Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin

2020 ◽  
Vol 47 (6) ◽  
pp. 509
Author(s):  
Melanie J. Young ◽  
Ludovic Dutoit ◽  
Fiona Robertson ◽  
Yolanda van Heezik ◽  
Philip J. Seddon ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Diet Composition ◽  
Pcr Primers ◽  
Fish Prey ◽  
Genus Level ◽  
Faecal Samples ◽  
Significant Difference ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
Diet Assessment

Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.

scholarly journals DNA metabarcoding quantifies relative abundances of arthropod taxa in songbird diets: validation with camera-recorded diets

2021 ◽  
Author(s):  
Yvonne Verkuil ◽  
Marion Nicolaus ◽  
Richard Ubels ◽  
Maurine Dietz ◽  
Jelmer Samplonius ◽  
...  
Keyword(s):  
Diet Composition ◽  
Arthropod Community ◽  
Cytochrome Oxidase Subunit ◽  
Free Living ◽  
Faecal Samples ◽  
Dna Metabarcoding ◽  
Lower Intestine ◽  
Quantitative Analyses ◽  
Ecological Applications ◽  
Relative Abundances

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of faecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free-living animals. This study validates that DNA metabarcoding of faeces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify relative abundances of dietary taxa. Validation was done with the hole-nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size-adjusted counts of food items delivered to nestlings were used to approximate provided biomass of prey orders and families and subsequently nestling faeces were assessed through DNA metabarcoding. To explore potential effects of digestion, stomach and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera-recorded taxa. Overall, and in each replicate year (N = 3), the relative abundances of size-adjusted prey counts and COI read numbers correlated at R=0.85 (CI:0.68-0.94) at order level and at R=0.75 (CI:0.67-0.82) at family level. Similarity in arthropod community composition between stomach and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.

Periphyton diversity in two different Antarctic lakes assessed using metabarcoding

2021 ◽  
pp. 1-9
Author(s):  
Paulo E.A.S. Câmara ◽  
Láuren M.D. De Souza ◽  
Otávio Henrique Bezerra Pinto ◽  
Peter Convey ◽  
Eduardo T. Amorim ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
South Shetland Islands ◽  
King George Island ◽  
Deception Island ◽  
Maritime Antarctic ◽  
Shetland Islands ◽  
Antarctic Lakes ◽  
Significant Difference

Abstract Antarctic lakes have generally simple periphyton communities when compared with those of lower latitudes. To date, assessment of microbial diversity in Antarctica has relied heavily on traditional direct observation and cultivation methods. In this study, sterilized cotton baits were left submerged for two years in two lakes on King George Island and Deception Island, South Shetland Islands (Maritime Antarctic), followed by assessment of diversity by metabarcoding using high-throughput sequencing. DNA sequences of 44 taxa belonging to four kingdoms and seven phyla were found. Thirty-six taxa were detected in Hennequin Lake on King George Island and 20 taxa were detected in Soto Lake on Deception Island. However, no significant difference in species composition was detected between the two assemblages (Shannon index). Our data suggest that metabarcoding provides a suitable method for the assessment of periphyton biodiversity in oligotrophic Antarctic lakes.

Seasonal and between-year variations in the diet of harbour seals in the Moray Firth, Scotland

1996 ◽  
Vol 74 (6) ◽  
pp. 1110-1121 ◽  
Author(s):  
D. J. Tollit ◽  
P. M. Thompson
Keyword(s):  
Diet Composition ◽  
Gadus Morhua ◽  
Prey Species ◽  
Temporal Variations ◽  
Short Term ◽  
Harbour Seals ◽  
Faecal Samples ◽  
Poor Indicator ◽  
Moray Firth ◽  
Merlangius Merlangus

Predictions concerning the effect of seals upon prey stocks require an understanding of temporal variations in diet composition. This study examined the extent of between-year and seasonal variations in the diet of harbour seals (Phoca vitulina) from the Moray Firth, Scotland, between 1989 and 1992. Analyses of fish otoliths and cephalopod beaks collected from 1129 faecal samples were used to derive estimates of the contribution made by each of 35 prey species, based on the number and mass consumed. The key prey, by mass, were sand eels (Ammodytidae) (47%), lesser octopus (Eledone cirrhosa) (27%), whiting (Merlangius merlangus) (6%), flounder (Platichthys flesus) (5%), and cod (Gadus morhua) (4%). Between-year and seasonal fluctuations in the contributions of these species were observed. Sand eels contributed 86–20% in summer and 91–49% in winter. Lesser octopus contributed 0–62% in summer and < 5% in winter, whilst whiting and cod contributed 2–34% in winter and 1–4% in summer. In contrast to 1988, clupeids were unimportant in winter. Differences in diet composition appeared to reflect local changes in the availability of food, especially overwintering clupeids. Results indicate that dietary information obtained from short-term studies can be a poor indicator of subsequent diet composition and should be treated with caution when used to predict the effect of seals on prey populations.

