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A biomolecular isolation framework for eco-systems biology.

Roume H, Muller EE, Cordes T, Renaut J, Hiller K, Wilmes P - ISME J (2012)

Bottom Line: The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods.To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest.The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.

View Article: PubMed Central - PubMed

Affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.

ABSTRACT
Mixed microbial communities are complex, dynamic and heterogeneous. It is therefore essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single samples to facilitate meaningful data integration, analysis and modeling. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin columns. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest. The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.

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Related in: MedlinePlus

Three-way comparison of microbial community metabolomes obtained from a LAO-enriched microbial community, river water filtrate and human feces. Each dot represents the relative abundance of a metabolite in the three different environmental samples. Exemplary metabolite signatures for each microbiome are highlighted with their respective abundance levels on the right. Error bars represent s.d.
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fig6: Three-way comparison of microbial community metabolomes obtained from a LAO-enriched microbial community, river water filtrate and human feces. Each dot represents the relative abundance of a metabolite in the three different environmental samples. Exemplary metabolite signatures for each microbiome are highlighted with their respective abundance levels on the right. Error bars represent s.d.

Mentions: Use of the developed standardized methodology further allows comparative analysis of different microbiomes. For example, it has not escaped our notice that an apparent enrichment in small RNA exists in human fecal samples (Figure 4b). Furthermore, to highlight potential signature metabolites for the three analyzed microbial communities, we contrasted the relative abundances of detected metabolites for each microbiome. For this, the metabolomic data sets from the respective microbiomes were subjected to a three-way comparative analysis (Supplementary Materials and methods). Clear differences in the metabolite composition of the three microbiomes are apparent, allowing the identification of specific signature metabolites for three microbiomes (Figure 6). For example, the enrichment of docosanol, a saturated fatty alcohol, in the LAO-enriched microbial community from the wastewater treatment plant may be explained by the wide use of this molecule as an emollient, emulsifier and thickener in cosmetics, nutritional and pharmaceutical products. Consequently, its presence may be expected in domestic wastewater and through its chemical properties would be enriched in LAOs. The pronounced enrichment of mannose, a simple sugar, in river water filtrate may be a direct result of photosynthesis by the dominant phototrophic organisms. Finally, a comparatively strong enrichment in citric acid was found in the human fecal samples. An increase of all metabolites involved in energy metabolism including citric acid was previously found in the serum of mice conventionally raised versus germ-free mice (Velagapudi et al., 2010). Our present results indicate that this elevated level may directly result from the metabolic activities of microbial communities in the gastrointestinal tract.


A biomolecular isolation framework for eco-systems biology.

Roume H, Muller EE, Cordes T, Renaut J, Hiller K, Wilmes P - ISME J (2012)

Three-way comparison of microbial community metabolomes obtained from a LAO-enriched microbial community, river water filtrate and human feces. Each dot represents the relative abundance of a metabolite in the three different environmental samples. Exemplary metabolite signatures for each microbiome are highlighted with their respective abundance levels on the right. Error bars represent s.d.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526178&req=5

fig6: Three-way comparison of microbial community metabolomes obtained from a LAO-enriched microbial community, river water filtrate and human feces. Each dot represents the relative abundance of a metabolite in the three different environmental samples. Exemplary metabolite signatures for each microbiome are highlighted with their respective abundance levels on the right. Error bars represent s.d.
Mentions: Use of the developed standardized methodology further allows comparative analysis of different microbiomes. For example, it has not escaped our notice that an apparent enrichment in small RNA exists in human fecal samples (Figure 4b). Furthermore, to highlight potential signature metabolites for the three analyzed microbial communities, we contrasted the relative abundances of detected metabolites for each microbiome. For this, the metabolomic data sets from the respective microbiomes were subjected to a three-way comparative analysis (Supplementary Materials and methods). Clear differences in the metabolite composition of the three microbiomes are apparent, allowing the identification of specific signature metabolites for three microbiomes (Figure 6). For example, the enrichment of docosanol, a saturated fatty alcohol, in the LAO-enriched microbial community from the wastewater treatment plant may be explained by the wide use of this molecule as an emollient, emulsifier and thickener in cosmetics, nutritional and pharmaceutical products. Consequently, its presence may be expected in domestic wastewater and through its chemical properties would be enriched in LAOs. The pronounced enrichment of mannose, a simple sugar, in river water filtrate may be a direct result of photosynthesis by the dominant phototrophic organisms. Finally, a comparatively strong enrichment in citric acid was found in the human fecal samples. An increase of all metabolites involved in energy metabolism including citric acid was previously found in the serum of mice conventionally raised versus germ-free mice (Velagapudi et al., 2010). Our present results indicate that this elevated level may directly result from the metabolic activities of microbial communities in the gastrointestinal tract.

Bottom Line: The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods.To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest.The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.

View Article: PubMed Central - PubMed

Affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.

ABSTRACT
Mixed microbial communities are complex, dynamic and heterogeneous. It is therefore essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single samples to facilitate meaningful data integration, analysis and modeling. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin columns. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest. The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.

Show MeSH
Related in: MedlinePlus