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Do it yourself! – Initial experiences with self-synthesized CsTFA for RNA-SIP analyses. METHODS IN MICROBIOLOGY 2022; 194:106432. [DOI: 10.1016/j.mimet.2022.106432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022]
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Wigley K, Egbadon E, Carere CR, Weaver L, Baronian K, Burbery L, Dupont PY, Bury SJ, Gostomski PA. RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm. J Appl Microbiol 2021; 132:1526-1542. [PMID: 34424588 DOI: 10.1111/jam.15264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 11/27/2022]
Abstract
AIMS Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm. METHODS AND RESULTS Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to 13 C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of 13 C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed 13 C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with 13 C. CONCLUSIONS Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.
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Affiliation(s)
- Kathryn Wigley
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Emmanuel Egbadon
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Carlo R Carere
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand
| | - Kim Baronian
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Lee Burbery
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand
| | - Pierre Y Dupont
- Institute of Environmental Science and Research Ltd, Christchurch, New Zealand
| | - Sarah J Bury
- National Institute of Water and Atmospheric Research Ltd, Wellington, New Zealand
| | - Peter A Gostomski
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
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Weis S, Schnell S, Egert M. Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation. Can J Microbiol 2020; 66:491-494. [PMID: 32134703 DOI: 10.1139/cjm-2019-0612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
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Ayala‐Mar S, Donoso‐Quezada J, Gallo‐Villanueva RC, Perez‐Gonzalez VH, González‐Valdez J. Recent advances and challenges in the recovery and purification of cellular exosomes. Electrophoresis 2019; 40:3036-3049. [PMID: 31373715 PMCID: PMC6972601 DOI: 10.1002/elps.201800526] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022]
Abstract
Exosomes are nanovesicles secreted by most cellular types that carry important biochemical compounds throughout the body with different purposes, playing a preponderant role in cellular communication. Because of their structure, physicochemical properties and stability, recent studies are focusing in their use as nanocarriers for different therapeutic compounds for the treatment of different diseases ranging from cancer to Parkinson's disease. However, current bioseparation protocols and methodologies are selected based on the final exosome application or intended use and present both advantages and disadvantages when compared among them. In this context, this review aims to present the most important technologies available for exosome isolation while discussing their advantages and disadvantages and the possibilities of being combined with other strategies. This is critical since the development of novel exosome-based therapeutic strategies will be constrained to the effectiveness and yield of the selected downstream purification methodologies for which a thorough understanding of the available technological resources is needed.
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Affiliation(s)
- Sergio Ayala‐Mar
- Tecnologico de MonterreySchool of Engineering and Science, AvEugenio Garza Sada 2501 SurMonterreyNLMexico
| | - Javier Donoso‐Quezada
- Tecnologico de MonterreySchool of Engineering and Science, AvEugenio Garza Sada 2501 SurMonterreyNLMexico
| | | | - Victor H. Perez‐Gonzalez
- Tecnologico de MonterreySchool of Engineering and Science, AvEugenio Garza Sada 2501 SurMonterreyNLMexico
| | - José González‐Valdez
- Tecnologico de MonterreySchool of Engineering and Science, AvEugenio Garza Sada 2501 SurMonterreyNLMexico
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Egert M, Weis S, Schnell S. RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Methods 2018; 149:25-30. [PMID: 29857194 DOI: 10.1016/j.ymeth.2018.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.
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Affiliation(s)
- Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany; Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
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Herrmann E, Young W, Reichert-Grimm V, Weis S, Riedel CU, Rosendale D, Stoklosinski H, Hunt M, Egert M. 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 2018; 10:nu10020179. [PMID: 29415499 PMCID: PMC5852755 DOI: 10.3390/nu10020179] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 01/30/2018] [Indexed: 02/07/2023] Open
Abstract
Resistant starch (RS) is the digestion resistant fraction of complex polysaccharide starch. By reaching the large bowel, RS can function as a prebiotic carbohydrate, i.e., it can shape the structure and activity of bowel bacterial communities towards a profile that confers health benefits. However, knowledge about the fate of RS in complex intestinal communities and the microbial members involved in its degradation is limited. In this study, 16S ribosomal RNA (rRNA)-based stable isotope probing (RNA-SIP) was used to identify mouse bowel bacteria involved in the assimilation of RS or its derivatives directly in their natural gut habitat. Stable-isotope [U13C]-labeled native potato starch was administrated to mice, and caecal contents were collected before 0 h and 2 h and 4 h after administration. 'Heavy', isotope-labeled [13C]RNA species, presumably derived from bacteria that have metabolized the labeled starch, were separated from 'light', unlabeled [12C]RNA species by fractionation of isolated total RNA in isopycnic-density gradients. Inspection of different density gradients showed a continuous increase in 'heavy' 16S rRNA in caecal samples over the course of the experiment. Sequencing analyses of unlabeled and labeled 16S amplicons particularly suggested a group of unclassified Clostridiales, Dorea, and a few other taxa (Bacteroides, Turicibacter) to be most actively involved in starch assimilation in vivo. In addition, metabolic product analyses revealed that the predominant 13C-labeled short chain fatty acid (SCFA) in caecal contents produced from the [U13C] starch was butyrate. For the first time, this study provides insights into the metabolic transformation of RS by intestinal bacterial communities directly within a gut ecosystem, which will finally help to better understand its prebiotic potential and possible applications in human health.
