Active fluorescent units (AFU)
An indicator of the number of microorganisms in a sample that are alive and active, as measured through a new ‘flow cytometry’ technique involving fluorescent labelling of cell parts and exposure to a laser beam.
You might have seen the acronym ‘CFU’ on your probiotics label, but what’s AFU?
AFU stands for Active Fluorescent Units. It’s an additional measurement that offers us a more precise view of the number of living and active microorganisms in a sample. Through AFU we are able to calculate all viable cells, including ones that are efficacious but not necessarily culturable (and therefore would not be counted in a traditional plated CFU measurement).
We determine AFU using a technique called ‘flow cytometry’. This may sound complicated, but it’s really just a sophisticated use of light and data. During testing, individual cells are tagged with fluorescent ‘markers’ and counted by a laser as they pass through a tube.
It’s pretty lit.
Antibiotics are a type of antimicrobial drug used in the treatment and prevention of bacterial infections. They may either kill or inhibit the growth of bacteria. Antibiotics are not effective against viruses such as the common cold or influenza.
Antibiotics (first discovered, quite accidentally, by Alexander Fleming in 1928) are a revolution of modern science. It goes without saying they have saved many lives and eradicated many diseases. However, we now know that antibiotic overuse comes at an alarming cost to our health.
See, antibiotics don’t discriminate between the good and the bad bacteria. They carpet-bomb your gut microbiome, killing target species but also wiping out many others, sending your inner world into dysbiosis. Studies have shown that your microbiome may take upwards of two years to fully recover from these detrimental effects.
Fun/scary fact: the CDC estimates that of the 154 million antibiotic prescriptions written across doctors’ offices and hospitals nationwide, 30% are unnecessary—with the majority of which are for infections that are not even bacterial. In other words, 47 million prescriptions in cases where antibiotics don’t even work. Process that for a second.
Inappropriate antibiotic treatment and overuse have also prompted bacteria to mutate and develop resistance. This could lead to a world where we are powerless against harmful bacteria, and minor infections and injuries become deadly.
The first rule of antibiotics? Try not to use them. The second rule of antibiotics? Use them really, really carefully.
P.S. The term ‘antibiotic’ literally means ‘against life’.
Bacteria is a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth’s crust. Bacteria live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
Bacteria ruled the world for three and a half billion years before humans even made an appearance. They continue to rule the world today. The truth is, we live in a microbial world, and not the other way around.
In fact, there are 38,000,000,000,000 of them living in and on you right now. They make up your microbiome and are essential to your health, performing functions like aiding in digestion, modulating immune responses, and producing vitamins and key metabolites.
Bacteria have historically had a bad rap—the discovery of some pathogenic ones like Mycobacterium tuberculosis and Escherichia coli sent us into germ hysteria, resulting in a century of antibiotic and antibacterial overuse, attempting to wipe them out of existence.
We now know that the overwhelming majority of bacteria are benign, and many are even beneficial, if not essential. It’s time we started taking care of them.
Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, biology, mathematics, statistics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. More broadly, bioinformatics is applied statistics and computing to biological science.
In the same way that humans have a genome (aka the collection of our DNA), microorganisms also contain and express countless genes. The combined genetic material of the microorganisms in a human body is known as the microbiome. But how do we even begin to untangle all this complex genetic information?
Bioinformatics is the study of complex mathematical analyses that enable us able to see patterns in the microbiome data that we wouldn’t see otherwise. For example we can spot links between changes in the microbiome and lifestyle factors (such as sleep, diet, or smoking). It can also show us the potential links between the health of the microbiome and diseases.
Remember: correlation doesn’t equal causation. Bioinformatics is for information gathering, not hypothesizing.
Butyrate (also known as butanoate) is the traditional name for the conjugate base of butyric acid (also known as butanoic acid). The formula of the butyrate ion is C4H7O2−. The name is used as part of the name of esters and salts of butyric acid, a short chain fatty acid.
You’re probably going to be hearing the word ‘butyrate’ a lot soon. But what is it exactly?
