. 2018 Dec 4;19(1):47–76. doi: 10.1111/1755-0998.12959

Table 1.

Examples of high‐throughput identification studies that focus on or include pathogens or pests

NGS technology	Sampling area, country	Sampled host species and substrate	Targeted taxa	Target DNA marker	Primers	Main results	Reference
Studies targeting pathogens
Sanger: MetT	Global	Homo sapiens: faeces	RNA viruses	All	None	Plant viruses prevail; humans may act as vectors	Zhang et al. (2005)
454: MetB	Pakistan	Orthoptera, Gastropoda: faeces	Plants	trnL (mini)	g + h	Different plant species prevail in diet of animal pests	Valentini et al. (2009)
454: MetT	Poland + Lithuania	Lycoperiscon esculentum: leaves	RNA viruses	All	None	Several previously unrecognized viruses detected	Adams et al. (2009)
Illumina: MetT	Peru	Manihot esculenta: leaves	SPFMV, SPCSV viruses	siRNA	None	Sequence of whole genomes using siRNA method	Kreuze et al. (2009)
454: MetT	CA, USA	Vitis vinifera: leaves	RNA viruses	All	Various	Sequence of whole genomes from known and unknown viruses	Al Rwahnih, Daubert, Golino, and Rowhani (2009)
454: WGS	Unknown	Phytophthora 4 spp.: cultures	Phytophthora	All	None	Host jumps are followed by rapid genome evolution in repeat‐rich regions	Raffaele, Farrer, Cano, Studholme, and MacLean (2010)
454: MetT	OK, USA + Costa Rica	15 angiosperm families: leaves	dsRNA viruses	All	RT–PCR primer	11 known virus families; thousands of novel host‐specific viruses	Roossinck et al. (2010)
Illumina: MetB	WA, Australia	17 wild plant species: leaves	ssRNA Viruses	All	Oligo‐d (T) primers for RT–PCR	Multiple novel viruses describe	Wylie, Luo, Li, and Jones (2012)
454: MetB	Italy	Phytophthora: mock community	Oomycetes: Phytophthora spp.	ITS1	ITS6 + ITS7	HTS method suited for detection of Phytophthora spp.	Vettraino, Bonants, Tomassini, Bruni, and Vannini (2012)
Ion Torrent: MetG	South Africa	Eucalyptus grandis: leaf, petiole, twig, wood	Fungi	ITS1	ITS1F^a + ITS2^a	Community dominated by Dothidiomycetes that harbour well‐known plant pathogens.	Kemler et al. (2013)
454: MetB	Finland	Picea abies: stumps	Basidiomycota	ITS	ITS1F^a + ITS4B^a	Phlebiopsis gigantea biocontrol does not affect fungal composition, lost 1 year after inoculation; Heterobasidion undetected	Terhonen et al. (2013)
Illumina: MetG	China	Hexapoda: mixed specimens	Hexapoda	None (mtDNA enriched)	None	High‐resolution identification of arthropods	Zhou et al. (2013)
Illumina: MetB	Panama	Woody plants: leaves	Bacteria	16S rRNA	799F + 1115R; PCRII_for + PCRII_rev	Communities dominated by a few core microbiome taxa	Kembel et al.. (2014)
454: MetB	Martinique, France	Arthropod predators	Metazoa	COI (mini)	Uni‐MinibarF1 + R1	Multiple insect pests make a strong contribution to diet	Mollot et al. (2014)
454: MetB	Spain	Soil, water	Phytophthora	ITS1	18Ph2F + 5.8S−1R	Greater species and phylogenetic richness in water samples	Catala, Pérez‐Sierra, and Abad‐Campos (2015)
Illumina: RAD‐seq	Germany	Fusarium graminearum: cultures	Fusarium graminearum	None	None	High levels of divergence in all populations	Talas and McDonald (2015)
Illumina: MetB	Germany	Arabidopsis thaliana tissues	Bacteria, Fungi, Oomycetes	16S rRNA ITS1. ITS2	2 pairs for each group	Pathogens regulate microbiome diversity; fungal and oomycete antagonism to bacteria	Agler et al. (2016)
Illumina: MetB	WA, USA	Populus trichocarpa: leaves	Fungi	ITS1	ITS1F^a + ITS2^a	Detection of species suppressing and facilitating rust infection	Busby, Peay, and Newcombe (2016)
