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The gut microbiota

The collection of microorganisms colonising the gastrointestinal tract is called the ‘gut microbiota’.

The human gut microbiota consists of 10-100 trillion symbiotic microorganisms (most of them bacteria, but also archaea, viruses and fungi), with a biomass of around 1 to 2 kg. In other words, the number of microorganisms in the gastrointestinal tract is one to ten times greater than the total number of human cells in the human body.

The relationship between humans and their gut microbiota is called a ‘symbiosis’. A symbiosis between two organisms means that they both need each other to survive. Bacteria in the human body have found a suitable ecosystem for their development. In exchange, these bacteria perform key functions in the body, as described below.

The word ‘microbiome’, when it is interchanged with ‘microbiota’, is often misused. A ‘microbiome’ actually consists of the collective genetic material of all the microorganisms in a specific environment (such as the gut for example). For instance, the human genome consists of about 23 000 genes, whereas the gut microbiome encodes around 10 million genes.

Like a fingerprint, the gut microbiota is unique to each individual, and is shaped early in life. Microbiota diversity increases from birth until the age of 3 to 5 years, when the composition and diversity of the gut microbiota reaches its adult stage and stable state. In adults, the microbiota is dominated by three bacterial phyla: Firmicutes, Bacteroidetes and Actinobacteria.

Bacteria are classified taxonomically according to different groups. From broadest to most specific, these are: phyla, classes, orders, families, genera, species and strains. Only a few phyla are represented in the gut microbiota, accounting for more than 160 species. The dominant gut microbial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, with the two first representing 90% of the gut microbiota.

Domain: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Genus: Homo
Species: Homo sapiens
Strain: Homo sapiens sapiens (you)
Domain: Bacteria
Phylum: Verrucomicrobia
Class: Verrucomicrobiae
Order: Verrucomicrobiales
Family: Akkermansiaceae
Genus: Akkermansia
Species: Akkermansia muciniphila
Strain: Akkermansia muciniphila MucT (AktiGut®)

The gut microbiota composition is influenced by many factors, some of which can be modified:

  • Diet and dietary habits (consumption of raw vegetables, consumption of alcohol, consumption of fried foods, intermediate fasting…)
  • Weight gain
  • Medication use (antibiotics, acid suppressants, anti-diabetic drugs, laxatives, antidepressants…) and surgery (colon resection, bariatric surgery…)
  • Breast- or infant formula feeding and introduction of solid food
  • Environment (rural vs. urban locations)
  • Lifestyle (exercise, sedentary lifestyle, stress, jetlag)

The gut microbiota composition is also influenced by other factors that are intrinsic and cannot be changed:

  • Ethnicity
  • Genetic background
  • Certain diseases
  • The anatomy of the intestinal tract (e.g., the large intestine has a higher microbial diversity compared to the small intestine)
  • Gestational age (preterm birth vs. full-term birth)
  • Delivery mode (vaginal delivery vs. C-section)
  • Age and aging
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There is a heritable, genetic component to our gut microbiota. Nevertheless, environmental factors related to diet, drugs, and anthropometric factors such as weight have a bigger influence on its composition.

Most importantly, the beneficial effects of the gut microbiota are highly dependent on its composition, which has been shown to change dramatically in several human disorders and diseases.

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Gut microbiota — at the intersection of everything? Patrice D. Cani, Nature Reviews Gastroenterology & Hepatology, 2017

Humans have a long history of symbiotic interactions with bacteria. Our microbiota has co-evolved with us over thousands of years, to form a complex and mutually beneficial relationship. Indeed, the gut microbiota performs functions that our human cells are not able to.