DNA-, RNA-, and protein-based stable-isotope probing for high-throughput biomarker analysis of active microorganisms

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F23%3A00576258" target="_blank" >RIV/60077344:_____/23:00576258 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1007/978-1-0716-2795-2_17" target="_blank" >http://dx.doi.org/10.1007/978-1-0716-2795-2_17</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-1-0716-2795-2_17" target="_blank" >10.1007/978-1-0716-2795-2_17</a>

Result language

angličtina

Original language name

DNA-, RNA-, and protein-based stable-isotope probing for high-throughput biomarker analysis of active microorganisms

Original language description

Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.

Czech name

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Czech description

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Type

C - Chapter in a specialist book

CEP classification

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OECD FORD branch

10606 - Microbiology

Project

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Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Book/collection name

Metagenomics: Methods and Protocols, Methods in Molecular Biology

ISBN

978-1-0716-2794-5

Number of pages of the result

22

Pages from-to

"Roč. 2555 (2023)"

Number of pages of the book

287

Publisher name

Humana

Place of publication

New York

UT code for WoS chapter

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