Also called antibacterials, antibiotics are types of molecules that can block the growth of certain bacteria and are commonly prescribed to treat bacterial infections as well as certain parasites. Antibiotics are useless against viruses like the ones that cause the common cold or flu.

An antibody, also called immunoglobulin, is a protein produced by the body’s immune system in response to the detection of the presence of a perceived foreign substance. This substance, called antigen, can be a bacterium, a parasite, or even molecules like proteins. The antibodies recognise antigens and latch onto them in order to remove them from the human body. Each antibody matches a unique antigen.

Any substance that can stimulate the production of antibodies and combine specifically with them.

Autoimmune disorders are a group of different conditions that arise when the immune system confuses its own healthy body tissues for antigens or foreign elements, and attacks them in order to destroy them. The exact cause for the onset of these disorders is still unknown. Around 80 different autoimmune disorders are known; severity changes depending on the attacked organ. Some autoimmune reactions are considered part of the mechanisms of diseases such as diabetes.


Bacteria are a large group of prokaryotic microorganisms (cells lacking a nucleus, as opposed to eukaryotic ones, that have nucleus, and that form the human body) that were among the first life forms to appear on Earth. They are commonly found in most of the planet’s habitats and live in symbiotic (mutually beneficial), commensal (eating from the same dish) or parasitic (living in or on another organism and benefiting from it) relationships with plants, animals and humans. Many people believe that all bacteria are pathogens. Although some of them can be harmful, most of them are beneficial and necessary for remaining in good health.

Bacteria are 10 to 50 times smaller than human cells. In the human body there are an estimated 40 trillion microorganisms, including at least 1000 different known species of bacteria with more than 3 million genes—that is, 150 times more genes than humans have. Large bacterial communities live on the skin and in our bodily cavities. The largest community lives in our guts: the gut microbiota.

A genus of bacterial species naturally present in a mammal’s gut. You can also find these bacteria in fermented foods (such as dairy products) or in dietary supplements.

Abdominal bloating is a condition in which the abdomen swells and gets tight. More common in women, it can cause belly pain that varies from mild to intense. It is provoked by excess gas, when said gas does not pass through belching or flatulence and therefore builds up in the stomach and intestines, or by an excessive reaction to normal gas production e.g. hypersensitivity of the bowel. In general, people suffering from bloating have flatter bellies in the morning that progressively become more distended over the day.


A species of bacteria that lives harmlessly in the gut of many people. In the gut’s microbial community, there is a balance between the “good” bacteria (beneficial) and potentially harmful ones (pathogenic). Problems begin when an imbalance occurs, often due to antibiotic treatment. If the quantity of C. difficile increases greatly, a variety of symptoms can arise, ranging from diarrhoea to inflammation of the colon.

C. difficile infections generally affect patients who have recently undergone antibiotic treatment or who are in hospitals or long-term care facilities. Faecal microbiota transplant (FMT) is being studied as a possible treatment for recurrent C. difficile infections. Some probiotics may prevent the occurrence of C. difficile in hospitalized adult patients who are treated with antibiotics.

The colon, also known as the large intestine, is the last part of the digestive tract. It allows the absorption of water and essential vitamins produced by gut bacteria and the transformation of non-digested residues, which is the origin of faeces. Shorter in length than the small intestine, with a longer transit time, the colon is considerably thicker in diameter and harbours the vast majority of the gut microbiota.

The term commensalism refers to a type of relationship between two different organisms that “eat from the same dish”. In this kind of relationship, neither benefits from the other or provokes any harm. It is therefore a neutral relationship. Other classes of relationships between organisms include mutualism, in which both organisms obtain benefits, or parasitism, where one profits from the other by harming it. Although “friendly” bacteria inhabiting our organism are usually referred to as commensal, research in this field suggests that the relationship between our gut microbiota and us is not merely commensal, but rather a mutualistic relationship.

This is a type of Inflammatory Bowel Disease (IBD) that can affect any part of the digestive system, from the mouth to the back passage, although it mostly occurs in the last section of the small intestine, the ileum, or the large intestine, the colon. Its most usual symptoms include diarrhoea, abdominal pain and extreme tiredness, as well as bloody stools and weight loss on occasion.