Butyrate is a short-chain fatty acid which fuels the cells lining your colon and strengthens your protective intestinal mucosa. It also has powerful anti-inflammatory effects beyond the gut, reducing oxidative stress (imbalance between free radicals and detoxifying antioxidants) and managing the production of regulatory T-cells (the ones that help your body distinguish between self and intruder).
Want more butyrate? Well, this is where the story gets interesting. Butyrate is a byproduct of certain bacteria and the work they do. You see, certain bacteria in your colon break down dietary fiber and produce short-chain fatty acids like butyrate in the process.
Clinical trials are experiments or observations done in clinical research. Such prospective biomedical or behavioral research studies on human participants are designed to answer specific questions about biomedical or behavioral interventions, including new treatments (such as novel vaccines, drugs, dietary choices, dietary supplements, and medical devices) and known interventions that warrant further study and comparison. Clinical trials generate data on safety and efficacy.
Raise your hand if you’ve ever thought about participating in a clinical trial as a quick way to make cash. All joking aside, these studies are carefully controlled and rely on human participants who are administered a treatment while being closely monitored.
Clinical trials help scientists assess both the safety and effectiveness of products and medications, and they’re essential to the advancement of science. They are critical for finding better ways of understanding, preventing, diagnosing, and treating our whole selves. Clinical trials are always evaluated by experts to ensure the participant’s health is safeguarded.
In addition, you may see the term “double blind”. This means that any information that may influence the behavior of the tester or the subject is withheld until after the test. This is important to prevent research outcomes from being ‘influenced’ by the placebo effect or observer bias.
So, if you’re ever questioning a claim a product makes, ask for the clinical trial data.
Clostridium difficile also known as C. difficile, C. diff is a species of Gram-positive spore-forming bacterium. Clostridia (members of the genus Clostridium and of the Clostridiaceae family) are anaerobic, motile bacteria, ubiquitous in nature, and especially prevalent in soil. Its vegetative cells are rod-shaped, pleomorphic, and occur in pairs or short chains. Under the microscope, they appear as long, irregular (often drumstick- or spindle-shaped) cells with a bulge at their terminal ends. C. difficile is catalase and superoxide dismutase negative and produces two types of toxins: enterotoxin A and cytotoxin B, which disrupts cytoskeleton signal transductions in the host.
File under: bacteria not to be taken lightly.
Clostridium difficile (C. diff) is a pretty gnarly pathogen. If you’re about to reach for hand sanitizer—please don’t—at last count, there were already 16 resistant strains reported. People most at risk are those with a compromised microbiota (this happens for a variety of reasons like poor diet, a weakened immune system, or antibiotics-overuse) and are often infected during hospital stays.
Infections caused by C. diff are particularly insidious. It’s a challenge to treat, frequently returning again and again, and each time requiring a more extreme treatment than the last. Fecal transplants have shown incredible potential in treating C. diff. And yes, that’s exactly what it sounds like—transplanting donor poop into and recolonizing the gut of a dysbiotic host.
Colonization occurs when microorganisms live on or in a host organism but do not invade tissues or cause damage. Colonization refers to the presence of microorganisms which can cause infection, but not to the infection itself. Having these microorganisms present does increase the risk of infection if the right environment occurs.
When microorganisms find a commodious place to take up residence, they naturally begin to grow and multiply—this is known as colonization. This term has also given way to one of our favorite myths around probiotics.
Many people incorrectly believe that probiotics must colonize our gut and alter the composition of our microbiome to have an impact. This is not true—in fact, outside of cases like fecal transplants, most probiotics don’t colonize. The introduction of beneficial microbes that pass through our gastrointestinal tract can influence many factors of our health. We call these ‘Transient Microbes’.
Dietary fiber or roughage is the indigestible portion of food derived from plants. It has two main components:
- Soluble fiber, which dissolves in water, is readily fermented in the colon into gases and physiologically active byproducts and can be prebiotic and viscous. This delays gastric emptying which, in humans, can result in an extended feeling of fullness.
- Insoluble fiber, which does not dissolve in water, is metabolically inert and provides bulking, or it can be fermented in the colon. Bulking fibers absorb water as they move through the digestive system, easing defecation.
