
Raphael Eisenhofer Philipona
School of Biological Sciences
Faculty of Sciences, Engineering and Technology
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
I am passionate about the natural world and protecting our vanishing biodiversity. Ultimately, I want my research to help inform conservation practices and to provide a unique angle through which to engage the public about our awesome (and unfortunately, very endangered) Australian mammal biodiversity.
Microbes have profoundly influenced the evolution of animals and are an important facet of their biology. My expertise is in applying metagenomic techniques to study microbial communities. I'm a firm believer in the power of interdisciplinary research to yield results greater than the sum of its parts, and I enjoy integrating my expertise on projects with researchers from other disciplines.
Key areas of research are:
The microbial ecology of Australian mammals.
Coevolution between Australian mammals and their microbes.
Discovering interactions between Australian mammals and their microbes, and determining what these interactions mean for mammal ecology and health.
Developing microbiota therapies for improving captive mammal health and conservation efforts.
Note: I'm currently living in Copenhagen (Denmark) where I'm employed as a post doctoral researcher at the Globe institute, University of Copenhagen.
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Appointments
Date Position Institution name 2021 - ongoing Adjunct assistant lecturer University of Adelaide 2021 - 2024 Postdoctoral researcher University of Copenhagen -
Awards and Achievements
Date Type Title Institution Name Country Amount 2018 Award School of Biological Sciences Postgraduate Academic Achievement Award University of Adelaide Australia 500 2016 Research Award Royal Society of South Australia Small Research Grant Royal Society of South Australia Australia 1500 2015 Scholarship Australian Postgraduate Award University of Adelaide Australia - 2014 Award Victoria Graduate Award Victoria University New Zealand $5000 2013 Scholarship Summer Research Scholarship Victoria University New Zealand $6000 2013 Achievement Included on the Dean's List for Academic Excellence Victoria University New Zealand - -
Language Competencies
Language Competency English Can read, write, speak, understand spoken and peer review -
Education
Date Institution name Country Title 2015 - 2018 University of Adelaide Australia PhD (Paleomicrobiology, Metagenomics) 2011 - 2014 Victoria University of Wellington New Zealand BSc (Honours) - Molecular Microbiology -
Research Interests
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Journals
Year Citation 2025 Pietroni, C., Gaun, N., Leonard, A., Lauritsen, J., Martin-Bideguren, G., Odriozola, I., . . . Eisenhofer, R. (2025). Hologenomic data generation and analysis in wild vertebrates. Methods in Ecology and Evolution, 16(1), 97-107.
2024 Welsh, B. L., & Eisenhofer, R. (2024). The prevalence of controls in phyllosphere microbiome research: a methodological review. New Phytologist, 242(1), 23-29.
Europe PMC12024 Næsborg-Nielsen, C., Mounsey, K., Wilkinson, V., Eisenhofer, R., Burridge, C. P., & Carver, S. (2024). Changes in the Skin Microbiota in Two Bare-nosed Wombats (Vombatus ursinus) with Differing Recovery Trajectories following Treatment for Sarcoptic Mange. Journal of Wildlife Diseases, 60(3), 734-738.
2024 Borry, M., Forsythe, A., Andrades Valtueña, A., Hübner, A., Ibrahim, A., Quagliariello, A., . . . Fellows Yates, J. A. (2024). Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Research, 12, 926.
Scopus2 Europe PMC12024 Eisenhofer, R., Wright, S., & Weyrich, L. (2024). Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ, 12, e16770-1-e16770-25.
Scopus12024 Eisenhofer, R., Nesme, J., Santos-Bay, L., Koziol, A., Sørensen, S. J., Alberdi, A., & Aizpurua, O. (2024). A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiology Spectrum, 12(4), 14 pages.
Scopus7 Europe PMC42024 Dosseto, A., Dux, F., Eisenhofer, R., & Weyrich, L. (2024). Assessing the Utility of Strontium Isotopes in Fossil Dental Calculus. Journal of Archaeological Method and Theory, 31(3), 1570-1584.
2023 Eisenhofer, R., Odriozola, I., & Alberdi, A. (2023). Impact of microbial genome completeness on metagenomic functional inference. ISME COMMUNICATIONS, 3(1), 5 pages.
WoS42023 Eisenhofer Philipona, R., Brice, K. L., Blyton, M. D., Bevins, S. E., Leigh, K., Singh, B. K., . . . Moore, B. D. (2023). Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time. PeerJ, 11, e14598-1-e14598-21.
Scopus5 WoS1 Europe PMC32023 Welsh, B. L., Eisenhofer Philipona, R., Bastian, S. E. P., & Kidd, S. P. (2023). Monitoring the viable grapevine microbiome to enhance the quality of wild wines. Microbiology Australia, 44(1), 13-17.
Scopus42023 Pirolo, M., Espinosa-Gongora, C., Alberdi, A., Eisenhofer, R., Soverini, M., Eriksen, E. Ø., . . . Guardabassi, L. (2023). Bacterial topography of the upper and lower respiratory tract in pigs. Animal Microbiome, 5(1), 13 pages.