454: MetB	Primorye, Russia	Fraxinus mandshurica: leaf, leaflets, rachises	Fungi (incl. Hymenoscyphus spp.)	ITS2	gITS7 + ITS4	Fungal composition similar in infected and uninfected leaves; H. fraxineus detected from 33% of samples	Cleary et al. (2016)
PacBio: MetaB	Mexico	Coffea arabica +Hemileia vastatrix: pustules	Fungi	ITS	ITS1F^a +ITS4	Communities diverse, differ geographically; potential biocontrol agents detected	James, Marino, Perfecto, and Vandermeer (2016)
Illumina: MetT	North America	Cultures of five fungal pathogens	RNA viruses	All	None	Tens of novel mycoviruses that may have biocontrol properties	Marzano et al. (2016)
Illumina: WGS	Variable	Erysiphales spp.: cultures	Erysiphales (Fungi)	None	None	Interspecific hybridization causes raise of novel pathogens	Menardo et al. (2016)
ON: WGS	Guinea	Homo sapiens: tissue samples	Ebola virus	None	None	Virus genome sequenced and detected in <60 min.	Quick et al. (2016)
Illumina: MetB	France	Raphanus sativus	Bacteria, Fungi	16S, gyrB, ITS1	515F+806b aF64+aR353 ITS1F^a+ITS2^a	Alternaria infection alters plant microbiome	Rezki et al. (2016)
Illumina: MetB	Estonia	Forest nursery soils	Oomycetes	ITS	ITS1Oo + ITS4ngs	HTS conditions suitable for identification of oomycetes	Riit et al. (2016)
454: MetB	Great Britain	Quercus spp.: bark, wood	Bacteria	16S rRNA	341f + 805r	Composition differs in healthy and infected tissue by acute oak decline	Sapp et al. (2016)
454: MetB	SA, Canada	4 crops: roots and soil	Fungi	ITS1	ITS1F^a + ITS2^a	Pathogens become dominant after crop rotations with legumes	Bainard et al. (2017)
454: MetB	Spain	Quercus ilex: roots, soil	Oomycetes, esp. Phytophthora	ITS1	ITS6^a + 5.8S−1R	Phytophthora sp. nov dominates	Catala, Berbegal, Pérez‐Sierra, and Abad‐Camposa (2017)
454: MetB	Norway	Fraxinus excelsior: leaves, petioles	Fungi (incl. Hymenoscyphus spp.)	ITS1, ITS2	ITS5^a + ITS2^a; gITS7 + ITS4	Fungal communities differ by season and infection rate; few reads of Hymenoscyphus spp. in ITS1 data	Cross et al. (2017)
454: MetB	Italy	Bark beetles: Orthotomicus erosus, Xyleborinus saxesenii	Fungi	ITS2	ITS3^a + ITS4	Bark beetles carry pathogenic fungi with exported timber	Malacrino et al. (2017)
454: MetB	Finland	Betula pendula: leaves	Fungi	ITS2	fITS7^a + ITS4	No effect of tree diversity and neighbourhood on pathogens	Nguyen et al. (2017)
Ion torrent: ddRAD sequences	Multiple	Hymenoscyphus fraxineus: ascocarps, isolates; H. albidus: isolates	Fungi: H. albidus, H. fraxineus	None	None	High genetic variation in E Asia compared to Europe; E Russia a likely source area for Europe; possibility to assign strain to a population	Sønstebø et al. (2017)
Illumina: MetB	France	Arabidopsis thaliana: tissues	Bacteria	gyrB	aF64+aR353	Pathogens co‐occur in diseased plants, differ in roots and leaves and seasonally	Bartoli et al. (2018)
PhyloChip	Netherlands	Arabidopsis thaliana: roots	Bacteria, Fungi	None	None	Pathogen‐induced root microbes induce systemic resistance in offspring	Berendsen et al. (2018)
Illumina: MetB	Slovenia, Germany	Centaurea spp.: rhizosphere	Nematodes	18S	3NDf + 1132rmod	MetB outperforms qPCR in nematode identification	Geisen et al. (2018)
ON: MetG	New Zealand	Rattus norvegicus: gut	All	None	None	Diet consists of various plants and insects incl. pests	Pearman et al. (2018)
Studies including pathogens
