The ruminant digestive tract (University of Minnesota, 1996), showing the rumen,

where most cellulose digestion takes place.

Microbiology
Cows' guts & microbes | Discovery of rumen microbes | Why
do cows need micro-organisms? | How many microbes live
in the rumen?| What types of bacteria are in the
rumen? | Rumen protozoa & fungi | How do rumen microbes
obtain energy? | Fermentation | Bibliography
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.

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.

Fig. 3. A scanning electron micrograph of Escherichia coli.

Source: Rocky Mountain Laboratories, NIAID, NIH, 2005.
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
LINK..... http://sci.waikato.ac.nz/farm/content/microbiology.html