medical case report recently made headlines supporting the notion that the bacteria inside our gut have something to do with the size of our gut.

Clostridium is a nasty strain of bacteria that is resistant to many antibiotics. Normally, the many other species of bacteria in the gut keep Clostridium in check, but when those friendly bacteria are wiped out during antibiotic therapy, Clostridium can thrive and produce severe inflammation (colitis) and diarrhea. This can develop into a serious illness that claims the lives of 14,000 Americans every year.

A novel way to treat this condition is through use of fecal microbiota transplant (FMT). In other words, the patient ingests the intestinal bacteria from a healthy person to replenish their own stock and get Clostridium back under control. We will leave it to your imagination as to how doctors collect the good bacteria, but let's just say you can make some decent money if you're willing and able to donate . Thankfully for patients, FMT is available in pill form.

As unappealing as it sounds, fecal transplants - which repopulate intestinal bacteria in the recipient - are proving to be very effective in treating some serious ailments.

As reported recently , a young woman with a stable weight of ~130 pounds had to undergo FMT to fight a Clostridium infection. The good news is that she beat the infection, but the bad news is that she gained 34 pounds in 16 months, classifying her as obese with a BMI of 33. Even more alarming is that she could not lose weight despite being on a supervised liquid diet and exercise program. The donor for the FMT (her teen daughter) was overweight, but otherwise in good health, so doctors are now recommending that FMT donors be of normal weight.

In light of this news, here's a beginner's guide to the tiny creatures calling you "home"...

You are not just a person – you are an ecosystem. Your body is home to trillions of microscopic critters, including viruses, bacteria, and fungi, living on or inside you. Collectively, these communities of microbes constitute what is called your “microbiome”.

And there are more of “them” than “you” – the number of microbes inhabiting your body is larger than the number of cells making up your body! To put this in perspective, it has been estimated that your microbiome weighs about 3 pounds. Good news if you’re on a diet – when you step on the scale tonight, feel free to subtract 3 pounds of stuff that isn’t “you” per se.

A new study concerning our microbiome seems to be coming out each week, so it is time we get to know our microbial roommates.

1. Where does your microbiome come from?

We are born virtually sterile, but quickly receive an infusion of bacteria from our mom, first through the birth canal and then through the milk. Over 900 species of bacteria have been found in breast milk, and these are the pioneers that settle into your gut, which appears to stabilize by the age of 3. Of potential interest are babies born by caesarean section or those who are fed formula instead of breast milk. Babies delivered via C-section do in fact have a different microbiome and may be at higher risk for certain types of allergies and obesity (more on this below). Our microbiome continues to receive fresh new imports as we move through, inhale, and ingest our environment.

How much of you is really you? There are more microbes in your body than the number of cells making up your body. We are just now beginning to appreciate the many things they do for us.

2. Your microbiome is like your own personal “germ cloud”.

You’ve probably noticed that everyone’s home smells a little different. Sometimes this is due to cooking, pets, or the amount of trash they let accumulate, but it is also due in part to the microbiome of the inhabitants . Researchers have found that you are surrounded by a “germ cloud”, and you leave pieces of your microbiome wherever you go like a trail of breadcrumbs. It might even be possible for police to use microbiomes to track people one day like they currently use fingerprints or DNA. In other words, you have a “microbiome fingerprint” that is left behind like a germ echo wherever you go.

This “germ cloud” may also explain how dogs can track people so easily. The byproducts generated by the millions of bacteria living on your skin are aromatic (odorous), producing a scent that is released into the air as you move. Animals with a keen sense of smell can get a whiff of these aromatic compounds and follow them to the source.

Speaking of “germ clouds”, if you ever wondered if it is possible to fart out germs, some brave scientists have sniffed out the answer to this question. You can read about the results here

3. Antibiotics substantially alter your microbiome.

they help us digest food, make vitamins, and build anti-inflammatory compounds. We take antibiotics to get rid of pathogenic bacteria that make us sick. The problem is they are not selective, so they destroy a lot of our friendly bacteria in addition to the bad guy. We need these friendly bacteria to do all sorts of things – to name just a few:they help us digest food, make vitamins, and build anti-inflammatory compounds.

Clostridium difficile, are naturally resistant to many antibiotics. When good bacteria are killed as collateral damage in an antibiotic treatment, the growth of Clostridium can run amok. These bacteria secrete a toxin that causes diarrhea and they can lead to a life-threatening superinfection in some patients. Another important thing our microbial friends do is keep infections in check. For example, yeast infections from pathogenic fungi can arise if good bacteria are not around competing for resources. And some bacteria, like the nasty, are naturally resistant to many antibiotics. When good bacteria are killed as collateral damage in an antibiotic treatment, the growth ofcan run amok. These bacteria secrete a toxin that causes diarrhea and they can lead to a life-threatening superinfection in some patients.

4. Your microbiome may protect you from allergies or obesity.

Several recent studies have correlated unusual microbiome composition with the presence of certain allergies. Dr. Hans Bisgaard has shown that infants harboring fewer species of gut bacteria have an increased risk of developing certain allergies as they grow up. More recently, Dr. Catherine Nagler has shown that certain bacterial species offer protection from peanut allergies .

Dr. Martin Blaser has found that administration of penicillin to mice soon after birth altered their gut microbiome in such a way that it made them more prone to obesity as adults. Remarkably, the tendency to grow obese is transferrable to germ-free mice – in other words, by transplanting the microbes from the penicillin treated mice to normal mice made the normal mice more susceptible to weight gain.

Studies such as these make it tantalizing to speculate that we may be able to treat certain ailments in humans by altering our microbiome with specific probiotic regimens. Maybe they could even slip these bacteria into our peanut butter instead of deadly Salmonella

5. How do scientists study the microbiome?

Advances in DNA sequencing have allowed scientists to rapidly map the genomes for many microbial species, which provides us with a “genomic fingerprint”. We can process samples swabbed from the skin or body cavities, or process stool samples, for DNA sequencing. Usually just sequencing the 16S ribosomal RNA gene is enough to distinguish one bacteria species from another.

It should be mentioned that some scientists are issuing cautions about over-interpreting microbiome studies . Many of the studies altering the microbiome have been performed in mice, so it remains to be determined to what extent the findings can be extrapolated to humans. Furthermore, many of the methods used to alter the microbiome in lab animals do not faithfully mimic what humans do with antibiotics. For example, in some studies the investigators give large doses of antibiotics over unusually long periods of time to see an effect in lab animals, which does not equate to the typical dosing of antibiotics in humans. Finally, many of these studies are correlative and have not yet definitively demonstrated causation. There is a big difference between correlation and causation

6. So should I take my microbiome into my own hands?

Much more research needs to be done to assess the true impact of the microbiome versus other factors that come into play, such as host genetics, diet, and the environment. It is argued that some microbiome studies are hyped up and way overblown . Long story short: if you or your child becomes sick with an infectious agent, it is not wise to withhold antibiotic treatment out of fear that it will cause allergies or obesity. If you are overweight, a healthier diet and plenty of exercise is going to do much more than any probiotic pill. In fact, there is little evidence that the popular probiotics on the market do anything to remedy the wide-ranging health problems some claim to treat, although there is data showing potential benefit in treating some gastrointestinal maladies , especially acute diarrhea caused by rotavirus.

Go here to learn more about the NIH human microbiome project.

Bill Sullivan, Ph.D. Contributed by:Bill Sullivan, Ph.D.

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Science (New York, N.Y.), 345 (6200), 1048-52 PMID: Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, & Gilbert JA (2014). Longitudinal analysis of microbial interaction between humans and the indoor environment.(6200), 1048-52 PMID: 25170151

Journal of Allergy and Clinical Immunology, 128 (3), 646-65200000 DOI: Bisgaard, H., Li, N., Bonnelykke, K., Chawes, B., Skov, T., Paludan-Müller, G., Stokholm, J., Smith, B., & Krogfelt, K. (2011). Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age(3), 646-65200000 DOI: 10.1016/j.jaci.2011.04.060

Cell, 158 (4), 705-721 DOI: Cox, L., Yamanishi, S., Sohn, J., Alekseyenko, A., Leung, J., Cho, I., Kim, S., Li, H., Gao, Z., Mahana, D., Zárate Rodriguez, J., Rogers, A., Robine, N., Loke, P., & Blaser, M. (2014). Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences(4), 705-721 DOI: 10.1016/j.cell.2014.05.052

Proceedings of the National Academy of Sciences DOI: Stefka, A., Feehley, T., Tripathi, P., Qiu, J., McCoy, K., Mazmanian, S., Tjota, M., Seo, G., Cao, S., Theriault, B., Antonopoulos, D., Zhou, L., Chang, E., Fu, Y., & Nagler, C. (2014). Commensal bacteria protect against food allergen sensitizationDOI: 10.1073/pnas.1412008111

American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists, 67 (6), 449-58 PMID: Williams NT (2010). Probiotics.(6), 449-58 PMID: 20208051