Dr Mike Taylor

Senior Lecturer in Microbiology

Senior Lecturer in Microbiology


Phone: +64 9 3737599 x82280
Thomas Building, Level 3, Room 334C
Email: mw.taylor@auckland.ac.nz

Research Interests

Our research group investigates the ecology of microorganisms associated with animal “hosts”, with recent expansion into study of the human microbiome. Host-microbe interactions range from being pathogenic in nature, to microbes acting as a food source, to tightly linked symbioses in which both partners benefit. Understanding which microorganisms are associated with which hosts - and why - is central to our research. To this end, we employ a range of molecular and cultivation-based approaches, and utilise a number of different “hosts” in our research. Our main areas of research interest are summarised below…

Microbiology of autism spectrum disorder (ASD)

Autism is a major human health issue, affecting as many as 1 in 88 children. Gastrointestinal problems, perhaps indicative of a disrupted microbial community in the gut, are commonly associated with ASD. Furthermore, a number of recent studies have indicated differences in the gut microbiota of people with and without ASD, though few consistent patterns have yet emerged. In order to better understand the role of the gut microbiome in ASD, we have recently started to investigate the composition and activities of the faecal microbiota among people with ASD. This work is done in close collaboration with University of Auckland geneticists Jessie Jacobsen, Russell Snell and Klaus Lehnert, as well as Auckland neurologist Roz Hill and biochemist Dave Greenwood, and fits within the wider framework of the Minds for Minds research campaign (www.mindsforminds.org.nz).


Role of the microbiome in sinus disease

Chronic rhinosinusitis (CRS) is a miserable condition which causes its sufferers to feel as if they have a permanent head cold. It is a major health problem in Western societies, affecting approximately 5% of the population and adding a considerable financial burden to healthcare systems. While the causes of CRS remain poorly understood, it is becoming increasingly evident that bacteria growing within the sinuses have a role to play. In close collaboration with Richard Douglas and Kristi Biswas at the University of Auckland’s Department of Surgery, we are applying cultivation-dependent and –independent (molecular) techniques to determine the composition, abundance and in situ activities of the microbial community associated with CRS.


Fluorescence in situ hybridisation image of bacteria (red cells) within infected sinus tissue. Image courtesy of K. Biswas.

Microbial ecology of endangered New Zealand species

Animals provide a diverse array of habitats for microorganisms to colonise, and virtually all animals form symbiotic relationships with one or more microbial species. Due to its environmental heterogeneity and extended period of geographic isolation (>50 million years), New Zealand houses a unique variety of animal host organisms. Unfortunately, many of these animals are endangered, and we are actively investigating the microbiology of some of these species in order to (a) better understand the role of microbes in the biology of these endemic host animals, and (b) utilise this microbiological knowledge to aid in the conservation and management of key endangered species. Much of our research so far has concentrated on the critically endangered parrot, the kakapo (Strigops habroptilus), though we are also examining other bird and also reptile species, such as Duvaucel’s gecko (Hoplodactylus duvauceli). This work is done in cooperation with the Department of Conservation’s Kakapo Recovery Programme (kakaporecovery.org.nz/), the NZ Centre for Conservation Medicine (www.conservationmedicine.co.nz), and ecologists including Dianne Brunton and Manuela Barry at Massey University, and Dan Tompkins at Landcare Research.


The critically endangered kakapo. Image courtesy of D. Waite.

Marine sponge microbiome

Marine sponges harbour a dense and diverse community of microorganisms, which contribute substantially to the biology of the host sponge. We have been studying the microbiology of sponges for more than a decade, and although our work in this area is being wound back, it does remain an active part of our research programme. Our collaborators in this area include Nicole Webster (Australian Institute of Marine Science), Ute Hentschel (University of Wuerzburg), James Bell (Victoria University of Wellington), Jose Montoya (Marine Sciences Institute, Barcelona) and Peter Schupp (University of Oldenburg).


Current team members

  • David Waite (PhD student) – Microbiology of the critically endangered NZ parrot, the kakapo
  • Melissa D’souza (PhD student) – Soil bacteria of the Ross Sea Region, Antarctica
  • Carmen Astudillo (PhD student) – Marine sponge microbiology
  • Rose Williams (MSc student) – Gut microbiome of the threatened Duvaucel’s gecko
  • Brett Wagner (MSc student) – Optimising procedures for extraction of nucleic acids from human stool samples
  • Elahe Kia (MSc student) – Urinary metabolic profiles of children with autism spectrum disorder
  • Dean Brown (MSc student) – Gut microbiota and autism spectrum disorder
  • Mike Hoggard (Research Assistant / Biomed (Hons) student) – Role of the sinus microbiome in chronic rhinosinusitis
  • Jeremy Raynes (SBS summer student) – Microbiology of chronic rhinosinusitis


