', Functional Ecology, vol 31, no 12 , pp 2330 - 2343.
  • Jeffries, T., Schmitz Fontes, M., Harrison, D., Van-Dongen-Vogels, V., Eyre, B., Ralph, P. and Seymour, J. (2016), 'Bacterioplankton dynamics within a large anthropogenically impacted urban estuary', Frontiers in Microbiology, vol 6 .
  • Delgado Baquerizo, M., Maestre, F., Reich, P., Jeffries, T., Gaitan, J., Encinar, D., Berdugo, M., Campbell, C. and Singh, B. (2016), 'Microbial diversity drives multifunctionality in terrestrial ecosystems', Nature Communications, vol 7 .
  • Colombo, F., Macdonald, C., Jeffries, T., Powell, J. and Singh, B. (2016), 'Impact of forest management practices on soil bacterial diversity and consequences for soil processes', Soil Biology and Biochemistry, vol 94 , pp 200 - 210.
  • Jeffries, T., Curlevski, N., Brown, M., Harrison, D., Doblin, M., Petrou, K., Ralph, P. and Seymour, J. (2016), 'Partitioning of fungal assemblages across different marine habitats', Environmental Microbiology Reports, vol 8, no 2 , pp 235 - 238.
  • Messer, L., Mahaffey, C., Robinson, C., Jeffries, T., Baker, K., Isaksson, J., Ostrowski, M., Doblin, M., Brown, M. and Seymour, J. (2016), 'High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation', The ISME Journal, vol 10, no 6 , pp 1499 - 1513.
  • Trivedi, P., Delgado Baquerizo, M., Trivedi, C., Hu, H., Anderson, I., Jeffries, T., Zhou, J. and Singh, B. (2016), 'Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships', The ISME Journal, vol 10 , pp 2593 - 2604.
  • Delgado Baquerizo, M., Maestre, F., Reich, P., Trivedi, P., Osanai, Y., Liu, Y., Hamonts, K., Jeffries, T. and Singh, B. (2016), 'Carbon content and climate variability drive global soil bacterial diversity patterns', Ecological Monographs, vol 86, no 3 , pp 373 - 390.
  • Dann, L., Rosales, S., Mckerral, J., Paterson, J., Smith, R., Jeffries, T., Oliver, R. and Mitchell, J. (2016), 'Marine and giant viruses as indicators of a marine microbial community in a riverine system', MicrobiologyOpen, vol 5, no 6 , pp 1071 - 1084.
  • Jeffries, T., Ostrowski, M., Williams, R., Xie, C., Jensen, R., Grzymski, J., Senstius, S., Givskov, M., Hoeke, R., Philip, G., Neches, R., Drautz-Moses, D., Chenard, C., Paulsen, I. and Lauro, F. (2015), 'Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll', Scientific Reports, vol 5 .
  • Nielsen, D., Pernice, M., Schliep, M., Sablok, G., Jeffries, T., Kuhl, M., Wangpraseurt, D., Ralph, P. and Larkum, A. (2015), 'Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians', Environmental Microbiology, vol 17, no 10 , pp 4121 - 4132.
  • Maestre, F., Delgado Baquerizo, M., Jeffries, T., Eldridge, D., Ochoa, V., Gozalo, B., Quero, J., Garcia-Gomez, M., Singh, B. and et al, .. (2015), 'Increasing aridity reduces soil microbial diversity and abundance in global drylands', Proceedings of the National Academy of Sciences of the United States of America, vol 112, no 51 , pp 15684 - 15689.
  • Messer, L., Doubell, M., Jeffries, T., Brown, M. and Seymour, J. (2015), 'Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary', Aquatic Microbial Ecology, vol 74, no 1 , pp 1 - 15.
  • Carney, R., Mitrovic, S., Jeffries, T., Westhorpe, D., Curlevski, N. and Seymour, J. (2015), 'River bacterioplankton community responses to a high inflow event', Aquatic Microbial Ecology, vol 75, no 3 , pp 187 - 205.
  • Tout, J., Jeffries, T., Petrou, K., Tyson, G., Webster, N., Garren, M., Stocker, R., Ralph, P. and Seymour, J. (2015), 'Chemotaxis by natural populations of coral reef bacteria', The ISME Journal, vol 9 , pp 1764 - 1777.
  • Dann, L., Mitchell, J., Speck, P., Newton, K., Jeffries, T. and Paterson, J. (2014), 'Virio- and bacterioplankton microscale distributions at the sediment-water interface', PLoS One, vol 9, no 7 .
  • Roudnew, B., Lavery, T., Seymour, J., Jeffries, T. and Mitchell, J. (2014), 'Variability in bacteria and virus-like particle abundances during purging of unconfined aquifers', Ground Water, vol 52, no 1 , pp 118 - 124.
  • Tout, J., Jeffries, T., Webster, N., Stocker, R., Ralph, P. and Seymour, J. (2014), 'Variability in microbial community composition and function between different niches within a coral reef', Microbial Ecology, vol 67, no 3 , pp 540 - 552.
  • Smith, R., Jeffries, T., Adetutu, E., Fairweather, P. and Mitchell, J. (2013), 'Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis', PLoS One, vol 8, no 11 .
  • Smith, R., Jeffries, T., Roudnew, B., Seymour, J., Fitch, A., Simons, K., Speck, P., Newton, K., Brown, M. and Mitchell, J. (2013), 'Confined aquifers as viral reservoirs', Environmental Microbiology Reports, vol 5, no 5 , pp 725 - 730.
  • Roudnew, B., Seymour, J., Jeffries, T., Lavery, T., Smith, R. and Mitchell, J. (2012), 'Bacterial and virus-like particle abundances in purged and unpurged groundwater depth profiles', Ground Water Monitoring and Remediation, vol 32, no 4 , pp 72 - 77.
  • Seymour, J., Doblin, M., Jeffries, T., Brown, M., Newton, K., Ralph, P., Baird, M. and Mitchell, J. (2012), 'Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current', Environmental Microbiology Reports, vol 4, no 5 , pp 548 - 555.
  • Smith, R., Jeffries, T., Roudnew, B., Fitch, A., Seymour, J., Delpin, M., Newton, K., Brown, M. and Mitchell, J. (2012), 'Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems', Environmental Microbiology, vol 14, no 1 , pp 240 - 253.
  • Jeffries, T., Seymour, J., Newton, K., Smith, R., Seuront, L. and Mitchell, J. (2012), 'Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient', Biogeosciences, vol 9, no 2 , pp 815 - 825.
  • Lavery, T., Roudnew, B., Seymour, J., Mitchell, J. and Jeffries, T. (2012), 'High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces', PLoS One, vol 7, no 5 .
  • Jeffries, T., Seymour, J., Gilbert, J., Dinsdale, E., Newton, K., Leterme, S., Roudnew, B., Smith, R., Seuront, L. and Mitchell, J. (2011), 'Substrate type determines metagenomic profiles from diverse chemical habitats', PLoS One, vol 6, no 9 .