Dietary fiber consists of non-starch polysaccharides and other plant components such as cellulose, resistant starch, resistant dextrins, inulin, lignins, chitins, pectins, beta-glucans, and oligosaccharides.
There are two types of fiber: insoluble and soluble. Both come from food material, both are indigestible by the human body, and both play a critical role in supporting digestion.
Insoluble fiber is what you’ve maybe heard referred to as “roughage”. It’s the tough matter found in food stalks, skins, and seeds and it doesn’t dissolve in water or get absorbed into the bloodstream. It adds bulk to the waste produced in the gut, which helps keep you regular.
Meanwhile, soluble fiber absorbs water to form a gel-like substance inside the digestive system. Sources include beans, oats, fruits, and avocados. Soluble fiber helps soften stool so it can slide through the GI tract more easily.
Fiber is in every fruit, vegetable, whole grain, and legume that you eat (so we’re still wondering why prunes get all the glory). Fiber in the daily diet contributes to a feeling of fullness, lowers cholesterol, and helps control blood sugar levels.
Fiber confers major benefits on humans but for many decades scientists didn’t really know why. Recent studies of the gut microbiome have revealed that the trillions of microbes in the colon may be responsible for some of the beneficial effects of fiber, such as the production of butyrate, a short-chain fatty acid responsible for powering cellular energy.
Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma. In certain organisms, these smaller substances are absorbed through the small intestine into the bloodstream. Digestion is a form of catabolism that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term mechanical digestion refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. In chemical digestion, enzymes break down food into the small molecules the body can use.
Your body can’t use your lunch in the form you ate it in. That’s what digestion is for—a five stage process that breaks your food down into minute components that can be absorbed into the bloodstream, extracting the nutrients and converting the unusable stuff into waste. Everything you eat or drink goes through digestion in the mouth, stomach, small intestine, large intestine, and finally, out the rectum (yes, poop).
But you don’t do all this work alone. Your gut bacteria is critical to each of these processes, breaking down complex compounds you otherwise can’t.
A gut missing these beneficial bacteria can lead to gastrointestinal disorders (Crohn’s, inflammatory bowel diseases, colitis) and even impact systemic health (obesity, diabetes, cancer).
In microbiome science, diversity is a measure of the variety of microorganisms within an environment. Diversity takes into account both the number of different microbial groups and how many microbes are in each of those groups.
Just like biodiversity in an ecosystem, diversity in our microbiome is generally a good sign. Unfortunately, there’s a mass extinction of microbes happening right inside our bodies, contributing to a surge of diseases that didn’t once exist—autoimmune, allergies, autism, asthma, diabetes, obesity, and more. In evaluating this rise of modern illnesses, scientists have studied communities all around the world who still observe a hunter-gatherer style of living. They’ve found that these communities have very similar microbiomes to one another, yet completely different from ours in the West, with guts containing up to 50% more bacterial species and twice as many bacterial genes.
While this research is extremely interesting, we must remember that in looking at the health of our ecosystem, diversity is only one factor to consider. While it is generally considered a marker of health, we must also look to the stability, structure, and function of our microbiomes.
An observed or measured outcome in a clinical trial to indicate or reflect the effect of the treatment being tested. An endpoint in a human study must be named in advance, so when the study is complete you can objectively deduce whether the treatment altered the variable.
When setting up a treatment or a study, we set an intentional endpoint as a way to measure the expected outcome. Given the uncertain nature of testing and variables, setting a threshold is extremely important for researchers.
We set up an endpoint before the study so that we have an objective stance as to whether the study had a positive outcome or not. As an example, I might say to you, “by taking this probiotic, the endpoint will be an improvement in skin health” and then we would commence the study and deem whether or not it was successful by the outcome of the ‘better skin’ endpoint.
It’s also important to note that an endpoint can be something you can easily notice, or something that’s impossible to notice with the naked eye (e.g. abundance of a certain type of immune cells within your body).
A eukaryote is any organism whose cells have a nucleus enclosed within membranes. Eukaryotes belong to the domain Eukaryota or Eukarya. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue.