Assoc. Prof. Jacqueline Beggs, University of Auckland
Assoc. Prof. James Bell, Victoria University of Wellington
Prof. Dianne Brunton, Dr Manuela Barry, Massey University
Dr Peter Deines, Massey University
Dr Richard Douglas, Kristi Biswas, Department of Surgery, University of Auckland
Daryl Eason, Deidre Vercoe, Ron Moorhouse, Department of Conservation
Dr Matthew Goddard, University of Auckland
Assoc. Prof. David Greenwood, Plant & Food Research
Prof. Ute Hentschel, University of Wuerzburg
Dr Jessie Jacobsen, Assoc. Prof. Klaus Lehnert, Prof. Russell Snell, University of Auckland
Dr Jose Montoya, Marine Sciences Institute (ICM-CSIC), Barcelona
Prof. Sally Poppitt, Human Nutrition Unit, University of Auckland
Prof. Peter Schupp, University of Wuerzburg
Dr Matthew Stott, GNS Science
Dr Dan Tompkins, Landcare Research
Dr Nicole Webster, Australian Institute of Marine Scienc

New Zealand Microbial Ecology Consortium (NZMEC)

The NZMEC is a special interest group of the NZ Microbiological Society (www.nzms.org.nz), convened by Mike Taylor and Matt Stott (GNS Science, Wairakei www.gns.cri.nz/who/staff/2150.html). The aim of the NZMEC is to facilitate interaction and collaboration among NZ-based microbial ecologists, and to disseminate relevant information such as job opportunities and recent publications – this is achieved by the Consortium’s website (www.nzmec.org.nz). We also hold biannual meetings which include seminars by some of the world’s leading microbial ecologists, and workshops on topics such as statistics for microbial ecology, and next-generation sequencing for microbial diversity studies. Please check out our website, or email Mike (mw.taylor@auckland.ac.nz) or Matt (m.stott@gns.cri.nz) if you are interested in joining or just learning more about NZMEC.

Selected Recent Publications

Dhami, M.K., Buckley, T.R., Beggs, J.R., and M W Taylor (2013). Primary symbiont of the ancient scale insect family Coelostomidiidae exhibits strict cophylogenetic patterns. Symbiosis, DOI: 10.1007/s13199-013-0257-8.

Waite, D., Deines, P., and M W Taylor (2013). Quantifying the impact of storage procedures for faecal bacteriotherapy in the critically endangered New Zealand parrot, the kakapo. Zoo Biology, DOI: 10.1002/zoo.21098.

Biswas, K., M W Taylor, and Turner, S.J. (2013). Successional development of biofilms in moving bed biofilm reactor (MBBR) systems treating municipal wastewater. Applied Microbiology and Biotechnology, DOI: 10.1007/s00253-013-5082-8.

Dhami, M.K., Weir, B.S., M W Taylor, and Beggs, J.R. (2013). Diverse honeydew-consuming fungal communities associated with scale insects. PLoS One 8: e70316.

Bell, J.J., Jones, T., Davy, S., M W Taylor, and Webster, N.S. (2013). Could some coral reefs become sponge reefs as our climate changes?. Global Change Biology 19: 2613-2624.

Simister, R.L., M W Taylor, Rogers, K., Schupp, P.J., and Deines, P. (2013). Temporal molecular and isotopic analysis of active bacterial communities in two New Zealand sponges. FEMS Microbiology Ecology 85: 195-205.

Giles, E., Kamke, J., Moitinho-Silva, L., M W Taylor, Hentschel, U., Ravasi, T., and Schmitt, S. (2013). Bacterial community profiles in low microbial abundance sponges. FEMS Microbiology Ecology 83: 232-241.

M W Taylor, Tsai, P., Simister, R.L., Deines, P., Ericson, G., Botte, E., Schmitt, S., and Webster, N.S. (2013). ‘Sponge-specific’ bacteria are widespread (but rare) in diverse marine environments. The ISME Journal 7: 438-443.

Simister, R.L., M W Taylor, Tsai, P., and Webster, N.S. (2012). Sponge-microbe associations survive high nutrients and temperatures. PLoS One 7: e52220.

Simister, R.L., M W Taylor, Fan, L., Crowe, M.L., Bruxner, T., Tsai, P., and Webster, N.S. (2012). Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge, Rhopaloeides odorabile. Environmental Microbiology 14: 3232-3246.

Hentschel, U., Piel, J., Degnan, S.M., and M W Taylor (2012). Genomic insights into the marine sponge microbiome. Nature Reviews Microbiology 10: 641-654.

