This is, and will remain, a work in progress. Your input is encouraged. If there is a term you think should be here, let us know! If you have an issue with how we defined a term, let us know that too! New terms will be added and old definitions will be updated as needed.
Please note this is not meant to be an exhaustive glossary of microbiological terms but rather an accessible resource for the public at large seeking to better understand the world of the microbiome.
Antibiotics
Substances (typically in the form of pharmaceuticals) designed to kill bacteria, the unintended consequence of which can included bacteria that are beneficial to your health.
Archaea
Bacteria-like microorganism that is part of your microbiota
Bacteriophage
A kind of virus that attacks specific bacteria and archaea. Considered a potential alternative to antibiotics.
Broad-Spectrum Antibiotics
Antibiotics designed to kill a wider variety of bacteria than a regular antibiotics.
Bacteria
Microscopic single-cell organism and an integral part of the human microbiota.
CFU
Colony Forming Units the term typically used to measure the number of “live” or viable probiotic microorganisms in a supplement or fermented food.
Colon
Your large intestine, and home to the vast majority of your microbes.
Dysbiosis
An imbalance or disruption of the microbiota that can lead to a host of conditions including irritable bowel syndrome (IBS).
FMT
Fecal Matter Transplant. A Process by with a person’s entire microbiota is replaced through the insertion of the microbiota of a healthy donor as derived from their fecal matter. Currently used to great success for treating Clostridium difficile (C. diff), a serious intestinal infection.
GI Tract
Abbreviation. See “Gastrointestinal Tract.”
Gastrointestinal Tract
Your food consumption, processing, and disposal system starting with your mouth and ending at your anus.
Gut Microbes
The microorganisms that reside in your “gut,” mostly in your colon. Together they can weigh two pounds and more.
IBS
See “Irritable Bowel Syndrome.”
Irritable Bowel Syndrome
A disorder of the large intestine that can include chronic gas, bloating, diarrhea and constipation.
Microbe
Synonym. See “Microorganism.”
Microbiome
Technically, the combined genetic material of the microorganisms within a particular environment. However, in the popular vernacular, the term has come to refer to the microorganisms themselves, and therefore is often used synonymously with “microbiota.” (We use “microbiome” in our name because regarding public awareness, that term is an order of magnitude better known than “microbiota,” and since Microbiome Bulletin is designed to be an outreach vehicle to the public at large, it made sense to have a name with which they would be familiar. Within our posts, we do try to use “microbiota” where appropriate.
Microbiota
The totality of the communities of microorganisms living both in and on your body.
Microorganism
An organism, typically single-celled, that is so small it cannot be seen without the aid of a microscope. Bacteria, archaea, fungi, and viruses.
Pathogen
An undesirable microorganism that causes harm or disease.
Phage
Short for “bacteriophage” (see “Bacteriophage”).
Prebiotic
A substance that can confer direct benefit to the desirable microorganisms or “probiotics” that are found primarily in your intestinal tract, the colon in particular. Usually a fermentable fiber and therefore a “food” or sustenance to those microorganisms. Pectin, a soluble fiber found in fruit is one example, as is inulin, a soluble fiber typically found in vegetables. Both, and more, are available as supplements as well.
Probiotic
A desirable microorganism that confers some health benefit to its human host (human being our primary focus at Microbiome Bulletin). Found in both fermentable foods (yogurt, kim chee, kefir, etc.) and in supplement form.
SFCAs
Abbreviation. See “Short Chain Fatty Acids.”
Short Chain Fatty Acids (SFCAs)
Short chain fatty acids include butyrate, propionate, and polyamine and confer a number of anti-inflammatory benefits, and serve as a major source of sustenance to the cells lining the walls of your intestines.
Synbiotics
A product that combines probiotics with complementary prebiotics. Not so much a thing in and of itself, but more a repackaging for marketing purposes. That’s not to say it’s not a good idea. I often will mix inulin powder in with my yogurt. Prebiotics “feeding” the probiotics if you will, but synbiotics are not some innovative new discovery. It’s just combing two things together.
Wow! Great article.
One of the few great article I have come across in a while. These set of definitions brought me back to my high school days where I have loads of biological terms to memorize. This is an eye opener for me and I learnt alot from the terms listed. I have already bookmarked the page in order to check on it anytime i wish to refer back to the system
Just by reading through your Microbiome glossary here, I’ve already managed to learn ten times more than I’ve ever known before on the subject (which is obviously a good thing!).
