New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

AbstractFood webs are important in understanding the structure, function, and behaviour of ecosystems, but, due to methodological limitations, are often poorly resolved in ways that impact food-web properties. Although DNA barcoding has proven useful in determining the diet of consumers, few studies have used this technique to determine food-web structure. These studies report mixed impacts on various food-web properties, but are limited by their taxonomic focus and their failure to evaluate DNA barcoding for both diet analysis and food-web structure. In this study, we show that, when compared to a morphological approach, DNA barcoding increases foodweb resolution by increasing the number and frequency of prey species identified in the stomach contents of eight species of Canadian boreal shield predatory fishes. In addition, we observed differences in food-web structure, such as increased generalism, habitat coupling, and omnivory, that have strong implications for food-web stability and dynamics. We conclude that DNA barcoding is a powerful tool to evaluate how resolution impacts foodweb properties and can help further our understanding of how food webs are structured by identifying feeding interactions in an unprecedented and highly detailed manner.

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A Comparison of Stomach and Fecal Samples for Diet Analysis of Grey Kangaroos

Wildlife Research ◽

10.1071/wr9880249 ◽

1988 ◽

Vol 15 (3) ◽

pp. 249 ◽

Cited By ~ 6

Author(s):

GL Norbury

Keyword(s):

Plant Species ◽

Stomach Contents ◽

Microscopic Analysis ◽

Dry Weight ◽

Stomach Content Analysis ◽

Diet Analysis ◽

Faecal Analysis ◽

Differential Digestion ◽

Free Ranging ◽

Species Proportions

In an experiment with four captive eastern grey kangaroos, Macropus giganteus, microscopic analysis of both stomach contents and faeces did not reflect the ingested dry weight proportion of most plant species in a fed diet. However, close agreement was obtained by correcting for unidentifiable microscopic fragments of plants. This suggests that differential digestion may not be as important an artefact of microscopic diet analysis as previously reported. Provided corrections are made, faecal analysis may be as reliable as stomach content analysis for describing relative proportions of plant species in the diet of macropodids. In contrast, differences in proportions of plant species between stomach and faecal samples from free-ranging western grey kangaroos, Macropus fuliginosus, suggest that faecal analysis may not be suitable for quantitative studies of diet selection (comparisons of plant species proportions in the diet with species proportions in the field) in areas with heterogeneous vegetation. In these situations, samples of stomach contents are considered more appropriate.

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Changes in the diet composition of Pygmy Cormorant Phalacrocorax pygmeus on Skadar lake (Southern Montenegro)

Acrocephalus ◽

10.2478/v10100-010-0003-8 ◽

2010 ◽

Vol 31 (144) ◽

pp. 21-26

Author(s):

Andrej Vizi ◽

Ondrej Vizi

Keyword(s):

Breeding Season ◽

Fish Species ◽

Fish Community ◽

Diet Composition ◽

Stomach Contents ◽

Breeding Population ◽

Diet Analysis ◽

Regional Population ◽

Species Specific ◽

Lake Fish

Changes in the diet composition of Pygmy Cormorant Phalacrocorax pygmeus on Skadar lake (Southern Montenegro) Diet changes of Pygmy Cormorant Phalacrocorax pygmeus, a piscivorous bird feeding primarily on fish up to 15 cm long, were studied on Skadar Lake. The breeding population on the lake was estimated at over 2,000 pairs in 2005 and 1,260 pairs in 2006, comprising about 5-8% of the regional population of SE Europe & Turkey. The first diet analysis, based on stomach contents of specimens hunted in the course of the breeding season, was carried out in the period 1973-1975 in order to identify the influence of the birds on commercial fishery. Further samples of regurgitated or accidentally dropped food items during the feeding of nestlings were collected and analyzed in the 2006 breeding season. Results from both periods are presented and changes in diet composition in the course of over 30 years are discussed. Between 1973-1975 and 2006, the Pygmy Cormorant's diet on Skadar Lake changed drastically. Only one fish species, Rudd Scardinius knezevici, was found to be common to both study periods. Pygmy Cormorant's diet in the period 1973-1975 consisted of 11 fish species (N = 224 specimens), belonging to five families. The most abundant fish species were Roach Rutilus ohridanus and Albanian Roach Pachychilon pictum. Diet analysis in 2006 revealed only six species (N = 98 specimens) from two families, and also showed that the introduced Goldfish Carassius auratus became a major food source for Pygmy Cormorant, constituting 84.7% of the total specimen number. Age class analysis of Goldfish items revealed that juvenile specimens (45-90 mm) comprised 89.0% of the total Goldfish compound. The study confirms that the Pygmy Cormorant is not a species-specific hunter and suggests it is not affected by the changes in composition of fish community in the littoral zone of the lake. Fish consumption by Pygmy Cormorants on Skadar Lake in 2006 was estimated at 45 t during the most intensive foraging period (June-August).