Scopus9 WoS42023 Maidment, T., & Eisenhofer, R. (2023). Pouch bacteria: an understudied and potentially important facet of marsupial reproduction. Microbiology Australia, 44(1), 41-44.
Scopus12023 Koziol, A., Odriozola, I., Leonard, A., Eisenhofer, R., José, C. S., Aizpurua, O., & Alberdi, A. (2023). Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors. mBio, 14(5), e01606-23-1-e01606-23-17.
Scopus8 Europe PMC52022 Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., & Penrose, B. (2022). Microbial biogeography of the wombat gastrointestinal tract. PeerJ, 10, e12982.
Scopus22022 Perry, T., West, E., Eisenhofer, R., Stenhouse, A., Wilson, I., Laming, B., . . . Grützner, F. (2022). Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes.. Frontiers in microbiology, 13, 1-11.
Scopus8 WoS1 Europe PMC52022 Næsborg-Nielsen, C., Eisenhofer, R., Fraser, T. A., Wilkinson, V., Burridge, C. P., & Carver, S. (2022). Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus). Parasites and Vectors, 15(1), 323-1-323-10.
Scopus5 WoS1 Europe PMC22022 Eisenhofer, R., Brice, K., Blyton, M. D. J., Bevins, S., Leigh, K., Singh, B., . . . Moore, B. (2022). Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time.
2022 Haas, F., Eisenhofer, R., Schreiber, M., Weyrich, L., & Rensing, S. (2022). Neanderthals did not likely consume <i>Physcomitrium patens</i> – a model moss species.
2022 Eisenhofer, R., Odriozola, I., & Alberdi, A. (2022). Impact of microbial genome completeness on functional metagenomics.
2021 Eisenhofer Philipona, R., Helgen, K. M., & Taggart, D. (2021). Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons). Animal Microbiome, 3(1), 4-1-4-14.
Scopus8 WoS7 Europe PMC72021 Weiss, S., Taggart, D., Smith, I., Helgen, K. M., & Eisenhofer Philipona, R. (2021). Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons). Animal Microbiome, 3(1), 13-1-13-14.
Scopus13 WoS7 Europe PMC82021 Farrer, A. G., Wright, S. L., Skelly, E., Eisenhofer, R., Dobney, K., & Weyrich, L. S. (2021). Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus. Scientific Reports, 11(1), 7456-1-7456-14.
Scopus17 WoS7 Europe PMC122021 Armbrecht, L., Eisenhofer, R., Utge, J., Sibert, E. C., Rocha, F., Ward, R., . . . Bowler, C. (2021). Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.. ISME communications, 1(1), 10 pages.
WoS8 Europe PMC52020 Eisenhofer Philipona, R., Kanzawa-Kiriyama, H., Shinoda, K. I., & Weyrich, L. S. (2020). Investigating the demographic history of Japan using ancient oral microbiota. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1812), 20190578-1-20190578-11.
Scopus26 WoS13 Europe PMC142020 Selway, C. A., Eisenhofer, R., & Weyrich, L. S. (2020). Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing. Journal of Pathology: Clinical Research, 6(2), 97-106.
Scopus33 WoS18 Europe PMC202020 Armbrecht, L., Herrando-Pérez, S., Eisenhofer, R., Hallegraeff, G. M., Bolch, C. J. S., & Cooper, A. (2020). An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Molecular Ecology Resources, 20(4), 906-919.
Scopus23 WoS17 Europe PMC122019 Eisenhofer, R., & Cooper, A. (2019). Fossils: A new home for microbes.. eLife, 8, 1-3.
Scopus1 WoS42019 Eisenhofer, R., Minich, J. J., Marotz, C., Cooper, A., Knight, R., & Weyrich, L. S. (2019). Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends in Microbiology, 27(2), 105-117.
Scopus610 WoS455 Europe PMC4172019 Eisenhofer, R., & Weyrich, L. S. (2019). Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ, 7(3), 1-24.
Scopus28 WoS16 Europe PMC172019 Weyrich, L. S., Farrer, A. G., Eisenhofer, R., Arriola Martinez, L., Young, J., Selway, C. A., . . . Cooper, A. (2019). Laboratory contamination over time during low-biomass sample analysis. Molecular ecology resources, 19(4), 982-996.
Scopus151 WoS114 Europe PMC972019 Eisenhofer, R., Anderson, A., Dobney, K., Cooper, A., & Weyrich, L. (2019). Ancient microbial DNA in dental calculus: a new method for studying rapid human migration events. Journal of Island and Coastal Archaeology, 14(2), 149-162.
Scopus16 WoS102018 Eisenhofer, R., & Weyrich, L. (2018). Proper authentication of ancient DNA is still essential. Genes, 9(3), 5 pages.
