One of my favorite papers of all time is Mark Davis’ (Stanford) 2015 paper: “Variation in the human immune system is largely driven by non-heritable influences.” Davis and team found that the human immune response is “very much shaped by the environment and most likely by the many different microbes an individual encounters in their lifetime.” In 2018 many studies added to this topic, including these two:

Microglial control of astrocytes in response to microbial metabolites

Lead author: Francisco J. Quintana, Harvard Medical School

The team found that, in a mouse model of multiple sclerosis, tryptophan created by the gut microbiome interacted with the AHR receptor on microglia/astrocytes. Subsequent changes in gene expression regulated communication between the cell types. The study is a great example of a growing trend: microbial metabolites can control immune signaling.

Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System.

Lead author: Paul Bollyky, Stanford University School of Medicine

Interaction of bacteriophages with mammalian immune cells (Bollyky et al)

The paper clarifies that bacteriophages (phages) directly interact with human cells +  impact/modulate the human immune response. It provides examples of how phages can modulate innate immunity via phagocytosis and cytokine responses. Phages can also impact adaptive immunity via effects on antibody production. The team also presents a computational model for predicting these complex and dynamic interactions. These models predict that phages may play important roles in shaping mammalian-bacterial interactions.