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Pregled bibliografske jedinice broj: 980433

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies


Panek, Marina; Čipčić Paljetak, Hana; Barešić, Anja; Perić, Mihaela; Matijašić, Mario; Lojkić, Ivana; Vranešić Bender, Darija; Krznarić, Željko; Verbanac, Donatella
Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies // Scientific reports, 8 (2018), 5143, 13 doi:10.1038/s41598-018-23296-4 (međunarodna recenzija, članak, znanstveni)


CROSBI ID: 980433 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

Autori
Panek, Marina ; Čipčić Paljetak, Hana ; Barešić, Anja ; Perić, Mihaela ; Matijašić, Mario ; Lojkić, Ivana ; Vranešić Bender, Darija ; Krznarić, Željko ; Verbanac, Donatella

Izvornik
Scientific reports (2045-2322) 8 (2018); 5143, 13

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
gut microbiota ; DNA extraction ; next generation sequencing technologies ; Illumina

Sažetak
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human feces by application of next-generation sequencing (NGS). However, the detected composition of the fecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for the 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 (Illumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of fecal samples although favoring 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 fecal microbiota. The differences included higher diversity observed with MiSeq and increased the 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.

Izvorni jezik
Engleski

Znanstvena područja
Interdisciplinarne prirodne znanosti, Temeljne medicinske znanosti, Kliničke medicinske znanosti



POVEZANOST RADA


Projekti:
IP-2013-11-5467 - Utvrđivanje sastava crijevne mikrobiote, upalnih markera, prehrambenog i endokrinog statusa u pacijenata s upalnom bolesti crijeva (MINUTE for IBD) (Verbanac, Donatella, HRZZ - 2013-11) ( CroRIS)
EK-EFRR-KK.01.1.1.01.0008 - Znanstveni centar izvrsnosti za reproduktivnu i regenerativnu medicinu – istraživanja novih platormi i potencijala (CERRM) (Volarević, Siniša; Vukičević, Slobodan; Ježek, Davor, EK - KK.01.1.1.01) ( CroRIS)

Ustanove:
Hrvatski veterinarski institut, Zagreb,
Medicinski fakultet, Zagreb,
Klinički bolnički centar Zagreb

Poveznice na cjeloviti tekst rada:

doi www.nature.com

Citiraj ovu publikaciju:

Panek, Marina; Čipčić Paljetak, Hana; Barešić, Anja; Perić, Mihaela; Matijašić, Mario; Lojkić, Ivana; Vranešić Bender, Darija; Krznarić, Željko; Verbanac, Donatella
Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies // Scientific reports, 8 (2018), 5143, 13 doi:10.1038/s41598-018-23296-4 (međunarodna recenzija, članak, znanstveni)
Panek, M., Čipčić Paljetak, H., Barešić, A., Perić, M., Matijašić, M., Lojkić, I., Vranešić Bender, D., Krznarić, Ž. & Verbanac, D. (2018) Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies. Scientific reports, 8, 5143, 13 doi:10.1038/s41598-018-23296-4.
@article{article, author = {Panek, Marina and \v{C}ip\v{c}i\'{c} Paljetak, Hana and Bare\v{s}i\'{c}, Anja and Peri\'{c}, Mihaela and Matija\v{s}i\'{c}, Mario and Lojki\'{c}, Ivana and Vrane\v{s}i\'{c} Bender, Darija and Krznari\'{c}, \v{Z}eljko and Verbanac, Donatella}, year = {2018}, pages = {13}, DOI = {10.1038/s41598-018-23296-4}, chapter = {5143}, keywords = {gut microbiota, DNA extraction, next generation sequencing technologies, Illumina}, journal = {Scientific reports}, doi = {10.1038/s41598-018-23296-4}, volume = {8}, issn = {2045-2322}, title = {Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies}, keyword = {gut microbiota, DNA extraction, next generation sequencing technologies, Illumina}, chapternumber = {5143} }
@article{article, author = {Panek, Marina and \v{C}ip\v{c}i\'{c} Paljetak, Hana and Bare\v{s}i\'{c}, Anja and Peri\'{c}, Mihaela and Matija\v{s}i\'{c}, Mario and Lojki\'{c}, Ivana and Vrane\v{s}i\'{c} Bender, Darija and Krznari\'{c}, \v{Z}eljko and Verbanac, Donatella}, year = {2018}, pages = {13}, DOI = {10.1038/s41598-018-23296-4}, chapter = {5143}, keywords = {gut microbiota, DNA extraction, next generation sequencing technologies, Illumina}, journal = {Scientific reports}, doi = {10.1038/s41598-018-23296-4}, volume = {8}, issn = {2045-2322}, title = {Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies}, keyword = {gut microbiota, DNA extraction, next generation sequencing technologies, Illumina}, chapternumber = {5143} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • Social Science Citation Index (SSCI)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


Citati:





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