Scopus12 WoS6 Europe PMC102017 Eisenhofer, R., Cooper, A., & Weyrich, L. (2017). Reply to santiago-rodriguez et al.: Proper authentication of ancient DNA is essential. FEMS Microbiology Ecology, 93(5), 3 pages.
Scopus11 WoS12 Europe PMC72016 Eisenhofer Philipona, R. A., Cooper, A., & Weyrich, L. S. (2016). Isolating viable ancient bacteria: what you put in is what you get out. Genome Announcements, 4(4), e00712-16.
Scopus3 WoS1 Europe PMC1- Inc, I. (n.d.). Reducing Run-to-Run Carryover on the MiSeq Using Dilute Sodium Hypochlorite Solution.
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Conference Papers
Year Citation 2023 Ta, C., Skelly, E., Handsley-Davis, M., Eisenhofer, R., Kaidonis, J., & Weyrich, L. S. (2023). Effects of long-term storage conditions on microbial composition in dental calculus. In AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY Vol. 180 (pp. 173-174). WILEY. -
Datasets
Year Citation - Philipona, R. E. (n.d.). Genomes-Used-For-Simulated-Metagenomes.
DOI- Philipona, R. E. (n.d.). Simulated_Metagenomes.
DOI- Philipona, R. E. (n.d.). List of assembly accessions for simulated MALT analyses.
DOI- Philipona, R. E. (n.d.). HOMD accessions.
DOI- Philipona, R. E. (n.d.). RefSeqGCS accessions.
DOI- Philipona, R. E. (n.d.). RefSeqGCS genome accessions.
DOI- Philipona, R. E. (n.d.). Simulated-Metagenome.xlsx.
DOI- Philipona, R. E. (n.d.). Final 16S rRNA gene bait design.
DOI- Philipona, R. E. (n.d.). SI Files.
DOI- Philipona, R. E. (n.d.). SI file 1.
DOI- Philipona, R. E. (n.d.). SI file 2.
DOI
Origin and Development of the Microbiome in a Marsupial Soil Engineer: the Southern Hairy-nosed Wombat (Lasiorhinus latifrons)
Funding scheme: FND000091: Schultz Foundation Partnership
Amount: $5,000
Using the human microbiota to trace the final stages of Polynesian settlement
Funding scheme: ORG113911: Royal Society of South Australia - Small Research Grant
Amount: $1,500
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Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2021 Co-Supervisor The role and inheritance of bacteria in the Australian native resin bee, Megachile tosticauda Doctor of Philosophy Doctorate Full Time Miss Elisabeth Mary Williamson 2021 Co-Supervisor Monitoring of the reintroduction of the Brush-Tailed Bettong Bettongia penicillate into the Southern Yorke Peninsula. Doctor of Philosophy Doctorate Full Time Miss Chloe Helen Frick 2020 Co-Supervisor Ecological and Genetic studies of Hairy-nosed Wombats (Lasiorhinus latifrons) Doctor of Philosophy Doctorate Full Time Ms Shannon Kleemann -
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2020 - 2023 Co-Supervisor Investigating the Influence of Fungicide Usage and Vineyard Disease Management on the Grapevine Microbiome and Wine Quality Doctor of Philosophy Doctorate Full Time Mr Brady Leigh Welsh 2019 - 2021 Co-Supervisor Low-biomass Human Microbiomes: Another Piece to the Puzzle for Non-communicable Diseases Doctor of Philosophy Doctorate Full Time Miss Caitlin Alyssa Selway -
Other Supervision Activities
Date Role Research Topic Location Program Supervision Type Student Load Student Name 2019 - ongoing Co-Supervisor Microbiome Development of the Southern Hairy-nosed Wombat University of Adelaide/University of Copenhagen Veterinary Masters program Master - Sesilje Weiss 2019 - ongoing Principal Supervisor Gut microbiome analysis of the Southern hairy-nosed wombat The University of Adelaide Ecology and Evolutionary Biology Honours Full Time Calvin Heath 2019 - ongoing Principal Supervisor Analysis of modern and ancient human oral viromes The University of Adelaide Molecular and Biomedical Science Honours Full Time Darcy Watson 2019 - ongoing Principal Supervisor Genomic analyses of periodontal disease-associated microorganisms in human dental plaque The University of Adelaide Molecular and Biomedical Science Honours Full Time Brady Welsh
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Committee Memberships
Date Role Committee Institution Country 2019 - ongoing Member General Committee Nature Conservation Society of South Australia Australia -
Memberships
Date Role Membership Country 2019 - ongoing Member Nature Conservation Society of South Australia Australia 2019 - ongoing Member Society for Conservation Biology Australia 2019 - ongoing Member The Australian Mammal Society Australia 2017 - ongoing Member Australasian Bat Society Australia 2017 - ongoing Member Bat Conservation International United States 2016 - ongoing Member Royal Society of South Australia Australia 2016 - ongoing Member The Australian Society for Microbiology Australia 2016 - ongoing Member American Society for Microbiology United States
Connect With Me
External Profiles