A solitary bacterium triggers the innate immune response in various ways. It can shed microbial elements such as lipopolysaccharides (LPS—sugar chains that dangle from bacterial cell walls) that act as MAMPs. Or it can be ingested by a dendritic cell that is feeling through the mucus layer for anything that is foreign—to name two. Bacteria do not want the innate immune response on constant alert. They become unhappy because they die. And more importantly to us, their macro-biont host becomes unhappy because he or she is sick (think about the last fever you had). An unhappy host leads to unstable bacterial communities. So our microbes have developed ways to dampen the immune response to their specific communities by passing signals through the mucus layer to the epithelial and immune cells that say, “shhh, all is well; we are here to work with you.”
Viruses and microbes are not passive participants in our holobiont, waiting for that moment when they can transform into vicious pathogens and make us sick. Just as our cells work to protect their biont territory and ensure genetic continuance, microbial cells do too. These bionts are feisty even if they aren’t deadly. They are working just as we are to grab the most energy from nutrients and to transform that energy into dissemination of their genes—fighting, nudging, grudgingly cooperating with each other. They are constantly acting inside of us, using the nutrient energy we bring in, to shape our guts and other aspects of our human bodies to their benefit. It is an orchestration of constant give and take.