The human microbiome is hot stuff these days. Hard to imagine we have only gained some understanding of its existence and importance since the Human Microbiome Project kicked off in 2008. Beneficial gut bacteria, it turns out, are very hard to study because they live an anaerobic (oxygen-free) life in our intestinal tract. It was only when their DNA could be studied (metagenomics) that we began to understand how big a deal they were in human health. A very big deal indeed, as they are thought to number in the trillions. Our understanding of their diverse identities can barely be described as sketchy.
I’ve been browsing my way through Missing Microbes. I love this book. Its author, Martin Blaser, is an MD who has been researching a much discussed bacterium, Heliobacter Pylori, for over 30 years. H. pylori, which has colonized the human gut for more than 50,000 years, was determined by the winners of the 2005 Nobel Prize in Physiology to be the cause of peptic ulcers which had previously been ascribed to stress. The bacterium has also been associated with stomach cancer.
But Blaser also believes H. pylori plays an important immunological role, and that our all-out antibiotic assault on it may be costing us in more ways than the increasing rates of antibiotic resistance which the Nobel winners had also predicted. Blaser and others speculate that since its loss in Western populations correlates to increases in autoimmune disorders, there may be more to this ancient bacterium that has for so long co-existed in the human gut. Adults who lack H. pylori may also be more susceptible to reflux (GERD) and heartburn that can themselves lead to esophageal cancers. And there is some evidence that it protects against allergies and asthma in childhood.
Blaser has a lot to say about antibiotic use in modern medicine as well as modern farming, and how these have contributed to making the modern microbiome a biological desert, and landed humans in a completely new and dangerous medical landscape.
As his book’s subtitle suggests, Blaser believes that antibiotic use has contributed to many of our modern ills. His work on antibiotics and obesity suggested that antibiotics administered in childhood may have the same effect farmers look for in their meat animals: accelerated growth, making them taller and fatter.
North American children are typically exposed to around 17 courses of antibiotics by the time they are 20, and another 13 by the time they are in their 30s. This doesn’t include the antibiotics they may receive from their mother through the placenta or breast milk, nor those consumed in drinking water, milk and meat. Children born of C-sections are also deprived of protective maternal bacteria from vaginal birth, and subject to direct or indirect antibiotics.
We don’t know yet what will be the long term effects of so many antibiotics on a developing brain and immune system in children, nor on public health as a whole. There are a lot of troubling correlations: people who used antibiotics in the month before a salmonella outbreak in Chicago got sicker than those who didn’t. Exposure of children to broad-spectrum antibiotics in the first two years of life (notably –mycin drugs) is associated with lifetime obesity. A Swedish study found a clear association between celiac disease onset following antibiotic use. Antibiotics impair our ability to excrete estrogen, leading to the modern ills of estrogen dominance (which affects men and children as well as women). Even short courses of antibiotics may permanently change our unique, personal microbiome, and there is no known way to permanently reinstate what’s been lost – even if we knew what that was.
Not all beneficial bacteria – or, like H. pylori, those that demonstrate amphibiosis, being sometimes beneficial and other times not – can be re-colonized into the human gut over the long term. H. pylori, for example, which is not just one but a family of microbes, is acquired in infancy and childhood in conditions that typically no longer exist in the Western world. (Blaser stresses replacing the term “infection” with “colonization” when speaking of our microbes. Since we have co-existed with some – like H. pylori – for millennia, the only thing we know for sure is that we don’t fully understand our biological history with them.)
Meanwhile, says Blaser, we can start by avoiding antibiotics wherever possible, particularly broad-spectrum ones that cause too much collateral damage. Avoiding c-section births except in medical emergencies, and re-evaluating the prophylactic use of antibiotics where c-sections are required would help protect children. Discussing with a pediatrician whether antibiotics are the appropriate first course of treatment for childhood ailments is crucial. Lobby for policies preventing the use of antibiotics in farming and meanwhile avoid conventionally raised meat and dairy. He’s lukewarm on probiotic supplements, prebiotics, and their hybrid synbiotics, mainly because we simply don’t know which bacteria are crucial, and there is little research and no standards for production. Fecal transplants are helpful for some conditions (but not DIY versions where the donor has not been screened for medical risks to the recipient).
Meanwhile, the research into this essential biological mystery is exploding in the scientific world. Let’s hope we can get enough scientific leverage on political will to reverse some of the excesses of antibiotics before we’ve killed off all that aids us.