MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

Riccardo Scotti; Stuart Southern; Christine Boinett; Timothy P. Jenkins; Alba Cortés; Cinzia Cantacessi

doi:10.1186/s40168-019-0782-7

Table 1 Studies from which bacterial 16S rRNA sequence datasets included in our meta-analysis were sourced, in chronological order. For each study, bibliographical references (including PubMed ID; PMID), as well as helminth parasite(s) and vertebrate host species under investigation, sequence data repository and corresponding accession number, are provided. The numbers of samples from helminth-infected and -uninfected hosts from each study included in the meta-analysis, and of raw and high-quality reads subjected to (re)processing are also included. Results from dataset (re)processing using MGnify are available in ENA MGnify (https://www.ebi.ac.uk/metagenomics/) using the accession numbers provided

From: MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

PMID	Ref.	Host	Parasite	Type of infection	Type/site of sampling	16S rRNA hypervariable region	Pipeline	Ref. DB	ENA Accession	MGnify accession	Sample size		Raw read count		High-quality read count
PMID	Ref.	Host	Parasite	Type of infection	Type/site of sampling	16S rRNA hypervariable region	Pipeline	Ref. DB	ENA Accession	MGnify accession	Uninfected	Infected	Uninfected	Infected	Uninfected	Infected
23925654	[39]	Hamster (Mesocricetus auratus)	Opisthorchis viverrini	Experimental	Colon	V7-V9	CloVR-16S	RDP	PRJNA188112	MGYS00003431	4	4	179,193	189,399	149,780	157,744
24795483	[40]	Human (Homo sapiens)	Necator americanus	Experimental	Faeces	V1-V3 V3-V5	QIIME	Greengenes	PRJNA244913	MGYS00003191	8	8	106,832	103,428	86,737	83,780
26377648	[25]	Mouse (Mus musculus)	Nippostrongylus brasiliensis	Experimental	Small intestine	V3-V4	QIIME	Greengenes	PRJNA255974	MGYS00003192	10	9	77,836	71,752	77,836	71,752
25942314	[41]	Mouse	Trichuris muris	Experimental	Caecum, faeces	V4	QIIME	Greengenes	PRJEB6560	MGYS00001732	80	60	3,253,762	2,438,665	3,034,081	2,306,376
26150661	[35]	Wild yellow-necked mouse (Apodemus flavicollis)	Multiparasites	Natural	Stomach, small intestine, caecum, colon	V1-V3	QIIME	Greengenes	PRJEB8312	MGYS00003181	38	93	1,790,824	4,990,294	1,723,425	4,865,341
25934152	[42]	Cat (Felis catus) Dog (Canis lupus familiaris)	Multiparasites	Natural	Faeces	V4	MR DNA	Greengenes	PRJNA276586	MGYS00003432	14	48	587,641	2,002,497	500,349	1,657,742
27912797	[43]	Cat	Toxocara cati	Natural	Faeces	V3-V4	QIIME	Greengenes	PRJNA349988	MGYS00003433	21	24	4,121,930	6,206,792	3,365,062	4,999,740
27827438	[44]	Human	N. americanus	Experimental	Small intestine	V3-V4	QIIME	Greengenes	PRJNA316208	MGYS00003180	12	12	7,855,514	6,597,567	7,025,186	5,918,376
26853110	[36]	Alpine goat (Capra aegagrus hircus)	Haemonchus contortus	Experimental	Abomasum	V3-V4	QIIME	Greengenes	PRJNA518079	MGYS00004556	5	12	1,213,261	3,302,574	1,196,878	3,263,552
28892494	[45]	Human	Multiparasites	Natural	Faeces	V3-V4	QIIME	Greengenes	PRJEB21999	MGYS00003147	22	11	8,388,179	4,934,705	7,777,849	4,506,626
30353019	[46]	Human	Strongyloides stercoralis	Natural	Faeces	V3-V4	QIIME2	Greengenes	PRJEB28700	MGYS00003148	11	20	1,946,889	2,578,359	1,873,123	2,487,145
30104612	[28]	Mouse	Schistosoma mansoni	Experimental	Small and large intestine	V4	QIIME	Greengenes	PRJEB29315	MGYS00003460	40	40	1,405,122	1,369,830	1,405,120	1,369,830
30149004	[47]	Mouse	Metagonimus yokogawai	Experimental	Caecum	V3-V4	Mothur	EzBioCloud	PRJNA481634	MGYS00003893	7	8	3,335,612	1,405,858	3,194,586	1,351,499
30323795	[48]	Human	Clonorchis sinensis	Natural	Faeces	V3-V4	QIIME	Greengenes	PRJNA486437	MGYS00003894	42	47	5,010,319	5,131,918	4,814,736	4,997,256
30643702	[49]	Human	Multiparasites	Natural	Faeces	V4	Mothur	RDP	PRJNA487588	MGYS00003908	6	16	88,768	338,701	86,195	328,849

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