Validation of DNA metabarcoding of fecal samples using cattle fed known rations

Scasta, John Derek; Jorns, T.; Derner, Justin D.; Lake, Scott; Augustine, David J.; Windh, Jessica L.; Smith, Travis

doi:10.1016/j.anifeedsci.2019.114219

Cited by 21 publications

(14 citation statements)

References 20 publications

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“…We suspect that result is a combination of high concentrations of pollen across the landscape during spring months and low digestibility of some vegetation species (Ando et al, 2018). Given that different functional groups and plant taxa differ in digestibility, some species likely show higher presence in feces (Scasta et al, 2019). This bias is not unique to diet analyses using DNA but is often reported in microhistological analyses of diet composition (Anthony and Smith, 1974;Dearden et al, 1975).…”

Section: Discussionmentioning

confidence: 99%

Variation in diet of desert bighorn sheep (Ovis canadensis nelsoni): Tradeoffs associated with parturition

et al. 2023

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Selection of forage and habitats is driven by nutritional needs of individuals. Some species may sacrifice nutritional quality of forage for the mother in favor of safety of offspring (risk-averse strategy), immediately following parturition. We studied diet quality and forage selection by bighorn sheep before and following parturition to determine how nutritional demands associated with rearing offspring influenced forage acquisition. We used desert bighorn sheep, Ovis canadensis nelsoni, to investigate that potential tradeoff. We captured and radio-collared female bighorn sheep from 2016 to 2018. We used vaginal implant transmitters (VIT)s in pregnant females to identify parturition and to capture and radio-collar neonates to monitor survival of young. We collected fecal samples throughout the breeding season and throughout the year to understand diet quality and composition throughout those temporal periods. We determined diet quality and composition for pre-parturient females, females provisioning offspring, females that lost offspring, and non-pregnant individuals using fecal nitrogen and DNA metabarcoding analyses. Additionally, we compared the diet quality and composition of offspring and adult females during the spring, as well as summer and winter months. Our results indicated differences in diet quality between individuals provisioning offspring and those whose offspring had died. Females that were provisioning dependent young had lower quality diets than those that lost their offspring. Diet composition among those groups was also markedly different; females that had lost an offspring had a more diverse diet than did females with dependent young. Diet quality differed among seasons, wherein offspring and adult females had higher quality diets during the spring months, with decreasing quality as the year progressed. Diet diversity was similar across seasons, although spring months tended to be most diverse. Our results support tradeoffs associated with risk-averse strategies made by adult females associated with parturition. Nutritional quality of forage was linked to provisioning status, indicating that females were trading diet quality for safety of offspring, but those females whose offspring had died selected high quality forages. Those results help explain habitat selection observed in mountain ungulates around parturition and provide further insight into the evolutionary processes and adaptive significance exhibited by those specialized artiodactyls.

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Section: Discussionmentioning

confidence: 99%

Variation in diet of desert bighorn sheep (Ovis canadensis nelsoni): Tradeoffs associated with parturition

et al. 2023

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“…These adaptations may affect the degradation of plant DNA. The few studies that have examined the accuracy of metabarcoding for herbivores focused primarily on domesticated and wild ruminants (Nakahara et al, 2016; Scasta et al, 2019; Willerslev et al, 2014), which also have a unique digestive strategy that differs from nonruminants (Holechek et al, 1982). To the best of our knowledge, diet metabarcoding has not been evaluated in a wild, nonruminant herbivore.…”

