Boosting natural history research via metagenomic clean-up of crowdsourced feces.

Rudolf Meier,Amrita Srivathsan,Niranjan Nagarajan

doi:10.1371/journal.pbio.3000517

Rudolf Meier, Amrita Srivathsan + Show 1 more

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https://doi.org/10.1371/journal.pbio.3000517

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Abstract

Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research—a major source of information on noncharismatic species—is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are “crowdsourced” during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a “metagenomic clean-up” on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace’s favorite collecting sites.

Highlights

Natural history research has been in steep decline over the past few decades [1,2,3]
Akin to a naturalist’s incidental field observations, a small number of fecal samples for noncharismatic mammal species may initially appear to be of limited value, but they can be very informative once they are fully evaluated
This is because fecal samples contain information on diet, genetics of the host, gut parasites, microbiome [19,20,21,22], and even hormones; i.e., these samples are inherently data-rich and multidimensional

Summary

Introduction

Natural history research has been in steep decline over the past few decades [1,2,3]. Akin to a naturalist’s incidental field observations, a small number of fecal samples for noncharismatic mammal species may initially appear to be of limited value, but they can be very informative once they are fully evaluated This is because fecal samples contain information on diet, genetics of the host, gut parasites, microbiome [19,20,21,22], and even hormones (e.g., cortisol [23]); i.e., these samples are inherently data-rich and multidimensional. The microbiomes of Rattus and Sundamys were diverse (1.5–15-fold higher, Fig 3A and 3B) but largely lacking with regard to microbial species producing chitinolytic enzymes It is time for a metagenomic initiative supporting natural history research in the 21st century. They would initiate data acquisition following approved protocols for the country in

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