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Microbiome studies have traditionally fallen into studies of who’s there and what are they doing. To address these questions, biologists often use next-generation sequencing. Sequencing the 16S rRNA reveals the identity of the organisms present while sequencing of all transcripts gives clues into what the microbes are doing.

But aside from sequencing, scientists can also study the microbiome by using engineered genetic tools and reporter microbes. Let’s take a look at a few of these methods below.

When you think about going to a scientific conference, you may think about sitting amongst a sea of chairs listening to talks all day. But nope, not at the American Society for Microbiology 2018 Microbe meeting. Soon after I arrived, I was looking through a paper-based, affordable, and portable microscope called the ‘foldscope’ (Dr. Prakash, Stanford University). Right there on the floor outside the lecture hall.

Knowing where bacteria are located within their host is often key to understanding their role in both health and disease. To observe bacteria in action, researchers have developed in vivo bacterial reporters that use fluorophores and luciferases to track bacteria in real time, but each of these reporters has its drawbacks. Acoustic reporter genes (ARGs) overcome these limitations by using gas vesicle reporters that are detectable by an inexpensive and widely available imaging platform: ultrasound.

Here at Addgene, we often refer to plasmids as lab or experimental tools. They certainly are very handy in research, but where did these tools come from and why do they exist in nature? Read on to learn more about environmental plasmids, and how they’ve helped us develop molecular biology tools for the lab.

Restriction enzyme cloning is the workhorse of molecular cloning; however, one of its biggest limitations is that sequence modifications can only be made at restriction enzyme cut sites. The lambda red system is an alternative method that can be used for cloning or genome engineering and is based on homologous recombination. It allows for direct modification of DNA within E. coli and is independent of restriction sites. The lambda red system is derived from the lambda red bacteriophage and its use as a genetic engineering tool is frequently called recombineering - short for homologous recombination-mediated genetic engineering.  It can be used to make an assortment of modifications: insertion and deletion of selectable and non-selectable sequences, point mutations or other small base pair changes, and the addition of protein tags. It also has the flexibility to modify the E. coli chromosome, plasmid DNA or BAC DNA.