You are born a blank slate, your ecosystems barren. As you emerge, you’re likely swathed in a mix of vaginal juices, dominated by lactobacillus. Your mother’s body is teeming with colonies—each interaction with it is an opportunity to culture your new body. For the next six months, your immune system is depressed to make room for colonization, especially of your digestive system: your gut microbiome.
These bacteria will help you digest and will protect you against pathogens. Your gut goes through what ecologists call succession—successive generations of organisms that settle into a lasting stability. These now-stable ecosystems comprise about half of your body’s cells and over 10,000 species.
In his book I Contain Multitudes: The Microbes Within Us and a Grander View of Life, Ed Yong compares the human body to an archipelago—each body part is an island that contains its own balanced ecosystem. Some of the islands may be inches apart in terms of space (like the large intestines and the vulva), but they’re worlds apart in terms of microbial diversity, with ecosystems as different as jungle, forest, desert.
We are in the age of disintegration, collapse, extinction, loss of diversity. It’s no less true for the invisible ecosystems of our skin, our stomachs, and our noses. For our invisible ecosystems though, the devastation is fueled by modern medicine. Imagine a terrorist on the loose in NYC, says Mark Smith, CEO at Finch Therapeutics, which develops microbiome therapeutics. “Rather than sending out a SWAT team for them, we’re just going to nuke the whole city.” This is the broad-spectrum antibiotic approach. “It’s important, and it saves peoples’ lives, but there’s a lot of collateral damage, and I think we’re really just starting to understand some of the potential consequences of that.”
In one of the most dramatic immediate consequences of antibiotic use, they can leave behind a devastated landscape ripe for an opportunist called C. Difficile. C. Diff is already present in about a third of people, but when the gut ecosystem is disrupted (through sometimes just a single course of antibiotics), it takes over, wracking the body with diarrhea, abdominal cramping, and ultimately kidney failure. The treatment, ironically, is more antibiotics, which sometimes works, but sometimes leaves patients vulnerable and with recurrent reinfections.
The biotic resistance hypothesis in invasion ecology posits that healthy, diverse ecosystems are much less likely to be vulnerable to an invasive species. The places we see these invaders take over without abandon (see kudzu in the Southeastern U.S.) are often those previously disturbed by humans. Holly Jones, associate professor of conservation biology and restoration ecology at Northern Illinois University, says, “As conservation biologists, the goal is to have the most diversity that you could possibly have, so that when your system gets hit by whatever stressor it is—say it’s like a drought or a flood or a fire or whatever—you have species that are adapted to those things.”