Community Fingerprinting

Community fingerprinting is a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present. In general, it is assumed that each different gene variant represents a different type of microbe. Community fingerprinting is used by microbiologists studying a variety of microbial systems (e.g. marine, freshwater, soil, and human microbial communities) to measure biodiversity or track changes in community structure over time. The method analyzes environmental samples by assaying genomic DNA. This approach offers an alternative to microbial culturing, which is important because most microbes cannot be cultured in the laboratory. Community fingerprinting does not result in identification of individual microbe species; instead, it presents an overall picture of a microbial community. These methods are now largely being replaced by high throughput sequencing, such as targeted microbiome analysis (e.g., 16s rRNA sequencing) and metagenomics. Community fingerprinting is a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present. In general, it is assumed that each different gene variant represents a different type of microbe. Community fingerprinting is used by microbiologists studying a variety of microbial systems (e.g. marine, freshwater, soil, and human microbial communities) to measure biodiversity or track changes in community structure over time. The method analyzes environmental samples by assaying genomic DNA. This approach offers an alternative to microbial culturing, which is important because most microbes cannot be cultured in the laboratory. Community fingerprinting does not result in identification of individual microbe species; instead, it presents an overall picture of a microbial community. These methods are now largely being replaced by high throughput sequencing, such as targeted microbiome analysis (e.g., 16s rRNA sequencing) and metagenomics. A fingerprinting analysis begins with an environmental sample (e.g. seawater or soil), from which total DNA is extracted. (Total DNA contains a mix of genetic material from all the microbes present in the sample.) A particular gene or DNA region is then selected as a target for analysis, under the assumption that each microbe species will have a different gene variant (also called a 'phylotype'). Different methods (see below) can be used to visualize the phylotypes present in a sample. Because the aim of community fingerprinting is to gain an overall understanding of community structure, it is a particularly useful technique for analyzing time-series data collected from the field. For example, one could study the pattern of microbial succession in a habitat, or one could examine the response of a microbial community to an environmental perturbation, such as the release of a pollutant. Depending on what information is desired, different genes may be targeted. The most common are small subunit ribosomal RNA (rRNA) genes, such as 16S rRNA. These genes are frequently used in microbial phylogenetic analyses, so well-established techniques exist for their study. Other genes of interest might be those that are key in various metabolic processes. The advantages of community fingerprinting are that it can be performed quickly and relatively cheaply, and the analyses can accommodate a large number of samples simultaneously. These properties make community fingerprinting especially useful for monitoring changes in microbial communities over time. Also, fingerprinting techniques do not require one to have a priori sequence data for organisms in a sample.A disadvantage of community fingerprinting is that it results in largely qualitative, not quantitative data. When using qualitative data, it can be difficult to compare patterns observed in different studies or between different investigators. Also, community fingerprinting does not directly identify taxa in an environmental sample, though the data output from certain techniques (e.g. DGGE) can be analyzed further if one desires identification. Some authors point to poor reproducibility of results for certain fingerprinting methods, while other authors have criticized the inaccuracy of abundance estimates and the inability of some techniques to capture the presence of rare taxa. For example, it is difficult for the DGGE method to detect microbes that comprise less than 0.5%-1% of a bacterial community.