454: MetT	Europe	Agricultural soils	All (esp. ammonia oxidizers)	None (AmoA)	None (various for AmoA)	Archaea are predominate ammonia oxidizers	Leininger et al. (2006)
454: MetB	Various	Various soils	Bacteria, Archaea	18S	787f + 1492rm	Richness and composition differ in agricultural and forest soils; pathogens undistinguished	Roesch et al. (2007)
454: MetG	China	Vector insect	Candidatus Liberibacter asiaticus	None	None	Plant pathogen genome recovered from mixed DNA samples	Duan et al. (2009)
454: MetB	France	6 tree plantations: soil	Fungi	ITS1	ITS1F^a + ITS2^a	Putative pathogen Ceratobasidiaceae sp. dominant in all sites	Buee et al. (2009)
454: MetB	KS, USA	Quercus macrocarpa: leaves in rural versus urban sites	Fungi	ITS1	ITS1F^a + ITS2^a	Both pathogens and endophytes common, habitat effect	Jumpponen and Jones (2009)
454: MetB	Americas	Soil	Bacteria	16S	27F + 338R	pH drives soil bacterial composition on a continental scale; pathogens undistinguished	Lauber, Zhou, Gordon, Knight, and Fierer (2010)
454: MetB	FL, USA + unknown	Individuals extracted from soil	Nematoda	18S; 28S	NF1 + 18Sr2b^a; D3a + D3b	Two markers recover nearly all taxa	Porazinska et al. (2009)
454: MetB	Costa Rica	Forest soil	Eukaryotes	18S; 28S	SSUF04 + SSUR22; NF1 + 18Sr2b^a	HTS of 18S and 28S rRNA genes can be used for eukaryote diversity studies	Creer et al. (2010)
454: MetB	Global	Indoor dust	Fungi	28S	LROR‐F + LR5F	Indoor dust reveals predominance of microfungi incl. plant pathogens	Amend, Seifert, Samson, and Bruns (2010)
454: MetB	Americas	Soil	Eukaryotes (esp. protists)	18S	F515^a + R1119^a	Distribution of protist phyla depends on climate; pathogens undistinguished	Bates et al. (2013)
454: MetB	KS, USA	Individuals extracted from soil	Nematoda	18S	NF1 + 18Sr2b^a	Quantification of taxa semiquantitative at best	Darby, Todd, and Herman (2013)
Illumina: MetB	NY, USA	Green roof and city park soil	Fungi	ITS1	ITS1F^a + ITS2^a	Fungal composition differs, pathogens undistinguished	McGuire et al. (2013)
Illumina: MetB	Germany	Grassland soil	Fungi	ITS1	ITSFI2^a + ITS2^a	Illumina HTS can be used to recover fungal diversity	Schmidt et al. (2013)
454: MetB	NC, TN, USA	3 tree species: roots	Bacteria, Fungi	16S, 18S, ITS, 28S	various	Soil origin explains endophytes better than host species; pathogens commonly detected	Bonito et al. (2014)
454: MetB	Portugal	Vitis vinifera: leaves	Bacteria, Fungi	16S, ITS2, 28S	V6F, V6R; ITS3^a + ITS4; D2F^a + D2R	Fungal richness declines but bacterial richness increases with time	Pinto et al. (2014)
454: MetB	Global	Soil	Fungi	ITS2	ITS3NGSmix + ITS4ngs	Plant pathogen richness peaks in tropics	Tedersoo et al. (2014)
454: MetB	Costa Rica	Reared individuals	Lepidoptera	COI	LepF1 + LepR1	HTS can be used in single‐specimen barcoding	Shokralla et al. (2014)
454: MetB	Italy	Olea europaea: fruits, leaves	Fungi	ITS2	ITS3^a + ITS4	Low diversity and high Colletotrichum abundance in rotten fruits	Abdelfattah, Nicosia, Cacciola, Droby, and Schena (2015)
Illumina: mtMetG	Spain	Coleoptera: bodies	Coleoptera	COI, etc.	None	Larval species and phylogenetic diversity greater in subsoil	Andujar et al. (2015)
Illumina: MetB	AK, USA + Canada	Populus balsamifera: leaves	Fungi	ITS1	ITS1FI2^a + ITS4	Proportion of pathogens declines northwards	Balint et al. (2015)
454: MetT	Europe	Soil	Eukaryotes	None	None, 18S extracted	High protist diversity incl. many pathogens	Geisen et al. (2015)
Illumina: MetB	USA	Dust	Fungi	ITS1	ITS1F^a + ITS2^a	Spore dispersal prediction for pathogens and other fungi	Grantham et al. (2015)
