Laboratory mice are often considered the scientific equivalent of identical twins – genetically identical and expected to look and behave the same. But new research from the Faculty of Science, Charles University, shows that this assumption doesn’t always hold true. The team discovered that the composition of the gut microbiota can dramatically influence the structure and function of the immune system – even in genetically identical animals. The study was published in the prestigious journal Gut Microbes.
“We were surprised by how much the absence of microbiota increased phenotypic variability. Germ-free mice were each a little different, while those with a normal microbiota were much more alike,” says Jan Pačes, first author of the article from the Laboratory of Cell Immunology at Charles University.
In addition to Peyer’s patches, the intestinal mucosa contains a rich assortment of smaller immune formations collectively referred to as SILT (scattered intestinal lymphoid tissue). Traditionally, these structures have been described as cryptopatches and isolated lymphoid follicles. In reality, their diversity is much greater – in the small intestine, one can find formations of various sizes and shapes, each with a unique cellular composition. In the image, all immune cells are shown in fuchsia, B lymphocytes in green, and T lymphocytes in red.
The researchers used a unique “green mouse” model (MHCII-EGFP knock-in), in which antigen-presenting cells can be visualized under a fluorescence microscope. This allowed for the first comprehensive quantitative mapping of gut-associated lymphoid tissues (GALT) – including Peyer’s patches, isolated lymphoid follicles, and mesenteric lymph nodes – in mice with different microbiota compositions: conventional (CV), germ-free (GF), and those colonized with the defined minimal microbiota OMM12.
Key findings include:
- Mice with a complex microbiota were more similar to each other than GF or OMM12-colonized mice.
- The absence of microbiota dramatically increased variability in the shape and size of gut immune organs.
- While OMM12 partly restored gut morphology, it failed to restore physiological immune cell numbers or fully replicate the functional immune status of conventional mice.
Along the way, the team also described a previously unknown immune structure – the immunovillus. This densely immune cell–packed villus-like projection was found mainly in mice with restricted microbiota and may represent an adaptation to a specific microbial environment.
The caecum is one of the key immune system centers in the digestive tract. The image shows the lymphoid tissue of the mouse caecum — displaying strikingly different organization depending on the presence of gut bacteria. The most compact structure is observed in mice with a normally diverse gut microbiota; in mice with reduced microbiota, these structures appear more sparse, and in animals completely lacking commensal bacteria, the original structure breaks down into individual lymphoid follicles.
Published in the high-impact journal Gut Microbes (top decile in the field), the study highlights the need to consider microbial context – not just genetics – when interpreting results from laboratory mouse models. Standardizing microbiota is essential for reproducibility, but current simplified microbial consortia such as OMM12 are not yet a perfect substitute for a natural complex microbiota.
Link to the article: DOI: 10.1080/19490976.2025.2543908