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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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

Institucijski repozitorij: Dr Med - digitalni repozitorij Medicinskog fakulteta Sveučilišta u Zagrebu

Citirajte ovaj rad

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, br. 1, 2018, str. 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 i Donatella Verbanac. "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies." Scientific Reports 8, br. 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), str. 5143. doi: doi:10.1038/s41598-018-23296-4

Panek M, Čipčić Paljetak H, Barešić A, Perić M, Matijašić M, Lojkić I, i sur.. Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies. Scientific Reports [Internet]. 23.03.2018. [pristupljeno 22.11.2024.];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, br. 1, str. 5143, Ožujak 2018. [Online]. Dostupno na: https://urn.nsk.hr/urn:nbn:hr:105:887030. [Citirano: 22.11.2024.]

Za citiranje koristite ovu mrežnu adresu: https://urn.nsk.hr/urn:nbn:hr:105:887030
Podaci o radu
Naslov (engleski)Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies
AutorMarina Panek
AutorHana Čipčić Paljetak
AutorAnja Barešić
AutorMihaela Perić
AutorMario Matijašić
AutorIvana Lojkić
AutorDarija Vranešić Bender
AutorŽeljko Krznarić
AutorDonatella Verbanac
Autorova ustanovaSveučilište u Zagrebu
Medicinski fakultet
Znanstveno / umjetničko
područje, polje i grana		BIOMEDICINA I ZDRAVSTVO
Kliničke medicinske znanosti
Sažetak (engleski)
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.
Ključne riječi (engleski)
Jezikengleski
Vrsta publikacijeZnanstveni rad - Izvorni znanstveni rad
Status objaveObjavljen
Vrsta recenzijeRecenziran
Verzija publikacijeObjavljena verzija rada (izdavačev PDF)
Naslov časopisaScientific Reports
Brojčani podacivol. 8, br. 1, str. 5143
p-ISSN2045-2322
DOIhttps://doi.org/doi:10.1038/s41598-018-23296-4
URN:NBNurn:nbn:hr:105:887030
Datum objave publikacije2018-03-23
URL dokumentahttp://doi.org/10.1038/s41598-018-23296-4
Vrsta resursaTekst
Prava pristupaOtvoreni pristup
Uvjeti korištenjaIkona licence Zaštićeno autorskim pravom.
Datum i vrijeme pohrane2024-03-28 10:18:41