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Microbiology
is the study of microbes - microscopic living organisms. This group
includes bacteria, fungi, and protozoa. This page looks at microbiology
in the context of the rumen - part of the digestive system of
cows and other ruminants.
Cows' guts and microbes
Cows' guts (their digestive tracts, or intestines) are packed with microscopic organisms: bacteria, fungi, and single-celled animals called protozoa.
They aren't alone in this - all animals carry a huge load of bacteria -
but the microbes that live in one special gut compartment in cows
(and other ruminants) are special: they digest cellulose.
This makes a whole new energy source available to the cow. There's a
lot of energy in cellulose, but most animals are simply unable to
digest it because they don't have the necessary enzymes. That's where
the microbes come in.
The ruminant digestive tract (University
of Minnesota, 1996), showing the rumen,
where most cellulose digestion takes place.
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When were rumen microbes first discovered?
The single-celled
animals (protozoa)
living in the rumen were first discovered in 1843. Later that century, other
researchers discovered that a range of bacteria also lived in this part of the
gut. By the end of the 19th century, scientists were coming to
realise that microorganisms were important in helping ruminant animals to gain
nutrients from their food (Hungate, 1966). For example, when they killed the
rumen bacteria in a sample of stomach contents (using an antiseptic) and then
mixed the fluid with cellulose, the cellulose wasn’t digested. But when rumen fluids and cellulose were mixed
together without an antiseptic, various gases and acids were produced, which
showed that the cellulose had been broken down. This was followed by research
looking at what was actually produced during rumen fermentation. It turned out
that one product, short-chain fatty acids, provided a large proportion of a
cow’s energy needs (Annison and Bryden, 1998).
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Why do cows need micro-organisms?
Now we know that cows need rumen
microorganisms to survive. Even though cows eat grass, they can’t digest it on
their own. This is because cows can’t make the enzymes needed to break down some parts of plant
cells. For example, cows can’t digest cellulose. To do this, they need an
enzyme called cellulase. This is why the microorganisms are so important- they
produce the cellulase and other enzymes necessary to break down the parts of
plant cells that the cow can’t digest. Many different types of microorganisms
live in cow guts, making different enzymes to break down different parts of
plants.
Protein-structure model of cellulase
The microorganisms digest the plant
material and produce short-chain fatty acids, which the cow can then absorb
through its gut wall and use for energy. As well as this, the cow also digests some
of the microorganisms every day as they are washed out of the rumen into the abomasum. So you could say
that the cow’s diet is actually made up of grass and microbes, not just the
grass that it eats.
How can the microorganisms stay alive if
some of them are always being digested by the cow? They keep their population
numbers up by growing very quickly - they need to be able to reproduce before
the food leaves the rumen. They can also attach themselves to solid lumps of food in the rumen to
avoid being flushed out with rumen liquids.
Cows and their gut microbes are an example of symbiosis
- two organisms living together. The relationship between cows and
their gut microorganisms is mutualistic. This means that both organisms
benefit from the relationship. The microbes get a suitable place to
live and a supply of food delivered to their door. The cow gets energy
from digesting the gut microbes and the short-chain fatty acids they produce.
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How many microbes live in the rumen?
The number of microbes in one drop of rumen
fluid is more than 10 times bigger than the number of people on Earth! (If there are 1012
microbes in 1ml of fluid, then 1 drop (1/20ml) contains 50,000,000,000.
And 2008 data from the US Census Bureau tell us that there are
around 6,602,000,000 people on Earth.)
That’s a
lot of microbes - about one thousand billion, or 1012, or
1,000,000,000,000 organisms per millilitre (Prescott, Harley & Klein, 2005).
To give you an idea of how many there are in total, the rumen may hold up to 95 litres of food & fluid.
There are all sorts of different types of microbes in the rumen, such as fungi,
bacteria and single-celled eukaryotic organisms called protozoans. There are also some archaea, which are ancient microorgansisms that
produce methane.
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What types of bacteria are found in the rumen?
Bacteria are the most important microbes
involved in ruminant digestion, and there are many different types in the rumen
(Prescott, Harley & Klein, 2005). Almost all of the rumen bacteria will die
if they are exposed to oxygen- they are obligately anaerobic (Hungate, 1975).
