. 2017 Nov 2;11(11):e0005916. doi: 10.1371/journal.pntd.0005916

Table 1. Scheme of reported investigations on a human or animal model gut “parasitome” by exploiting “omic” technologies.

Parasite	“Omic” approach	Sample	Technique	Major results	Reference
Ancylostoma caninum	Proteomics	Adult worm from small intestines of stray dogs	1-DE LC-ESI-MS/MS^a; protein or peptide OGE^b and shotgun LC-ESI-MS/MS	Description of proteins from the excretory/secretory products	[74]
Ancylostoma ceylanicum	Genomics	Hookworms culture and infection in golden hamster (Mesocricetus auratus)	Genomic library; Illumina sequencing	Complete sequence of hookworm genome and definition of temporal genes expression	[48]
Ancylostoma ceylanicum	Transcriptomics		RNA-seq library, Illumina sequencing		[48]
Blastocystis spp.	Metagenomics	Faecal DNA from 2 groups of patients, positive or negative for Blastocystis	NGS^c: Ion Torrent sequencing	Blastocystis colonisation is positively associated with increased bacterial diversity and with higher abundance of Clostridia class, Ruminococcaceae, and Prevotellaceae	[37]
Blastocystis spp.	Metagenomics	Faecal DNA from cohorts of healthy individuals and patients with Crohn’s disease, ulcerative colitis	NGS: WGS^d Illumina sequencing	Blastocystis colonisation is positively associated with species richness and with species present in lean individuals, such as the Prevotella or Ruminococcus enterotype	[33]
Blastocystis ST7	Proteomics	Axenic culture of an isolate obtained from a Singaporean patient with intestinal disorders	1-DE LC-ESI-MS/MS^a	Definition of secreted protease candidates for the effects induced at the parasite–host interface and involved in mucus degradation: legumain peptidase ACY95293.1, and cathepsin B peptidase CBK25506.2.	[72]
Cryptosporidium parvum	Proteomics	Excysted sporozoites from lambs	2-DE MALDI TOF^e; 1-DE LC-ESI-MS/MS; Shotgun MudPit^f LC-ESI-MS/MS	Definition of sporozoite proteome	[59]
	Proteomics	Excysted and non-excysted calf oocysts	Stable isotope labelling iTRAQ^g LC-ESI-MS/MS; Shotgun LC-ESI-MS/MS	Definition of excysted and non-excysted oocysts proteome; specific proteins augmented in excysted invasive sporozoites: many ribosomal (40S and 60S) and heat shock chaperonin (Hsp70 and Hsp90)	[60]
	Metabolomics	Human faecal samples	Untargeted GC-MS^h	Higher abundance of phenylalanine, valine, isoleucine, serine, succinic acid, and threitol, lower levels of xylose in infected sample; faecal metabolite profiles generated are able to identify infected individuals	[86]
	Metabolomics	Faecal sample from mice infected with S26 isolate (obtained from a naturally infected calf)	Chemical Derivatization GC-MS	Less abundant metabolites and intermediaries involved in energy metabolism (key nutrients scavenged by Cryptosporidium to supplement its metabolic pathway) were detected in infected mice than in uninfected mice	[87]
Encephalitozoon cuniculi	Proteomics	GB-M1 cultured in Madin-Darby canine kidney or human foreskin fibroblast cells	2-DE MALDI-TOF/ESI LC-MS/MS; Shotgun LC-ESI-MS/MS	Identification of a reference map of the major proteins expressed during late sporogony	[62]
Entamoeba histolytica	Proteomics	Axenic cultured trophozoites (strain HMI:IMSS)	2-DE LC-ESI-MS/MS	Identification of specific parasite proteins that promote host invasion	[68]
		Axenic cultured trophozoites (strain HMI:IMSS)	1-DE LC-ESI-MS/MS	Identification of the cell surface–associated proteome	[67]
		Axenic cultured trophozoites (strains HMI:IMSS and Rahman)	2-DIGEⁱ MALDI-TOF/ESI LC-MS/MS	Identification of important molecular component defining physiologically relevant virulence phenotype	[70]
Entamoeba histolytica and Entamoeba dispar	Proteomics	Axenic cultured trophozoites (strain HMI:IMSS of E. hystolytica and SAW760 of E. dispar)	2-DE MALDI-TOF	Identification of more proteins which are involved in Entamoeba pathogenicity	[69]
Entamoeba invadens	Transcriptomics	Axenic cultured trophozoites (IP-1 strain)	Affymetrix platform microarray	First description of transcriptional and metabolic regulatory networks dynamics taking place during E. invadens encystation	[89]
Entamoeba invadens	Metabolomics	Axenic cultured trophozoites (IP-1 strain)	CE^j-ESI-TOF-MS/MS		[89]
Giardia duodenalis	Metabolomics	Stool from patients with confirmed infection and controls with diarrhoea	GC-MS	First report of the Volatile Organic Compounds that could be biomarkers of Giardia infection	[88]
Giardia lamblia	Proteomics	Cultured WBC6 (ATCC catalog number 50803) trophozoites	1-DE LC ESI-MS/MS	Definition of the protein repertoire of peripheral and encystation-specific vesicles that have key roles in proliferation and transmission to a new host	[61]
Heligmosomoides polygyrus	Metagenomics	Distal ileum and cecal tip of C57BL/6 healthy and infected mice; L3 larvae and adult worms from duodenum of infected mice	NGS: 16S rRNA gene targeted amplification and Sanger-style sequencing; quantitative PCR clone library analysis	Infection significantly alters the gut microbiota with increased Lactobacillaceae bacterial load	[42]
