A biomolecular isolation framework for eco-systems biology

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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DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

“…The moose rumen sample was collected from an animal in Småland, Sweden, within an hour after the animal was shot. DNA was extracted as described by Roume et al (21). The extracted moose rumen DNA was submitted to the Science for Life Laboratory for TrueSeq library preparation and sequencing on an Illumina HiSeq (Illumina, Inc.), generating paired-end sequence reads that were 100 bp in length.…”

Sources and Functions of Extracellular Small RNAs in Human Circulation

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