Experimental Cell Biology II: Human microbiome
Microbiome vs microbiota Align the overlapping ends of the different reads
Microorganisms typically live in complex of DNA sequences and assemble them into a
microbial communities, and their activities are continuous sequence.
regulated by interactions with each other, with
their environment, and with other organisms.
The sites of the human body inhabited by
microorganisms include the mouth, nasal
cavities, throat, stomach, intestines, urogenital
tracts, and skin. The microbiota is the
community of commensal, symbiotic and
pathogenic microorganisms that share our
body. The collection of genes that are encoded
by the members of the microbiota is called the
metagenome. The microbiota is the collection of
genomes from all the microorganisms in the
environment. The human microbiome contains
around 3.3 million bacterial genes, humans Phylogeny and taxonomy of bacteria
only have 20.000-25.000 genes. The phylogenic tree is a branching diagram
showing the evolutionary relationships among
Microbiome research biological species based on similarities and
Microbiome researchers differences in their physical or genetic
use DNA sequencing characteristics.
technology (cultivation-
independent methods).
These methods focus on
sequencing specific
target regions that are
then amplified by PCR
and analyzed by next-
generation sequencing (NGS) or Sanger
Dideoxy Sequencing reactions to identify and
differentiate multiple microbial species from Taxonomy is the identification, naming and
complicated samples. They sequence the target classification of organisms. Classifications are
genes of 16S rRNA by using universal primers based on phylogenetic data.
to describe and compare the phylogeny and Nomenclature is the process of assigning names
taxonomy of bacteria in a database. This way to the taxonomic ranking of each living organism.
they can investigate the composition of the Each bacteria is assigned two names, a genus and
microbiota. It is also possible to find other a species name. In Escherichia coli, the genus is
members of the tree of life, such as archaea and Escherichia and the species is coli.
yeast, these are also part of the human
microbiome.
There are 4-6 phyla associated with the human
gut, which means that there are certain
There are also other applications to identify the conditions that only allow these 4-6 phyla to
microbiome, such as shotgun sequencing. In grow. The most dominant phyla are Bacteroidetes
this case, the whole genome is sequenced, but and firmicutes. The other phyla are
the DNA is isolated and randomly broken up Actinobacteria, Verrumcomicrobia,
into small segments. The computer can Proteobacteria and Fusobacteria.
, Microbes Gastrointestinal Microbiota
A microbe is a microorganism that causes The human digestive tract is a long folded tube of
disease or fermentation. It is estimated that nutrients mixed with microbes (bacteria). The
the microbes in the human microbiome gastrointestinal tract has about 400 m2 of surface
number between 10^13 and 10^14 cells, which area and is home to a total of about 10^13
is roughly the total number of human cells in microbial cells.
one single person. Together, the human body as
the host and its associated microbes are The stomach
recognized to constitute a host-microbiome The stomach plays a role in inactivating bacteria
supraorganism. The use of microbes as a due to the low pH. This means that the number of
metabolic model system led to the discovery of bacteria present in the stomach is relatively low.
their function in one cell, to understand their Though there are bacteria that live in the
function in all cells. This was important to stomach, for example, Helicobacter Pylori, which
understand microbial evolution and for the is associated with ulcers and gastric
discovery of DNA as the molecular basis of malignancies.
heredity 80 years ago.
This is an overview of the major microbial The intestines
populations in the body sites sampled by In the duodenum, the food from the stomach is
human microbiome projects. Diversity among blended with bile, bicarbonate and digestive
body sites was evaluated by 16S rRNA gene enzymes, which will increase the pH. When the
sequence analysis. Note that each body site food reaches the gut, the pH will be neutral.
tends to be dominated by one population type: In the colon are a lot of bacteria and archaea
skin by Propionibacterium species, oral by present. The colon is a fermentation vessel, with
Streptococcus species, urogenital by the microbiota using nutrients derived from the
Lactobacillus species, and gastrointestinal by digestion of food. Facultative aerobes such as
Bacteroides species. E.coli are present, they consume any remaining
oxygen, rendering the large intestine strictly
anoxic. Anoxia promotes the growth of obligate
anaerobes such as Clostridium and Bacteroides
species, these are de dominant species in the
colon. Also, Firmicutes are present, they are
important in the digestion of polysaccharide
polymers in plant fibres (cellulose and pectin).
Goblet cells in the colon produce mucin, which is a
slime layer that contains water-soluble proteins
and glycoproteins. There are no microorganisms
Biofilms
present in the mucus layer which protects the
The primary site of interaction between
epithelial cells. During the passage of food, water
humans and microbes is the surface areas of
is absorbed and turns into faeces. Bacteria
the epithelial cells. These surfaces are
compose about one-third of the weight of faecal
colonized by biofilms. Biofilms are a collection
matter and are continuously displaced downward.
of micro-organisms that stick together and
The bacteria that are lost are also continuously
often also to a surface and form a slimy
replaced by new growth. The time needed for the
extracellular matrix and use the epithelial
passage of material through the human
cells as a substrate.
gastrointestinal tract is about 24 h, and the
growth rate of bacteria in the lumen is one to two
The human gastrointestinal tract
doublings per day.
Bacterial diversity of faeces.
The results are pooled from
approximately 1 million
sequences of the 16S rRNA
gene. Members of the Bac-
teroidetes and Firmicutes
dominate the normal micro-
biota of the large intestine.