I was interested to see you mention IBS and Irritable Bowel Syndrome in the list and was wondering if you were planning to cover the subject in an upcoming article? I only ask as I have suffered with this over the last decade and I am always on the lookout for new information/angles on handling the condition?
Yes, I expect that kind of piece will likely come under the News and Research section. IBS is a huge issue, and encompasses a broad array of conditions. However, it is unquestionably related to the microbiota in one way or another, and rebalancing the microbiota will almost certainly play a part in future treatments.
I will keep a special eye out for developments in that area.
Thanks for this page, it’s good to have a glossary page as know we have a clear meaning of each word that we are looking for. for example IBS- this one I can relate to as I also suffer from ibs, and there are also a few more on there that I can also relate to- thanks for this
Hi admin, your blog on microbiome glossary is very educative.
I already have an understanding of some of the terms, such as: antibiotics, bacteria, colon, gastrointestinal tract, gut microbes,, micro organism, pathogen, and probiotics. But terms like : microbiota, phage, prebiotic, synbiotic, are completely foreign words to me.
Although, I’m an engineer, this new addition to my vocabulary is needful.
My wife is currently on antibiotics and I was explaining to her that good bacteria is dying in addition to the harmful bacteria. I just showed this to her and she said, “Wow, you were right!”. I have taken probiotics myself for the purpose of maintaining health but I have have never heard of prebiotics. Does the microbiome affect conditions like Heartburn also?
It certainly can. I’ll be writing about this in the future, but for now, check out this article.
This is a very well put together glossary term to a lot of things that can go on in our digestion system, of course some of the words also apply to the rest of our body as well. I was just reading an article the other day on Bacteriophage and had to look up what it was. They are really bizarre futuristic looking things even though they were discovered a very long time ago by accident, and I guess vaccines and antibiotics replaced the attention they were getting years ago. Now, we know the dangers of both and it is time to revisit Bacteriophage as a possible solution. Nature provided us the way to cure ourselves, but we are always so determined to invent something and not rely on nature. That is arrogance which has costed us years and years of overlooking better options. Sorry, I get on a soap box about these things. Thanks, for triggering my brain cells to wake up today this is a well put together list.
What a great resource within your website. I am very much interested in probiotics and how they help our systems and this glossary helps to answer many questions. May I ask when taking antiobiotics should we increase our probiotics regimen or keep it the same? I often wonder if it’s depleting more than it’s helping. Thank you for putting this glossary together, this will definitely be a go to page for me in the future.
What a great resource within your website. I am very much interested in probiotics and how they help our systems and this glossary helps to answer many questions. May I ask when taking antiobiotics should we increase our probiotics regimen or keep it the same? I often wonder if it’s depleting more than it’s helping. Thank you for putting this glossary together, this will definitely be a go to page for me in the future.
It’s generally believed that taking probiotics during (preferably hours apart) or after a round of antibiotics helps to restore, or at least kick start, the process of restoring your helpful gut flora.
There was a recent study that suggested the opposite was true. That was only one study, and I still hear doctors recommending probiotics, but I think the topic bears watching, like so much to do with the microbiota!
Wow! This is quite a list, but an interesting one though. Reminds me of those years back at school doing biology.
I understood your definition of FMT ( fecal matter transplant) but I didn’t get to see the meaning of Fecal Matter itself, would have helped me understand the term better.
This is a very good resource, will always come back to it, when I have biological terms to deal with.
Cheers..
Funny you should mention that. The thought did occur to me. Fecal matter is basically poop. When I come up with a more refined way to say “poop,” I’ll add it to the definition!
I love this Microbiome Glossary already and have bookmarked it so that I can always go back and check what more words have been added. My kids ask me for the meaning of these words when they hear or read them on supplement bottles or advertisements and I have to go searching,so this is a good place to quickly dash into and find what I am looking for. I’m not sure if it’s something possible but I was wondering,can you add a audio beside some of the not so common words so that a novice can play it and know how exactly to pronounce them. But this is a cool one. I likey!
You know, that’s a very interesting idea. I might be able to do that. I’m gong to be adding video to the site, but audio would be more appropriate in this particular case.
Thanks for the idea!