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RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2046))

Abstract

The RNA-SIP technology allows for linking the structure and function of complex microbial communities, that is, the identification of microbial key players involved in distinct degradation and assimilation processes under in situ conditions. Being dependent on RNA, this technique is particularly suited for environments with high numbers of very active, that is, significantly RNA-expressing microorganisms, such as intestinal tract samples. We use RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in order to better understand the functionality of these medically and economically important nutrients in human and animal intestinal environments.

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References

  1. Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8(1):51. https://doi.org/10.1186/s13073-016-0307-y

    Article  PubMed  PubMed Central  Google Scholar 

  2. Sender R, Fuchs S, Milo R (2016) Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164(3):337–340. https://doi.org/10.1016/j.cell.2016.01.013

    Article  CAS  PubMed  Google Scholar 

  3. Riedel CU, Schwiertz A, Egert M (2014) The stomach and small and large intestinal microbiomes. In: Marchesi JR (ed) The human microbiota and microbiome. CABI, Wallingford, pp 1–19

    Google Scholar 

  4. Walsh CJ, Guinane CM, O'Toole PW et al (2014) Beneficial modulation of the gut microbiota. FEBS Lett 588(22):4120–4130. https://doi.org/10.1016/j.febslet.2014.03.035

    Article  CAS  PubMed  Google Scholar 

  5. Krumbeck JA, Maldonado-Gomez MX, Ramer-Tait AE et al (2016) Prebiotics and synbiotics: dietary strategies for improving gut health. Curr Opin Gastroenterol 32(2):110–119. https://doi.org/10.1097/MOG.0000000000000249

    Article  CAS  PubMed  Google Scholar 

  6. Manefield M, Whiteley AS, Griffiths RI et al (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68(11):5367–5373. https://doi.org/10.1128/AEM.68.11.5367-5373.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Manefield M, Whiteley AS, Ostle N et al (2002) Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun Mass Spectrom 16(23):2179–2183. https://doi.org/10.1002/rcm.782

    Article  CAS  PubMed  Google Scholar 

  8. Lueders T, Dumont MG, Bradford L et al (2016) RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes. Curr Opin Biotechnol 41:83–89. https://doi.org/10.1016/j.copbio.2016.05.001

    Article  CAS  PubMed  Google Scholar 

  9. Herrmann E, Young W, Rosendale D et al (2017) Determination of resistant starch assimilating bacteria in fecal samples of mice by in vitro RNA-based stable isotope probing. Front Microbiol 8:1331. https://doi.org/10.3389/fmicb.2017.01331

    Article  PubMed  PubMed Central  Google Scholar 

  10. Herrmann E, Young W, Rosendale D et al (2017) RNA-based stable isotope probing suggests Allobaculum spp. as particularly active glucose assimilators in a complex murine microbiota cultured in vitro. Biomed Res Int 2017:1829685. https://doi.org/10.1155/2017/1829685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Young W, Egert M, Bassett SA et al (2015) Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing. Nutrients 7(4):2109–2124. https://doi.org/10.3390/nu7042109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Egert M, de Graaf AA, Maathuis A et al (2007) Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing. FEMS Microbiol Ecol 60(1):126–135. https://doi.org/10.1111/j.1574-6941.2007.00281.x

    Article  CAS  PubMed  Google Scholar 

  13. Kovatcheva-Datchary P, Egert M, Maathuis A et al (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11(4):914–926. https://doi.org/10.1111/j.1462-2920.2008.01815.x

    Article  CAS  PubMed  Google Scholar 

  14. Herrmann E, Young W, Reichert-Grimm V et al (2018) In vivo assessment of resistant starch degradation by the caecal microbiota of mice using RNA-based stable isotope probing - a proof-of-principle study. Nutrients 10(2). : pii: E179. https://doi.org/10.3390/nu10020179

    Article  PubMed Central  Google Scholar 

  15. Tannock GW, Lawley B, Munro K et al (2014) RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel. Appl Environ Microbiol 80(7):2240–2247. https://doi.org/10.1128/AEM.03799-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Berry D, Loy A (2018) Stable-isotope probing of human and animal microbiome function. Trends Microbiol 26:999. https://doi.org/10.1016/j.tim.2018.06.004; pii: S0966-842X(18)30139-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Egert M, Weis S, Schnell S (2018) RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Methods 149:25–30. https://doi.org/10.1016/j.ymeth.2018.05.022

    Article  CAS  PubMed  Google Scholar 

  18. Forbord B, Osmundsen H (1993) Isolation of DNA and RNA from Streptococcus sobrinus OMZ176 using CsTFA gradients. Int J Biochem 25(12):1975–1980

    Article  CAS  Google Scholar 

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Correspondence to Markus Egert .

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Weis, S., Schnell, S., Egert, M. (2019). RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment. In: Dumont, M., Hernández García, M. (eds) Stable Isotope Probing. Methods in Molecular Biology, vol 2046. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9721-3_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9721-3_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9720-6

  • Online ISBN: 978-1-4939-9721-3

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