Unprecedented Symbiont Eukaryote Diversity Is Governed by Internal Trophic Webs in a Wild Non-Human Primate

Wilcox, Justin; Hollocher, Hope

doi:10.1016/j.protis.2018.03.001

Cited by 11 publications

(8 citation statements)

References 75 publications

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“…First, it eliminates the need to discard most of the sequence data as is the case universal primers are used alone. It is true that sequencing to greater depth can still allow access to eukaryome diversity, but this is inefficient and expensive (Wilcox and Hollocher, ). Second, blocking primers have been successfully used to access the eukaryome, but there is no universal blocking primer that will eliminate all or even most animals, so blocking primers tend to be specific to a particular study (Belda et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…All of them have been applied in free‐living environments but their success differs when used in animal‐associated ones. The main issue is that the sequences recovered from PCR using universal 18S primers are mostly from the host and not its microeukaryotic microbiome (Parfrey et al ., ; Wilmes et al ., ; Wilcox and Hollocher, ), sometimes by many orders of magnitude. One solution to this problem is to use blocking primers in the PCR reaction, which are chemically modified primers (with a C3 spacer) that target the host 18S rRNA and will prevent the extension during the PCR when using universal primers.…”

Section: Introductionmentioning

confidence: 99%

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Validation of a universal set of primers to study animal‐associated microeukaryotic communities

Campo

Pons

Herranz

et al. 2019

Environmental Microbiology

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Summary The application of metabarcoding to study animal‐associated microeukaryotes has been restricted because the universal barcode used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the host. As a result, when host‐associated microbial eukaryotes are analysed by metabarcoding, the reads tend to be dominated by host sequences. We have done an in silico validation against the SILVA 18S rRNA database of a non‐metazoan primer set (primers that are biased against the metazoan 18S rRNA) that recovers only 2.6% of all the metazoan sequences, while recovering most of the other eukaryotes (80.4%). Among metazoans, the non‐metazoan primers are predicted to amplify 74% of Porifera sequences, 4% of Ctenophora, and 15% of Cnidaria, while amplifying almost no sequences within Bilateria. In vivo, these non‐metazoan primers reduce significantly the animal signal from coral and human samples, and when compared against universal primers provide at worst a 2‐fold decrease in the number of metazoan reads and at best a 2800‐fold decrease. This easy, inexpensive, and near‐universal method for the study of animal‐associated microeukaryotes diversity will contribute to a better understanding of the microbiome.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Validation of a universal set of primers to study animal‐associated microeukaryotic communities

Campo

Pons

Herranz

et al. 2019

Environmental Microbiology

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“…However, recent studies using this approach have focused mainly on characterizing a single compartment of biodiversity, including the nemabiome (or more broadly the helminthic community) of terrestrial species [39,107–109]. To our knowledge, this is the one of the first study to attempt to identify, without a priori , all parasitic eukaryotic taxa present on teleost fish species using a universal metabarcoding approach [110]. Even if this approach was initially intended to characterize the bacterial communities of some fish species, it has allowed us to detect parasitic species belonging to different phyla (Table 2) [29,35,41].…”

Section: Discussionmentioning

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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“…In addition, 18S rRNA targeted high-throughput sequencing detected threefold the diversity of parasite species (n = 6) compared to gross adult parasite recovery (n = 2), suggesting that combined molecular and adult parasite recovery represents an important tool for characterising the parasite community of a given host. Comparative studies in other species, including wild rats ( Rattus norvegicus and R. rattus ), found 18S rRNA targeted high-throughput sequencing to be at least as sensitive as traditional count methods ( Hino et al, 2016 ; Tanaka et al, 2014 ), and detects a broad diversity of intestinal eukaryotes in long-tailed macaques ( Macaca fascicularis ) and spotted hyenas ( Crocuta crocuta ) ( Heitlinger et al, 2017 ; Wilcox and Hollocher, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Parasites of an Arctic scavenger; the wolverine (Gulo gulo)

Watson

Hailer

Lecomte

et al. 2020

International Journal for Parasitology: Parasites and Wildlife

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Parasites are fundamental components within all ecosystems, shaping interaction webs, host population dynamics and behaviour. Despite this, baseline data is lacking to understand the parasite ecology of many Arctic species, including the wolverine ( Gulo gulo ), a top Arctic predator and scavenger. Here, we combined traditional count methods (i.e. adult helminth recovery, where taxonomy was confirmed by molecular identification) with 18S rRNA high-throughput sequencing to document the wolverine parasite community. Further, we investigated whether the abundance of parasites detected using traditional methods were associated with host metadata, latitude, and longitude (ranging from the northern limit of the boreal forest to the low Arctic and Arctic tundra in Nunavut, Canada). Adult parasites in intestinal contents were identified as Baylisascaris devosi in 72% (n = 39) of wolverines and Taenia spp. in 22% (n = 12), of which specimens from 2 wolverines were identified as T. twitchelli based on COX1 sequence. 18S rRNA high-throughput sequencing on DNA extracted from faeces detected additional parasites, including a pseudophyllid cestode ( Diplogonoporus spp. or Diphyllobothrium spp.), two metastrongyloid lungworms ( Angiostrongylus spp. or Aelurostrongylus spp., and Crenosoma spp.), an ascarid nematode ( Ascaris spp. or Toxocara spp.), a Trichinella spp. nematode, and the protozoan Sarcocystis spp., though each at a prevalence less than 13% (n = 7). The abundance of B. devosi significantly decreased with latitude (slope = -0.68; R 2 = 0.17; P = 0.004), suggesting a northerly limit in distribution. We describe B. devosi and T. twitchelli in Canadian wolverines for the first time since 1978, and extend the recorded geographic distribution of these parasites ca 2000 km to the East and into the tundra ecosystem. Our findings illustrate the value of molecular methods in support of traditional methods, encouraging additional work to improve the advancement of molecular screening for parasites.

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Unprecedented Symbiont Eukaryote Diversity Is Governed by Internal Trophic Webs in a Wild Non-Human Primate

Cited by 11 publications

References 75 publications

Validation of a universal set of primers to study animal‐associated microeukaryotic communities

Validation of a universal set of primers to study animal‐associated microeukaryotic communities

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

Parasites of an Arctic scavenger; the wolverine (Gulo gulo)

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