Section: Introductionmentioning

confidence: 99%

Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal

Stapleton

Weinstein

Greenhalgh

et al. 2022

Molecular Ecology Resources

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DNA metabarcoding is widely used to determine wild animal diets, but whether this technique provides accurate, quantitative measurements is still under debate. To test our ability to accurately estimate the abundance of dietary items using metabarcoding, we fed wild‐caught desert woodrats (Neotoma lepida) diets consisting of constant amounts of juniper (Juniperus osteosperma, 15%) and varying amounts of creosote (Larrea tridentata, 1%–60%), cactus (Opuntia sp., 0%–100%) and commercial chow (0%–85%). Using metabarcoding, we compared the representation of items in the original diet samples to that in the faecal samples to test the sensitivity and accuracy of diet metabarcoding, the performance of different bioinformatic pipelines and our ability to correct sequence counts. Metabarcoding, using standard trnL primers, detected creosote, juniper and chow. Different pipelines for assigning taxonomy performed similarly. While creosote was detectable at dietary proportions as low as 1%, we failed to detect cactus in most samples, probably due to a primer mismatch. Creosote read counts increased as its proportion in the diet increased, and we could differentiate when creosote was a minor and major component of the diet. However, we found that estimates of juniper and creosote varied. Using previously suggested methods to correct these errors did not improve accuracy estimates of creosote, but did reduce error for juniper and chow. Our results indicate that metabarcoding can provide quantitative information on dietary composition, but may be limited. We suggest that researchers use caution when quantitatively interpreting diet metabarcoding results unless they first experimentally determine the extent of possible biases.

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“…To date, feeding trials 39 , comparisons of diet reconstructions from microhistology and fecal DNA 40 , and isotopic estimates of the relative contribution of C 3 and C 4 species 4 , 41 all support the validity of fecal DNA for diet reconstructions. One feeding trial did not, but that was conducted with dried hay that likely would have caused cpDNA degradation among species 42 .…”

Section: Discussionmentioning

confidence: 99%

Seasonal patterns of bison diet across climate gradients in North America

Craine

2021

Sci Rep

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North American plains bison (Bison bison) have been reintroduced across their former range, yet we know too little about their current diet to understand what drove their past migrations as well as observed continental-scale variation in weight gain and reproduction. In order to better understand the seasonal diets of bison at the continental scale, bison fecal material was collected monthly from April to September in 2019 across 45 sites throughout the conterminous United States. Fecal material was analyzed for dietary quality using near infrared spectroscopy and dietary composition with DNA metabarcoding. As observed in previous research, dietary quality peaked in June and was on average greatest for sites with cold, wet climates. Yet, in April, dietary quality was highest in warmer regions, likely reflecting earlier phenology of plants in southern than northern regions. Independent of climate and season, bison that consumed more warm-season grasses had lower dietary protein concentrations. Interpreting the relative abundance of sequences from different plant species as the relative intake of protein from those species, only 38% of bison protein intake came from grasses. An equal amount of dietary protein came from legumes (38%) and 22% from non-leguminous forbs. Seasonal shifts in bison diet were also clear, in part, following the phenology of functional groups. For example, cool-season grass protein intake was highest in May, while legume protein intake was highest in August. Comparing data taken in June and September 2018 in a previous study with corresponding data in 2019, on average, June [CP] was 20% higher in 2019 than 2018, while September [CP] did not differ between years. Dietary functional group composition was generally similar in amounts and relationships with climate between years, yet in September 2019, legumes contributed 20% more protein and warm-season grasses 14% less than in September 2018. In all, this research demonstrates that bison consistently rely on eudicots for protein with the functional group composition of their diet in some ways consistent across space and time, but also spatially and temporally variable. The early-season inversion of plant quality gradients would have been a strong driver of migratory behavior for large numbers of bison optimizing protein intake. As most bison currently experience protein deficiency, optimizing protein intake under current non-migratory conditions will require increasing the relative abundance of high-protein species such as N2-fixing species.

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Validation of DNA metabarcoding of fecal samples using cattle fed known rations

Cited by 21 publications

References 20 publications

Variation in diet of desert bighorn sheep (Ovis canadensis nelsoni): Tradeoffs associated with parturition

Variation in diet of desert bighorn sheep (Ovis canadensis nelsoni): Tradeoffs associated with parturition

Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal

Seasonal patterns of bison diet across climate gradients in North America

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