This disorder often begins gradually and becomes worse over time. People with Crohn’s disease sometimes go for long periods without any symptoms or very mild ones, known as remission periods. These phases can be followed by very troublesome periods during which the disease flares up. The exact cause of this disorder is unknown, although researchers point out some factors like genetics, an immune system anomaly that causes it to attack healthy bacteria in the gut, smoking or environmental factors (curiously, the disease is more common in Western countries than in the world’s developing areas).


Also called dysbacteriosis, it refers to an imbalance of microbial colonies, either in number or type, that have colonized the human body. This is most common in the digestive tract, but it can happen in any exposed surface or mucous membrane. Dysbiosis can affect digestion, absorption of nutrients, production of vitamins and controlling the growth of harmful microorganisms. A wide range of factors, such as changes in dietary habits or antibiotic use, can influence the delicate microbial balance and thus, lead to dysbiosis. Researchers believe that it may have a role in disorders such as Inflammatory Bowel Disease (IBD), chronic fatigue, obesity or even certain cancers.


The microbial community living in our gut is a unique combination of different types and amounts of bacteria. It is not a permanent bacterial mix, but an evolving one that can be affected by our diet, environmental factors, medicinal treatments, etc. Scientific research in the frame of the European MetaHit Project (2008 – 2012) has been able to identify and characterise three main different microbiota groups or enterotypes.

A species of bacteria (from the family Enterobacteraceae) that normally lives in the guts of people and animals. Most E. coli strains are harmless and play an essential role in keeping the digestive system healthy, helping to digest food and producing Vitamin K. However, some E. coli bacteria are pathogenic and can cause disease. The harmful serotypes can be transmitted through contaminated water or food or through contact with animals or other infected people.


Also known as faecal transplant or stool transplant, this term refers to the process of transplantation of faecal samples (with its bacteria and metabolites) from a healthy individual into a person with an unbalanced microbiota. Although this procedure has been proven to be effective in patients suffering from resistant C. difficile infection, its use has not yet been authorized in a general basis. Experts continue working on this technique, and no consensus has been reached so far on its potential adverse effects.

Fermentation is a chemical process by which an organism converts sugars and carbohydrates present in food into an acid or an alcohol. Humans have used it for centuries to turn raw materials into assimilable final products, in food such as yogurt, kefir, cheese, bread, wine and beer, or even chocolate.


This was the name previously given to the bacterial communities inhabiting our intestines. Researchers now prefer the term gut microbiota, as bacteria do not belong to the vegetable world. Some scientists also use one term or the other depending on the techniques used to identify the bacteria. They use microbiota to refer to bacteria found through sequencing techniques and gut flora to name bacteria found through (older) culturing techniques.

This is the name given to the community of microorganisms inhabiting the length and breadth of the mammalian gastrointestinal tract. The composition of this microbial community is host specific. Each individual’s gut microbiota can undergo endogenous and exogenous alterations. It is sometimes called human flora, microflora or gut flora. These terms, however, are less used by scientists as it leads to the incorrect idea that tiny plants colonise us, while the microorganisms making up our microbiota are actually different kinds of microbes.


Human Microbiome Project. Launched in 2008, it was a five-year US National Institutes of Health (NIH) project that had the aim of identifying and characterising microbial communities found at multiple human body cavities and looking for correlations between changes in the microbiome and human health and diseases.

See gut flora / gut microbiota.

This term refers to the biological community of microorganisms living in the environment of the human gut. Although the bacteria belong to different groups and are present in our digestive systems in different quantities, they work as a team, playing an essential role in helping digest food, boosting the immune system, preventing infections and even influencing mood and behaviour.


The immune system is generally known as the body’s defence system against infectious organisms and other invaders. It is made up of a network of cells, tissues and specialized organs that communicate with each other and act through a cascade of biological reactions that involves cytokines. The immune response acts to destroy and eliminate the detected agent in order to prevent it from causing any harm to the host.

Inflammation is the body’s biological response as it aims to fight against an aggression. It can be characterized by specific symptoms such as redness, swelling, a feeling of heat or pain, or altered functions of the involved organ. Infection is caused by bacteria, viruses or fungi, whereas inflammation is part of our innate immunity and does not necessarily imply an infection.

