Raphael Eisenhofer Philipona

Research Interests

Conservation and Biodiversity Genetics Microbial Genetics Microbiology

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
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.
DOI Scopus1 WoS1 Europe PMC2
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.
DOI
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.
DOI
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.
DOI
2024 Welsh, B. L., & Eisenhofer, R. (2024). The prevalence of controls in phyllosphere microbiome research: a methodological review. New Phytologist, 242(1), 23-29.
DOI Scopus3 WoS3 Europe PMC4
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.
DOI 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.
DOI Scopus5 Europe PMC3
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.
DOI Scopus7
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.
DOI Scopus3 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.
DOI Scopus21 WoS20 Europe PMC16
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.
DOI Scopus1 WoS1
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.
DOI WoS31
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.
DOI Scopus8 WoS7 Europe PMC4
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.
DOI Scopus4 WoS4
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.
DOI Scopus11 WoS9
2023 Maidment, T., & Eisenhofer, R. (2023). Pouch bacteria: an understudied and potentially important facet of marsupial reproduction. Microbiology Australia, 44(1), 41-44.
DOI Scopus2 WoS2
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.
DOI Scopus18 WoS19 Europe PMC18
2022 Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., & Penrose, B. (2022). Microbial biogeography of the wombat gastrointestinal tract. PeerJ, 10, e12982.
DOI Scopus2 WoS1 Europe PMC2
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.
DOI Scopus12 WoS12 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.
DOI 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.
DOI
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.
DOI
2022 Eisenhofer, R., Odriozola, I., & Alberdi, A. (2022). Impact of microbial genome completeness on functional metagenomics.
DOI
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.
DOI Scopus11 WoS12 Europe PMC11
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.
DOI Scopus17 WoS19 Europe PMC15
2021 Weiss, S., Taggart, D., Smith, I., Helgen, K. M., & Eisenhofer, R. (2021). Host reproductive cycle influences the pouch microbiota of wild Southern Hairy-nosed Wombats (Lasiorhinus latifrons).
DOI
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.
DOI Scopus20 WoS18 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.
DOI WoS22 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.
DOI Scopus28 WoS26 Europe PMC22
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.
DOI Scopus45 WoS43 Europe PMC36
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.
DOI Scopus32 WoS31 Europe PMC21
2019 Eisenhofer, R., & Cooper, A. (2019). Fossils: A new home for microbes.. eLife, 8, 1-3.
DOI 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.
DOI Scopus720 WoS700 Europe PMC656
2019 Eisenhofer, R., & Weyrich, L. S. (2019). Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ, 7(3), 1-24.
DOI Scopus30 WoS27 Europe PMC24
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.
DOI Scopus174 WoS165 Europe PMC153
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.
DOI Scopus17 WoS17
2018 Eisenhofer, R., & Weyrich, L. (2018). Proper authentication of ancient DNA is still essential. Genes, 9(3), 5 pages.
DOI 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.
DOI 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.
DOI Scopus4 WoS3 Europe PMC1
- Inc, I. (n.d.). Reducing Run-to-Run Carryover on the MiSeq Using Dilute Sodium Hypochlorite Solution.
DOI

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

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

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