Here we'll look at some of the most important bacterial groups in the rumen -
their relatives include some very useful microbes as well as some that make us
sick.
But first - something on how they're classified.
Classification
Because
there are so many organisms out there, we need a classification system to keep
track of all of them. We classify organisms at different levels, grouping
similar organisms together. For example, humans:
Domain Eukaryota
Kingdom Animalia
Phylum Chordata
Class Mammalia
Order Primates
Family Hominidae
Genus Homo
species sapiens
So, back to the bacteria.
Phylum
Firmicutes
Class Lactobacillales
The Lactobacillales are usually harmless to
humans- not all germs will make you sick! “Lacto” means “milk,” and this gives us a clue
about where these bacteria are found and what they're used for - making cheese and yoghurt. Others are
used to make beer and wine.
However, there are also harmful bacteria in
this group, such as Staphylococcus aureus, which can cause infections,
boils, abscesses and pneumonia in humans. You may have heard of “super bugs”
infecting people in hospitals- these are often strains of S. aureus
which have evolved to become resistant to antibiotics.
One species from this group, Streptococcus
bovis, uses a wide diet of different food sources in the rumen, such as
sugars and proteins, to make short-chain fatty acids.
Class Clostridia
This class contains some important rumen
bacteria that are able to digest a wide range of plant materials. Butyrivibrio
fibrisolvens, a member of this class, is able to ferment a wide range of
substrates, including cellulose, xylan (a structura polysaccharide similar to cellulose), proteins, sugars
and fats. Close relatives of these rumen microorganisms are also found in the
human gut (Fig. 1.). Other relatives of these bacteria are responsible for the
diseases tetanus and botulism.
Fig. 1. Clostridium
difficile obtained from a human gut.
Source: Wiggs, 2007.
Phylum
Bacteroidetes
A large proportion of rumen bacteria belong
to this group. These bacteria are rod-shaped and cannot survive in the presence
of oxygen - they are obligate anaerobes (Fig. 2) (Prescott, Harley & Klein,
2005). An important member of this group
that is found in the rumen is Bacteroides succinogenes, a cellulose fermenter (Hungate,
1966).
Fig. 2. Bacteroides
biacutis. Source: Dowell, 2006.
Phylum
Proteobacteria
The phylum Proteobacteria is the largest
and most diverse group of bacteria. They have many different shapes and ways of
living. Some are free-living, some are parasitic, and others form mutualistic
relationships with other organisms, such as those found in the rumen. Many
Proteobacteria are responsible for diseases in animals and humans, such as Salmonella
sp., which can cause
typhoid.
This order contains some bacteria found in
the guts of other animals as well as ruminants. Just like cows, we need gut
microorganisms to help digest our food. Escherichia coli (Fig. 3) is
found in the guts of humans and animals.
Methane-producing
bacteria (Phylum Euryarchaeota)
These organisms belong to the domain Archaea,
an ancient group separate from the eukaryotes and bacteria. The Archaea in
the rumen use hydrogen gas and carbon dioxide to produce methane. This
regulates fermentation in the rumen by lowering the amount of hydrogen gas,
allowing bacteria which produce hydrogen to carry on metabolising. Some species
that produce methane in the rumen include Methanobrevibacter ruminantium,
Methanobacterium formicicum and Methanomicrobium mobile.
Note: Bacterial names
Bacteria are often named for their shape.
The name coccus comes from the Greek word meaning “granules” and is used
to name spherical cells, such as those shown below (Fig. 4.). Rod-shaped
bacteria are also very common- these are called bacilli. Spiral-shaped
cells are called Spirilla, and if they are flexible, spiral-shaped
bacteria are called spirochaetes. What about the bacteria Staphylococcus?
Staphyle means “bunch of grapes” in Greek, and coccus means
“granules”, so Staphylococcus means “bunches of granules”- which is just
what they look like (Fig. 4).
Fig. 4. Scanning electron micrograph of Staphylococcus aureus. Source: Ardurino and Carr, 2007.
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What about protozoa and fungi?
Protozoa
Most of the protozoa found in the rumen are
ciliates (phylum Ciliophora). Many ciliates use cilia (tail-like
structures) to move around, and to move food particles into their mouths. Most
ciliates do not live inside another organism, but some exist in the rumen, such as Entodinium.
