Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome
Open accessAbstract
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.
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Blastocystis sp. was identified by applying previously validated methods and thresholds.
“We identified Blastocystis sp. by applying previously validated methods and thresholds.47”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [47]
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Self-citationOn the road to strain-resolved comparative metagenomics
Segata, N. (2018) · mSystems · doi:10.1128/msystems.00190-17 · Cited by 127 · see citing works
Response of the human gut and saliva microbiome to urbanization in Cameroon
Lokmer, A., Aflalo, S., Amougou, N., Lafosse, S., Froment, A., Tabe, F. E., Poyet, M., Groussin, M., Said-Mohamed, R., & Ségurel, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-59849-9 · Cited by 46 · see citing works
Cinek, O., Polackova, K., Odeh, R., Alassaf, A., Kramná, L., Ibekwe, M. U., Majaliwa, E. S., Ahmadov, G., Elmahi, B. M. E., Mekki, H., et al. (2021) · Parasites & Vectors · doi:10.1186/s13071-021-04859-3 · Cited by 32 · see citing works
Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population
Manara, S., Selma-Royo, M., Huang, K. D., Asnicar, F., Armanini, F., Blanco-Miguez, A., Cumbo, F., Golzato, D., Manghi, P., Pinto, F., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.04.011 · Cited by 30 · see citing works
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- Authors
- Beghini, F., Pasolli, E., Truong, T. D., Putignani, L., Cacciò, S. M., & Segata, N.
- Affiliations
- University of Trento (IT)
- Bambino Gesù Children's Hospital (IT)
- Istituto Superiore di Sanità (IT)
- Corresponding author
- Cacciò, Simone M
- Segata, Nicola
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-08-22
- Volume
- 11
- Issue
- 12
- Pages
- 2848-2863
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC5702742
- OpenAlex
- W2747743284
- Cited by
- 201
- References
- 82
- Citations by year
- 2026: 16 · 2025: 31 · 2024: 20 · 2023: 18 · 2022: 37 · 2021: 30 · 2020: 13 · 2019: 17 · 2018: 17 · 2017: 1 · 2014: 1
- FWCI
- 5.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The ISME Journal (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Iris (University of Trento) (submittedVersion, cc-by-nc-sa)
- Funders
- European Commission (707345, 643476, HORIZON2020, H2020, 618833)
- Ministero dell’Istruzione, dell’Università e della Ricerca (FIR RBFR13EWWI, RBFR13EWWI, H2020)
- Fondazione Cassa Di Risparmio Di Trento E Rovereto (2013.0239)
- Horizon 2020 Framework Programme (#643476, 707345)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Parasitology › Parasitic Infections and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Blastocystis, human gut microbiome, Blastocystis subtypes, prevalence, asymptomatic colonization, dysbiosis, colorectal cancer, Crohn's disease, body mass index, Methanobrevibacter smithii, archaea, microbial community composition, draft genome sequence, unicellular eukaryotes
- MeSH terms
- Adolescent, Adult, Aged, Crohn Disease, Feces, Female, Humans, Male, Middle Aged, Prevalence, Blastocystis, Gastrointestinal Tract, Young Adult, Metagenomics, Dysbiosis
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