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Affiliation(s)
- Elena Herrmann
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Wayne Young
- AgResearch Limited, Food Nutrition and Health Team, Grasslands Research Centre, Palmerston North 4474, New Zealand;
- Riddet Institute, Massey University, Palmerston North 4474, New Zealand
- High-Value Nutrition, National Science Challenge, University of Auckland, Auckland 1142, New Zealand
| | - Verena Reichert-Grimm
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Severin Weis
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Douglas Rosendale
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Halina Stoklosinski
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Martin Hunt
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Markus Egert
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
- Correspondence: ; Tel.: +49-7720-307-4554
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Herrmann E, Young W, Rosendale D, Conrad R, Riedel CU, Egert M. Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing. Front Microbiol 2017; 8:1331. [PMID: 28790981 PMCID: PMC5522855 DOI: 10.3389/fmicb.2017.01331] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/30/2017] [Indexed: 01/01/2023] Open
Abstract
The impact of the intestinal microbiota on human health is becoming increasingly appreciated in recent years. In consequence, and fueled by major technological advances, the composition of the intestinal microbiota in health and disease has been intensively studied by high throughput sequencing approaches. Observations linking dysbiosis of the intestinal microbiota with a number of serious medical conditions including chronic inflammatory disorders and allergic diseases suggest that restoration of the composition and activity of the intestinal microbiota may be a treatment option at least for some of these diseases. One possibility to shape the intestinal microbiota is the administration of prebiotic carbohydrates such as resistant starch (RS). In the present study, we aim at establishing RNA-based stable isotope probing (RNA-SIP) to identify bacterial populations that are involved in the assimilation of RS using anaerobic in vitro fermentation of murine fecal material with stable [U13C] isotope-labeled potato starch. Total RNA from these incubations was extracted, processed by gradient ultracentrifugation and fractionated by density. 16S rRNA gene sequences were amplified from reverse transcribed RNA of high and low density fractions suspected to contain labeled and unlabeled RNA, respectively. Phylogenetic analysis of the obtained sequences revealed a distinct subset of the intestinal microbiota involved in starch metabolism. The results suggest Bacteroidetes, in particular genera affiliated with Prevotellaceae, as well as members of the Ruminococcacea family to be primary assimilators of resistant starch due to a significantly higher relative abundance in higher density fractions in RNA samples isolated after 2 h of incubation. Using high performance liquid chromatography coupled to isotope ratio mass spectrometry (HPLC-IRMS) analysis, some stable isotope label was recovered from acetate, propionate and butyrate. Here, we demonstrate the suitability of RNA-SIP to link specific groups of microorganisms with fermentation of a specific substrate. The application of RNA-SIP in future in vivo studies will help to better understand the mechanisms behind functionality of a prebiotic carbohydrate and its impact on an intestinal ecosystem with potential implications for human health.
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Affiliation(s)
- Elena Herrmann
- Faculty of Medical & Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
| | - Wayne Young
- AgResearch Ltd., Food Nutrition and Health Team, Grasslands Research CentrePalmerston North, New Zealand
| | - Douglas Rosendale
- The New Zealand Institute for Plant & Food Research Ltd.Palmerston North, New Zealand
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of UlmUlm, Germany
| | - Markus Egert
- Faculty of Medical & Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
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RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1829685. [PMID: 28299315 PMCID: PMC5337319 DOI: 10.1155/2017/1829685] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria in a complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic conditions for 0, 2, and 4 h with 40 mM [U13C]glucose. Isopycnic density gradient ultracentrifugation and fractionation of isolated RNA into labeled and unlabeled fractions followed by 16S rRNA sequencing showed a quick adaptation of the bacterial community in response to the added sugar, which was dominated by unclassified Lachnospiraceae species. Inspection of distinct fractions of isotope-labeled RNA revealed Allobaculum spp. as particularly active glucose utilizers in the system, as the corresponding RNA showed significantly higher proportions among the labeled RNA. With time, the labeled sugar was used by a wider spectrum of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U13C]glucose, with lactate, acetate, and propionate being the principal 13C-labeled fermentation products, and suggested that "cross-feeding" occurred in the system. RNA-SIP combined with metabolic profiling of 13C-labeled products allowed insights into the microbial assimilation of a general model substrate, demonstrating the appropriateness of this technology to study assimilation processes of nutritionally more relevant substrates, for example, prebiotic carbohydrates, in the gut microbiota of mice as a model system.
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