Intestinal Biotope

Scientists have just discovered a new organ. This is an organ made up not of human cells but of bacteria. This discovery has revolutionised our perception of the human body and opens the way to a whole new understanding of some diseases.

The Digestive System

• The gastrointestinal tract (GIT)

Its role: This is responsible for digesting food, breaking it down into proteins, carbohydrates, lipids, mineral salts, trace elements and other substances that the body can use. The GIT also enables the transport and absorption of these nutrients through the intestinal mucous into the bloodstream. 

The GIT is made up of several organs: the mouth, the oesophagus, the stomach, the small intestine and the colon.
The colon is what we are interested in and it carries out three functions that are important to the body:
- The digestion and absorption of food not yet digested,
- The concentration of faecal matter through the absorption of water and electrolytes,
- The storage and elimination of faeces.
- On a functional level, the colon can be divided into parts, separated by the transverse colon:
- The right colon (caecum and ascending or proximal colon) plays a major role in absorbing water and electrolytes, as well as fermenting undigested sugars,
- The left colon (descending or distal colon, sigmoid colon and rectum) intervenes primarily in the storing and elimination of stools.
- Their vascularisation is completely different which may explain the difference in their functions.

• Digestion

Between the mouth and the anus, food undergoes multiple chemical and mechanical transformations. These transformations can be divided into three phases depending on the place (organ) where the food is converted into nutrients:

- The buccal and oesophageal phase
- The gastric phase
- The intestinal phase
Source: Faculty of Medicine, Laval University (fr)


Intestinal biotope or flora

- So what is normal intestinal flora?

Flora refers to the ensemble of micro organisms in a given place. Intestinal flora is made up of the entire microbial community living in the intestine. That amounts to between 1,000 billion and 100,000 billion bacteria.

• Intestinal biotope

Normal intestinal flora contains around 1012-14 bacteria, or, depending on your age, 10 to 20 times as many cells as there are in the body. That gives you an idea of how important this "living microbiological world" is. 

The bacteria living in a person in normal conditions are commensal or saprophytic bacteria as opposed to pathogenic bacteria.

biotope intestinal
• Intestinal Biotope. Source : Journal de pédiatrie et de puériculture (2009) (fr)


• The composition of intestinal flora

Intestinal flora forms a complex ecosystem made up of hundreds of species.

The majority of these bacteria are obligate anaerobic (Conway, 1995).
Forty of these species represent 99% of the biotope (Macfarlane and Macfarlane, 1997). Some 80% of existing bacteria have not yet been identified. Certain micro-organisms found in large numbers are described as autochthonous bacteria.


The colonic flora comes in two states:

- A planktonic state : in which the bacterial populations are free-flowing in isolation in the colonic environment.
- A sessile state : in which the bacteria fix on to particles of food or intestinal mucus, thus forming a biofilm (Macfarlane et al.1997, Probert and Gibson, 2002).

The mucus forms a physical barrier to potentially pathogenic organisms present in the intestinal lumen (Lee et al., 2003).
Mucus possesses:
- The ability to prevent pathogenic agents from adhering to epithelial cells. This property is in part down to mucins (the main component of mucus) produced by epithelial cells.
- The characteristic of also constituting a micro-environment for autochthonous micro flora by forming nutrients and oxygen. (Palestrant et al., 2004).
- Some bacteria are more suited to the sessile state than to the planktonic. The micro-organisms most often detected in mucous tissue are the Bacteroides and Fusobacterium. Other bacteria such as Bifidobacterium spp., Spirochaetes spp., Helicobacter spp., E- coli and gram-positive cocci are also capable of growing in intestinal mucus (Probert and Gibson, 2002). The states vary depending on ethnicity and diet

Source: Collection of electronic thesis and dissertations, Laval University (fr)

• The role of intestinal flora

Intestinal mucus has an active surface of considerably more than 300 m². It is constantly exposed to a very great quantity of antigens of food or bacterial origin. Bacterial intestinal flora plays an essential role in immune, intestinal and peripheral systems.

This intestinal biotope constitutes a "barrier" that limits colonisation by pathogenic bacteria. The stability of intestinal flora comes from microbial interaction within the intestinal flora in the form of competitions over nutritional substratum or places to lock on to and changes to the intestinal environment through the products of bacterial metabolism: pH, bacteriocins and organic acids etc. So the intestinal flora is a major biotope, vital to the acquisition and maintenance of digestive functions.
Source: Journal de pédiatrie et de puériculture (2009) (fr)


• Stress factors for intestinal floral

A certain number of therapeutic, toxic or dietary factors can have a lasting effect on the flora.

- Antibiotic treatment

Whether taken orally or intravenously, all antibiotic treatments should be fully recommended and suited to the situation - i.e. targeted.

Also, antibiotics issuing from the agricultural world, given to animals to dope or treat them before they are slaughtered, will have repercussions on our flora. They appear in the bloodstream and therefore in the muscle of the animal - in other words in the meat we eat. So in the end, eating meat amounts to taking broad-spectrum antibiotics.
An antibiotic is an agent that destroys bacteria, so to defend itself against this aggressor, the bacteria mutate to be able to fight the antibiotic or release proteins aimed at fighting it. Given the many, many treatments of this kind, we can understand very well that in the end such medication, even with targeted use of antibiotics, will no longer help us as bacteria are becoming multi-resistant. Within hospitals, this multi-resistance is creating an unparalleled public health problem and the next plague: nosocomial infections.