In the rumen, two types of ciliates are found; the holotrichs and the
spirotrichs. The holotrichs convert soluble sugars into starch,
while spirotrichs consume starch and cellulose (Hungate, 1975).
Fungi
The fungi in the rumen
are a bit different
to the mushrooms in your local supermarket. They are very small (Fig.
5) - note that the scale bar on this diagram is 50µm, or 50
millionths of a metre.
Unlike mushrooms, rumen fungi don’t need oxygen to survive: they
are anaerobes. Rumen fungi have
been shown to digest cellulose and xylans, which shows that they may play a
role in helping the ruminant host to digest plant matter.
Fungi are very important to humans. They
are excellent recyclers, breaking down animal and plant matter into molecules
that can be re-used by other organisms. Yeasts, a type of fungi, are used to make
bread, wine and beer. Fungi also cause many diseases in plants and animals,
such as the human diseases athlete’s foot and ringworm.
Fig. 5. Candida albicans, the fungus that causes thrush in humans, magnified 200 times. Source: Y tambe, 2005
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How do rumen microbes obtain energy?
To
obtain energy for growth and reproduction, organisms must break down
large molecules into smaller ones. This process gives energy and is
called catabolism. For growth to occur, larger molecules are made from
smaller ones, using up energy. This process is called anabolism. Both
processes are part of cellular metabolism.
When plant material, such as
grass, enters a cow's stomach, microorganisms immediately get to work
to break it down. They do this with enzymes. Ruminants are unable to
synthesise the enzymes needed to digest cellulose and other plant
compounds. The microbes in the rumen, however, are able to make the
various enzymes needed to hydrolyse cellulose, proteins, sugars and other materials.
Rumen bacteria need carbon dioxide, nitrogen, sodium, and volatile fatty acids
to grow (Hungate, Bryant & Mah, 1964). Some bacteria use only one
type of food, but others use a range of different types (Table 1). Many
bacteria are able to digest cellulose. Many can also digest xylan, a
type of complex carbohydrate similar to cellulose. Others can digest proteins, or sugars such as amylose and lactose.
Glucose is released when cellulose is digested. Various microbes then ferment the glucose to produce short-chain fatty acids
(SCFAs). The SCFAs are then taken up and used by the host animal.
Carbon dioxide and methane gas are also produced by the microbes and
are excreted by the host (e.g. in exhaled air & by belching).
Table
1. Sources of carbon, energy and electrons and their definitions. (Modified
from Prescott, Harley & Klein, 2005)
| Carbon sources |
|
| -Autotrophs |
Main carbon source is CO2 |
| -Heterotrophs |
Use carbon found in other organisms |
| Energy sources |
|
| -Phototrophs |
Light |
| -Chemotrophs |
Organic or inorganic compounds |
| Electron sources |
|
| Lithotrophs |
Inorganic molecules |
| Organotrophs |
Organic molecules |
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Fermentation
Because
there is very little oxygen present in the rumen, the microorganisms there must
obtain energy from their food anaerobically (without oxygen). This is done
through a process called fermentation. Fermentation involves the breakdown of
glucose into alcohols or acids. Sound familiar? Fermentation is also used to
make alcoholic drinks such as beer and wine. As we’ll see, it doesn’t yield as
much energy as aerobic respiration.
Before
fermentation can occur, larger molecules present in the plant material, such as
lipids, proteins and polysaccharides,
must first be broken down into their component parts. This is done by hydrolysis. Through hydrolysis, lipids are broken down
into glycerol and fatty acids; proteins into amino acids, and polysaccharides
into glucose and other simple sugars. Here, we’ll look at fermentation using
glucose.
Whether
there is oxygen present or not, the first step of respiration is glycolysis. In
this process, glucose is broken down to form a compound called pyruvate. Glycolysis
also generates 2 ATP molecules (the cell’s energy carriers) and 2 of NADH.
In
anaerobic environments like the rumen, glycolysis may be followed by homolactic
fermentation. This is a ‘recycling’ step that doesn’t generate any more ATP.
