The Monstrous Microbiome: Good Bowel Buddies


DIY Fecal Transplants – putting the “Y” in DIY

A few weeks ago, I received an email from a friend with a link to one person’s journey through the valley of the shadow of poor gut health to the eventual crest over into the promised land of microbial-intestinal paradise. All achieved with a Do -It-Yourself fecal transplant.

If you just read that and went – wait … DIY fecal transplant? — that is the same, dumbfounded, slow blink realization that I had when I clicked on that link. Reading through the testimony and step-by-step guide I was reduced to tears as I laughed at the glorious one liners and anecdotes. Despite my amusement, the author of the website is entirely serious in their step-by-step instructions, key tips and tricks and, especially, in their belief in the power of good microbes in the all the right places. But, honestly, despite the misguided nature of their website, they are right about one thing – the power of bacteria and their influence on our health.

Now it’s not all shits and giggles (I am so sorry, I couldn’t help myself), fecal transplants are a real deal, medical procedure. I was first introduced to the idea of fecal transplants a few years back, sitting in a microbiology class during my short, misguided stint in nursing school. It was presented as a new approach at curing resistant Clostridium Difficile infections – or C. Diff for short.

Bad Bowel Buddies

C. Diff infections are nasty, dangerous events that generally kick those who are already down right in the gut. C. Diff is a type of bacteria that exists in very small amounts within the normal flora (your body’s resident bacteria) of your intestinal track. They are kept in check by the other “good” bacteria that populate the cozy folds of your intestinal wall. These are opportunistic pathogens, meaning they will seize the perfect moment to gain control over your guts and wreak havoc on your insides. Carpe Diem and the like.

C. Diff is an anaerobic (does not need oxygen), spore forming (can package its DNA into a very tough shell go to sleep and hang around for MONTHS), toxin producing bacteria that cause inflammation and diarrhea. In some cases, this inflammation is so severe it leads to bowel perforation (a hole where you do not want one) and death. If your bowel manages to stay intact, the dehydration that follows severe diarrhea could kill you too.

The infection generally occurs in patients who are on long term or very potent intravenous antibiotics; recently hospitalized; immunocompromised; and/or post surgical patients. In short, C. Diff is a bastard.

Now, if that wasn’t horrible enough – this hardy little microbe can be very difficult to destroy.  This has to do with C. Diff’s ability to bundle itself into a spore. Spore forming bacteria are pretty amazing but also pretty terrifying things, and are responsible for some pretty nasty illnesses. Other spore forming clostridia bacteria include those that cause tetanus and botulism – some horrifying illnesses that involve prolonged muscle spasms and muscle paralysis, respectively.

And then there is anthrax, a deadly, spore-forming, bacillus bacteria that has been harnessed for biochemical warfare and bioterrorism. Oh, behold the wondrous power of microbes.

But wait, it gets even better.

C. Diff has a reputation for developing resistance to the course of antibiotics that are used to treat the infection. Just when you think you’ve gotten rid of the thing, a few resistant rods drifting in your intestines wage a Viking raid on your intestinal epithelium, conquering and pillaging your gut.

This is where the fecal transplants come in.

Fecal Transplants

Please, do not attempt a DIY fecal transplant at home. It would be, pretty much, the most uncomfortable, horrifying experience of your life. According to the DIY website and step-by-step guide, it involves: a kitchen funnel, a big brown towel, a diagram of the colon and some personal lubricant (or coconut oil!).  Oh, and some other person’s fecal matter. Please, save the big brown towel and personal lubricant for more fun activities that don’t involve an enema of another person’s poop. Unless, of course, that’s your idea of a wild night, then you may want to rethink your life choices. Not judging, really.

Fecal transplants are a relatively new therapy, and the process of getting someone else’s feces into your bowel is pretty similar to the horrifying steps outlined in the DIY version – minus the kitchen funnel and coconut oil. There are only two ways to the intestines, meaning there are limited avenues to get the good microbes where they need to be. Unfortunately, it generally involves some very unpleasant placements of tubes. Although, with fecal transplant proving itself to be an effective tool in treating C. Diff infections, capsule forms are being engineered to deliver the microbes to where they need to be — minus the tubes. You can unclench now.

