DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates

Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing

Consisting of diverse groups of organisms, parasites are among the least studied pathogens despite their enormous impacts on humans, livestock, and wildlife. In particular, little is known about their host specificity and diversity in wildlife. Here, using multiple primer pairs and sequencing 18S rRNA genes of diverse groups of parasites, we aimed to investigate fecal parasitomes of carnivorous wildlife in Korea, namely, the raccoon dog (Nyctereutes procyonoides), the leopard cat (Prionailurus bengalensis), and the Eurasian otter (Lutra lutra). A total of 5 host-specific parasite species were identified, including 2 from raccoon dogs, 2 from leopard cats, and 1 from Eurasian otters. In addition, numerous parasite species of their prey animals were detected in their feces. It was found that the parasitome composition varied between host animals, and it was thought that the difference was attributed to the difference in prey animals, as numerous small mammal parasites were detected from feces of leopard cats inhabiting inland areas and fish parasites from feces of Eurasian otters and raccoon dogs inhabiting waterside areas. Furthermore, 5 zoonotic parasites known to infect humans were identified at the species level. Wildlife-associated zoonoses are expected to increase as the proximity between humans and wildlife increases due to urbanization. Vigilance may be necessary, such as by monitoring parasites in wildlife feces, as was done in this study.

Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains

Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.

Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities

The Eurasian otter Lutra lutra is a generalist carnivore that is widely distributed in many aquatic ecosystems. Based on its inherent attributes of opportunistic foraging behaviour and broad dietary range, it is naturally considered a potential sampler of the diversity of aquatic vertebrates. To test the ability and efficiency of otters as a diversity sampler, we used DNA metabarcoding to investigate the composition in vertebrates of the diet of otters that inhabit a forest stream area in northeast China. Twenty vertebrate prey taxa were detected in 98 otter spraints. Otter diet mainly comprised aquatic fishes (59.4%) and amphibians (39.0%). We also used traditional approaches to investigate fish communities at 60 sampling sites in the same area to determine the relationship between fish population composition in the environment and otter diet. The comparison revealed that 28 species of fish were distributed in this area, of which five are simultaneously detected in otter spraints. This indicates that molecular analysis of the diet of otters is not an ideal approach for investigating fish diversity, at least when using the 12SV5 primer pair. Based on a review of the available molecular research on otter diet, we conclude that the low species resolution may be due to the presence of many closely-related prey species in native habitats and lack of suitable barcodes. Considering the remarkable power of diet metabarcoding analysis in capturing elusive and rare species, it represents an approach that can compensate for the defects associated with fishing methods and we suggest that it can be used as an auxiliary means of measuring traditional fish diversity.

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea

The leopard cat (Prionailurus bengalensis), an endangered species in South Korea, is a small feline widely distributed in Asia. Here, we investigated the diet of leopard cats in the inland areas of Korea by examining their fecal contents using vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing. Shotgun metagenomic sequencing revealed that the feces were rich in DNA not only of vertebrates but also of arthropods and plants, but care should be taken when using shotgun metagenomic sequencing to identify vertebrates at low taxonomic levels (e.g., genus level), as it was often erroneous. Meanwhile, vertebrate mitochondrial 12S rRNA gene sequencing was found to be accurate in the genus-level identification, as the genera identified were consistent with the Korean fauna. We found that small mammals such as murids were their main prey. By using these two sequencing methods in combination, this study demonstrated that accurate information about the overall dietary content and vertebrate prey of leopard cats could be obtained. We expect that the continued community efforts to expand the genome database of wildlife, including vertebrates, will alleviate the problem of erroneous identification of prey at low taxonomic levels by shotgun metagenomic sequencing in the near future.

Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison

The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.

Using DNA metabarcoding and a novel canid-specific blocking oligonucleotide to investigate the composition of animal diets of raccoon dogs (Nyctereutes procyonoides) inhabiting the waterside area in Korea

The raccoon dog (Nyctereutes procyonoides) is known to be an opportunistic generalist who feeds on a wide variety of foods. Historically, their diet has been investigated by morphological observation of undigested remains in feces, requiring specialized knowledge such as osteology, zoology, and phytology. Here, we used DNA metabarcoding of vertebrate 12S rRNA gene and invertebrate 16S rRNA gene to investigate their fecal contents. Additionally, we developed a blocking oligonucleotide that specifically inhibits the amplification of the canid 12S rRNA gene. We confirmed that the blocking oligonucleotide selectively inhibit the amplification of raccoon dog’s DNA without significantly changing the composition of the preys’ DNA. We found that the main foods of raccoon dogs in our study area, the waterside of paddy fields in Korea, were fishes such as Cyprinidae and insects such as mole crickets, which makes sense given the Korean fauna and their well-known opportunistic feeding behaviors. As a method to conveniently and objectively investigate feeding habits of raccoon dogs, this study provided baseline information on DNA metabarcoding. By using DNA metabarcoding, it is expected that the diet habits and ecology of raccoon dogs will be better understood by future research.

