Dr Raphael Eisenhofer Philipona
School of Biological Sciences
College of Science
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.
| Date | Position | Institution name |
|---|---|---|
| 2021 - ongoing | Adjunct assistant lecturer | University of Adelaide |
| 2021 - 2024 | Postdoctoral researcher | University of Copenhagen |
| 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 | Competency |
|---|---|
| English | Can read, write, speak, understand spoken and peer review |
| 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 |
| Year | Citation |
|---|---|
| 2026 | Williamson, E., Hill, K., Eisenhofer, R., & Hogendoorn, K. (2026). Experimental evidence for the absence of a functional gut microbiome in the solitary bee <i>Megachile tosticauda</i>. FEMS Microbiology Letters, 373, 11 pages. |
| 2026 | Eisenhofer, R., Alberdi, A., & Woodcroft, B. J. (2026). Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. Msystems, 11(4), 1-15. Scopus1 WoS1 |
| 2026 | Marcos, S., Odriozola, I., Aizpurua, O., Eisenhofer, R., Mak, S. S. T., Martin-Bideguren, G., . . . Alberdi, A. (2026). Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth. Isme Communications, 6(1), 13 pages. Scopus2 WoS1 |
| 2025 | Williamson, E. M., Hammer, T. J., Hogendoorn, K., & Eisenhofer, R. (2025). Blanking on blanks: few insect microbiota studies control for contaminants.. mBio, 16(4), e0265824. Scopus11 WoS10 Europe PMC7 |
| 2025 | Williamson, E., Hill, K., Hogendoorn, K., & Eisenhofer, R. (2025). The bacterial community associated with the solitary resin bee Megachile tosticauda throughout its life cycle.. FEMS Microbiol Ecol, 101(4), 10 pages. Scopus1 WoS1 Europe PMC1 |
| 2025 | Wilson, I., Perry, T., Eisenhofer, R., Rismiller, P., Shaw, M., & Grutzner, F. (2025). Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).. FEMS Microbiol Ecol, 101(5), 11 pages. |
| 2025 | Werner, L. E., Kleemann, S. L., Dix, S. K., Van Dijk, K., Biffin, E., Waycott, M., . . . Taggart, D. A. (2025). The influence of season, habitat and diet on the faecal microbiome of the yellow-footed rock-wallaby (Petrogale xanthopus xanthopus). Australian Journal of Zoology, 73(4), 17 pages. Scopus1 WoS1 |
| 2025 | Fierer, N., Leung, P. M., Lappan, R., Eisenhofer, R., Ricci, F., Holland, S. I., . . . Greening, C. (2025). Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Nature Microbiology, 10(7), 1570-1580. Scopus63 WoS62 Europe PMC34 |
| 2024 | 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. Scopus1 Europe PMC1 |
| 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. [version 2; peer reviewed: 1 approved, 3 approved with reservations]. F1000Research, 12, 926-1-926-35. Scopus7 Europe PMC4 |
| 2024 | Pietroni, C., Gaun, N., Leonard, A., Lauritsen, J., Martin-Bideguren, G., Odriozola, I., . . . Eisenhofer, R. (2024). Hologenomic data generation and analysis in wild vertebrates. Methods in Ecology and Evolution, 16(1), 97-107. Scopus14 |
| 2024 | 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. Scopus4 WoS3 Europe PMC3 |
| 2024 | 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), e03590-23-1-e03590-23-14. Scopus32 WoS31 Europe PMC23 |
| 2024 | 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. Scopus3 WoS2 |
| 2024 | Welsh, B. L., & Eisenhofer, R. (2024). The prevalence of controls in phyllosphere microbiome research: a methodological review. New Phytologist, 242(1), 23-29. Scopus4 WoS4 Europe PMC4 |
| 2023 | Eisenhofer, R., Odriozola, I., & Alberdi, A. (2023). Impact of microbial genome completeness on metagenomic functional inference. ISME Communications: New Developments in Microbial Ecology, 3(1), 12-1-12-5. Scopus40 WoS37 |
| 2023 | 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. Scopus11 WoS11 Europe PMC9 |
| 2023 | 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. Scopus5 WoS5 |
| 2023 | 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. Scopus19 WoS15 |
| 2023 | Maidment, T., & Eisenhofer, R. (2023). Pouch bacteria: an understudied and potentially important facet of marsupial reproduction. Microbiology Australia, 44(1), 41-44. Scopus3 WoS4 |
| 2023 | 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. Scopus22 WoS23 Europe PMC19 |
| 2022 | Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., & Penrose, B. (2022). Microbial biogeography of the wombat gastrointestinal tract. PeerJ, 10, e12982. Scopus4 WoS3 Europe PMC5 |
| 2022 | 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. Scopus15 WoS14 Europe PMC11 |
| 2022 | 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. Scopus8 WoS5 Europe PMC6 |
| 2022 | 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. Europe PMC2 |
| 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. Scopus16 WoS16 Europe PMC14 |