Now, it is not the feces we really want. Unfortunately, that’s just the delivery vehicle — a way to keep the colonies of beneficial bacteria happy, alive and thriving until they reach their new intestinal environment. The treatment relies on the transplanted bacteria to settle down, lay down roots and maybe buy that house with the white picket fence at the corner of the Sigmoid colon. We want something called colonization to happen – lots of health promoting, beneficial bacteria sticking to your intestinal wall, choking out the C. Diff and reclaiming territory lost to the toxic pathogenic microbe.

Fecal transplants may have a future that doesn’t involve the feces. Something called RePoopolate took bacteria from an optimal donor, purified it and cultured three dozen different strains. It’s more like a probiotic– a capsule filled with good microbes and none of the BS (or in this case I guess it would be HS). The trial was given to a very small amount of people, not even a handful (two C. Diff patients), and it appeared to be an effective treatment. Unfortunately, the small population size doesn’t make this trial very statistically relevant — one can not draw any conclusions based on only two patients. Some, not so encouraging news, is that another poop-free transplant, Ser-109, failed in a clinical trial a few years back.  They are pushing through with a new phase of a clinical trial this year, so perhaps we will see a future of poop-free microbe laden transplants. One can only hope.

Now, not surprisingly, there is a dark side to fecal transplants. Like the DIY guides found deep in the bowels of the internet, there is also a prevalent idea that it is a cure all.

A miracle.

A saving grace to those afflicted with a variety of ailments from irritable bowel syndrome to autism. That’s some pretty dangerous thinking.

First of all, not all bacteria are created equal and the transplantation of your friend’s, or spouse’s, or a stranger’s bowel buddies into your intestines can have severe consequences. Let’s jump back to the DIY fecal transplants for a second. If that specimen is not rigorously tested, you could be potentially exposing yourself to a variety of diseases, from hepatitis to HIV. That’s not the only obstacle, if the sample is disease free, the bacterial colonies may not be the ones you want. It’s not a one size fits all — there needs to be some vetting and customization when it comes down to what bacteria we are going to let spend the night in our colons.

Now, secondly, animal studies have shown transplanted microbes can cause a whole host of trouble that include obesity, irritable bowel syndrome and psychiatric aliments. Bear in mind, these are animal models, so we can’t extrapolate this with confidence to the human population; however, it shows that transplanting microbes is not without its risks. In fact, it may create the very problems people are trying to cure.

The Weird, Wonderful Microbiome

Now we have already touched on the microbiome but haven’t really explored what it is. And honestly, within the confines of this one blog post, I won’t be able to do it justice. The “omes” are so complex; and the sheer number and variety of “omes” are astounding.  There is, of course, the microbiome and the genome (which hopefully everyone knows about) but there are also the more obscure ones hanging around. For example, we also have the proteome, the kinome and the connectome – that is the systematic study and organization of proteins, kinases (really cool enzymes that have a hand in a ton of functions) and neural connections, respectfully. Amazing!

So, the microbiome is just the collection and organization in the study of microbes. And it is everywhere. You have your individual, personalized microbes living on your skin and inside you gut. It’s that normal flora I was talking about. Good bacteria that we have developed a cooperative relationship with. They keep things in check and in return they get all they need from living on and in us.

We are all unique.We have a completely different flora then the person next to us — the microbes on my skin are a different combination of species compared to the person sitting next to me in the library. There are various populations taking up residence on all of us. Its is, essentially, its own universe.

One of the most incredible things is that we appear to share the same microbial flora with the people we live with. If we cohabitate long enough, our microbes will eventually synch. It’s almost romantic.

