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How the Microbiome Influences Our Health
By YASEMIN SAPLAKOGLU

We are never alone. In addition to 30 trillion human cells, our bodies are home to some 39 trillion microbes — bacteria, fungi and protozoa that live in our gut, lungs, mouth, nose, skin and elsewhere throughout the body. The assemblies of organisms found in and on our body, the “microbiota,” are parts of broader microbial habitats, or “microbiomes,” that encompass all the viral and cellular genomes, encoded proteins and other molecules in their local environment.

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These microbes play many roles, from protecting against pathogens and tuning our immune responses to digesting food and synthesizing nutrients. Because of this, when a microbiome is thrown into disarray — such as through bad diet, infectious disease, medications or environmental factors — it can have a ripple effect on our health. Unhealthy microbiomes have been linked to cancer, heart and lung diseases, inflammation, and inflammatory bowel disease. Microbes are even thought to regulate the gut-brain axis, a communication highway that connects the brain to the enteric nervous system, which controls the intestines.

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What’s New and Noteworthy

Where does our microbiome come from? Several studies over the past year have yielded insights. Babies acquire most of their microbes from mom at birth and in the months that follow. But it turns out that mothers don’t only share microbial organisms with babies — they also share microbial genes. In a 2022 study published in Cell, scientists revealed that short sequences of DNA called mobile elements can hop from the mother’s bacteria to the baby’s bacteria, even months after birth. As I reported in Quanta, it’s likely that these genes could help seed a more capable gut microbiome in the baby, which in turn could further develop the baby’s immune system.

Transmission doesn’t only happen at birth. In fact, microbiomes are incredibly dynamic and can change drastically throughout a person’s lifetime. In a Quanta article published last year, I reported on the most comprehensive global analysis of microbiome transmission to date. Using new genomics tools, a team of Italian biologists traced more than 800,000 strains of microbes between families, roommates, neighbors and villages in 20 countries. They discovered that microbes hop extensively between people, especially between spouses and roommates, who spend a lot of time together. These findings suggested that some diseases that aren’t considered contagious might have a contagious aspect to them, if they involve the microbiome. However, that idea is speculative and will surely be debated and studied in the coming years.

Insights into how we acquire the microbiome and how it impacts our bodies don’t just come from studies of humans. Other animals also have microbiomes that are critical for their health and development — and several recent studies have drawn links between gut microbes and the brain. In 2019, Quanta reported that fear behavior differs between mice with different microbiomes, and in 2022 we reported on the ways microbiomes influence social skills and brain structure in zebra fish.
https://www.quantamagazine.org/how-microbiomes-affect-fear-20191204/?mc_cid=455286e60c&mc_eid=b89cb9fee3

Science published a paper describing how a diverse microbiota helps protect against pathogens by consuming a wide variety of nutrients — leaving fewer nutrients available for potential pathogens.
https://www.science.org/doi/10.1126/science.adj3502?mc_cid=455286e60c&mc_eid=b89cb9fee3

MIT Technology Review unpacked a fraught ethical conflict around how scientists conduct microbiome research. In search of healthful microbes that may have been lost from industrialized and sanitized populations, some researchers are collecting feces from hunter-gatherer societies — raising concerns in those communities about consent, equity and impact.
https://www.technologyreview.com/2023/12/18/1085384/the-hunter-gatherer-groups-at-the-heart-of-a-microbiome-gold-rush/?mc_cid=455286e60c&mc_eid=b89cb9fee3

Scientific American dove into research on the microbiome of the kākāpō, an endangered parrot from New Zealand, in hopes of garnering insights to save the birds from extinction.
https://www.scientificamerican.com/article/rare-animals-microbiomes-harbor-survival-secrets/?mc_cid=455286e60c&mc_eid=b89cb9fee3

Nature magazine reported on the discovery of “weird” flat circles of RNA, smaller than viruses, which the researchers called “obelisks,” and which colonize human gut microbiota.
https://www.nature.com/articles/d41586-024-00266-7?mc_cid=455286e60c&mc_eid=b89cb9fee3