Scientists headed by a team at the University of Chicago have shown how genetic differences in the immune system can impact on the types of bacterial communities that colonize the gastrointestinal system. Their studies, in germ-free mice colonized with microbiomes from conventionally reared animals, found that while the makeup of the donor microbiome was the key factor in determining the recipient microbiome, genetic differences in the immune systems of the recipients also played a role. “When the input is standardized, you can compare mice of different genetic strains and see what these genetics do to the microbiome in recipient mice,” said Alexander Chervonsky, MD, PhD, who is a senior author of the team’s study, which is published in Cell Reports. “This approach allowed us to tell whether there was a genetic influence, and indeed there is.” Chervonsky and colleagues report their findings in a paper titled, “Polymorphic Immune Mechanisms Regulate Commensal Repertoire.”

The bacteria that naturally live in and on us provide essential functions that are required for our very survival, the authors wrote. The composition of microbial communities varies between individuals and is influenced by a range of factors, including “… the mode of transmission during birth, breastfeeding, alimentary infections, and diet.” Previous studies have suggested that host genetics can also impact on microbial communities—identical twins tend to have more similar microbiomes than do non-identical twins—but, as the team continued, “ … two important questions remain unanswered: to what extent and which host’s polymorphic mechanisms are involved in shaping the repertoire of the commensals.”

It’s not possible to genetically modify humans, so these types of questions are investigated using animal models, which also has “intrinsic problems,” the authors commented, due to “legacy,” or “batch” effects when using the same mouse strains at different experimental institutions. “These discrepancies arise because, even with other environmental factors held constant, variation in the colonizing input microbiota define the outcomes,” the team noted. Effectively, the results of transferring microbes from one mouse to another are largely determined by the microbiome of the source animal, what kind of food they eat, where they live, etc. Even if researchers in two different labs use the same breed strain of mice with the same genetic backgrounds, the microbiome of recipients won’t be exactly the same. “Input defines the output,” Chervonsky said.

To overcome these issues, Chervonsky, who is a microbiome researcher, and microbiologist Tatyana Golovkina, PhD, co-senior author of the reported study, placed highly controlled constraints on their experiments. They transferred the microbiome from one conventionally raised mouse to many genetically identical mice held at the University of Chicago’s gnotobiotic—germ-free—mouse facility. These animals are bred and raised to completely lack bacteria in their bodies, including their digestive tracts, so that they represent a blank slate for microbiome transfer research.

Chervonsky and Golovkina carried out numerous studies where they transferred the microbiomes from one source mouse to different recipients, some of which had the same genetic backgrounds and some with slight differences in the genetic makeup of their immune systems. The team then worked with Aly A. Khan, PhD, a pathologist at the University of Chicago, and Dionysios Antonopoulos, PhD, a microbiologist from Argonne National Laboratory, to analyze the genomes of microbiomes in the recipient mice and their offspring, and to compare the effects of different immune system genes.

“First, we sought to define to what extent the input microbiota determines the outcome of colonization experiments,” the investigators explained. “Second, we sought to test whether the abundance of specific microbes was associated with the genetic background of the host.”

The immune system comprises innate, or hardwired mechanisms to fight of invading pathogens, in combination with adaptive immunity that learns as it encounters different pathogens and uses T cells and B cells to target unique receptors on foreign invaders. The authors reasoned that, “the microbiomes are likely shaped by different forces, including immune (innate and adaptive) mechanisms, which differ in the ways that they sense the microbiota and in the effector mechanisms triggered by recognition. Adaptive mechanisms based on T-cell reactivity and/or T cell-dependent antibody responses rely on antigen presentation by molecules of the major histocompatibility complexes (MHCs) expressed on the surface of specialized cells.”

The researchers found that while adaptive immunity had some effect on certain strains of bacteria in the resulting microbiomes, the overall effects of this were relatively minor. In some cases, bacteria took advantage of the adaptive immune response to thrive. Chervonsky and Golovkina also tested microbiome transfer into mice that were congenic, or genetically the same, except for differences in part of the genome’s MHC locus, which determines adaptive immunity. They found that the majority of differences in recipient microbiome could be attributed to innate polymorphic genes, or different variations of genes in the major histocompatibility complexes.

“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 differences in the outcome are those which are polymorphic but not part of the adaptive immune response.” The researchers say the implications of their findings are that “total control over the enormous body of microorganisms by the host immunity is unlikely (probably due to its extremely high cost) and that both non-polymorphic control mechanisms and other natural forces could be involved.”

“The host’s polymorphic mechanisms affect the gut microbiome, and both innate (anti-microbial peptides, complement, pentraxins, and enzymes affecting microbial survival) and adaptive (MHC-dependent and MHC-independent) pathways influence the microbiota,” the authors concluded. “However, we find it remarkable that the host-determined polymorphic influences on microbial composition are limited in scope and target only select microbial lineages.”

Golovkina hopes this work will set an example for how to standardize microbiome studies. Using standard tools like germ-free mice to carefully control the conditions of experiments, researchers can build upon previous work instead of conducting one-off, standalone experiments. “We expect that further carefully arranged and controlled studies of genetically modified gnotobiotic animals using engineered communities of different complexities will elucidate the input of individual genetic mechanisms in host-commensal symbiosis,” the researchers commented.

“There are standards in many different types of research, but they’re almost nonexistent in microbiome research,” Golovkina said. “We’re trying to set up a standard of analysis for these questions about how to compare differences in microbial composition.”

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