Assessing the Diet of a Predator Using a DNA Metabarcoding Approach

The diet of top predators is vital information needed to determine their ecological function and for their conservation management. However, the elusive habit and low population density of many predators constrains determination of their diets. While the morphological identification of scat contents is the traditional method, DNA metabarcoding has lately proven a more efficient and accurate method of identifying prey taxa. We applied DNA metabarcoding to analyzing the diet of the Eurasian otter (Lutra lutra), a top predator in freshwater ecosystems, using 12S and 16S rRNA mitochondrial primers target vertebrate prey. Diet did not vary among different data removal thresholds of 0.1, 1, 3, and 5%, comprising fishes (>90%), amphibians and birds (>2%), and occasionally mammals (<2%). Both 12S and 16S primers revealed similar otter diets, indicating that a single set of primers with a higher threshold is cost-effective for detecting the main prey taxa. Using 12S primers and a 5% threshold, we found no seasonal variation of otter diet in the Tangjiahe National Nature Reserve. A different prey community was found outside the reserve, which resulted in different prey composition for otters. However, prey taxon richness was not different between otters in- and outside the reserve. Otters preferred Schizothorax spp., the largest-sized fish species in the reserve, whereas they mainly preyed on Triplophysa bleekeri, a small-sized fish species, outside the reserve. Otters’ flexible feeding strategy reflect their high adaptability. However, greater human disturbance outside the reserve may present significant challenges to otters by altering prey communities and reducing prey profitability. Combining fecal DNA metabarcoding and local fish survey will provide opportunities for more detailed studies on the impact of different levels of human disturbances on prey communities and otters.

The host-specific resistome in environmental feces of Eurasian otters (Lutra lutra) and leopard cats (Prionailurus bengalensis) revealed by metagenomic sequencing

Investigation of feces of wildlife, which is considered as reservoirs, melting pots, vectors and secondary sources of antimicrobial resistance genes (ARGs), provides insights into the risks and ecology of ARGs in the environment. Here, we investigated microbiomes, virulence factor genes (VFGs) of bacterial pathogens, and resistomes in environmental feces of Eurasian otters (Lutra lutra) and leopard cats (Prionailurus bengalensis) using shotgun metagenome sequencing. As expected, the taxonomic compositions of bacteria were significantly different between the animals. Importantly, we found that the compositions of ARGs were also significantly different between the animals. We detected ARGs including iri, tetA(P), tetB(P), floR, sulII, strA, strB, tetW and tetY. Some of them were significantly more abundant in either of the host animals, such as strA, strB and tetY in Eurasian otters, and tetA(P), tetW and iri in leopard cats. We also found that some ARGs were selectively correlated to particular VFGs-related bacteria, such as tetA(P) and tetB(P) to Clostridium, and iri to Mycobacterium. We also found that there were positive correlations between Acinetobacter and ARGs of multiple antimicrobial classes. The host-specific resistomes and VFGs-related bacteria may be due to differences in the host's gut microbiome, diet and/or habitat, but further investigation is needed. Overall, this study provided important baseline information about the resistomes of the wildlife in Korea, which may help the conservation of these endangered species and assessment of human health risks posed by ARGs and bacterial pathogens from wildlife.

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Fecal ARGs and VFGs were investigated in wild Eurasian otters and leopard cats.

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The ARGs and VFGs were widespread in both the host animals.

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Certain ARGs and VFGs were differentially more abundant in either of the hosts.

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Multiple ARGs showed positive correlations with Acinetobacter VFGs.

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Consistent monitoring of ARGs in wildlife is needed from a One Health perspective.

Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

A barcoding-based scat-analysis assessment of Eurasian otter Lutra lutra diet on Kinmen Island

While it is well known that Eurasian otters principally feed on fishes and crustaceans, their detailed diet taxonomies are not fully understood. This is partly due to their nocturnal behavior and the limited resolving power of traditional morphological identification from scat. A suitable, reliable molecular method for diet studies is therefore needed.I performed a series of Sanger-sequencing reactions, utilizing nine primer sets for Eurasian otter diet research. These are mainly based on the barcoding concept to determine the taxonomic composition of spraints. The primer sets target different types of animals, amplifying each separately. This procedure was used to detect the prey contents of 64 spraint samples collected from Kinmen Island. Through high-resolution gel electrophoresis and sequencing, it was evident that PCR products could be successfully amplified by the different primer sets and from spraint samples comprising multiple prey species.Extracted DNA from all spraint samples was PCR-amplified with 9 primer sets. In total, 16 prey types were identified across all 64 samples. Fourteen were identified at the species level.The aim of this study was to develop and apply a novel diet research method to Eurasian otters. Eight of the primers are universal primers designed for COI segments of different animal groups, and one primer set was designed specifically for tilapia groups. This method can be applied to study the diets of not only Kinmen Eurasian otter populations, but also other Eurasian otter populations and other small carnivorous animals.

DNA-based detection of Leptospira wolffii, Giardia intestinalis and Toxoplasma gondii in environmental feces of wild animals in Korea

Leptospira, Giardia intestinalis and Toxoplasma gondii infections are reported in humans and animals worldwide, but molecular surveillance of these pathogens in Korean wildlife is still limited. Here, we examined the prevalence of these pathogens in environmental feces of Eurasian otters, leopard cats and raccoon dogs using nested PCR followed by DNA sequencing. G. intestinalis was detected in all of three animals, while T. gondii was detected only in leopard cats. Leptospira wolffii was detected in raccoon dog and Eurasian otter. Our results suggest that these animals can act as a reservoir of these zoonotic pathogens. Consistent monitoring of these pathogens in wildlife is needed to prevent from their infections in humans and livestock in Korea.

Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

Understanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach

Background

The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities.

Methods

DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians).

Results

Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior.