You’re Only Half Human: The Microbes in and among Us

I’m sure I wasn’t the only child who loved the taste of liquid amoxicillin– “the pink stuff” as I called it. Being a child of the ’80s with frequent ear infections, I practically lived on the stuff. I remember when I was about three years old, I snuck into our fridge and realized that the lid to one of the bottles hadn’t been fastened properly. Like a child who’s found the cookie jar completely unattended, no parent in sight, I stood there and drank half a bottle. I don’t remember what unpleasant intestinal upset may’ve ensued the following day. All I knew was the pink stuff wadelicious.

I was a child of the Antibiotic Era. I was also delivered by c-section, a growing trend at the time which has only more recently started its decline. I’m still not absolutely certain how medically necessary the c-section was; I was 6 days late and the doctor informed my mother quote, “The barn door’s too small!”, indicating that her pelvis wasn’t able to accommodate a vaginal birth. My mother’s really only slightly below average in size, and while I was definitely a larger baby at 21″, 8.12 lbs., I wasn’t a monstrosity either. I’ve heard conflicting opinions from medical folk, some saying that for most births the “barn door” is rarely too small and the election for c-section was moreso a trend in obstetrics of the era. But in any case, I was yanked from the womb, smacked on the butt, and somehow amidst all the hubbub still managed to achieve a good APGAR score. By 4 months of age, however, I had developed an allergy to breastmilk and I was promptly and permanently put on soy formula. It was the Triple Hit. I c-sectioned, formula-fed, and antibioticked my way through birth, infancy, and childhood. And now at age 31, I have irritable bowel syndrome (IBS), asthma, and frequent sinus and ear infections. Coincidence?


There’s growing evidence to suggest that antibiotic over-use correlates with imbalanced gut and respiratory microflora. These microflora consist of symbiotic and commensal bacteria, fungi, and archaea. For those not familiar, a “symbiosis” is when two organisms benefit one another, in this case in a host-microbe relationship. “Commensalism” is when one organism benefits from another, meanwhile the other is neutrally affected. Sometimes there is a fine line between symbiosis, commensalism, and parasitism, the latter in which one organism benefits at the expense of another. In the case of certain microbes, they may be neutral or beneficial when the host animal is in good health, but become harmful when the animal is ill or the microfloral populations become imbalanced. The single-celled fungus, yeast, is a great example: under healthy conditions a certain amount of yeast can be beneficial, helping to keep numbers of other potentially harmful microbes in check; but most women are all too familiar with how overproliferation of yeast can easily turn into an infection. Alas, symbiont-turned-parasite.

According to the microbial ecologist, Jack Gilbert, the ~100 trillion microflora in your gut weigh about 2-5 lbs., depending on your size. And that’s not even considering those organisms which reside in your respiratory tract, genitalia, and on your skin. You’re absolutely crawling with them. But contrary to our traditional belief that “cleanliness is next to Godliness”, many of these little guys take part in a vital symbiosis with ourselves. Did you know, for instance, that scientists have found that our microflora play an important role in the education of the intestinal immune system which can last our entire lifetimes? [1] There are also microbes necessary for the digestion of certain foods we eat, like milk and the lactobacilli that break down the sugar lactose into a digestable form, or the breakdown of fiber into simple sugars by Bacteroides [2]. We have been evolving with our microbial partners for so long that parts of our anatomy and physiology are dependent on the presence of our microbes.

When microbial populations are imbalanced in the case of diseases like IBS, certain probiotics can also help restore health. For instance, O’Mahony et al. (2005) reported that patients with IBS treated with the bacterium, Bifidobacterium infantis, for 8 weeks showed significant improvements in their conditions. In addition, the researchers also tested the patients’ cytokine levels prior to treatment and found that the ratio between IL-10 (an anti-inflammatory cytokine) and IL-12 (a pro-inflammatory cytokine) was skewed towards inflammation. Remarkably, this imbalance was normalized by the Bifidobacteria.

Bifidobacterium within the colon. Borrowed from here.

Breastmilk is one of the primary sources of Bifidobacteria, in contrast to other food sources [3]. Sadly, breastfeeding in the Western world saw a marked decline between the 1800s-1960s. Why? It was considered lower-class and uneducated to breastfeed one’s child and was even discouraged by the medical establishment [4]. It causes one to wonder whether trends in microflora within Western populations may not have been permanently affected by the deliberate refusal to breastfeed.

Other factors may also play into microfloral trends in Western culture. A larger study carried out in 2006 in the Netherlands reported that:

  • Infants born through c-section tended to have higher numbers of Clostridium difficile and lower numbers of Bifidobacteria and Bacteroides (vaginal birth is an important source for maternal-infant infection).
  • Babies that were formula fed as opposed to breastfed had higher numbers of C. difficile, E. coli, Bacteroides, and Lactobacilli.
  • Infants who were hospitalized or who were premature tended to have higher levels of C. difficile.

So not only does breastfeeding play an important role in maternal-to-infant microbial transfer but a vaginal birth does as well, via the infant swallowing vaginal fluid during labor. Just consider the trend in the last few decades of the number of cesarian sections women have had. There are times, granted, in which a c-section is unavoidable. But there was also a growing trend up into the 1990s for mothers to voluntarily elect to have c-sections. In 2003, MacKenzie et al. reported that between 1976 and 1996, the number of cesarian sections in a single maternity unit in a large district teaching hospital more than doubled. Interestingly, maternal election remained constant over those decades and the primary reasons for increased c-sections were medical, i.e., fetal distress, failed labor induction, failed 1st- and 2nd-stage labor progression, breech presentation, and twins. It would be interesting to determine whether these trends were actually due to increases in truly problematic births or due to shifting trends in medical intervention.

If you consider your body as a walking collection of cells, you’ll find that your 100 trillion eukaryotic cells share their community with a similar number of prokaryotic cells. Granted, their much smaller prokaryote sizes mean that were you to collect your microbes into a single space they’d probably be no larger than, say, your liver. But nevertheless, they are a part of your body, another organ as it were. Only this organ is much more diverse, much more adaptable, and while you need certain numbers of certain types of microbes to develop properly and maintain good health, too many of those same symbionts can cause disease as well. Unlike your own eukaryotic cells, your microbes don’t selflessly commit suicide when something goes wrong for the good of the larger community of cells. In spite of their necessity, there is an essence of microbial selfishness and they are known to take advantage of a bad situation. Granted, symbionts’ and commensals’ relative aggressiveness towards their host system has undoubtedly been selected against over the epochs. After all, they don’t want to kill you! They just want food and shelter.


But your general health is dependent on the delicate balance of your microbial ecosystem. Without that, it may lead to chronic digestive, respiratory, vaginal, and skin diseases. And our modern era, characterized by antibiotic overuse, c-section-crazed obstetrics, and the refusal to breastfeed, may be at fault for an apparent rise in microbial-host borne diseases.

So what can you do about it? Well, thankfully trends seem to be reversing in terms of breastfeeding and natural births. But the decline in antibiotic use is comparatively slower. If your doctor prescribes you an antibiotic for something, ask questions, raise concerns, and ask if there are safer alternatives for treatment. And most importantly, if your doctor doesn’t have the time or patience to address these matters, find a new doctor who does. In addition, if you’re considering the use of probiotics or prebiotics to help treat a medical condition, be sure to thoroughly investigate the effectiveness of the particular product you’re interested in. Pro- and prebiotics are not well regulated by the FDA in the United States and you may not be getting what you’re paying for. Do your homework and ask your doctor for recommendations. Your local pharmacist may also be a good resource.

Best of luck!

2 responses to “You’re Only Half Human: The Microbes in and among Us

  1. Hi Emily –

    Nice posting.

    The piece about our recent findings on the unexpected effects of c-sections and early life antibiotic use got me thinking about some papers I ran across when I thought about my early days coming up. I don’t know if your teenage and college years were like mine, but I tried my hand at alcohol with reckless abandon. Then, twenty years later, ran into these.

    Oh well.

    – pD

    • Very interesting! Thankfully I never had a taste for alcohol, although I was certainly a Mountain Dew binge drinker (which I can only imagine the horrors it did to my GI tract!). But also interesting the sex differences in the brain following alcohol consumption. I wonder how much for females the effect is due to the reparative properties of estrogen on the brain and plasticity…

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