Mention the word bacteria, and most of us will think of the worst things. In reality, there are good bacteria and bad bacteria, and the former are critical for our health and survival. Most of the friendly bacteria inside us reside in our gut, namely the stomach, and small and large intestines. There, they coexist with a motley group of other microorganisms numbering in the trillions. These include archaea (closely related to bacteria), fungi, parasites and viruses. Picture a bustling city on a weekday morning, the sidewalks thronging with people rushing to get to work or to appointments. At a microscopic level, that is how this huge colony of microbes – known as our microbiota – looks like. And the “city” they reside in is called the microbiome. In a healthy person, these “bugs” coexist peacefully; the microbiome is even labeled a supporting organ because it plays so many key roles in promoting the smooth daily operations of the human body, from the gut to the immune system and the skin.

Each of us has a unique microbiota that is originally determined by our DNA inherited by birth. Later on, environmental exposures and diet can change our microbiome, making it more or less resilient to disease. Regardless of how it evolves over time, the good bacteria in our microbiome are indispensable to our health. They regulate our digestive functions by ensuring that the right food gets properly processed and that toxins are neutralized. They also regulate the immune system by producing short-chain fatty acids (SCFA) that control inflammatory responses to protect the health of cells lining the gut and the skin. They even help fight viral infections by producing specialized proteins to detect invading viruses and striking them before they do greater damage. This is a new discovery, first reported in a 2022 issue of the prestigious journal, Science. Said Alex Gao, a biochemist at Stanford University and lead author of the paper: “We tested 24 different phages (viruses that solely target and kill bacteria) spanning nine phage families, and found that there was almost this across-the-board activation” of Avs. The proteins were recognizing three-dimensional folds and shapes of the viral proteins, and not their DNA sequences. This form of protein shape recognition doesn’t have a lot of precedent in molecular biology.” [1]

Once detected, the good bacteria strike out at the phages, killing them but also killing their own kind. While this may sound like cellular suicide, bacteria live in colonies with strong genetic similarity. By destroying themselves, infected cells can protect neighbors that are essentially their twins, which makes perfect sense as an evolutionary strategy.

Note

[1] Alex Gao et al. Prokaryotic innate immunity through pattern recognition of conserved viral protein. Science, 12 Aug 2022, Vol 377, Issue 660