Microbial Ecology

Human Microbiome

Computational Biology


This information has been contributed by Doctor Jeffries.

Current Projects

Title: Diet, gut microbiota and the evolution of lifespan and reproduction
  • Australian Research Council (ACRG)
Western Researchers: John Hunt, Thomas Jeffries and Markus Riegler
Years: 2022-02-01 - 2026-02-02
ID: P00027204

Previous Projects

Title: Causes and consequences of biogeochemical mismatches during drought
  • Australian Research Council (ACRG)
Western Researchers: Uffe Nielsen, Thomas Jeffries and Yolima Carrillo Espanol
Years: 2019-05-01 - 2023-07-01
ID: P00024809
Title: Investigation of micro-organisms inhabiting sediment ponds at a NSW mine site
  • Department of Planning and Environment
Western Researchers: Thomas Jeffries and Val Spikmans
Years: 2021-05-01 - 2023-05-01
ID: P00027500


Current Supervision

Thesis Title: Bacterial Biofilms and Antibiotic Resistance
Field of Research:

Previous Supervision

Thesis Title: Taxonomic and Environmental Annotation of Bacterial 16S rRNA gene sequences via Shannon Entropy and Database Metadata Terms
Field of Research: Biological Sciences; Microbiology; Biological Sciences, N.e.c.; Other Natural And Physical Sciences

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