Microbial ecologists are hampered by a lack of knowledge of the physiology and metabolic capacity of most microorganisms; in fact, many are characterized solely by their ribosomal DNA and nothing else. Genomic data, the holy grail for understanding the metabolic capabilities of an organism, is currently only available for those microbes which can be cultured in the laboratory due to a need for relatively large quantities of contaminant-free DNA. At present, community DNA sequencing can only provide fragmented and gene based information. With single cell genomics these difficulties can be circumvented and will allow for the sequencing of the masses. 
Results/Conclusions

Using flow cytometry and whole genome amplification we have succeeded in producing high quality genomic data from Escherichia coli and Bacillus subtilis. For organisms that can be cultured in the laboratory (even in a community context) we have also developed a technique for producing higher quality data by creating artificial polyploidy prior to cell sorting and genomic amplification. Single cell genomics will allow for a much greater understanding of environmental microorganisms and their ecological impact.