Waite, D.W., Deines, P., and M W Taylor (2012). Gut microbiome of the critically endangered New Zealand parrot, the kakapo (Strigops habroptilus). PLoS One 7: e35803.

Dhami, M.K., Turner, A.P., Deines, P., Beggs, J.R., and M W Taylor (2012). Ultrastructural and molecular characterisation of a bacterial symbiosis in the ecologically important scale insect family Coelostomidiidae. FEMS Microbiology Ecology 81: 537-546.

Simister, R.L., Deines, P., Botte, E., Webster, N.S., and M W Taylor (2012). Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environmental Microbiology 14: 517-524.

Schmitt, S., Tsai, P., Bell, J., Fromont, J., Ilan, M., Lindquist, N., Perez, T., Rodrigo, A., Schupp, P., Vacelet, J., Webster, N., Hentschel, U., and M W Taylor (2012). Assessing the complex sponge microbiota - core, variable and species-specific bacterial communities in marine sponges. The ISME Journal 6: 564-576.

Schmitt, S., Hentschel, U., and M W Taylor (2012). Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges. Hydrobiologia 687: 341-351.

Webster, N.S., and M W Taylor (2012). Marine sponges and their microbial symbionts: love and other relationships. Environmental Microbiology 14: 335-346.

Schmitt, S., Deines, P., Behnam, F., Wagner, M., and M W Taylor (2011). Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges. FEMS Microbiology Ecology 78: 497-510.

M W Taylor, Hill, R.T., and Hentschel, U. (2011). Meeting report: First International Symposium on Sponge Microbiology. Marine Biotechnology 13: 1057-1061.

Simister, R.L., Schmitt, S., and M W Taylor (2011). Evaluating methods for the preservation and extraction of DNA and RNA for analysis of microbial communities in marine sponges. Journal of Experimental Marine Biology & Ecology 397: 38-43.

Kamke, J., M W Taylor, and Schmitt, S. (2010). Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. The ISME Journal 4: 498-508.

M W Taylor, Loy, A., and Wagner, M. (2010). Microarrays for studying the composition and function of microbial communities. In: The Microbiology of Activated Sludge, pp. 397-411, eds. Seviour, R., and Nielsen, P.H. IWA Publishing, London..

Webster, N.S., M W Taylor, Behnam, F., Lücker, S., Rattei, T., Whalan, S., Horn, M., and Wagner, M. (2010). Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environmental Microbiology 12: 2070-2082.

S A Lawrence, R O’Toole, M W Taylor and S K Davy (2010). Subcuticular Bacteria Associated with Two Common New Zealand Echinoderms: Characterization Using 16S rRNA Sequence Analysis and Fluorescence in situ Hybridization. Biol. Bull. 218, 95-104, 2010.

Schmitt, S., and M W Taylor (2009). Sponges – an evolutionary success story. Biologist 56: 74-78.

Steger, D., Ettinger-Epstein, P., Whalan, S., Hentschel, U., de Nys, R., Wagner, M., and M W Taylor (2008). Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges.. Environmental Microbiology 10: 1087-1094.

M W Taylor, R W Thacker and U Hentschel. (2007). Evolutionary insights from sponges. Science 316: 1854-1855..

D Steger, P Ettinger-Epstein, S Whalan, U Hentschel, R de Nys, M Wagner and M W Taylor. (2007). Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges . Environmental Microbiology, in press..

M W Taylor, R Radax, D Steger and M Wagner. (2007). Sponge-associated microorganisms: evolution, ecology and biotechnological potential.. Microbiology and Molecular Biology Reviews 71: 295-347.

S R Longford, N Tujula, G Crocetti, A J Holmes, C Holmström, S Kjelleberg, P D Steinberg and M W Taylor. (2007). Comparisons of diversity of bacterial communities associated with three marine eukaryotes. . Aquatic Microbial Ecology 48: 217-229..

U Hentschel, K Usher and M W Taylor. (2006). Marine sponges as microbial fermenters.. FEMS Microbiology Ecology 55: 167-177..

M W Taylor, P J Schupp, R de Nys, S Kjelleberg and P D Steinberg. (2005). Biogeography of bacteria associated with the marine sponge Cymbastela concentrica.. Environmental Microbiology 7: 419-433.

M Wagner and M W Taylor. (2005). Isotopic-labelling methods for deciphering the function of uncultured micro-organisms.. In: SGM Symposium 65: Micro-organisms and earth systems - advances in geomicrobiology, pp. 1-10, eds. Gadd, G.M., Semple, K.T., and Lappin-Scott, H.M. Cambridge University Press, Cambridge..