prikaz prve stranice dokumenta Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies
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Scientific paper - Original scientific paper
Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies
Scientific Reports, 8 (2018), 1; 5143. https://doi.org/doi:10.1038/s41598-018-23296-4
Panek, Marina; Čipčić Paljetak, Hana; Barešić, Anja; Perić, Mihaela; Matijašić, Mario; Lojkić, Ivana; Vranešić Bender, Darija; Krznarić, Željko; Verbanac, Donatella

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Panek, M., Čipčić Paljetak, H., Barešić, A., Perić, M., Matijašić, M., Lojkić, I. ... Verbanac, D. (2018). Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies. Scientific Reports, 8. (1), 5143. doi: doi:10.1038/s41598-018-23296-4

Panek, Marina, et al. "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies." Scientific Reports, vol. 8, no. 1, 2018, p. 5143. https://doi.org/doi:10.1038/s41598-018-23296-4

Panek, Marina, Hana Čipčić Paljetak, Anja Barešić, Mihaela Perić, Mario Matijašić, Ivana Lojkić, Darija Vranešić Bender, Željko Krznarić and Donatella Verbanac. "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies." Scientific Reports 8, no. 1 (2018): 5143. https://doi.org/doi:10.1038/s41598-018-23296-4

Panek, M., et al. (2018) 'Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies', Scientific Reports, 8(1), p. 5143. doi: doi:10.1038/s41598-018-23296-4

Panek M, Čipčić Paljetak H, Barešić A, Perić M, Matijašić M, Lojkić I, and sur.. Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies. Scientific Reports [Internet]. 2018 March 23 [cited 2024 May 06];8(1):5143. doi: doi:10.1038/s41598-018-23296-4

M. Panek, et al., "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies", Scientific Reports, vol. 8, no. 1, p. 5143, March 2018. [Online]. Available at: https://urn.nsk.hr/urn:nbn:hr:105:887030. [Accessed: 06 May 2024]

Metadata
Title (english)Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies
AuthorMarina Panek
AuthorHana Čipčić Paljetak
AuthorAnja Barešić
AuthorMihaela Perić
AuthorMario Matijašić
AuthorIvana Lojkić
AuthorDarija Vranešić Bender
AuthorŽeljko Krznarić
AuthorDonatella Verbanac
Author's institutionUniversity of Zagreb
School of Medicine
Scientific / art field,
discipline and subdiscipline		BIOMEDICINE AND HEALTHCARE
Clinical Medical Sciences
Abstract (english)
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for collection and storage of faecal samples (native and OMNIgene.GUT system) and bacterial DNA extraction (MP Biomedicals, QIAGEN and MO BIO kits), using two NGS platforms for 16S rRNA gene sequencing (Ilumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of faecal samples although favouring Sutterella genus. MP provided superior DNA yield and quality, MO BIO depleted Gram positive organisms while using QIAGEN with OMNIgene.GUT resulted in greatest variability compared to other two kits. MiSeq and IT platforms in their supplier recommended setups provided comparable reproducibility of donor faecal microbiota. The differences included higher diversity observed with MiSeq and increased capacity of MiSeq to detect Akkermansia muciniphila, [Odoribacteraceae], Erysipelotrichaceae and Ruminococcaceae (primarily Faecalibacterium prausnitzii). The results of our study could assist the investigators using NGS technologies to make informed decisions on appropriate tools for their experimental pipelines.
Keywords (english)
Languageenglish
Publication typeScientific paper - Original scientific paper
Publication statusPublished
Peer reviewPeer review
Publication versionPublished version
Journal titleScientific Reports
Numberingvol. 8, no. 1, p. 5143
p-ISSN2045-2322
DOIhttps://doi.org/doi:10.1038/s41598-018-23296-4
URN:NBNurn:nbn:hr:105:887030
Publication2018-03-23
Document URLhttp://doi.org/10.1038/s41598-018-23296-4
Type of resourceText
Access conditionsOpen access
Terms of useLicence In copyright icon
Created on2024-03-28 10:18:41