The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research
Year: 2026
Type: article
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.
Source: Animal Microbiome
Authors: Kevin D. Kohl, Rindy Anderson, Catherine Andreadis, Marcella D. Baiz, Kasun H. Bodawatta, Felipe Campos-Cerda, Jaime A. Chaves, Anne B. Clark, Maria S. Costantini, Gabrielle L. Davidson, Charli S. Davies, Maurine W. Dietz, Melanie Florkowski, Sarah M. Hird, Jennifer L. Houtz, William H. Karasov, Sarah A. Knutie, Haw Chuan Lim, Nicholas A. Mason, Melissah Rowe, Elizabeth N. Rudzki, Priscilla A. San Juan, Heather R. Skeen, Morgan C. Slevin, Shane Somers, Annie G. West, Sarah F. Worsley, Elin Videvall, Brian K. Trevelline
Institutions: University of Pittsburgh, Florida Atlantic University, University of Notre Dame, University at Buffalo, State University of New York, University of Copenhagen, Universidad Nacional Autónoma de México, San Francisco State University, Binghamton University, University of Illinois Urbana-Champaign, Illinois Natural History Survey, Prairie Research Institute, University of East Anglia, University of Jyväskylä, University of Groningen, Texas A&M University, University of Connecticut, Allegheny College, University of Wisconsin–Madison, George Mason University, Louisiana State University, Netherlands Institute of Ecology, Natural History Museum of Los Angeles County, Princeton University, Field Museum of Natural History, University College Cork, University of Auckland, Uppsala University, Kent State University
Language: English
Topic: Gut microbiota and health
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,190
Awards: Using the immune system to understand vertebrate-microbiome interactions and evolution, G5861975270, Assembly of the gut microbiome from birth to weaning: a cross-species comparison in wild mammals, IMAGiNE: Collaborative Research: Epigenetic potential and range expansion in the house sparrow
OpenAlex ID: W7161582593