Congratulations to Beth on publishing an important Open Access review in Molecular Ecology!
The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation.
This paper means a lot to me, and to the group, for a number of reasons.
First and foremost, it spotlights a hugely important and often downplayed issue for folks doing dietary DNA metabarcoding work -- and similar amplicon sequencing applications with microbiomes, environmental DNA, ancient DNA, pathogens, etc. It documents a long history of reliance on abundance-filtering strategies in our bioinformatic pipelines that may inadvertently introduce more ecologically relevant errors than they eliminate. Folks tend to be well aware of the errors that our pipelines target (trace contamination, sequence errors), and they tend to be aware that abundance filtering is an imperfect solution. But at the end of the day we are trying to learn something new about ecology and the environment, and that means we need to be more attuned to how these filters impact our downstream biological interpretations. Over the years, I have worked with countless researchers to grapple with this issue in particular -- including authors, reviewers, and editors on both sides of peer review -- and I have tried to help alleviate the strain that this imbalance between the need to filter contaminants vs. the need to preserve signal in the data can cause. Researchers in the field have long needed a thoughtful review like this one to help guide the way. I hope it will inspire discussions, debates, thoughtful introspection... and ultimately progress toward more robust applications in the field.
Second and equally important, all of the molecular data presented in this paper were generated by students in my Conservation in the Genomics Age course at Brown (BIOL 1515/2015) in 2018 and 2020. Under the leadership of Patrick (TA in 2018) and Beth (co-instructor in 2020), the students received a shipment of fecal samples from Yellowstone National Park, extracted DNA, did PCR and sequencing, ran bioinformatics, and helped us come to grips with the results. I am so proud of everything we accomplished together with students in both of these classes, and I want to highlight the roles of coauthors Violet Sackett and Camille Tulloss who both stuck with the project and completed independent studies that contributed to this outcome.
Third, we have all benefited from Beth's steady leadership on this project and in the lab. The pandemic has been hard on everyone. Beth took the reins on this work remotely and under trying circumstances. I have been blown away by her intellect, ambition, insight, knowledge, skill, and resourcefulness. This review spotlights a pervasive issue that I have felt researchers in the field needed to have for years, and all credit to Beth for making it successful. It sets a very strong foundation for the most exciting work that Beth has in the pipeline... :)
Fourth, finally, and not at all least, this paper is rooted in our long-term collaboration with Park Scientists from Yellowstone National Park, including coauthors McGarvey and Geremia. It highlights both the need to gain new understanding of wildlife diets -- not to simply rest on preconceived notions about what animals eat -- and the critical importance of ensuring the data will be both useful and robust for downstream decision-making. When the outcome of an analysis really matters, researchers will benefit from approaching their work using the types of thoughtful and thorough approaches we illustrate in this paper.
Congrats Beth and colleagues! This is an important contribution to the field.
Littleford-Colquhoun BL, Freeman PT, Sackett VI, Tulloss CV, McGarvey LM, Geremia C, Kartzinel TR. 2022. The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation. Molecular Ecology 10.1111/mec.16352.
The lab has much to celebrate as we close out another semester, even despite the disruptions of COVID-19.
A pair of recent papers from the lab were highlighted for the creative use of DNA metabarcoding to solve problems and ask new questions in fields that span ecology and biomedical science.
1. Our recent paper documenting variation in diet-microbiome linkages in African megafauna was highlighted on the cover of PNAS, Brown University's news, The Division of Biomedicine's 'Kudos' memo, and in the media. This open access paper reflects the results of a long-term collaboration with Rob Pringle from Princeton, Paul Musili from the National Museums of Kenya, a creative honors thesis by Julianna Hsing, and the microbiome-bioinformatics chops of current grad student Bianca Brown.
2. Our recent paper in mSystems creatively translated the DNA metabarcoding approaches that we've been using for wildlife research into a biomedical context to evaluate the plant component of human diets. Using DNA-based evidence of human diet composition could be highly complementary to the current standard of asking human subjects to maintain diet logs in research on human health and nutrition. The paper was highlighted as Editor's pick in the area of Clinical Science and Epidemiology by the journal, as well as in a thoughtful commentary by Frank Maixner, who further highlighted the connections between this work and the fields of archaeology and ancient DNA. The paper was co-led by Aspen Reese based on samples from a prior experimental study investigating the influences of diet interventions on human gut microbiomes, which was led by Lawrence David.
The full text of this exciting new paper is online today: Feeding immunity: physiological and behavioral responses to infection and resource limitation. The article appears in a special feature of Frontiers in Immunology entitled Wild immunity -- the answers are out there. Congratulations to Sarah Budischak, Andrea Graham, and coauthors!
One of the most exciting aspects of this paper is the idea of "rewilding laboratory mice" to begin understanding the ecology of this model organism in genetics and medicine. What happens when lab mice are infected with an intestinal parasite, put outside, and tasked with surviving in a world with limited resources?
Add on top of that all of the exciting technology brought together to probe this creative experiment for mechanism -- PIT tags, DNA metabarcoding, NMR spectroscopy -- and you've got the makings of a classic. In this experiment, custom-built feeding devices capable of tracking foraging behavior, paired with DNA metabarcoding, revealed compensatory feeding behaviors by mice that otherwise might have masked the effects of infection.
Especially relevant to research in our lab, a hormone called leptin that serves as an indicator of hunger and body fat was correlated with consumption of different species of wild plants. Animals with higher leptin concentrations tended to eat more protein-rich clovers and other legumes than did animals with lower leptin, potentially pointing to different foraging behaviors and differential selectivity for wild foods as mechanisms for dealing with infection while reestablishing a dietary niche after generations in the laboratory. Although the effect sizes for the DNA metabarcoding data were small, these tantalizing trends highlight the importance of these measurements and the value of the technique. A valuable contribution.
Proud to contribute to a paper by Adam Pellegrini and coauthors that was just published in Ecology Letters: "Convergence of bark investment according to fire and climate structures ecosystem vulnerability to future change" (PDF).
Our work finds that some ecosystems contain tree species that are well adapted to the predicted changes in global fire regimes due to climate change, while others are composed of trees that may be particularly vulnerable. The paper was highlighted on Princeton's homepage and in Nature News!