Gut microbiota single cell

Gut microbiota single cell identification: increasing accuracy and resolution


Among the topics that are the subject of our Monitoring and Intelligence System’s activities, there is one that we think could be particularly interesting for our clients.

Have you ever heard anything about microbiota? If you are interested in animal nutrition, it is very likely that the answer is yes!

We like to think of microbiota as a community of many individual bacteria that are from many different species and that live symbiotically.

Considering that these commensal bacterial communities are strictly associated with the physiology of the host, it is expected that such community can change or even affect the health of the host.

Therefore, to understand these interactions, it is important to know what kind of bacteria (taxa) are in the microbiota and how many cells of each kind are in these bacterial communities.

Although measuring the microbiota composition at the single-cell level is difficult, good news comes from Japan where a new method called Barcoding Bacteria for Identification and Quantification (BarBIQ) has been developed. A key difference between BarBIQ and usual methods is that BarBIQ quantifies the number of cells for each OTU, while conventional methods measure the number of amplified sources of 16S rRNA gene molecules (i.e: 16S rRNA gene abundance from cells, genome copy number and extracellular DNA), which may affect the quantification of the intestinal microbiota.

Feature image: Pathompong Thongsan, licensed under iStock.

According to the results of the study recently published in Nature, BarBIQ approach allows the classification of single bacterial cells into taxa and quantifies how many cells there are in each taxon. Since BarBIQ can define microbiota at the single-cell level, it is expected that it can provide a deep and more accurate taxonomic classification and functional inferences of microbial ecosystems.

In the original work, Jin et al., (2022) demonstrate the usefulness of BarBIQ to robustly quantify cultured bacterial strains from the human gut in a model community. Furthermore, by applying this method to murine cecal microbiota, they were able to get a highly reproducible cell abundance quantification, showing also that BarBIQ allowed to discover that dietary vitamin A impacts the composition of microbiota in two different locations of the murine cecum.

This condition, that other methods were not able to identify, shows that BarBIQ can be able not only to visualize the global microbiota and individual bacterial members but also allows an effective understanding of gut microbiota functions.

Since BarBIQ enables microbiota qualitative and quantitative characterization at the single-cells level, we can say that the method is meant to be a keystone for microbiota studies.

Therefore, it could be very useful to develop new ingredients, additives, or nutraceutical products such probiotics or prebiotics.


Our client knows that we can help them to identify, characterize and quantify microbial populations and strains present in their products.

And you? Are you aware that DATAOMICS can assist you in the development of new microbiota-based products?

If you are curious to explore this field…

Contact us!

Reference of the open access paper:

Jin, J., Yamamoto, R., Takeuchi, T. et al. High-throughput identification and quantification of single bacterial cells in the microbiota. Nat Commun 13, 863 (2022).


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