For a way better written, and more in-depth journey into the microbiome, check out Ed Yong’s book I Contain Multitudes. His exploration isn’t limited to the human microbiome, instead the book covers the microbiome of all multicellular organisms – from pangolin to the coral reef – and what it all means.


Image: -Gut Bacteria Might Guide The Workings Of Our Minds –

Brain Gut Connection

The last word on the human microbiome might sound a little out there, but there is some hard science behind it.

Unbeknownst to most of us, there is a tiny, second brain living in your abdomen and it communicates and influences the big guy in the skull. Seriously. It’s called the gut-brain axis, and it is described in one study (This one here) as a “bidirectional communication network that monitors and integrates gut functions and links them to cognitive and emotional centers in the brain.” Meaning the gut and the brain appear to talk to each other and may even have a strong influence on one another.

When we think of neurons we generally think of the ones in our brain that snap, crackle and pop when we have an sudden idea or when we reach out to touch someone. However, neural tissue is intimately intertwined within our gut with a staggering number of neurons that, according to some sources, outnumber the spinal cord. The Enteric Nervous System, or ENS, is the name for the mesh of neurons that tell your gut what to do. Not only does it tell your entrails how to behave, it appears to be signaling messages to your brain via the tenth cranial nerve, the vagus nerve.

Your gut also uses neurotransmitters. A whopping 90% percent of your body’s serotonin is used and synthesized in your gut. Altered levels of serotonin are thought to play a role in not only digestive diseases, like IBS, but also diseases beyond the gut, like osteoporosis.

So, if you are mulling over the idea that your gut is actually a very long, squirmy, squiggly brain and you feel like it’s more science fiction than science, it actually gets a little weirder. Cue the microbes.

As we explored earlier, the microbiome plays a huge role in a lot of aspects of our health. There is emerging evidence that the gut microbiome may play a large role in CNS and brain function as well. For example, there is an apparent link between the use of antibiotics and altered mental states – psychiatric side effects like depression and even psychosis. On the flip side, in mice, the stress of untreated bacterial infections may also lead to disruptions in memory and cognition. Microbes appear to be capable of influencing the grey matter in many different ways, at least when we are looking at animal models.

In fuzzy little mice models, altering the microbes of the gut with antibiotic like agents caused a change in behaviour and increased the expression of a chemical called brain-derived neurotrophic factor or BDNF. An altered expression of BDNF has been suggested to play a role in a variety of neuropsychatric disorders, including Schizophrenia.

Antibiotics aren’t the only culprits, diet and alcohol use also appear to influence and alter the composition of those good bowel buddies. And, as evidence keeps coming in, this disruption of our gut’s inhabitants may have a crucial role in behaviour, cognition and memory…at least when we look at mice brains.

The End of the Road

Now, if you have survived my awful poop jokes and heavy-handed wit, we have reached the end of the line when it comes to the human microbiome and the gut, at least as far as this post is concerned. It was an long journey from C. Diff and DIY fecal transplants to the unnerving idea that our brains may be under the influence of the microbes bouncing around in our squiggly entrails.

In the end, we’re not only a skin suit of endogenous biomolecules and chemicals, but we are also a comfy home to tiny living things that may have a huge hand in the fate of our health and even the inner workings of our nervous system.  So, be kind to your microbes and they might not engage in a full fledged mutiny on your bowels and brain.

Also, put down the kitchen funnel and leave the fecal transplants to the experts.


I Contain Multitudes: The microbes within us and a grander view of life. Ed Yong
The Power of Poop (
From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Rogers. Nature. Molecular Psychiatry
Think Twice: How the Gut’s “Second Brain” Influences Mood and Well-Being. Scientific America
Brain-Derived Neurotrophic Factor and Neuropsychiatric Disorders. Autry. 2012
Serotonin in the Gut: What Does It Do? Bornstein. 2012. Frontiers Neuroscience
Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Petrof. 2013
CDI. Seres Therapeutics
Medical Microbiology. Murray. 2016
First Image: Erin Mattthews
Second Image:

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