B io Factsheet

www.curriculum-press.co.uk Number 322

The bacteria in our bodies

This Factsheet:
• Explains the term microbiome.
• Explains how our microbiome keeps us healthy.
• Outlines the evidence that the over-use of antibiotics and our
increasingly high sugar, high fat diet may be harming our
microbiome, making us more susceptible to bowel disease and
auto-immune disease.
The microbiome is the genetic material of all the microbes - bacteria,
fungi, protozoa and viruses - that live on and inside the human body.
Microbes outnumber our human cells ten to one – each of us has more
than 100 trillion microbes.
The bacterial composition of mother’s milk is also heavily influenced
by the method of delivery and whether or not the mother is obese.
As children get older the number of bacterial species which they host
increases but again, many factors affect the bacterial composition of
the young child’s gut.
A study comparing children from Europe, who had a high fat, high
animal protein, high sugar and starch but low fibre diet, with children
from Burkino Faso who had a diet that contained low levels of fat and
animal protein but high fibre and plant polysaccharides found that
the two groups had very different microbial populations in their guts.

Examples: Bacteria keep us healthy

• Respiratory System -- Mouth, Pharynx, Lungs The evidence that our bacteria keep us healthy came from good old-
• Streptococci, Candida, Neisseria fashioned scientific observation.
• Skin - Staphylococcus, Trochosporon
• Stomach -H Pylori, Streptococcus • In 2000 a French gastroenterologist took tissue samples from
• Intestines - Lactobacilli, E Coli patients with Crohn’s disease – chronic gut disorder
• Breast milk - Streptococcus, Staphylococcus, Serratis,
Corynebacteria • DNA analysis of the gut tissue revealed a shortage of one common
• Urogenital System – Bladder, Uterus, Vagina Lactobacilli) species of bacteria - Faecalibacterium prausnitzii

Role of the microbiome
• Food digestion
• Regulation of immune system
• Production of vitamins B12, thiamine and riboflavin, and vitamin
K, which is needed for blood coagulation
• Regulation of fat storage
• Regulation of drug metabolism
• Renewal of gut epithelial cells
• Skin moisturisation
This Factsheet concentrates on the role of the microbiome in regulating
our immune system.
The intestine of a new born is a sterile environment – there are no
bacteria. But very quickly a microbiome develops. The composition
of this flora is determined by factors such as
• delivery mode: vaginal vs. C-section
• the cleanlinesss of the delivery environment
• feeding mode: breast milk vs. formula
• the degree to which antibiotics are used
• the flora of the mothe ’s skin
• the bacterial composition of the aerial environment
Whether the infant is breast fed or not seems particularly significant in
determining microfloral composition. Several studies have suggested
that prebiotics in breast milk (e.g. glycoconjugates) promote the
growth of certain bacteria e.g. Bifidobacteri and breast milk usually
contains several hundred species of bacteria not found elsewhere in
the mother’s body.
• When this bacterium was injected into mice it protected them
against exper­imentally induced intestinal inflammatio
• Mixing F. praus­nitzii with human immune cells in a test tube,
induced a strong anti-inflammatory response
A healthy adult maintains an ecosystem of trillions of bacterial
cells. Every adult has a unique microflora and each person’s exact
composition changes daily. The vast majority of bacteria live in the
large intestine and there is a lot of evidence that they play a key role
in interacting positively with our immune system.
Scientists have identified that key parts of this microflora are branches
of the clostridial group and are known as clostridial clusters. One of
their roles is to inhabit the mucus lining of the gut and to block the
passage of pathogenic bacteria. F. praus­nitzii is part of one of these
clostridial groups and many studies have shown that patients with
depleted levels of this species are more likely to suffer inflammato y
bowel diseases.
More generally, it is possible that it is disruption to these clusters
that is responsible for the increasing incidence of bowel disorders.
Disruption could be caused by antibiotics, sanitary practices such as
colonic irrigation and our increasingly high sugar and high fat diet.
Use of antibiotics early in life may be particularly damaging: Young
mice given high doses of vancomycin were found to have reduced levels
of clostridial clusters, reduced levels of T cells and were more likely
to develop asthma and auto-immune disease later in life.

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Autoimmune disease
Autoimmune diseases such as Type 1 diabetes, rheumatoid arthritis, muscular dystrophy and multiple sclerosis are associated with disruption
to the microbiome. Disruption allows pathogenic bacteria to accumulate, changing gene activity and metabolic processes. In turn, this can
lead to an abnormal immune response in which our immune system turns against our own cells and tissues.

The role of f bre

We do not have enzymes that can digest fibre but the clostridial clusters do. These release useful metabolites that appear to assist the
immune system but also provide nutrients to cells lining the colon. Many of these cells secrete mucus.

This mucus appears extremely important in keeping us healthy. Mucus contains compounds that repel certain potentially harmful microbes
and provides a source of nutrients – complex sugars - for other non-pathogenic bacteria.

A healthy gut microflora f clostridial clusters enables us to ferment more of the soluble fibre we ingest, releasing metabolites such as short
chain fatty acids that appear to stimulate the production of regulatory T cells, improving immune function.

If we reduce our levels of clostridial clusters with a low-fibre, high sugar and fat diet, we deplete our mucus layer in the colon, reducing production
of T cells, disrupting the immune response and allowing pathogenic bacteria access to the gut wall. This, it is hypothesised is the cause of the
increase in bowel conditions e.g. Crohn’s disease.

Human Microbiome Project (HMP)

The Human Microbiome Project (HMP) is a large scale US – based collaborative study of the role of bacteria, fungi and viruses in our bodies.

Scientists are trying to identify the species present and how changes in the microbiome might cause diseases such as inflammatory bowe
disease, diabetes and atherosclerosis and how these changes might be prevented or reversed.

DNA sequencing is used to identify which microbes live where.

Sampling points in the HMP

• 10,000+ species identified so far

• Each person’s microbiome is unique

Nasal

• A person’s microbiome is heavily influenced by method of birth and whether they

Oral received breast milk – which contains 600+ species

• Antibiotics found to kill useful species at the same time as they were killing the
target pathogen
Skin

• Destruction of useful microbiome species enables colonisation of the gut by

pathogens such as Clostridium difficile.
Gastro-
intestinal
The HMP is stimulating more research on probiotics, particularly the usefulness of
Urogenital
directly ingesting the useful bacterial species.

The hope is that our knowledge of an individual’s microbiome will lead to the
development of personalised medicines.

References
Gut microbiome: Velasquez-Manoff M (2015) The Peacekeepers Velasque NATURE 518
Sokol, H. et al. (2008). Faecalibacterium prausnitzii is an anti-inflammatory commensal bacteriu
identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105,

Acknowledgements:
This Factsheet was researched and written by Kevin Byrne.
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