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Gastric emptying of ingested fat emulsion in rats: implications for studies of fat-induced satiety

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.1996.270.3.r688 ◽

1996 ◽

Vol 270 (3) ◽

pp. R688-R692 ◽

Cited By ~ 3

Author(s):

M. I. Friedman ◽

I. Ramirez ◽

M. G. Tordoff

Keyword(s):

Gastric Emptying ◽

Stomach Contents ◽

Lipid Phase ◽

Phenol Red ◽

Rat Stomach ◽

Fat Emulsion ◽

Time Points ◽

Behavioral Studies ◽

Marked Suppression ◽

Behavior Of Rats

Evidence that ingested fat acts in the intestine to produce satiety stems from studies showing that intraintestinal infusion of fat emulsion inhibits eating behavior of rats. In this study, we determined the appropriateness of infusion parameters used in these behavioral studies by measuring gastric emptying rates of both the aqueous and lipid components of Intralipid ingested normally by rats. Stomach contents were collected at different times 0-40 min after rats ingested Intralipid containing [14C]polyethylene glycol (PEG) and phenol red (PR) and were assayed for PEG, PR, and fat. The proportion of ingested fat remaining in the stomach was significantly greater than the proportion of ingested PEG or PR at all time points examined. Despite initial gastric emptying of fat during ingestion, consumption of Intralipid (0.5 or 1.1 kcal/ml) did not suppress subsequent solid food intake. The results indicate that 1) ingested fat emulsion rapidly partitions in the rat stomach into an aqueous phase, which empties rapidly, and a lipid phase, which empties slowly, and 2) normal ingestion of Intralipid is not immediately satiating. These observations raise questions about the physiological significance of the rapid and marked suppression of feeding behavior produced by intraintestinal infusion of Intralipid.

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Cage culture with tilapia induces alteration in the diet of natural fish populations: the case of Auchenipterus osteomystax

Brazilian Journal of Biology ◽

10.1590/s1519-69842010000500015 ◽

2010 ◽

Vol 70 (4) ◽

pp. 1021-1030 ◽

Cited By ~ 12

Author(s):

L. Strictar-Pereira ◽

AA. Agostinho ◽

LC Gomes

Keyword(s):

Condition Factor ◽

Feeding Activity ◽

Stomach Contents ◽

Sampling Period ◽

Temporal Variations ◽

Nutritional Condition ◽

Diet Analysis ◽

Nutrient Inputs ◽

The Individual ◽

Stomach Weight

Fish rearing in cages installed in reservoirs has developed rapidly in Brazil over the last decade. However, this type of aquaculture induces some changes in the environment because of the high quantity of nutrients released into the surroundings. This study evaluated trophic changes resulting from these nutrient inputs into the diet, feeding activity and nutritional condition of Auchenipterus osteomystax, an insectivore that alternatively feeds on zooplankton. Fish were sampled with gillnets in two tilapia (Oreochromis niloticus) experimental caging aquaculture areas of the Rosana reservoir (Paranapanema River), at different distances from the cages. Samplings were carried out for 90 days (before the cages were installed and 30 and 60 days after installation). Diet analysis was based on 250 stomach contents evaluated with occurrence and volumetric methods, combined into a Feeding Index. The spatial and temporal variations in feeding activity were inferred by the stomach repletion index (stomach weight). The relative condition factor was used to evaluate the individual nutritional condition of the sampled fish. Insects and zooplankton accounted for more than 85% of the diet in any sample. Insects predominated before caging culture started and at the end of the sampling period, whereas zooplankton predominated 30 days after caging began. The repletion index increased at 30 days after caging in both areas when the condition factor was the lowest, with some recovery at the end of this period. The input of nutrients near caging areas caused a short elevation in zooplankton availability, which promoted changes in the diet of this opportunist species, increasing its feeding activity. However, these changes appeared to be unsustainable due to the poor nutritional condition of the individuals.