Inflammatory Bowel Disease (or IBD) covers Crohn’s disease and ulcerative colitis. Both disorders are characterized by an excessive swelling of the wall of one section of the digestive tract.

Irritable Bowel Syndrome (IBS) is a common functional disorder of the gut affecting 15% to 20% of people worldwide (with a higher prevalence in women). Irritable Bowel Syndrome is the main motivation behind gastroenterology consultations. Researchers believe it may originate from an unbalanced gut microbiota.


Lactobacillus is a type of rod-shaped bacteria that normally inhabits our oral, digestive and genital cavities. It is also present in some fermented foods like yogurts or dietary supplements. Its name comes from its ability to convert lactose and other sugars into lactic acid. Due to their effectiveness, lactobacilli are normally used for treating and preventing diarrhoea, including some infectious types such as rotavirus diarrhoea in children or traveller’s diarrhoea.


The term metagenome refers to the entire collection of microbial genes found in a particular environment (or ecosystem). Metagenomics is the the method used to analyze this metagenome. It reflects the potential capacity of a specific ecosystem, what action their gens can implement. It also reflects which microorganisms are present.

A project financed by the European Commission under the 7th FP program between 2008 and 2012. Its main objective was to establish associations between the genes of the human intestinal microbiota and our health (or our diseases). The researchers focused on two disorders of increasing importance in Europe: Inflammatory Bowel Disease (IBD) and obesity.

The term ‘microbial ecology’ is used to refer to the study of microbes and their interactions with the environment, as well as with plants, animals and each other. Although they are the tiniest creatures on Earth, they have a deep impact on humans and the planet. That is why scientists believe the study of microbial ecology can lead us to find better solutions to environmental restoration, food production and bioengineering, for instance.

Researchers usually refer to the human microbiome when talking about the entire collection of genes found in all of the microbial cells living in the human body. It is sometimes confused with microbiota, the word used to define the hundreds of trillions of microorganisms living in the human body.

It is the name given to the community of microorganisms that reside either on the surface or in different cavities of the body: the skin, the mouth, the ears, the vagina or the gastrointestinal tract, among others. (See gut microbiota)

Often wrongly used as a synonym of the word “microbe”, microorganisms are single- or multiple-cell organisms, so tiny that they cannot be seen with the naked eye (microscopic). Microorganisms are diverse and include parasites, bacteria, archaea, fungi and viruses. Microorganisms are the oldest form of life on Earth. The study of microorganisms is called microbiology.

The mucosa is a thin tissue layer that lines hollow organs, such as the mouth, uterus, lungs and the urinary and digestive tracts. The glands covering this tissue release a thick fluid called mucus. It is also the most highly differentiated layer of the GI tract. Structurally and functionally, it is the most complex and important area, as key absorptive functions take place on its surface.


The WHO defines obesity and overweight, as abnormal or excessive fat accumulation that constitutes a risk to health. Both overweight and obesity are major risk factors for a great number of chronic and serious diseases, such as diabetes, cardiovascular conditions and cancer.


A pathogen is an infectious biological agent that can produce a disease in its host. The term is most used to describe microorganisms like virus, bacteria or fungi, among others. These agents can disrupt the normal physiology of plants, animals and humans.

Prebiotics are functional non-digestible food components (such as certain kinds of fiber) that stimulate the activity or the growth of some specific groups of bacteria, e.g. bifidobacteria and lactic acid bacteria. Scientific studies have proved that both prebiotics and probiotics have several beneficial effects on the host’s health, especially in terms of digestive and immune functions.

According to the 2001 WHO/FAO definition, probiotics are “live microorganisms which, when administered in adequate amount, confer a health benefit on the host”. They are commonly consumed as part of fermented food, e.g. yogurt, or as dietary supplements.


The relationship established between two organisms that need each other to survive is called symbiosis. Bacteria have a long history of symbiotic interactions with humans, and they have even evolved in symbiosis with other microbes and with their hosts. In fact, humans have trillions of bacteria living in their digestive tracts, and these bacteria have found a suitable ecosystem for their development. As they break down food that humans can’t digest by themselves, they produce energy and the vitamins we need.