Spatial map provides a new view of the gut flora

What microbes are in your gut and where are they?

Researchers at Cornell University have developed imaging tools to create complex spatial maps of the locations and identities of hundreds of different microbial species, including those that make up the gut flora. This tool helps scientists understand how complex communities of microorganisms interact with each other and their environment, that is, us.

Team treatise, “Highly multiplexed spatial mapping of microbial communitiesWas published in Nature on December 2nd. The lead authors of this treatise are Hao Shi and M. Eng, doctoral students. ’18.

“There is a community of bacteria that live in our bodies and play an important role in human health and biology, and these microorganisms are rich in diversity. This is a list of bacterial species that exist in the community. You can tell from technologies such as DNA sequencing that create the. ” Iwijn De Vlaminck, Robert N of Life Science and Technology at Meinig School of Biomedical Engineering. Associate Professor Noyce and lead author of the treatise.

“But the tools for understanding the spatial interactions between these microorganisms are very limited, and these are the metabolism of these communities and how these microorganisms interact with their hosts. It’s very obviously important to understand, “he said.

De Vlaminck and Shi set out to create an imaging method using a two-step process called microbiome mapping with high phylogenetic resolution by fluorescence in situ hybridization (HiPR-FISH).They collaborated with co-author’s lab Warren Zip Fell, Associate Professor of Biomedical Engineering, and Iranabrit, Associate Professor and Mong Family Sesquicentennial Faculty Fellow of Biomedical Engineering incorporates additional imaging and microbiome expertise.

To identify microbial communities, researchers designed oligonucleotide probes that target specific bacterial cells based on the presence of the signature gene sequence 16S ribosomal RNA, and labeled the cells with another fluorophore. I have created a probe for a group. The team then laser-illuminates the fluorescent marker using a confocal microscope, decodes the fluorescence spectrum using machine learning and custom software, interprets the image, and is efficient and costly at single-cell resolution. We have created a highly effective technology.

Researchers have created a palette of spatial maps with a mixture of 10 basic colors, each capable of “painting” a total of 1,023 possible color combinations of E. coli fluorescently labeled with a unique binary barcode.

“The imaging itself leads to a very beautiful and rich image where all the bacterial cells are in different colors,” says De Vlaminck. “But for a quantitative understanding of microbial interactions, cell-cell distances, cluster size, etc., these can be interpreted in a computer-automated way so that this image can be converted into a digitized representation. Must be a community. “

The team applied the technology to two different systems: the mouse gut flora and the human oral plaque microflora. In the case of the gut flora, we were able to demonstrate how antibiotic treatment disrupts the spatial relationships between different bacteria.

Spatial mapping can be an important tool for studying and, in some cases, treating a variety of bacterial-induced diseases, including inflammatory bowel disease, colorectal cancer, and infectious diseases.

“We’re trying to dig deeper into the biology of systems where the microbiome plays an important role and understand how these types of spatial dynamics change in the presence of ongoing disease,” Shi said. Stated. “I would like to see if it provides clues and therapeutic insights that can be used to help people.”

The co-author is Benjamin Grodner, a doctoral student. Researcher Joan Sessing Lenz. Research support specialist Qiaojuan Shi.

The study was supported by Kavli Institute, Cornell University Nanoscale Science Institute And the National Institutes of Health (NIH). Researchers used the Cornell BRC-Imaging Facility, which is supported by New York State Stem Cell Science and NIH.