Bioprocessing Part 1: Fermentation

>>We all know something about fermentation. It’s a process used countless times each day
to make a variety of dairy products, baked goods and beverages.
We sometimes think of it as letting foods go bad, but in a controlled way.
With a little help, milk becomes yogurt… bread rises…
and grains decompose, creating alcoholic beverages and alternative fuels. >>But looking at these examples only gives
us a clue as to what’s really happening and how we can use the power of fermentation to
cost-effectively create a broad array of biological products. >>So, what is fermentation? A cell can be thought of as a micro-factory.
These cells can be bacteria, fungi or specific cells from mammals, plants or insects. In
Biotechnology, these cells are used to manufacture a product in a process called fermentation. >>For yogurt, buttermilk and cheese, we use
bacteria. To make breads and alcoholic beverages we
use yeast – a fungus! And the production of some vaccines requires
the growth of mammalian cells that are infected with a specific virus. >>The product the cells manufacture is usually
a chemical the cells contain naturally… or a substance that the cells have been genetically
altered to create… or even a metabolic waste product of the organism’s
growth – like one of our examples, alcohol! >>There are too many everyday products created
by commercial-scale fermentation to even list, but some common ones include: amino acids,
biopharmaceuticals, dyes, enzymes, food products, lipids, steroids and vitamins. [Music Fades, Nat Sound of Process Establishes,
Under For VO] >>Fermentation is a reasonably simple process.
A cell is selected based on its ability to produce the desired product.
A seed stock of cells is put into a small amount of media. Media provides the nutritional
products the cell needs to grow. When the population of cells has grown and
consumed most of the nutrients, it’s moved into a larger vessel with more growth media,
and the process repeats… This “scaling-up” is complete when the quantity
of cells is large and healthy enough to transfer into a production vessel – often referred
to as a bioreactor or fermentor. >>With plenty of fresh media now available
and under tightly controlled conditions, the cells grow and manufacture product.
When the fermentation is complete, the product is harvested. >>Fermentation is known as an “upstream” biotechnology
process. It occurs early in the production flow, before Recovery, Purification, Formulation,
Filling and Packaging. To better understand the fermentation process,
we should first find out a little bit about the cells we use and what they may require
to reproduce and stay healthy. Different cells have different needs. Some
are aerobic – they need oxygen – while others are anaerobic and do not require oxygen. >>All cells require nutrition. A properly
formulated media contains the necessary nutrients to allow cells to grow and produce.
The fermentor mixes the cells evenly throughout the media to suspend the cells and supply
the oxygen necessary for growth. Effective and efficient fermentation requires
rigorous monitoring and control of the environment within the bioreactor.
Key factors include temperature, pressure, pH – which is a measure of how acidic or alkaline
the media is, oxygen – usually measured as dissolved oxygen within the media, and nutrient
levels. Although the environment and the media are
tailored to the needs of specific cells, the lifecycle of almost all batches follows a
predictable pattern. The growth pattern has four phases: Lag, Exponential
or Log, Stationary and Death. >>When a cell is first introduced to fresh
media, it has to adapt to its new environment. This creates a lull or Lag in the growth timeline.
After the organism adapts, the batch takes off! The cells begin dividing at a constant
rate – an Exponential or Logarithmic (or “Log”) increase; doubling, then doubling again, and
on and on… As the nutrients in the media are consumed,
toxic metabolic waste products build up, cells begin to die, and growth slows.
When it reaches the point that just as many cells are dying as are dividing, the batch
enters the Stationary phase. This is the point at which the key nutrients
are completely consumed, the fermentation is stopped and the fermented broth is harvested.
If the fermentation were allowed to continue, the cells would enter the Death phase. More
cells die than divide, and – similar to the Exponential phase – the death rate increases
logarithmically. Now that we have a basic understanding of
how Fermentation works, let’s look at an actual process and see how it all comes together. For our sample process we will look at the
production of Green Fluorescent Protein, or GFP.
GFP is broadly used as a biological marker. It’s a fluorescent dye that’s very well tolerated
by most cells and doesn’t interfere with normal cellular function.. In the GFP fermentation process, we’ll need
to add an antibiotic to protect the purity of the batch, and then – late in the process
– a biochemical inducer to “turn on” the GFP gene
Our materials for this process will include: A bacteria seed stock – in this case E. coli
– that has been genetically enhanced to produce GFP…
the basic ingredients for a compatible media which include nutrients, stabilizers, an antibiotic
and an antifoaming agent… and IPTG which is the biochemical inducer
that “switches-on” the GFP gene. The equipment that we’ll be using includes
a 300 liter bioreactor, a UV/Vis Spectrophotometer to monitor the
optical density, which is a measure of the concentration of cells in the bioreactor –
a glucose analyzer, to measure glucose, a key nutrient –
an off-line, pH meter to help track the acid/base balance, and adjust on-line measurements,
if needed… and a Broth Tank for our final product. The bioreactor is equipped with a water jacket