As the progenitors of evolution, eukaryotes will forever sit on the throne of life’s kingdom. They’re responsible for the birth of all complex life on Earth, including plants, animals, and us humans.
At one point in our planet’s history, only two domains of life existed: bacteria and archaea. And in one unlikely and incredible moment, archaea and bacteria shared genes, and this union formed the first eukaryotes. Basically, it was the most game-changing evolution to take place on Earth. On a philosophical level, they’re basically responsible for everything from the stegosaurus to Shakespeare.
And on a superzoom level, eukaryotes are characterized by elaborate, multicellular structures, possessing a nucleus enclosed within membranes.
In food science, fermentation is how microorganisms like yeasts or bacteria convert carbohydrates to simpler compounds (alcohol or organic acids) in the absence of oxygen. Fermentation occurs naturally but can be tightly controlled to produce specific foods and beverages.
Fermentation is a natural process that happens without human interference or intention (that’s how early civilizations ‘discovered’ wine from juice that sat out for too long). That being said, the process can be tightly controlled to produce specific foods and beverages such as kombucha, kimchi, and kefir.
Food or beverage made by harnessing the growth of microorganisms. Every fermented food has both a substrate (the item being fermented) and live microbes that feed on the substrate while transforming it into something different. Fermented foods (including vegetable, fruit, dairy, and meat substrates) have been consumed for thousands of years in cultures around the world.
You probably know this as foods like sourdough, kimchi, yogurt, sauerkraut, miso, or beverages like kombucha.
Fun fact: humans have been fermenting food since the Neolithic times. The earliest types were beer, wine, and leavened bread and cheeses. These were followed by the pickling vegetables and fermentation of milk products in East Asia. In many cases, fermentation was accidental, if not serendipitous. In fact, many of these early societies had no idea what caused the sudden, dramatic change to these food substrates and often attributed it to divine intervention—the Egyptians praised Osiris for beer brewing and at many early Japanese miso and shoyu breweries, workers bowed to a shrine daily. We now know that we can thank invisible microorganisms for these delicious and often nutritious things.
Folate is a type of vitamin B needed for humans to perform critical functions such as the production of red blood cells. Although folate can be obtained from the diet, microorganisms in the colon produce a stable supply of the most easily absorbed form of folate and are important influencers of a person’s folate status. Folates occur naturally in many foods, especially dark green leafy vegetables, liver, and lentils.
The vitamin folate (aka B-9) is widely known for its role in fertility, pregnancy, and preventing serious birth defects. But did you know it also supports critical functions like the production and maintenance of red blood cells and DNA? Women are routinely told to fortify their bodies with folate, typically through nutrition-rich foods like leafy greens, avocados, and citrus fruits, or in the synthetic form—folic acid, via supplements.
When you take a folic acid supplement, it goes through a metabolic pathway in your liver to convert it into the bioavailable form of folate called methylfolate (5-MTHF). This is the form your body can use. 20-40% of women actually have a genetic mutation called MTHFR that prevents them from processing synthetic folic acid into usable folate. And for them, folic acid just sits in their liver, and over time, the buildup can actually be toxic.
The good news is, microbes in your gut can synthesize a number of essential vitamins—folate being one of them. So instead of relying on external supplementation, you can actually help your internal pharmacy create what it needs to thrive.
Strozzi GP, Mogna L. “Quantification of Folic Acid in Human Feces After Administration of Bifidobacterium Probiotic Strains.” Journal of Clinical Gastroenterology 2008 Sep;42 Suppl 3 Pt 2:S179-84. Accessed 2018 April 28 https://www.ncbi.nlm.nih.gov/pubmed/18685499 DOI:10.1097/MCG.0b013e31818087d8
Sugahara H, Odamaki T, Hashikura N, Abe F, Xiao J. “Differences in Folate Production by Bifidobacteria of Different Origins.” Bioscience Microbiota Food Health 2015; 34(4): 87–93. Web 2015 Aug 5. Accessed 2018 April 28 https://www.jstage.jst.go.jp/article/bmfh/34/4/34_2015-003/_article DOI:10.12938/bmfh.2015-003
A functional unit of your gastrointestinal system, organized as a multi-layer system, made up of two main components: a physical barrier surface and a deep functional barrier. The gut barrier is able to discriminate between pathogens and commensal microorganisms, organizing the immune tolerance and the immune response to pathogens. From the outer layer to the inner layer, the physical barrier is composed of gut microbiota, mucus, epithelial cells, and the innate and adaptive immune cells forming the gut-associated lymphoid tissue.
