NGS-based microbial contaminant identification
A manufacturer of bottled juices for consumption noticed debris in juice bottles as well as a sour, bad odor. Attempts to obtain microbial isolates from the juices …Read more
Microbial communities are the dominant life form on our planet. Even your body hosts as many bacterial cells as it does your own cells. Genomics and bioinformatics tools can unlock this hidden world and allows to explore the microbial diversity, composition and functional capacity of these communities. Studying microbial communities, also referred to as metagenomics, is of fundamental interest for understanding the biosphere. In addition this offers great promise for utilising the most numerous organisms on the planet to improve our own quality of life.
Metagenomics is a relatively new field that studies the presence and interactions of microorganisms in a sample. Increased realisation of the importance of microorganisms and the microbiome comes at a time when Next-Generation Sequencing techniques that enable the investigation of microbial communities have become both easier and cheaper. The number of microbial diversity and metagenomics studies has exploded in the last years. For this reason many researchers want to know how to succesfully implement a workflow for microbial diversity studies. A typical microbial diversity study comprises the following steps:
The first step for metagenomics is the sampling. This has to be done very precise, as this can introduce first bias. E.g. when soil samples are investigated, sampling next to the roots of a plant or one cm away from it will lead to a significant difference in microbial composition. Secondly from the samples the genetic material needs to be isolated from the samples. Especially when you want to quantify the amount of microorganisms this is a crucial step. Many isolation methods will introduce a bias, as some bacteria will lysate more easily than others. The preferred isolation method may even differ for different sample types, like faeces, water or soil samples. Read more about the importance of nucleic acid isolation in this blog. After isolation of the genetic material the material needs to be prepared for sequencing and a sequencing technology needs to be selected. Also these are criticial steps for the outcome of your microbial diversity study.
The last step of your study is the bioinformatics analysis, including read mapping, annotation and metagenome assembly. The right tools need to be selected for accurate taxonomic classification, quantification of microbial communities and species richness (so-called alpha diversity). In addition, functional properties of the microorganisms in the samples are reviewed by adding annotations and via metabolic pathway reconstruction. Also for this the optimal pipelines need to be selected for data analysis and presentation of the data.
Since there are many pitfalls in these kind of studies, implementing a workflow for microbial diversity and metagenomics studies is challeging. When you would like to consult one of the BaseClear experts, don’t hesitate to contact us via our contact form. We are happy to discuss how we can help you get started.
Patrick Koning – Marketing director BaseClear B.V.