around the vessel to regulate temperature, and integrated sensors to monitor key environmental
factors, including dissolved oxygen, pH, internal temperature, water-jacket temperature and
vessel pressure. The reactor also has an agitator, dedicated
ports for adding seed stock and media ingredients, separate ports for acid and base supplement,
air filters for supply and exhaust, and valves for drawing samples and for harvesting.
Most fermentation and monitoring functions can be managed from the bioreactor’s dedicated
process controller. Before the fermentation process can begin,
the area must be prepared. Preparation includes removing equipment and
material that won’t be used in the process… Cleaning and sanitizing the area and equipment…
and sterilizing equipment as required by the SOPs – Standard Operating Procedures.
Sterilization is used to eliminate unwanted microorganisms which can grow naturally in
the fermentation media and process equipment. Also, all required materials and documentation
should be gathered and prepared… and all Process Control software should be
loaded and verified. The Fermentation batch process will be guided
and documented with the BPR – Batch Process Record.
The Batch Record leads the operator through the process, step-by-step…
with each step requiring a sign-off and separate verification.
This record also includes spaces for documenting key times, activities and instrument readings. The GFP fermentation process really begins
with the expansion of our bacteria seed stock. After removing the specially modified E-coli
from the freezer and thawing it… It’s used to inoculate a small amount of fresh
media in a shaker flask. After the number of cells has reached the
target amount, the thriving cells are ready for fermentation.
Meanwhile, in the Fermentation area, operators begin with a complete check of all critical
equipment. Valves, caps and lines are checked, hoses
are tightened… probes are verified and calibrated.
and 10 kilograms of HPW – High Purity Water – is added to the vessel. The bioreactor is brought up to normal process
pressure and held there in order to check for leaks.
The pressure is monitored over a 30 minute period.
If a leak is detected, the problem is corrected and the test is run again.
Once the reactor passes the test, we are ready to mix the media in the vessel.
The agitator is turned on, and the ingredients are added:
Yeast Extract… Tryptic Soy Broth…
Ammonium chloride… Sodium biphosphate…
Monopotassium phosphate… and an Antifoam compound. Once all the initial ingredients are in, another
10 kilograms of High Purity Water is added… all ports and valves are closed…
all condensate valves are opened… and the bioreactor begins an SIP – Sterilize-In-Place
cycle. The target for sterilization is 121 degrees
Celsius for 30 minutes. As soon as the temperature climbs to the targeted
temperature, the condensate valves are closed, and the SIP cycle completes automatically. Both the vessel and the media are now sterile
– And we’re ready to add the final ingredients
to our media. The glucose hose is attached to the vessel
the connection is steamed to sterilize it and the separately sterilized glucose-antibiotic
solution is pumped into the vessel. Then a manual pH reading of the media is taken
and the bioreactor is set up for its fermentation cycle.
After the inoculation hose is connected to the reactor
and steamed for 20 minutes the expanded seed stock is pumped into the
reactor containing the media. Fermentation now begins. The operator takes
zero hour readings and begins to regularly monitor batch temperature, agitator RPMs,
dissolved oxygen levels, pH, vessel pressure, optical density, air flow rate and glucose
concentrations. Optical Densities and glucose concentrations
are of particular interest, so they’re graphed as well as documented.
When the targeted levels of glucose and optical density are achieved,
it’s time to add IPTG to the vessel to activate or turn on the expression of the Green Fluorescent
Protein in the cells. After allowing enough time for the cells to
produce green fluorescent protein usually 5 hours more, final readings are taken
and a sample is drawn to check the percentage of cell solids. The product is now referred to as “broth.”
The broth, which contains spent media and cells, is complete when the key nutrient,
glucose, is mostly consumed, and the batch has reached the desired concentration. The batch is then cooled down, pumped into
a broth tank… and labeled with the batch number, volume,
time and date. [Bright, Rhythm-Driven Music Establishes,
Then Under For VO] The Fermentation process is now complete! The harvested broth will now move downstream
to the Recovery process where the cells will be ruptured to free the Green Fluorescent
Protein and the protein will be separated from the
other broth components.


  1. Thanks for the video, it helped me a lot. I was wondering what specific model of Sartorius bioreactor is the one showed on this video. Thanks!

  2. Excellent,
    I plan to use in my course for Industrial Microbiology. how could I do it without violate your c/p rights??

  3. at 9:45, why the growth chart is like that? why is it started with OD=0. During 0 hour inoculum should be added so the value could not be zero.

  4. at 7:06, why did the person pipette lots of bubbles. There should not be any bubbles during pipetting, that is very basic.

  5. Are these videos available for corporate training? If so, where can we get licensing details and pricing? Tnx!

  6. Really very useful video!!! thank you for explaining the entire process stepwise!!!!… i can get a better view on this process

  7. Biopharmaceutical Process Development and Manufacturing focus on the development and practices involved in providing cost-effective, regulated manufacturing of biopharmaceutical products in a timely manner.

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