With over 100 times the surface area of your skin (seriously, it’s the equivalent of two tennis courts and thickness of one cell wall, or half a human hair), the gut is the largest exposed external surface on your body. On a daily basis, it deals with the food you eat, the molecules you inhale, and at times, the potential toxins that are in our food, air, and water. If your intestinal lining is damaged or compromised (you’ve probably heard of this being referred to as ‘leaky gut’), substances that don’t belong in your body can enter the bloodstream, triggering various reactions including inflammation, allergies, irritable bowels, migraines, pain, and fatigue.
Your gut barrier has two jobs: to absorb beneficial nutrients and protect against harmful substances. The inner lining of your small and large intestines are merely one cell thick (that’s about half a human hair!). Beneficial bacteria take up space along your epithelial wall and its mucus lining, maintaining your gut barrier integrity.
Iemoli E, Trabattoni D, Parisotto S, Borgonovo L, Toscano M, Rizzardini G, Clerici M, Ricci E, Fusi A, De Vecchi E, Piconi S, Drago L. “Probiotics Reduce Gut Microbial Translocation and Improve Adult Atopic Dermatitis.” Journal of Clinical Gastroenterology 2012 Oct;46 Suppl:S33-40. Accessed 2018 April 28. https://www.ncbi.nlm.nih.gov/pubmed/22955355 DOI:10.1097/MCG.0b013e31826a8468
Takeda Y, Nakase H, Namba K, Inoue S, Ueno S, Uza N, Chiba T. “Upregulation of T-bet and Tight Junction Molecules by Bifidobacterium Longum Improves Colonic Inflammation of Ulcerative Colitis.” Inflamm Bowel Dis. 2009 Nov;15(11):1617-8. Accessed 2018 April 28. https://www.ncbi.nlm.nih.gov/pubmed/19161180 DOI:10.1002/ibd.20861
The collection of genes expressed by the microorganisms living in the human digestive tract. These include bacteria, archaea, fungi, and viruses. In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body.
The relationship between gut microbiota and host is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids (SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host.
Your gut microbiota is the collection of microorganisms (bacteria, archaea, fungi, viruses) that live in your gastrointestinal tract. This is the bulk of your microbiome, containing tens of trillions of microorganisms and weighing about as much as your brain. In humans, the gut microbiota is established at one to two years after birth, and by that time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.
Your mother passes you your microbiome during birth. The process of receiving these foundational microbes is called seeding. It’s generally regarded to start at birth (though new research is starting to propose that microbial transmission could occur in the womb via the placenta), through the vaginal canal, skin-to-skin contact, and breastfeeding.
These first microbes colonize your gastrointestinal system and form the foundation of your immune system, serving as the instructors of what’s dangerous and what’s not. By the first few years of life, they stabilize into what is called the steady-state microbiome, resembling more or less what you have today.
The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.
The biological chain of events that explains how a treatment works.
In short, a mechanism is the explanation of exactly how a treatment works. This biological chain of events is the definitive reason substances cause health benefits, but not all are easily defined. It is not uncommon for studies to prove the efficacy of a certain treatment without understanding the direct mechanisms behind it. For example: dietary fiber. We all know fiber is an important part of a properly functioning digestive system but we haven’t figured out the exact steps that lead there. While there are theories, the complete mechanism is still unknown.
A probiotic, for example, might have a health benefit that depends on several mechanisms within the human body. Scientists explain phenomena by describing mechanisms that could produce it. Wherever possible and supported by research, we should make connections between mechanism, benefit, and the resulting structure-function claim.