454: MetB	FL, USA	Scolytidae bark beetles: mycangia	Fungi	ITS2	gITS7 + ITS4	Composition differs among species; several yeasts and plant pathogens besides mutualists	Kostovcik et al. (2015)
454: MetB	Italy	Fruit fly: Bactrocera oleae	Fungi	ITS2	ITS3^a + ITS4	Fruit fly carries spores of both pathogens and biocontrol agents; males and females differ	Malacrino, Schena, Campolo, Laudani, and Palmeri (2015)
Illumina: MetB	Costa Rica	1,010 trapped individuals	Arthropoda	COI	Ill_LCO1490 + Ill_C_R; Ill_B_F + Ill_HCO2198	Low match between morphology, Sanger sequencing and HTS	Shokralla et al. (2015)
454: MetB	Italy	Fragaria vesca: fruits, leaves	Fungi	ITS2	ITS3^a + ITS4	Fungicides reduce the dominant species Botrytis cinerea	Abdelfattah, Wisniewski, Nicosia, and M.G., Cacciola, S.O., & Schena, L. (2016)
454: MetB	Estonia	Forest soil	Eukaryotes	ITS2	ITS3NGSmix + ITS4ngs	Pathogen composition is relatively most affected by plant neighbourhood	Bahram et al. (2016)
Illumina: MetB	Panama	Plantation forest soil	Fungi	28S	NL1 + NL4	Pathogens respond more strongly to vegetation than saprobes and mutualists	Kivlin and Hawkes (2016)
Illumina: MetG	Brazil	Predator arthropods: gut	All	None	None	Insect pests are important food sources	Paula et al. (2016)
454: MetB	Estonia + Finland	Forest soil	Eukaryotes	ITS2	ITS3NGSmix + ITS4ngs	Plant pathogens respond negatively to soil C:N ratio; nematodes have site‐specific drivers	Tedersoo, Bahram, et al. (2016)
454: MetB	The Netherlands	Agricultural soils	Fungi	ITS2: ¹³C enriched	ITS9^a + ITS4	Pathogen: mycorrhiza ratio of active community declines with succession	Hannula et al. (2017)
Illumina: MetG	Great Britain	Solanum tuberosum: rot	All	None	None	Detection of taxonomic and functional profile of potato rot spots	Doonan et al. (2017)
Illumina: MetB	MN, USA	Agricultural soil	Fungi	ITS2	ITS1F^a + ITS2^a	Pathogens are relatively more abundant in high‐biomass plant communities	Cline et al. (2017)
Ion Torrent: MetB	Greenland	Tundra soil	Fungi	ITS2	fITS7^a + ITS4	Pathogens were more prevalent in highly stressed habitats	Grau et al. (2017)
Illumina: MetB	North America	Helianthus annuus: roots, leaves, seeds	Bacteria, Fungi	16S; ITS1	515F + 806r; ITS1F^a + ITS2^a	Proportion of pathogens greater in older than recent varieties	Leff, Lynch, Kane, and Fierer (2017)
Illumina: MetB	NY + MA, USA	Forest soil	Fungi	ITS2	fITS7^a + ITS4	Pathogen richness is greater in Alliaria petiolata infested sites	Anthony, Frey, and Stinson (2017)
454: MetB	Estonia	Pinus sylvestris forest soil	Eukaryotes	ITS2	ITS3NGSmix + ITS4ngs	Plant pathogen richness increase at higher soil moisture	Hiiesalu, Bahram, and Tedersoo (2017)
PacBio: MetB	Papua New Guinea + Estonia	Forest and nursery soil	Eukaryotes (esp. fungi, oomycetes)	18S, ITS, 28S	Multiple	Longer amplicons: higher resolution, less artefactual taxa; full ITS‐based identification of oomycetes	Tedersoo et al. (2017)
Illumina: MetB	S Europe	Bat Miniopterus schreibersii: faeces	Animals	COI, mt16S	ArtF1c + ArtR2c; Coleop16Sc + Coleop16Sd	Pests constitute >50% of prey	Aizpurua et al. (2018)
Illumina: MetB	SA, Australia	Soil in successional habitats	Fungi	ITS (ITS1 analysed)	ITS1F^a + ITS4	Pathogen abundance declines with ecosystem naturality	Yan et al. (2018)

MetB, metabarcoding; MetG, metagenomics; metT, metatranscriptomics; ON, Oxford Nanopore; WGS, whole‐genome sequencing.

Poorly performing primer(s).