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Table 1 Examples of metabarcoding and metagenomics approaches for the detection of helminth species in faecal samples or cultures

From: Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics

Methodology

Phylum

Nucleic acid of choice

Host

Platform

Matrix

Gene/marker or reference loci

References

NA

Nematoda

DNA

NA

NA

In silico

12S, 16S, ITS-2

[110]

Metabarcoding

Nematoda

DNA

Rat

MiSeq Illumina

Faeces

18S (V4-V5, V7-V8, V9)

[86]

Metabarcoding

Nematoda

DNA

Rat

MiSeq Illumina

Faeces

28S (D3-D4, D4-D5, D3-D5, D4-D6)

[86]

Metabarcoding

Platyhelminthes

DNA

Rat

MiSeq Illumina

Faeces

18S (V4-V5, V7-V8, V9)

[86]

Metabarcoding

Platyhelminthes

DNA

Rat

MiSeq Illumina

Faeces

28S (D3-D4, D4-D5, D3-D5, D4-D6)

[86]

Metabarcoding

Platyhelminthes

DNA

Various

NA

Environmental

18S (V4, V7,V8-V9, V9)

[87]

Metabarcoding

Nematoda

DNA

Rat

MiSeq Illumina

Worms

18S

[88]

Metabarcoding

Cestoda

DNA

Rat

MiSeq Illumina

Worms

18S

[88]

Metabarcoding

Nematoda

DNA

Cattle

MiSeq Illumina

Larvae/faeces

ITS-2

[97]

Metabarcoding

Nematoda

DNA

Sheep

MiSeq Illumina

Larvae

ITS-2

[98]

Metabarcoding

Nematoda

DNA

Cattle

MiSeq Illumina

Larvae

ITS-2

[99]

Metabarcoding

Nematoda

DNA

Sheep

MiSeq Illumina

Eggs and larvae

ITS-2

[100]

Metabarcoding

Nematoda

DNA

Rufus mouse lemur

454 Roche

Larvae

18S

[107]

Metabarcoding

Nematoda

DNA

Wild reindeer

MiSeq Illumina

Larvae

ITS-2

[111]

Metabarcoding

Nematoda

DNA

Sheep

MiSeq Illumina

Larvae

ITS-2; see also [97]

[116]

Metabarcoding

Nematoda

DNA

Roe deer

MiSeq Illumina

Larvae

ITS-2; see also [97]

[113]

Metabarcoding

Nematoda

DNA

Wild ruminants

MiSeq Illumina

Larvae

ITS-2; see also [97]

[112]

Metabarcoding

Nematoda

DNA

Bison

MiSeq Illumina

Larvae

ITS-2; see also [97]

[108]

Metabarcoding

Nematoda

DNA

Horse

MiSeq Illumina

Larvae

ITS-2; see also [97]

[109]

Metabarcoding

Nematoda

DNA

Gorillas, Mangabey

MiSeq Illumina

Larvae

ITS-2

[114]

Metagenomics

Nematoda

DNA

Primate

Hiseq Illumina

Faeces

18S, COI

[105]

Metagenomics

Nematoda, Platyhelminthes

DNA

Human

MiSeq Illumina

Faeces

Unavailable

[106]

  1. ITS-2 Second internal transcribed spacer, NA not applicable