| 2021 | 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. Scopus17 WoS18 Europe PMC16 |
| 2021 | Weiss, S., Taggart, D., Smith, I., Helgen, K., & Eisenhofer, R. (2021). Host reproductive cycle influences the pouch microbiota of wild Southern Hairy-nosed Wombats (Lasiorhinus latifrons). |
| 2021 | 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. Scopus21 WoS20 Europe PMC16 |
| 2021 | 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. WoS24 Europe PMC10 |
| 2020 | 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. Scopus30 WoS28 Europe PMC24 |
| 2020 | 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. Scopus52 WoS49 Europe PMC41 |
| 2020 | 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. Scopus36 WoS34 Europe PMC22 |
| 2019 | Eisenhofer, R., & Cooper, A. (2019). Fossils: A new home for microbes.. eLife, 8, 1-3. Scopus1 WoS4 |
| 2019 | 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. Scopus835 WoS796 Europe PMC730 |
| 2019 | Eisenhofer, R., & Weyrich, L. S. (2019). Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ, 7(3), 1-24. Scopus30 WoS27 Europe PMC25 |
| 2019 | 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. Scopus189 WoS171 Europe PMC174 |
| 2019 | 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. Scopus20 WoS19 |
| 2018 | Eisenhofer, R., & Weyrich, L. (2018). Proper authentication of ancient DNA is still essential. Genes, 9(3), 5 pages. Scopus13 WoS10 Europe PMC14 |
| 2017 | 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 PMC7 |
| 2016 | 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. Scopus4 WoS3 Europe PMC2 |
| - | Inc, I. (n.d.). Reducing Run-to-Run Carryover on the MiSeq Using Dilute Sodium Hypochlorite Solution. |
| 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. |
| 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 |
| Year | Citation |
|---|---|
| 2024 | Wilson, I., Perry, T., Eisenhofer, R., Rismiller, P., Shaw, M., & Grutzner, F. (2024). Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus). DOI |
| 2024 | González-Pech, R., Howe, C., Lizcano-Sandoval, L., Eisenhofer-Philipona, R., Marciniak, S., Roitman, S., . . . Medina, M. (2024). A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change. DOI Europe PMC1 |
| 2024 | Eisenhofer, R., Alberdi, A., & Woodcroft, B. (2024). Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. DOI Europe PMC2 |
| 2023 | Eisenhofer, R., Nesme, J., Santos-Bay, L., Koziol, A., Sørensen, S. J., Alberdi, A., & Aizpurua, O. (2023). A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. DOI |
| 2022 | Eisenhofer, R., Odriozola, I., & Alberdi, A. (2022). Impact of microbial genome completeness on functional metagenomics. DOI |
| 2021 | Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., & Penrose, B. (2021). Microbial biogeography of the wombat gastrointestinal tract. DOI |
| 2021 | Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., & Penrose, B. (2021). Do faecal samples represent the primary site of microbial plant fermentation in hindgut fermenters?. DOI |
| 2020 | Weiss, S., Taggart, D., Smith, I., Helgen, K. M., & Eisenhofer, R. (2020). Host Reproductive Cycle Influences the Pouch Microbiota of Wild Southern Hairy-Nosed Wombats (Lasiorhinus Latifrons). DOI |
| 2020 | Weiss, S., Taggart, D., Smith, I., Helgen, K. M., & Eisenhofer, R. (2020). Host reproductive cycle influences the pouch microbiota of wild Southern Hairy-nosed Wombats (Lasiorhinus latifrons). DOI |
| 2020 | Eisenhofer, R., Helgen, K., & Taggart, D. (2020). Signatures of Landscape and Captivity in the Gut Microbiota of Southern Hairy-nosed Wombats (Lasiorhinus Latifrons). DOI |
| 2018 | Eisenhofer, R., & Weyrich, L. S. (2018). Assessing alignment-based taxonomic classification of ancient microbial DNA. 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
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 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 |
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 2021 - 2025 | Co-Supervisor | The Identity, Acquisition, and Function of Bacteria in the Australian Solitary Resin Bee Megachile tosticauda | Doctor of Philosophy | Doctorate | Full Time | Miss Elisabeth Mary Williamson |
| 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 |
| 2020 - 2025 | Co-Supervisor | The Effects of Rainfall and Drought on Southern Hairy-nosed Wombat (Lasiorhinus latifrons) Ecology and Fitness | Doctor of Philosophy | Doctorate | Full Time | Ms Shannon Kleemann |
| 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 |
| 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 |
| Date | Role | Committee | Institution | Country |
|---|---|---|---|---|
| 2019 - ongoing | Member | General Committee | Nature Conservation Society of South Australia | Australia |
| 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 |