Helminths (Trichuris spp., Ascaris spp., hookworm)	Metagenomics	Faecal sample of helminth-infected or uninfected indigenous Malaysians and New York City residents	NGS: V4 16S rRNA gene targeted amplification; Illumina sequencing	Significant effect of helminth colonisation on the diversity, bacterial community structure and function of the gut microbiota	[45]
Necator americanus	Metagenomics	Faecal samples of experimentally infected human volunteers (affected by celiac disease) on a gluten-free diet	NGS: 16S rRNA gene targeted amplification; 454 pyrosequencing	Hookworm infection did not have a major impact on the community structure of the intestinal microbiota	[41]
	Metagenomics	Prior and post dietary gluten exposure faecal samples of experimentally infected human patients (affected by celiac disease)		Microbial species richness increases during the challenge with escalating doses of dietary gluten, a potential mechanism by which hookworm infection could positively impact gluten-induced inflammation and intestinal immune homeostasis	[40]
	Genomics	L3i and adult worms from intestines of Golden Syrian Hamster infected subcutaneously with the Anhui strain	NGS: WGS and 454 pyrosequencing	Draft genome sequence and postgenomic analyses to unveil the immunobiology of human hookworm disease	[49]
	Transcriptomics		Rna-seq: Roche/454 and Illumina cDNA libraries; Genome Sequencer Titanium FLX and Illumina sequencing
	Proteomics		OGE and shotgun LC-ESI-MS/MS; protein microarray
	Metabolomics	Urine and blood samples from infected and control Syrian hamsters	¹H NMR^k	Unveil the biochemical consequences of infection	[90]
	Metabolomics	Urine and blood samples from infected and control Syrian hamsters coinfected with Schistosoma japonicum	¹H NMR^k	Unveil the biochemical consequences of infection	[91]
Strongyloides stercoralis	Transcriptomics	Parasites from faecal samples of infected individual of the endemic area of La Safor (Valencia, Spain) and propagated on axenic culture	cDNA library, 454 pyrosequencing	First comprehensive database of third larval stage transcripts	[65]
Strongyloides stercoralis	Proteomics		Shotgun LC-ESI-MS/MS	First study of the S. stercoralis proteome	[64]
Taenia solium	Proteomics	Gravid proglottids from Peruvian patients' stools	LC fractionation and MALDI TOF MS/MS	Definition of oncosphere proteome	[63]
Taenia solium	Proteomics	Metacestodes from naturally infected pigs in Zambia and Perú	1-DE LC-ESI-MS/MS	First report of the metacestode excretion/secretion proteome	[73]
Trichinella spiralis	Proteomics	Worms (isolated from the small intestine of infected rats) cocultured with different strains of bacteria	iTRAQ bidimensional LC-ESI-MS/MS	Comprehension of microbe-induced alterations in the survival and reproduction of T. spiralis in vitro: Lactobacillus bulgaricus and L. acidophilus were beneficial; Salmonella enterica and Escherichia coli O157:H7 (EHEC) were not	[76]
Trichuris suis	Metagenomics	Luminal colon content of control and infected piglets	NGS: 16S rRNA gene targeted amplification and WGS 454 pyrosequencing	Identification of the infection significant impact on the proximal colon microbiota composition at both the phylum and genus levels (key genera: Mucispirillum, Succinivibrio, and Ruminococcus) supported by metabolic and functional data	[43]
Trichuris suis	Metabolomics	Luminal colon content of control and infected piglets	GC-MS		[43]
Trichuris trichiura	Genomics	A clinically isolated adult male	NGS: WGS, Illumina sequencing	High-quality draft genome assembly	[79]
	Transcriptomics	Stool sample of infected Ecuadorian children	NGS: Ion Torrent sequencing	First transcriptomic analysis of the adult stage of the human whipworm	[78]
	Proteomics	Stool sample of infected Ecuadorian children	Shotgun LC-ESI-MS/MS	Identification of proteins with immunomodulatory effects	[77]
Unknown parasites	Metagenomics	Wild rat faeces	NGS: V9 18S rRNA gene targeted amplification; Illumina sequencing	Novel method to determine host alimentary tract parasite infections	[50] [51]

^a 1-DE LC-ESI-MS/MS: monoDimensional gel Electrophoresis Liquid Chromatography-ElectropSprayIonisation-tandem Mass spectrometry

^b OGE: OFFGEL fractionation by isoelectric focusing

^c NGS: Next Generation Sequencing

^d WGS: Whole Genome Sequencing

^e 2-DE MALDI TOF: biDimensional Matrix-Assisted Laser Desorption/ionization Time-of flight mass spectrometry

^f MudPit: Multi-dimensional Protein Identification technology

^g iTRAQ: isobaric Tags for Relative and Absolute Quantitation

^h GC-MS: gas chromatography-mass spectrometry

ⁱ 2-DIGE: bidimensional-DIfference Gel Electrophoresis

^j CE: Capillary electrophoresis

^{k 1}H NMR: Proton Nuclear Magnetic Resonance spectroscopy