It is in hospitals that we find the greatest concentration of highly pathogenic germs.

- The negative effect of antibiotic treatments

Antibiotic treatments have a destructive effect on certain strains of bacteria of the commensal flora and thus leave the path clear for re-colonisation by and the development of pathogenic bacteria on which the antibiotic is ineffective.

This results in a competition and the following conclusion:
That an antibiotic treatment should always be followed by a controlled bacterial re-colonisation.
But 80% of colonic bacteria have not yet been identified. There is a major problem…

- The use of antacid treatments

Treating gastroesophageal reflux disease or gastroesophageal ulcers with anti H2 considerably alters the flora. Gastric alkalinisation removes one of the main barriers preventing potentially pathogenic bacteria from colonising.

It has been shown that antacid treatments increase the risk of infectious diarrhoea.[Canani RB, Cirillo P, Roggero P, et al. Therapy with gastric acidity inhibitors increases the risk of acute gastroenteritis and community-acquired pneumonia in children. Pediatrics 2006; 117:e817—20.]

- Invasive medical actions

Interventions or invasive gestures that do not pass through an acid barrier such as the stomach are responsible for the whole problem of transmission from an infection to septicaemia.
This proves that urinary and kidney infections (pyelonephritis) have major septic repercussions. And the proximity of orifices to the emitting orifice only aggravates the problem.

- Lack of dietary fibre

A diet that includes little or no fibre does not help the creation or upkeep of a balanced flora, leaving the path clear for pathogenic flora..

- Acute gastroenteritis

A commonplace viral or bacterial acute gastroenteritis (AGE) alters the intestinal flora. This can include acute infectious diarrhoea, one of the effects of which is a long-lasting imbalance in intestinal flora.
Source: Journal de pédiatrie et de puériculture (2009) (fr)
- Heavy metals
The absorption of heavy metals like copper or zinc (through fish that are at the top of the food chain such as tuna and swordfish), turns saprophytic bacteria into pathogenic bacteria. This concept is very new and is prompting us to reflect on the toxic products we consume.

• The constitution of intestinal flora in children

- Intestinal flora is constituted in the first months of our lives. Built up during several stages of life, it is formed as successive colonies of bacteria attach themselves:
- Colonisation of the alimentary tract 
While in the mother's uterus, the foetus has a sterile intestinal tract. The colonisation of the alimentary tract happens extremely quickly, beginning straight after birth. During this first stage, this colonisation is mainly a function of environmental factors and the birthing method. Indeed, children born by caesarean section will not be colonised by the same micro-organisms as children born by the natural route (Moreau et al., 1986). In addition, environmental and hygiene conditions following the birth can also influence the acquisition of intestinal flora.
During the first days of life, a succession of micro flora gets to work: 
- During Day One, the redox potential for the colonic environment favours the establishment of a micro flora dominated by aerobic micro organisms mainly comprising streptococci and enterobacteria (flora of the skin).
(Favier et al., 2002; Moreau et al., 1986 ; Sakata et al., 1985).
- After Day Two or Day Three, the obligate anaerobic micro flora begin to colonise the colonic habitat; Bifidobacteria seems to establish itself first followed by Bacteroides, Clostridium and Fusobacterium (Chierici et al., 1997; Moreau et al., 1986).
- This stage of colonic habitat colonisation is not affected by the dietary regime of the infant (breast milk or formula). It is only after this micro flora is established that the nature of the milk will foster the development of certain strains of bacteria among all the potential strains that could develop in the colon. 
Source: Collection of electronic thesis and dissertations, Laval University (fr)
Source: Swiss medical revue - 2012 (fr)

The revolution

It is estimated the intestinal flora comprises some 400 to 600 different species of bacteria. They form a biomass of 1012-14 bacteria and contain 100 times more genes than the whole of the human genome.
At birth, the alimentary tract is sterile and the process of bacterial colonisation begins.
Several factors influence this initial process: the gestational age, the method of birth, neonatal nutrition and genetic factors.
The Intestinal flora continues to develop until the infant is two years old and then reaches a definitive state which, under normal circumstances, should remain stable until adulthood.

The intestinal flora is subjected to multiple factors that may alter or disrupt it. This dysbiosis is nothing other than an imbalance between commensal bacteria and pathogenic bacteria. Dysbiosis has proven to be the common denominator in the emission of pathogenic bacteria.
Bacterial infections such as Clostridium Difficile, Klebsielles, Pseudomonas and Echerichia Coli are responsible for and guilty of the deaths of thousands of people who were not in a life-threatening situation.
So the emissary is the colon and the point of entry is the urethra.
The prevalence of these conditions proves that proximity is a preponderant factor.


Awareness of these mechanisms and the modulation of the composition of intestinal flora are at the heart of current concerns. The new theories acknowledge faecal danger as being at the root of hospital-acquired or nosocomial infections. Indeed, all themes converge on the implication of micro-organisms issuing from the colon in the pathogenesis of nosocomial infections.
The consequence of this is the reorganisation of how we handle human waste in institutions and that means designing innovative technology.
Innovative technology in the full knowledge of the process of resistance to antibiotics but also in how faecal matter is collected and disposed of.