The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research

To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.

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Publication Details

Journal
Animal Microbiome
Published
2026-05-18
DOI
https://doi.org/10.1186/s42523-026-00579-0
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research

Melanie Florkowski, Gabrielle L. Davidson, Heather R. Skeen, Annie G. West et al.
Animal Microbiome
Environmental DNA in Biodiversity Studies
article

The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research

Melanie Florkowski, Gabrielle L. Davidson, Heather R. Skeen, Annie G. West, Elizabeth N. Rudzki, Sarah M. Hird, Haw Chuan Lim, Maurine W. Dietz, Felipe Campos-Cerda, Kasun H. Bodawatta, Jaime A. Chaves, Maria S. Costantini, Elin Videvall, Charli S. Davies, Melissah Rowe, Nicholas A. Mason, Kevin D. Kohl, Brian K. Trevelline, Marcella D. Baiz, Sarah F. Worsley, Jennifer L. Houtz, Morgan C. Slevin, Anne B. Clark, Catherine Andreadis, Sarah A. Knutie, Shane Somers, Rindy Anderson, Priscilla A. San Juan, William H. Karasov
article en

Abstract

To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.

Animal MicrobiomeVol. 8(1)
University of Notre Dame (US), University of East Anglia (GB), Allegheny College (US), Uppsala University (SE), Binghamton University (US), University of Copenhagen (DK), Houston Museum of Natural Science (US), University of Wisconsin–Madison (US), University of Connecticut (US), Kent State University (US), University of Auckland (NZ), University of Illinois Urbana-Champaign (US), George Mason University (US), Universidad Autónoma de la Ciudad de México (MX), University of Groningen (NL), University of Pittsburgh (US), Princeton University (US), University College Cork (IE), Natural History Museum of Los Angeles County (US), Field Museum of Natural History (US), Netherlands Institute of Ecology (NL), University at Buffalo, State University of New York (US), Florida Atlantic University (US), San Francisco State University (US), Universidad Nacional Autónoma de México (MX), Texas A&M University (US), University of Jyväskylä (FI)
National Science Foundation, Vetenskapsrådet, Directorate for Biological Sciences, National Astronomical Observatories, Chinese Academy of Sciences
Zero hunger
Openalex Percentile: Top 6%
Environmental DNA in Biodiversity Studies
DOIOpen Access PDFOpenAlex
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