The research used gnotobiological or germ-free mice that are raised so that, from their birth, they do not have any bacteria in the body and act as blank slates in which to observe what happens when they are colonized by bacteria . Well, after populating the organism of these rodents with microbes from mice raised in a conventional way, what was seen was that, although the composition of the microbial input largely determined the microbiome of the recipient mice, the genetic differences between the strains of mice too.
“When the input is standardized, you can compare mice of different genetic strains and see what this genetics does to the microbiome in recipient mice,” said Alexander Chervonsky, lead author of the new study published in Cell Reports and Chairman of the Committee on Immunology at the University of Chicago. “This approach allowed us to know if there was a genetic influence, and indeed there is . So the next question was:” What mechanisms are involved? “
One of the challenges microbiome researchers faced is that it can be difficult to compare the results of experiments due to “inherited effects.” When scientists transfer microbes from one mouse to another, the result is largely determined by the microbiome of the source animal , what kind of food it eats, where it lives … So even if researchers in two different laboratories use exactly the same breed of mice with the same genetic background, they will see two different images when they analyze the microbiome of the recipients. “Entry defines exit,” Chervonsky said.
To overcome this, Chervonsky and study co-author Tatyana Golovkina transferred microbes from a conventionally bred mouse to many genetically identical and gnotobiological rodents . The researchers repeated the operation many times, transferring microbes from a single mouse to many recipients, some with similar genetic backgrounds and others with minor differences in their immune systems. They later worked with pathologist Aly A. Khan and Argonne National Laboratory microbiologist Dionysios Antonopoulos to analyze the resulting microbe genome sequences in recipient mice and their offspring and compare the effects of different immune system genes.
Animals have two primary types of immunity: innate immunity , which uses standard and hard-wired mechanisms to defend against pathogens, and adaptive immunity which “learns” as it encounters different pathogens and uses T cells and B cells to target. to its unique recipients. Some of the Chervonsky and Golovkina mice used in the experiments were genetically the same, except for differences in part of the genome called the major histocompatibility locus (MHC), which determines adaptive immunity.
When they examined how these different immune mechanisms shaped the microbiomes of recipient mice, the researchers found that while adaptive immunity had some effect on certain strains of bacteria , overall the effects were not dramatic. In some cases, the bacteria even took advantage of the adaptive immune response to thrive. Instead, most of the differences they saw could be attributed to innate polymorphic genes, or to different gene variations in the MHC.
“Manipulation of the adaptive system leads to some changes, but to our surprise, they were not dramatic,” Chervonsky said. “The vast majority of the mechanisms that determine the differences in outcome are those that are polymorphic but are not part of the adaptive immune response.”
Golovkina said she hopes this work will serve as an example to standardize microbial studies. The gnotobiotic facility is a key component of ongoing research on the immune system, genetics, and microbiome under the umbrella of the Duchossois Family Institute at the University of Chicago. Using standard tools such as germ-free mice to carefully monitor the conditions of the experiments, researchers can build on previous work rather than conducting single, independent experiments.
“There are standards in many different types of research, but they are almost non-existent in microbial research,” Golovkina said. “We are trying to establish a standard of analysis for these questions on how to compare differences in microbial composition.”
Referencia: “Polymorphic immune mechanisms regulate commensal repertoire,” was supported by the National Institutes of Health, the Department of Defense and the National Institute of Diabetes and Digestive and Kidney Diseases. Additional authors include Leonid Yurkovetskiy (currently at the University of Massachusetts), Joseph Pickard (currently at the University of Michigan), Kelly O’Grady and Renée de Pooter from the University of Chicago.