Homolactic fermentation converts pyruvate into lactate and converts the NADH
produced in glycolysis back into NAD+ so that it can be used again.
In our own cells (like those of all eukaryotes), where oxygen is
present, further energy can be produced from pyruvate using the Krebs cycle and
oxidative phosphorylation, producing a net total of 36 ATP per glucose
molecule. However, this is ruled out in the anaerobic environment of the rumen.
The sparknotes site has a diagram showing how fermentation works.
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Bibliography & useful websites
Useful
links
http://www.textbookofbacteriology.net/
An
online textbook written by an American university professor containing good
general information about microbiology, also with some information on how
microbes can affect human health
Bibliography
Annison,
E. F. & W. L. Bryden.1998. Perspectives on ruminant nutrition and
metabolism. Nutrition Research Reviews 11:173-198
Bauchop,
T. 1977. Foregut fermentation. In: R. T. J. Clarke and T. Bauchop (Ed.). Microbial
Ecology of the Gut (pp. 223-250). London: Academic Press.
Clarke,
R. T. J. 1977. Protozoa in the rumen ecosystem. In: R. T. J. Clarke and T.
Bauchop (Ed.). Microbial Ecology of the Gut (pp. 251-275). London:
Academic Press.
Church, D. C. (Ed.) 1988. The
Ruminant Animal: Digestive Physiology and Nutrition. Englewood Cliffs, New
Jersey: Prentice Hall.
Hespell,
R. B. 1987. Biotechnology and modifications of the rumen microbial ecosystem. Proceedings
of the Nutrition Society 46:407-413
Hungate,
R. E. 1950. Mutualisms in Protozoa. Annual Review of Microbiology
4:53-66
Hungate,
R. E. 1966. The Rumen and its Microbes. London: Academic Press.
Hungate,
R. E. 1975. The rumen microbial ecosystem. Annual Review of Ecology and
Systematics 6: 39-66
Hungate,
R. E., M. P. Bryant & R. A. Mah. 1964. The rumen bacteria and protozoa. Annual
Review of Microbiology 18:131-166.
Macy,
J. M. & I. Probst. 1979. The biology of gastrointestinal bacteroides. Annual
Review of Microbiology 33:561-594
Prescott,
L. M., J. P. Harley & D. A. Klein. 2005. Microbiology. Sixth
Edition. New York: McGraw-Hill.
Tajima, K., R. I. Aminov, T. Nagamine, K. Ogata, M.
Nakamura, H. Matsui & Y. Benno. 1999. Rumen bacterial diversity as
determined by sequence analysis of 16S rDNA libraries. FEMS Microbiology
Ecology 29(2):159-169
Thain,
M. & M. Hickman. 2001. The Penguin Dictionary of Biology. Tenth
Edition. London: Penguin Books.
U. S. Census Bureau. 2008. U.S. and World Population Clocks- POPClocks.
Accessed on 16.04.08 from http://www.census.gov/main/www/popclock.html
Image
credits
Ardurino,
M. J. and Carr, J. 2007. Electronic scanner image of
Staphylococcus aureus. Accessed on 06/04/08 from http://en.wikipedia.org/wiki/Image:Staphylococcus_aureus_01.jpg
Dowall, V. R.
2006. One of many en:commensal anaerobic Bacteroides spp. in the
gastrointestinal tract—cultured in blood agar medium for 48 hours. Accessed on
02/04/08 from http://en.wikipedia.org/wiki/Image:Bacteroides_biacutis_01.jpg
Rocky Mountain
Laboratories, NIAID, NIH. 2005. Escherichia
coli: Scanning electron micrograph of Escherichia coli,
grown in culture and adhered to a cover slip. Accessed on 02/04/08 from http://en.wikipedia.org/wiki/Image:EscherichiaColi_NIAID.jpg
Wiggs,
L. S. 2007. Scanning electron micrograph of Clostridium difficile
bacteria from a stool sample. Accessed on 02/04/08 from http://upload.wikimedia.org/
Y tambe, 2005.
Microscopic image (200-fold magnification) of Candida albicans ATCC
10231, grown on cornmeal agar medium with 1% Tween80. Accessed on 02/04/08 from
http://en.wikipedia.org/wiki/Image:Candida_albicans.jpg
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