Microbiome Glossary

Microbiome Glossary

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.


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.


Bacteria-like microorganism that is part of your microbiota


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.


Microscopic single-cell organism and an integral part of the human microbiota.


Colony Forming Units the term typically used to measure the number of “live” or viable probiotic microorganisms in a supplement or fermented food.


Your large intestine, and home to the vast majority of your microbes.


A microorganism that derives some benefit from its host but does neither obvious harm nor good in return.


An imbalance or disruption of the microbiota that can lead to a host of conditions including irritable bowel syndrome (IBS).


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.


A taxonomic rank just above species. For example, modern humans are referred to as “Homo sapiens,” of the genus “Homo,” and species, “sapien.”  Likewise, a common probiotic microorganism, “Lactobacillus casei,” is of the genus “Lactobacillus,” and the species, “casei.”

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 Flora

The microorganisms residing in your gut including bacteria, fungi, and archea.

Gut Microbes

The microorganisms that reside in your “gut,” mostly in your colon. Together they can weigh two pounds and more.


See “Irritable Bowel Syndrome.”

Irritable Bowel Syndrome

A disorder of the large intestine that can include chronic gas, bloating, diarrhea and constipation.


Synonym. See “Microorganism.”


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.


The totality of the communities of microorganisms living both in and on your body.


An organism, typically single-celled, that is so small it cannot be seen without the aid of a microscope. Bacteria, archaea, fungi, and viruses.


A microorganism that derives some benefit from its host and in return confers some benefit.


An undesirable microorganism that causes harm or disease.


A microorganism that derives some benefit from its host but in the process does some harm to its human host.


Short for “bacteriophage” (see “Bacteriophage”).


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.


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.


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.


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.