Protein-Lipid Communication between Intestinal Cells and Gut Microbes Boosts Immunity in Mice

The human gut is home to trillions of microbes that not only aid in digestion but also play a key role in shaping our immune system. These microbes communicate with the body by releasing a range of molecules that influence how immune cells grow and function.

To maintain a healthy balance between host defense and microbial coexistence, the body deploys a variety of defense tools—such as mucus, antimicrobial proteins, antibodies, and complement proteins—to control microbial activity and fend off harmful invaders. But one question lingers. And that is, can our bodies selectively recognize and manage specific bacteria among this incredibly diverse microbial community?

A research team headed by Qian Youcun, PhD, from the Shanghai Institute of Nutrition and Health (SINH) of the Chinese Academy of Sciences (CAS), and Song Xinyang, PhD, at Center for Excellence in Molecular Cell Science of CAS, turned to germ-free and conventional laboratory mice to investigate this question. Their study uncovered a surprising new way that the body interacts with gut microbes to help maintain intestinal health, and is the first, the team suggests, to show that the host can selectively target specific microbes by recognizing their unique lipid signatures. The results could point to new possibilities for developing next-generation treatments that work by tuning interactions between the microbiota and the immune system.

The team reported on their findings in Nature, in a paper titled “Targeting symbionts by apolipoprotein L proteins modulates gut immunity.”

The microorganisms inhabiting the mammalian gut live in symbiosis with their host, the authors wrote. “These microorganisms facilitate nutrient absorption and metabolism, as well as directing the development of the host immune system through various metabolites or structural molecules they produce.” As the intestinal immune system matures it also develops “sophisticated defence mechanisms” to cope with immunological challenges, both from its own microbiota and from invading pathogens, the authors further explained. They were interested to investigate whether the host can evolve tactics to selectively target specific microbiota, and also “how this immune-microbial mutualism benefits the development and functionality of the intestinal immune system.”

The researchers began by using advanced protein analysis techniques to compare gut lining samples from germ-free mice and conventional lab mice. This comparison led to the identification of a previously less characterized protein called APOL9, which was much more abundant in regular mice with gut microbes. “Apol9a/b belong to the APOL family and have been identified as interferon-stimulated genes,” they noted. “However, they have not been associated with targeting commensal microorganisms.” Further experiments showed that this protein was mainly produced by cells in the intestinal lining.

Their results, they noted, “… suggest that both mouse and human gut APOL molecules bind to microorganisms in a conserved manner and have a preference for engaging Bacteroidales species within the gut microbiome.”

Digging deeper, and focusing mechanistic studies on Bacteroides thetaiotaomicron, the researchers discovered that APOL9’s ability to recognize these bacteria depends on a unique fat molecule called ceramide-1-phosphate (Cer1P), which is found on the bacterial surface. When this molecule was removed using gene editing, APOL9 could no longer bind to the bacteria. Their study finding, they reported, “suggest that both mouse and human APOL proteins are likely to bind to commensal Bacteroidales species through their membrane anionic Cer1Ps rather than other lipids.”

Interestingly, unlike typical antimicrobial proteins that kill bacteria, APOL9 does not harm the microbes it binds to. It causes them to release tiny bubbles called outer membrane vesicles (OMVs)—nanometer-sized sacs filled with bacterial molecules. These OMVs can be taken up by the host’s immune system and used to boost immune readiness. The researchers found that OMVs enhance interferon-gamma (IFN-γ) signaling and increase the amount of MHC-II molecules on intestinal cells. These latter molecules are essential for training a unique group of T cells (CD4+CD8αα+) that help maintain immune balance in the gut. Ileal CD4+CD8αα+ intraepithelial lymphocytes (IELs) have been shown to possess both cytotoxic and regulatory properties, the authors noted, and are “crucial for maintaining immune tolerance and anti-infection responses in the gut.”

To better understand APOL9’s role in immune defense, the researchers used a widely accepted mouse model to study the effects of removing the gene. When exposed to Salmonella typhimurium (STm) bacteria, mice lacking APOL9 showed a weaker immune response and more widespread bacterial infection. “Our findings indicated that APOL9a/b neither directly bound to and killed STm nor were required for the intracellular clearance of the organism,” they noted. However, when treated with OMVs derived from the bacteria, these mice displayed stronger immune activity and fewer signs of infection. “… mice deficient in Apol9a/b exhibited higher mortality rates … more severe gut inflammation … and greater gut bacterial burden and dissemination to non-gut organs … whereas OMV administration ameliorated STm infection in Apol9a/b-deficient mice.”

“The specific interaction between APOL9 and Cer1P highlights a finely tuned molecular ‘dialogue’ forged through long-term coevolution between the host and its microbiota. In the future, we plan to explore the role of human APOL2 and investigate whether modulating this pathway can strengthen the intestinal immune barrier,” said study research lead Qian.

This study is the first to show how a host protein can specifically recognize bacterial lipids, thus triggering beneficial immune responses. It also highlights a new way the body actively shapes the gut microbiome—not just by tolerating microbes, but by communicating with them to maintain balance. “These findings also improve our understanding of how hosts benefit from mutualistic relationships with commensal bacteria through the microbiota-targeting proteins they deploy,” the authors concluded. “Our data show how a host-elicited factor benefits gut immunological homeostasis by selectively targeting commensal ceramide molecules.”