Imaging of microbiomes by atomic force microscopy is a fast and efficient method to get an overview of the microbial diversity and the overall structure of the microbiome. Distinct microbiomes occupy many habitats in the environment and are especially relevant in human health. Human microbiomes are essential to the epithelia they live on, form symbiotic relationships with the human cells and help defend against many pathogenic invaders.

Human microbiomes have become a focus area in medical microbiology as we discover how much of an impact they have on our health and how they could potentially be used to treat diseases. Especially the gut microbiome has received a lot of attention because of the many health conditions it is involved in. The oral and skin microbiomes shown below are also interesting because the underlying epithelia naturally slough cells that are easy to pick up noninvasively and analyze.

Oral microbiome samples collected from cheek swabs. The overview image shows several epithelial cells bound together. These cells are disc-shaped, about 50 um in diameter and around 1 um tall, and are almost completely keratinized. An individual cell shows two different types of bacteria on its surface, two long bacilli and a few isolated cocci. After eating, the number of bacteria increases dramatically.

Skin microbiomes are also easy to collect by gently scraping or blotting. Skin epithelial cells show more pronounced stress fibers and bacteria are mostly found in better protected areas between cells.

Human microbiomes are also perfect test subjects for correlative light and atomic force microscopy done here on and LS-AFM. This setup allows standard light microscopy imaging that is routinely used in microbiology diagnostics, and adds micro to nanoscale information of a defined area. The LS-AFM is also designed to perform these experiments in liquid, allowing measurements on live cells.

An oral microbiome imaged correlatively by bright field light microscopy and atomic force microscopy, leading to re-interpret the light microscopy data. Where do you think you see bacteria and where are they really?

Once again, the AFM shines because of the minimal sample preparation and the quick nanoscale data it can deliver on microbiome samples. The TT-2-AFM is fully sufficient to study microbiomes as most features are at least several nanometers tall.  An HR-AFM with superior noise floor is only needed when measuring individual biomolecules like DNA and proteins. Both TT-2 and HR-AFM can be used with the dunk and scan liquid scan cell to image live microbiome samples in medium or buffers, and the top view microscope can deliver reflective correlation with microscale features. When correlation with transmitted brightfield or fluorescence light microscopy is needed, the LS-AFM is used, either dry or in liquid. Microbiome samples can also be stained (e.g. gram stain or live-dead fluorescence assays) and correlative imaging can be performed before coverslipping.