Počet záznamů: 1
Suitability and setup of next-generation sequencing-based method for taxonomic characterization of aquatic microbial biofilm
- 1.
SYSNO ASEP 0508091 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Suitability and setup of next-generation sequencing-based method for taxonomic characterization of aquatic microbial biofilm Tvůrce(i) Bakal, Tomáš (MBU-M) RID
Janata, Jiří (MBU-M) RID, ORCID
Sabová, Lenka (MBU-M)
Grabic, V. (CZ)
Žlábek, V. (CZ)
Najmanová, Lucie (MBU-M) RIDZdroj.dok. Folia Microbiologica. - : Springer - ISSN 0015-5632
Roč. 64, č. 1 (2019), s. 9-17Poč.str. 9 s. Jazyk dok. eng - angličtina Země vyd. CZ - Česká republika Klíč. slova gradient gel-electrophoresis ; phylogenetic-relationships ; community structure Vědní obor RIV EE - Mikrobiologie, virologie Obor OECD Microbiology CEP GA15-04258S GA ČR - Grantová agentura ČR LQ1604 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy ED1.1.00/02.0109 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy Způsob publikování Omezený přístup Institucionální podpora MBU-M - RVO:61388971 UT WOS 000455916000002 EID SCOPUS 85048533213 DOI 10.1007/s12223-018-0624-1 Anotace A robust and widely applicable method for sampling of aquatic microbial biofilm and further sample processing is presented. The method is based on next-generation sequencing of V4-V5 variable regions of 16S rRNA gene and further statistical analysis of sequencing data, which could be useful not only to investigate taxonomic composition of biofilm bacterial consortia but also to assess aquatic ecosystem health. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant, however, the non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The bias of the method is assessed with respect to the employment of a non-quantitative step (PCR amplification) to obtain quantitative results (relative abundance of identified taxa). This aspect is often overlooked in ecological and medical studies. We document that sequencing of a mixture of three merged primary PCR reactions for each sample and further evaluation of median values from three technical replicates for each sample enables to overcome this bias and gives robust and repeatable results well distinguishing among sampling localities and seasons. Pracoviště Mikrobiologický ústav Kontakt Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Rok sběru 2020 Elektronická adresa https://link.springer.com/article/10.1007%2Fs12223-018-0624-1
Počet záznamů: 1