Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals

Aivelo, Tuomas; Medlar, Alan

doi:10.1017/s0031182017000610

Cited by 36 publications

(35 citation statements)

References 116 publications

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“…Identification of individual strongylid species/haplotypes occurring in these communities in noninvasively collected faecal samples using traditional molecular methods (e.g., single nematode amplification and sequencing) is almost impossible (Avramenko et al, ; Lichtenfels et al, ; Pafčo et al, ; Roeber, Jex, & Gasser, ). On the contrary, high‐throughput sequencing (HTS) provides a powerful tool for such analyses (Aivelo & Medlar, ; Avramenko et al, ; Lott, Hose, & Power, ; Tanaka et al, ). Recently, we applied a HTS approach relying on ITS‐2 metabarcoding on a two NHP host‐model system, and showed sufficient sensitivity for strain‐level profiling of strongylid nematodes and sufficient robustness against false positives (Pafčo et al, ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms?

et al. 2019

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The close phylogenetic relationship between humans and nonhuman primates (NHPs) can result in a high potential for pathogen exchange. In recent decades, NHP and human interactions have become more frequent due to increasing habitat encroachment and ecotourism. Strongylid communities, which include members of several genera, are typically found in NHPs. Using optimized high‐throughput sequencing for strain‐level identification of primate strongylids, we studied the structure of strongylid communities in NHPs and humans co‐habiting a tropical forest ecosystem in the Central African Republic. General taxonomic assignment of 85 ITS‐2 haplotypes indicated that the studied primates harbour at least nine genera of strongylid nematodes, with Oesophagostomum and Necator being the most prevalent. We detected both host‐specific and shared strongylid haplotypes. Skin‐penetrating Necator gorillaehaplotypes were shared between humans and gorillas but Necator americanus were much more restricted to humans. Strongylid communities of local hunter‐gatherers employed as trackers were more similar to those of gorillas compared to their relatives, who spent more time in villages. This was due to lower abundance of human‐origin N. americanus in both gorillas and trackers. Habituated gorillas or those under habituation did not show larger overlap of strongylids with humans compared to unhabituated. We concluded that the occurrence of the human‐specific strongylids in gorillas does not increase with direct contact between gorillas and humans due to the habituation. Overall, our results indicate that the degree of habitat sharing between hosts, together with mode of parasite transmission, are important factors for parasite spillover among primates.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms?

et al. 2019

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“…This technique has already revolutionized our understanding of microbial diversity [31–33] and its use is booming in the field of eukaryotic diversity [12–13,34–35]. Metabarcoding allows a more in-depth investigation of entire parasite communities [36–39], including all life stages. Tanaka et al .…”

Section: Introductionmentioning

confidence: 99%

Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach

et al. 2019

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Next‐generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.

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“…and other intestinal helminth parasites. Furthermore, the development of more robust molecular methods, such as metabarcoding, promises to benefit the assessment of parasite communities in the years to come ( Aivelo and Medlar, 2017 ; Avramenko et al, 2015 ; Tanaka et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

Lurking in the dark: Cryptic Strongyloides in a Bornean slow loris

Frías

Stark

Lynn

et al. 2018

International Journal for Parasitology: Parasites and Wildlife

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Within host communities, related species are more likely to share common parasitic agents, and as a result, morphological similarities have led researchers to conclude that parasites infecting closely related hosts within a community represent a single species. However, genetic diversity within parasite genera and host range remain poorly investigated in most systems. Strongyloides is a genus of soil-transmitted nematode that has been reported from several primate species in Africa and Asia, and has been estimated to infect hundreds of millions of people worldwide, although no precise estimates are available. Here we describe a case of infection with a cryptic species of Strongyloides in a Bornean (Philippine) slow loris (Nycticebus menagensis) living within a diverse community of several primate species in the Lower Kinabatangan Wildlife Sanctuary, Malaysian Borneo. Fresh fecal samples were collected from five primate species and nematode larvae cultured from these samples were selected for phylogenetic analyses. Sequences obtained for most larvae were identified as S. fuelleborni, grouping into three different clusters and showing no aggregation within specific hosts or geographic location. In contrast, a set of parasite sequences obtained from a slow loris clustered closely with S. stercoralis into a different group, being genetically distinct to sequences reported from other primate hosts, humans included. Our results suggest that although S. fuelleborni infects all haplorrhines sampled in this primate community, a different species might be infecting the slow loris, the only strepsirrhine in Borneo and one of the least studied primates in the region. Although more data are needed to support this conclusion, we propose that Strongyloides species in primates might be more diverse than previously thought, with potential implications for ecological and evolutionary host-parasite associations, as well as epidemiological dynamics.

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Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals

Cited by 36 publications

References 116 publications

Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms?

Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms?

Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach

Lurking in the dark: Cryptic Strongyloides in a Bornean slow loris

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