scholarly journals Parasitology and urban livestock farming in Nigeria : prevalence of ova in faecal and soil samples and animal ectoparasites in Makurdi

2007 ◽  
Vol 78 (1) ◽  
Author(s):  
E.A. Omudu ◽  
E.U. Amuta
Keyword(s):  
Test Tube ◽  
Soil Samples ◽  
Helminth Parasites ◽  
Livestock Farming ◽  
Chi Square ◽  
Zoonotic Infections ◽  
Faecal Samples ◽  
Significant Difference ◽  
Flotation Technique ◽  
Chi Square Analysis

Domestic environmental pollution resulting from urban livestock farming was investigated in Makurdi using parasitological techniques. The test tube flotation technique was used for the parasitological analysis of animal faecal matter and soil samples collected from residential premises. Ectoparasitic fauna of dogs, goats, sheep and cattle cohabiting with humans within the same residential compound were also collected and identified. The hand-picking and body brushing methods were employed to search for ticks, fleas, lice and mites. Of the 150 soil samples examined, 55 (36.7 %) were positive for 1 or more eggs of helminth parasites. There was no significant difference in the distribution of eggs in the soil samples from the 3 areas sampled (c2=0.046, df=2, P>0.05). Ascaris species were the dominant parasite eggs found. Of the 180 faecal samples examined, 107 (59.4 %) were positive for 1 or more eggs of helminth parasites. Chi-square analysis showed no significant difference in the level of infection of different animal faeces sampled (c2=5.74, df=4, P>0.05). Ascaris species were again the dominating helminth parasite eggs found. There was also no significant difference in the prevalence of helminth eggs in the animal faecal samples from the 3 areas sampled (c2=5.99, df=4, P>0.05). A total of 1908 ectoparasites was recovered (ticks: 32.80 %; lice: 22.43 %; fleas: 22.06% and mite: 22.69 %). There was no significant difference in infestation animals between sexes (c2=0.10, df=4, P>0.05). The predominant genus encountered for ticks were Amblyomma, while Linognathus (43.90%), Ctenocephalides (97.38%) and Sarcoptes (58.89 %) were most predominant for lice, fleas and mites respectively. The public health implications of the findings, especially as these relate to the increasing incidence and prevalence of zoonotic infections, are discussed.

scholarly journals FEEDING HABITS AND HELMINTH PARASITES OF SARDINE (S. PILCHARDUS) AND ANCHOVY (E. ENCRASICOLUS) IN THE ADRIATIC SEA

2015 ◽  
Vol 17 (1) ◽  
pp. 216 ◽  
Author(s):  
B. ZORICA ◽  
V. ČIKES KEČ ◽  
O. VIDJAK ◽  
I. MLADINEO ◽  
D. EZGETA BALIČ
Keyword(s):  
Diet Composition ◽  
Feeding Habits ◽  
Stomach Contents ◽  
Stomach Content Analysis ◽  
Helminth Parasites ◽  
Significant Difference ◽  
Prey Composition ◽  
One Year ◽  
Paratenic Hosts ◽  
Hysterothylacium Aduncum

We examined the stomach contents of two of the most economically and ecologically important small pelagic fish species, the sardine, Sardina pilchardus and the anchovy, Engraulis encrasicolus, obtained monthly from commercial purse-seine catches operating on Croatian fishing grounds during a one-year period (January–December, 2011). Both species generally showed a similar diet, with copepod and decapod larvae as dominant prey groups. The composition of anchovy and sardine stomach contents was not size- or sex-related, but throughout the year, a significant difference in diet composition was observed for each species as well as between species. Two gastrointerstinal helminths; the digenean Parahemiurus merus and nematode Hysterothylacium aduncum, were recorded during the stomach content analysis. Differences in population dynamics between the two parasites are congruent with differences in the prey composition of sardine and anchovy, reflecting fine-tuned interactions in the trophic web between parasites and intermediate or paratenic hosts included in the sardine and anchovy diet.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals VP1 DNA sequences of JC and BK viruses detected in urine of systemic lupus erythematosus patients reveal no differences from strains expressed in normal individuals

2000 ◽  
Vol 81 (11) ◽  
pp. 2625-2633 ◽  
Author(s):  
Signy Bendiksen ◽  
Ole Petter Rekvig ◽  
Marijke Van Ghelue ◽  
Ugo Moens
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Pregnant Women ◽  
Dna Sequences ◽  
Lupus Erythematosus ◽  
Urine Samples ◽  
Virus Reactivation ◽  
Systemic Lupus ◽  
Significant Difference ◽  
Multiple Sclerosis Patients ◽  
Urine Specimens

The ubiquitous human polyomaviruses BK (BKV) and JC (JCV) persist with no adverse effects in immunocompetent individuals. Virus-induced pathogenesis has been linked to virus reactivation during impaired immune conditions. Previous studies have shown a significant difference between the VP1 DNA sequences of JCV obtained from control urine samples and those in progressive multifocal leukoencephalopathy brain samples. This difference could not be detected when comparing normal control urinary JCV DNA with DNA sequences from chronic progressive multiple sclerosis patients. Since BKV and JCV are readily activated in systemic lupus erythematosus (SLE) patients, the presence of specific strains, related to VP1 DNA sequences, was investigated in these patients. VP1 DNA sequences in 100 urine samples from 21 SLE patients and 75 urine samples from 75 healthy pregnant women were analysed and compared to previously reported sequences. The results show that the VP1 sequence profiles of JCV and BKV excreted by SLE patients do not differ significantly from those excreted by immunocompetent individuals. The European JCV subtypes 1A or 1B were represented among all JCV-positive urine specimens, while BKV VP1 sequences showed complete, or almost complete, identity with the MM or JL strains. Different urine samples from the same patient collected over a 1 year period were predominantly stable. BKV VP1 DNA in urine specimens from healthy pregnant women was only detected during the third trimester of their pregnancy. These results argue against SLE-specific JCV and BKV strains and suggest reactivation of the viruses rather than recurrent re-infections of patients with SLE.

scholarly journals New PCR Primer Pairs Specific for Cryptococcus neoformans Serotype A or B Prepared on the Basis of Random Amplified Polymorphic DNA Fingerprint Pattern Analyses

1999 ◽  
Vol 37 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Francisco Hideo Aoki ◽  
Tamae Imai ◽  
Reiko Tanaka ◽  
Yuzuru Mikami ◽  
Hideaki Taguchi ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Serotype A ◽  
Specific Pcr ◽  
Fingerprint Pattern ◽  
Serotype B ◽  
Pcr Primer

Thirty-three strains of Cryptococcus neoformans were isolated from clinical specimens, including specimens from AIDS patients in Brazil, and were classified into two serotypes; we detected 31 and 2 strains of serotypes A and B, respectively. Random amplified polymorphic DNA (RAPD) fingerprint pattern analyses of these strains of serotypes A and B showed that the patterns were similar for strains of each serotype when three 10-mer primers were used as the RAPD primers. Comparative studies of the fingerprint patterns of the study isolates with those of the reference strains also showed that the RAPD patterns for strains of each serotype were related and that most of the fingerprint bands existed commonly for all strains of each serotype tested. The common RAPD bands (an approximately 700-bp band for serotype A and an approximately 450-bp band for serotype B) were extracted and the DNA sequences were determined. Using this information, we prepared two and one PCR primer pairs which were expected to be specific for C. neoformans serotypes A and B, respectively. Use of each PCR primer combination thus prepared for serotype A or B was 100% successful in identifying the respectiveC. neoformans serotypes, including the 33 clinical isolates tested in the present study. Among these combinations, one for serotype A was found to amplify DNA from C. neoformans serotype B as well as serotype A. Serotype B-specific PCR primer pairs amplified DNA from not only serotype B strains but also from serotype C strains. The usefulness of other serotype-specific PCR primers for clinical C. neoformans isolates is discussed.

scholarly journals Diet Composition and Seasonal Fluctuations in the Feeding Habit of Snow Barbel (Schizothorax plagiostomus) in River Indus, Pakistan

2018 ◽  
Vol 46 (1) ◽  
pp. 8
Author(s):  
Muhammad Qayash Khan ◽  
Muhammad Zubair Anjum ◽  
Shamim Akhter ◽  
Irfan Khattak ◽  
Abid Ali
Keyword(s):  
Diet Composition ◽  
Feeding Activity ◽  
Fish Fauna ◽  
Feeding Habit ◽  
Gut Contents ◽  
Catch Per Unit Effort ◽  
Food Items ◽  
Unit Effort ◽  
Significant Difference ◽  
River Indus

Background:Schizothorax plagiostomus is widely distributed in river Indus and is most important food fish in Pakistan. The feeding habit of fish is directly related to the size of fish, its metabolic rate and environmental temperature. The accurate description of fish diet and feeding habit is a very important aspect in fisheries management for the purpose of species conservation, breeding and culture. The present work was aimed to investigate the specie abundance, the diet composition and seasonal variations in the feeding habit of Snow barbell Schizothorax plagiostomus.Materials, Methods & Results: A total of 1799 fish specimens were caught at the confluence of six tributaries along river Indus at Indus Kohistan, northeastern Pakistan. The fish were collected by 5-panels of gill net during first week of each month. The site specific Catch Per Unit Effort (CPUE) and season specific CPUE of fish fauna were assessed. For the gut content analysis 240 samples (99 male and 141 females) of S. plagiostomus were selected on monthly basis. Frequency of occurrence method and volumetric method were applied to record the different food items in the gut of S. plagiostomus. The physico-chemical parameters, NO3 concentration and dissolved Co2 of water from different localities of river Indus were recorded month wise by Hach sensION 156 meter, Horiba LAQUA Nitrate Meter and EA80 meter respectively. Significant difference was observed in water temperature during the four seasons. Except alkalinity no other water parameter showed significant variation across different localities. The results showed that highest Mean CPUE was observed for Darel Stream (0.55) and lowest for Jalkot stream (0.26). Peak abundance of fish was recorded in the month of November with a mean catch of 44.50, mean CPUE of 0.74 and mean Kruskal-Wallis rank value of 63.25. Spirogyra and Ulothrix occurred as maximum food items in the gut of S. plagiostomus during summer while their minimum amount occurred during autumn. According to the ranking index spirogyra and ulothrix ranked higher with significant difference in comparison to other food items. The results showed that S. plagiostomus is phytophagous in its feeding habit, which consumed mainly algae attached to stones and pebbles during the whole year. However, the presence of some secondary items such as animal matter, detritus, sand and mud might be due to the distinct availabilities of food along the seasons. The highest feeding activity of S. plagiostomus was recorded during summer while the lowest one occurred during autumn, spring and winter. Discussion: Catch per unit effort (CPUE) is an indirect measure of the abundance of a target species. It is used as an index of stock abundance in fisheries and conservation biology. During the study low fish fauna was found in River Indus as reported previously. Majority of the fish occurred in snow fed river tributaries in the study area as these tributaries are comparatively less turbulent. Previous studies have also recorded that Schizothoracine generally prefer clean waters. The present findings of gut contents analysis showed clearly that S. plagiostomus is a phytophagous fish which scrap and consumed spirogyra and ulothrix attached to stones and pebbles. Earlier it was reported that mouth of S. plagiostomusis is inferior, wide, with deep lower jaw having keratinized cutting edge and the lower lip is folded and expanded with numerous papillae making it best suited for scrapping algae attached to stones and pebbles. The highest feeding activity was observed during warmer months as compared to cold months. S. plagiostomus spawn twice in a year in autumn and in spring. The highest feeding activity of S. plagiostomus seems to be link with a reflex of recovery strategy due to physiological process of gonadal development.

scholarly journals PIMBA: a PIpeline for MetaBarcoding Analysis

2021 ◽  
Author(s):  
Renato R. M. Oliveira ◽  
Raissa L S Silva ◽  
Gisele L. Nunes ◽  
Guilherme Oliveira
Keyword(s):  
Environmental Samples ◽  
Next Generation Sequencing Data ◽  
Ecological Studies ◽  
Sequencing Data ◽  
Monitoring Method ◽  
Computational Tools ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
User Friendly ◽  
Generation Sequencing

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, and mBRAVE have been widely used in ecological studies. However, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the softwares mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines.

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