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Dr. Burkhardt Flemer


Burkhardt Flemer

033701 - 78 212


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2017- now             

  • Postdoctoral researcher, Leibniz Institute for Vegetable and Ornamental Crops, Dr. Rita Grosch, Großbeeren, Germany


  • Postdoctoral researcher, APC Microbiome Institute, Prof. O’Toole, University College Cork, Ireland





  • PhD Microbiology, University College Cork, Ireland, Thesis title: Antimicrobial activities and diversity of sponge derived microbes, Supervisor: Prof. Alan Dobson


  • Diplom (FH) Biotechnology, Beuth Hochschule, Berlin, Germany and Hochschule Anhalt, Koethen, Germany, Diploma thesis at the Alfred-Wegener-Institute for Polar- and Marine Sciences, Title: “Diversity of Antarctic Sea Ice Algae”, Supervisor: Dr. Klaus Valentin.



ORCID ID: 0000-0003-4614-4432

Research Gate:

Google scholar:




  1. Flemer B, Herlihy M, O’Riordain M, et al, Tumour-associated and non-tumour-associated microbiota in colorectal cancer – and beyond, invited addendum, in print, Gut Microbes.
  2. Flemer B, Warren RD, Barrett MP, et al, 2018, The oral microbiota in colorectal cancer is distinctive and predictive, Gut [BMJ], Published Online First: 07 October 2017. doi: 10.1136/gutjnl-2017-314814
  3. Flemer B*, Gaci N*, Tottey W, et al, 2017, Faecal microbiota variation across the lifespan of the healthy laboratory rat, Gut Microbes, 2017, 8(5), pp. 428-439, doi:10.1080/19490976.2017.1334033, *equal contribution.
  4. O’Toole PW, Flemer B, 2017, From culture to high-throughput sequencing and beyond: a layperson’s guide to the ‘omics’ and diagnostic potential of the microbiome, Gastroenterology Clinics, 2017, 46 (1), pp. 9 – 17.
  5. O’Toole PW, Flemer B, Studying the microbiome, “omics” made accessible, Seminars in Liver Disease, 2016, 36, pp. 306-311.
  6. Flemer B, Lynch DB, Brown JMR, et al, 2017, Tumour-associated and non-tumour-associated microbiota in colorectal cancer, Gut [BMJ], 2017, 66, pp. 633-643.
  7. Kennedy J, Flemer B, Jackson SA, et al, 2014, Evidence of a putative deep sea specific microbiome in marine sponges, PLoS One, 2014 Mar 26, 9(3):e91092, doi: 10.1371/journal.pone.0091092, eCollection 2014.
  8. Jackson SA, Flemer B, McCann A, et al, Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges, PLoS One, 2013 Dec 30, 8(12):e84438, doi: 10.1371/journal.pone.0084438, eCollection 2013.
  9. Flemer B, Kennedy J, Margassery LM, et al, 2012, Diversity and anti-microbial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp., Journal of Applied Microbiology, 2012, 112, pp. 289-301.
  10. Kennedy J, Flemer B, Jackson SA, et al, 2010, Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism, Marine Drugs, 2010, 8, pp. 608-628.



  1. Sheehan D, Brown JMR, Flemer B, et al, Mechansims Underpinning Successful Faecal Microbiota Transplantation (FMT) for Recurrent Clostridium Difficile Infection, Gastroenterology 152(5):S47-S48, April 2017.



  1. Jackson SA, Kennedy J, Margassery LM, Flemer B, et al, Marine Sponges – Molecular Biology and Biotechnology, In Prof. S.K.Kim (Ed.): Springer Handbook of Marine Biotechnology (pp. 219-254), Berlin Heidelberg, Springer.



  1. Flemer B, O’Toole PW, Shanahan F, et al, Methods of determining colorectal cancer status in an individual, Patent application submitted to the European Patent Office.