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Diet analysis of Alaska Arctic snow crabs (Chionoecetes opilio) using stomach contents and δ13C and δ15N stable isotopes

Deep Sea Research Part II Topical Studies in Oceanography ◽

10.1016/j.dsr2.2015.11.009 ◽

2017 ◽

Vol 135 ◽

pp. 124-136 ◽

Cited By ~ 21

Author(s):

Lauren M. Divine ◽

Bodil A. Bluhm ◽

Franz J. Mueter ◽

Katrin Iken

Keyword(s):

Stable Isotopes ◽

Stomach Contents ◽

Diet Analysis ◽

Δ13c And Δ15n ◽

Chionoecetes Opilio ◽

Snow Crabs

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In vivo studies on the digestion of bovine caseins in the rat stomach

Journal of Dairy Research ◽

10.1017/s0022029900021749 ◽

1981 ◽

Vol 48 (2) ◽

pp. 319-326 ◽

Cited By ~ 11

Author(s):

Guy Miranda ◽

Jean-Pierre Pelissier

Keyword(s):

Amino Acid ◽

Skim Milk ◽

Amino Acid Content ◽

Stomach Contents ◽

In Vivo Studies ◽

Total Amino Acid ◽

Rat Stomach ◽

Trichloracetic Acid ◽

Total Amino Acid Content

SummaryThe action of gastric proteinases on bovine caseins was studied in vivo on rats fed skim-milk, or whole casein in water or whole casein in mineral solution, by analysing the gastric content after 30 min digestion. Clotting of the diet in the stomach greatly reduced the rate of gastric emptying. The proteolysis of caseins observed by gel electrophoresis appeared to follow a different pathway for the 3 different diets. The amino acid compositions of the trichloracetic acid sediments of the stomach contents did not differ between the 3 diets. The presence of free amino acids in the stomachs at significant levels (0·8–5 % of the total amino acid content) was observed.

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New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

10.1101/363622 ◽

2018 ◽

Author(s):

Nikki E. Freed ◽

William S. Pearman ◽

Adam N. H. Smith ◽

Georgia Breckell ◽

James Dale ◽

...

Keyword(s):

Stomach Contents ◽

Ground Truth ◽

Diet Analysis ◽

Sampling Location ◽

Metagenomic Sequencing ◽

Genomic Databases ◽

Promising Alternative ◽

Constrained Ordination ◽

Wide Range ◽

Long Read

AbstractBackgroundUsing metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore Technologies (ONT) MinION. Using an amplification-free approach, we profiled the stomach contents from wild-caught rats.ResultsWe conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla that include plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrate the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items, and show that at the family-level, false positive taxon assignments are approximately 97.5% accurate. We also suggest a way to mitigate for database biases in metagenomic approaches. Finally, we implement a constrained ordination analysis and show that we can identify the sampling location of an individual rat within tens of kilometres based on diet content alone.ConclusionsThis work establishes proof-of-principle for long-read metagenomic methods in quantitative diet analysis. We show that diet content can be quantified even with limited expertise, using a simple, amplification free workflow and a relatively inexpensive and accessible next generation sequencing method. Continued increases in the accuracy and throughput of ONT sequencing, along with improved genomic databases, suggests that a metagenomic approach to quantification of animal diets will become an important method in the future.

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Population Characteristics of Yellow Perch in Dead Lake, Florida

Journal of Fish and Wildlife Management ◽

10.3996/082018-jfwm-068 ◽

2019 ◽

Vol 10 (2) ◽

pp. 296-303

Author(s):

Scott M. Bisping ◽

Ted J. Alfermann ◽

Patrick A. Strickland

Keyword(s):

Yellow Perch ◽

Age Groups ◽

Relative Weight ◽

Stomach Contents ◽

High Water ◽

Limited Range ◽

Population Characteristics ◽

Diet Analysis ◽

Thermal Refugia ◽

Total Length

Abstract In Florida, the Yellow Perch Perca flavescens is known to exist only in the Apalachicola River watershed. We conducted a 2-y study (2015–2016) to assess population characteristics of Yellow Perch in Dead Lake, Florida. We also measured summertime (June–September 2016) water temperatures to identify temperature differences between two sections (West Arm Creek and the main pool) of Dead Lake. Using electrofishing, we collected 564 Yellow Perch ranging from 72 to 343 mm total length from West Arm Creek. An age sample showed Yellow Perch ranged in age from 0 to 6 y and strong year classes were produced in 2013 and 2015. High mean total length at age suggests Yellow Perch in Dead Lake are a fast-growing population, likely a result of limited abundance and a long growing season. This study showed low mean relative weight (Wr, 2015: 70; 2016: 67), which is similar to other southeastern populations. Stomach contents and diet analysis showed no differences between age groups, which suggests that Yellow Perch are opportunistic feeders. Dead Lake showed high water temperatures (≥28°C) during the summer months, but the spring-fed Stone Mill Creek may provide thermal refugia that allow fish to avoid stressful temperatures in the main pool of Dead Lake in summer. Limited awareness among anglers, coupled with low abundance and the fish's limited range in the state, likely contributes to the lack of exploitation of Yellow Perch in Florida.

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