The intermediate end product of metabolism. The term metabolite is usually restricted to small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory, and inhibitory effects on enzymes, defense, and interactions with other organisms. A primary metabolite is directly involved in normal “growth”, development, and reproduction.
As bacteria carry out the activities they need to sustain themselves (their version of ‘eating’) they take bigger compounds and turn them into smaller compounds called metabolites (or “small molecules”). Metabolites are naturally formed as substances are broken down. Basically, metabolites are a little like bacterial poop: the end product of what they metabolize.
Most molecules are small (obviously) but metabolites are officially called “small molecules” because they have a lower molecular weight than, say, protein molecules. This allows them to enter and interact with other cells. Bacteria in the gut produce various metabolites when they break down non-digestible carbohydrates (i.e. dietary fibers), including short-chain fatty acids like butyrate (which powers your cells), that can benefit your health.
The genetic material of all the microbes (bacteria, fungi, protozoa and viruses) that live in an ecosystem. In common use, “microbiome” is synonymous with “microbiota”—the collection of microorganisms (themselves) in the environment.
There’s a community of 38,000,000,000,000 (that’s 38 trillion) microorganisms, mostly bacteria, living in and on your body. The majority of them reside in your gastrointestinal tract, but many others live in diverse places like your mouth, your skin, and your armpits. They represent 50% of you by cell count. Collectively, the genes harbored in these trillions of microbial cells constitute your microbiome.
Altogether, it weighs about 3-5 pounds (about the same as your brain) and is now being considered by some a ‘lost organ’.
So where did your microbiome come from? You probably remember from sixth grade biology that you inherit your genes from your parents. But did you know that your mother passes you your microbiome too? The process of receiving these foundational microbes is called seeding. They colonize your gastrointestinal system at birth (through the vaginal canal, skin-to-skin contact, breastfeeding, and interacting with your surrounding environment) and form the foundation of your immune system, serving as the instructors of what’s dangerous and what’s not.
Scientists in the field are excited about the potential of the microbiome as another lens through which we program, sustain, and enhance health.
Microscopic organisms (also referred to as microbes) that exist in their single-celled form or in a colony of cells. These organisms, which cannot be seen with the naked eye, include bacteria, archaea, viruses, algae, protozoa, and fungi.
Microorganisms are so small they generally require a microscope to see. The vast majority of them pose no real threat to humans, plants, or animals. In fact, many co-evolved with us and serve beneficial functions we couldn’t thrive without.
Mycelium is the vegetative part of a fungus or fungus-like bacterial colony, consisting of a mass of branching, thread-like hyphae. Fungal colonies composed of mycelium are found in and on soil and many other substrates. A typical single spore germinates into a homokaryotic mycelium (which cannot reproduce sexually). When two compatible homokaryotic mycelia join and form a dikaryotic mycelium, they form fruiting bodies such as mushrooms.
Mycelium is part of a fungus that consists of a mass of slim, branch-like structures, capable of producing spores which absorb nutrients from the environment to grow the fungus. The size of mycelia can range from microscopic to large and visible to the naked eye, with the largest mycelium known is in Oregon and stretches 3.8 kilometres and is 2,200 years old.
The coolest thing is that it has properties like that of a natural glue. When you introduce it to agricultural waste, it binds everything together to create a positive-impact resource, replacing unsustainable synthetics like polystyrene or polyethylene. We worked with some mycelium experts at a company called Ecovative to grow our packaging trays out of mycelium. This means they contain no petroleum and degrade naturally in the soil within 30 days.
Peer review is the evaluation of work by one or more people of similar competence to the producers of the work (peers). It constitutes a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are employed to maintain standards of quality, improve performance, and provide credibility.
Peer review is central to how science works; it ensures scientific studies are of high quality and build on each other in order to advance overall knowledge in a field. In the end, we’re all part of team humanity, and this is part of that structure.
Substrates that are selectively utilized by host microorganisms, conferring a health benefit.
Prebiotics are commonly referred to as ‘the food that feeds your probiotics’. To an extent, this is true. Prebiotics typically refer to a class of plant compounds or fibers that support the growth of beneficial bacteria in the gut.
