Abstract
Original language | English |
---|---|
Pages (from-to) | 2848-2863 |
Number of pages | 16 |
Journal | ISME Journal |
Volume | 11 |
Issue number | 12 |
DOIs | |
Publication status | Published - 2017 |
Keywords
- bacterium
- bioinformatics
- cancer
- colonization
- genomics
- microbial community
- microorganism
- parasite
- Archaea
- Bacteria (microorganisms)
- Blastocystis
- Eukaryota
- Methanobrevibacter smithii
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Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. / Beghini, F.; Pasolli, E.; Truong, T.D. et al.
In: ISME Journal, Vol. 11, No. 12, 2017, p. 2848-2863.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome
AU - Beghini, F.
AU - Pasolli, E.
AU - Truong, T.D.
AU - Putignani, L.
AU - Cacciò, S.M.
AU - Segata, N.
N1 - Cited By :3 Export Date: 16 April 2018 Correspondence Address: Cacciò, S.M.; Department of Infectious Diseases, Istituto Superiore di SanitàItaly; email: simone.caccio@iss.it References: Alfellani, M.A., Stensvold, C.R., Vidal-Lapiedra, A., Onuoha, E.S.U., Fagbenro-Beyioku, A.F., Clark, C.G., Variable geographic distribution of Blastocystis subtypes and its potential implications (2013) Acta Trop, 126, pp. 11-18; Alfellani, M.A., Taner-Mulla, D., Jacob, A.S., Imeede, C.A., Yoshikawa, H., Stensvold, C.R., Genetic diversity of Blastocystis in livestock and zoo animals (2013) Protist, 164, pp. 497-509; Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool (1990) J Mol Biol, 215, pp. 403-410; Andersen, L.O.B., Bonde, I., Nielsen, H.B., Stensvold, C.R., A retrospective metagenomics approach to studying Blastocystis (2015) FEMS Microbiol Ecol, 91, p. fiv072; Andersen, L.O.B., Nielsen, H.V., Stensvold, C.R., Waiting for the human intestinal Eukaryotome (2013) Soc Microb Ecol, 7, pp. 1253-1255; Andersen, L.O.B., Stensvold, C.R., Blastocystis in health and disease-Are we moving from a clinical to a public health perspective (2015) J Clin Microbiol, 54, pp. 524-528; Aronesty, E., Comparison of sequencing utility programs (2013) Open Bioinformatics J, 7, pp. 1-8; Audebert, C., Even, G., Cian, A., Blastocystis, I.G., Loywick, A., Merlin, S., Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota (2016) Sci Rep, 6, p. 25255; Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing (2012) J Comput Biol, 19, pp. 455-477; Bart, A., Wentink-Bonnema, E.M., Gilis, H., Verhaar, N., Wassenaar, C.J., Van Vugt, M., Diagnosis and subtype analysis of Blastocystis sp.in 442 patients in a hospital setting in the Netherlands (2013) BMC Infect Dis, 13, p. 389; Breiman, L., Random forests (2001) Machine Learning, 45, pp. 5-32; Budroni, S., Siena, E., Dunning, H.J.C., Seib, K.L., Serruto, D., Nofroni, C., Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination (2011) Proc Natl Acad Sci USA, 108, pp. 4494-4499; Cantarel, B.L., Korf, I., Robb, S.M., Parra, G., Ross, E., Moore, B., MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes (2008) Genome Res, 18, pp. 188-196; Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T., TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses (2009) Bioinformatics, 25, pp. 1972-1973; Cekin, A.H., Cekin, Y., Adakan, Y., Tasdemir, E., Koclar, F.G., Yolcular, B.O., Blastocystosis in patients with gastrointestinal symptoms: A case-control study (2012) BMC Gastroenterol, 12, p. 122; Clark, C.G., Van Der Giezen, M., Alfellani, M.A., Stensvold, C.R., Recent developments in Blastocystis research (2013) Adv Parasitol, 82, pp. 1-32; Denoeud, F., Roussel, M., Noel, B., Wawrzyniak, I., Da Silva, C., Diogon, M., Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite (2011) Genome Biol, 12, p. 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PY - 2017
Y1 - 2017
N2 - The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14.9%), its non-random and ST-specific distribution, and its ability to cause persistent (asymptomatic) colonization. These findings, along with the higher prevalence observed in non-westernized individuals, the lack of positive association with any of the disease considered, and decreased presence in individuals with dysbiosis associated with colorectal cancer and Crohn's disease, strongly suggest that Blastocystis is a component of the healthy gut microbiome. Further, we found an inverse association between body mass index and Blastocystis, and strong co-occurrence with archaeal organisms (Methanobrevibacter smithii) and several bacterial species. The association of specific microbial community structures with Blastocystis was confirmed by the high predictability (up to 0.91 area under the curve) of the microorganism colonization based on the species-level composition of the microbiome. Finally, we reconstructed and functionally profiled 43 new draft Blastocystis genomes and discovered a higher intra subtype variability of ST1 and ST2 compared with ST3 and ST4. Altogether, we provide an in-depth epidemiologic, ecological, and genomic analysis of Blastocystis, and show how metagenomics can be crucial to advance population genomics of human parasites. © The Author(s) 2017.
AB - The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14.9%), its non-random and ST-specific distribution, and its ability to cause persistent (asymptomatic) colonization. These findings, along with the higher prevalence observed in non-westernized individuals, the lack of positive association with any of the disease considered, and decreased presence in individuals with dysbiosis associated with colorectal cancer and Crohn's disease, strongly suggest that Blastocystis is a component of the healthy gut microbiome. Further, we found an inverse association between body mass index and Blastocystis, and strong co-occurrence with archaeal organisms (Methanobrevibacter smithii) and several bacterial species. The association of specific microbial community structures with Blastocystis was confirmed by the high predictability (up to 0.91 area under the curve) of the microorganism colonization based on the species-level composition of the microbiome. Finally, we reconstructed and functionally profiled 43 new draft Blastocystis genomes and discovered a higher intra subtype variability of ST1 and ST2 compared with ST3 and ST4. Altogether, we provide an in-depth epidemiologic, ecological, and genomic analysis of Blastocystis, and show how metagenomics can be crucial to advance population genomics of human parasites. © The Author(s) 2017.
KW - bacterium
KW - bioinformatics
KW - cancer
KW - colonization
KW - genomics
KW - microbial community
KW - microorganism
KW - parasite
KW - Archaea
KW - Bacteria (microorganisms)
KW - Blastocystis
KW - Eukaryota
KW - Methanobrevibacter smithii
U2 - 10.1038/ismej.2017.139
DO - 10.1038/ismej.2017.139
M3 - Article
VL - 11
SP - 2848
EP - 2863
JO - ISME Journal
JF - ISME Journal
SN - 1751-7362
IS - 12
ER -