Diet Analysis of Leopoldamys Neilli, a Cave-dwelling Rodent in Southeast Asia, Using Next-Generation Sequencing from Feces

Latinne, Alice; Galan, Maxime; Waengsothorn, Surachit; Rojanadilok, Prateep; Eiamampai, Krairat; Sribuarod, Kriangsak; Michaux, Johan

doi:10.4311/2013lsc0100

Cited by 5 publications

(4 citation statements)

References 29 publications

(39 reference statements)

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“…Digestion pass-through rates, for example, can be quite rapid in other rodent species and experimental studies have reported rates ranging from 0.5–13 hours [51, 52]. Soininen et al [50] reported high variability in recovered diet components among individual fecal samples from two small voles ( Microtus oeconomus and Myodes rufocanus ), and high fecal-sample variability has been reported elsewhere [62, 63]. Nonetheless, we expect population-level comparisons based on large samples to be robust to intra-individual noise.…”

Section: Discussionmentioning

confidence: 99%

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

et al. 2016

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Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

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Section: Discussionmentioning

confidence: 99%

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

et al. 2016

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“…The importance of visual diet analysis cannot be ignored, especially when we want to know exactly which prey part the predator is consuming (Latinne et al 2014) or to quantify predation. In this study, with visual identification we found that seeds were the most commonly eaten plant part in the diet of the 3 pest species.…”

Section: Discussionmentioning

confidence: 99%

Diet analysis of small mammal pests: A comparison of molecular and microhistological methods

Khanam

Howitt

Mushtaq

et al. 2016

Integrative Zoology

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Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species.

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“…More recently, several diets based on faeces of a broad panel of mammal species encompassing herbivores, bats, carnivores, and rodents among others, have been successfully analyzed with molecular techniques using DNA barcoding (Soininen et al 2009;Zeale et al 2011;Galan et al 2012;Shehzad et al 2012;Latinne et al 2014). The different prey species and plant taxa contained in the faeces are identified by amplifying small and highly variable DNA fragments with universal primers and by using them as barcodes.…”

Section: Introductionmentioning

confidence: 99%

A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces

et al. 2015

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The Pyrenean desman (Galemys pyrenaicus) is a small endangered semi-aquatic mammal endemic to the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its diet from this material using next-generation sequencing methods. We amplified and sequenced a small DNA minibarcode (133 bp) of the COI gene in twenty-four putative faeces samples of Pyrenean desman and successfully identified the species in 16 samples. Other identified species were mammals, birds and amphibians, evidencing the potential application of our methods to a larger panel of taxa. In the Pyrenean desman faeces, we were able to identify nineteen prey species with a positive match (more than 98% of identity with a reference sequence) and eleven putative prey species with lower identity scores (90-96%). The nineteen species belonged to four orders and eleven families among which Trichoptera and Hydropsychidae were the most frequent, respectively. Future improvements could be obtained by extending the reference DNA sequence collection to reach precise identifications over the Desman's range and by increasing the sampling to gain a better knowledge of the local diet of this endangered species. Such information is of great importance to propose the best management measures for its conservation.

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Diet Analysis of Leopoldamys Neilli, a Cave-dwelling Rodent in Southeast Asia, Using Next-Generation Sequencing from Feces

Cited by 5 publications

References 29 publications

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

Diet analysis of small mammal pests: A comparison of molecular and microhistological methods

A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces

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