However, new observations about how these and other substances interact with our gut microbes, reveal a broader definition. Scientists now argue that the growth of specific microbes is less relevant—what we do care about is what these microbes are metabolizing.
The evolved, and now official, definition, published by the International Scientific Association for Probiotics and Prebiotics, refers to prebiotics as ‘substrates that are selectively utilized by host microorganisms conferring a health benefit’. In English: nutrients used by bacteria to help you thrive. This has broadened the path to introduce new classes of non-fermentable prebiotic compounds like polyphenols that are metabolized by gut bacteria into beneficial metabolites.
Probiotics are live microorganisms which, when administered in adequate amounts, confer a health benefit on the host.
This is the official definition of a probiotic, co-authored by our Chief Scientist, Dr. Gregor Reid, in a joint FAO / WHO working group in 2001.
Let’s break it down:
Live microorganisms: This refers to strains of beneficial bacteria that are consumed. ‘Live’ is a critical word here, and in science, we refer to this as ‘survivability’. To confer benefits, microorganisms must survive the many stages of digestion (think stomach acid and bile), past the small intestine, and make it into the colon, where their work begins.
Adequate amounts: This is very important, and you’ll generally see quantities enumerated on a label as a certain billion or trillion CFU. Each probiotic is associated with an effective dosage, and this dosage amount is arrived at through clinical study.
Health benefit: So you’ve taken some live bacteria in the right amounts. But are they actually doing anything for you? To satisfy the definition of a probiotic, the live cultures must demonstrate a proven health benefit. This means each specific strain (not just the species) must have been clinically verified to cause a beneficial change in the body.
Host: That’s you!
The process by which you receive your foundation microbes.
You probably remember from sixth grade biology that you inherit your genes from your parents. But did you know that your mother passes your microbiome on to you when you are born?
Seeding is generally regarded to start at birth (though new research is starting to propose that microbial transmission or priming could occur in the womb via the placenta), through the vaginal canal, skin-to-skin contact, and breastfeeding. Eventually, the surrounding environment—other moms, dads, siblings, dogs, the ground, nature—continues to contribute to this microbial biodiversity.
These first microbes colonize your gastrointestinal system and help to set the foundation of your immune system, serving as the instructors of what’s dangerous and what’s not. Within the first few years of life, they stabilize into what is called the steady-state microbiome, resembling more or less what you have today.
A complex system consisting of a large number of individual organisms that function together to behave as if it were an ecosystem and to gain a biological advantage.
A curious and inquisitive, perspective-shifting organism, who questions relentlessly, thinks differently, takes the time to understand holistically, and believes everything is connected. An activist for the bettering of humanity and our planet. Sometimes referred to as: ‘a person who lives scientifically’.
In other words, you.
Any type of a close and long-term interaction between two different biological organisms, be it mutualistic, commensal, or parasitic. The organisms, each termed a symbiont, may be of the same or of different species.
An interaction between organisms that live closely together. Normally when we think of symbiosis we think of something that benefits both organisms in some way—but in reality, symbiosis can be neutral to one of the partners or can even harm one of them. It all depends on the context.
Lynn Margulis, a celebrated, boundary-pushing biologist, argued that we have to understand symbiosis in order to understand how every living thing on Earth evolved. Organisms in symbiosis—from clownfish and anemones to rhinos and tick birds—have their reasons for sticking together. And inevitably, there are outcomes and consequences. (Evolutionarily or otherwise.) It’s complicated.
A sour food that results when bacteria consume the sugars in milk. The bacteria in yogurt must include Streptococcus thermophilus and Lactobacillus bulgaricus, with other species being optional.
Yoghurt is food produced by bacterial fermentation of milk. This process produces lactic acid, which acts on milk protein to give yoghurt its texture and characteristic tart flavor. Traditionally made yoghurt can be a very healthy and nutritious addition to our diets, but many commercial varieties have been… well, soured. Modern yoghurts are often pasteurized, killing the live microorganisms, and then doused in sugar, stripping it of its nutritional benefits.