Monday, March 31, 2008


This is considered the "MILLION DOLLAR QUESTION" by all who run industrial fermentation process. Determining when to start and when to terminate a fermentation process is akin to playing shares on the stock market. The similarity between the two situations are the same. It is always very easy to start a fermentation process anytime but it is more difficult to determine the exact time to terminate the fermentation process.

If we terminate too early we might end up with lesser amount of fermentation products being formed and more raw substrates remaining underutilized by the microbes. If we terminate it too late, we might have higher amount of fermentation products formed and little or nothing of the raw substrate remaining in the fermentor (THEORETICALLY SPEAKING)

The catch is even though the second option seems more favourable but the cost of producing the fermentation products at the end part of the fermentation process will increase per unit of fermentation product formed.The rate of fermentation product decreases at the end stages but the costs of maintaining the fermentation in terms of time, energy will be higher.

The most important guideline to determine when to terminate the fermentation process will be ECONOMICS! Further in fermentation processes involving microorganisms even if we switch off the fermentation process, the process of fermentation is still active and on going in the fermentation vat
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Saturday, March 29, 2008


In most fermentation especially involving liquid substrate fermentation, water is the main medium of the fermentation reaction. In fermentor, the vessel supports the fermentation broth which is a water based suspension supporting all the different components of the fermentation process such as the substrate, microorganisms and the fermentation products. As the fermentation process in the fermentor represents different phases such as solids, liquids and gases, it is most important in a successful fermentation that a homogenous condition or composition is attained throughout the fermentation broth. There must not be dead zones or physical and chemical gradients formed anywhere in the fermentor.

In reality however, this homogenous condition throughout the fermentor is difficult to achieve except at small scale fermentors where homogenous mixing is easily obtained by efficient stirring by the stirrer. In very large bioreactors, it is quite difficult to achieve homogenous conditions throughout the fermentor. This is one of the biggest problem facing any scale up exercise involving large fermentors.

Efficient mixing of a fermentor are affected by many parameters especially:
1 Size and geometry of fermentor
2 Power
3 Fermentation broth rheology
4 Stirrer design and configuration

Mixing of the fermentation broth is a very complex phenomenon and it changes temporaly and spatially. Sometimes in most fermentation technology books or practicals the phenomenon of mixing is so often oversimplified and explained in terms of primary, secondary and tertiary mixings. It assumes so much on the laminar concept of flows when in reality it is far more complex

Thus it is important to carry out water or flow tracing studies to observe visually how the mixing pattern of the fermentation broth appears at different parametric conditions in order to achieve the optimal mixing conditions and to detect formation of dead zones and formation of gradients so that steps can be taken to solve the problem.

Many courses in fermentation technology often try to demonstrate the phenomenon of mixing by using erroneous models. One poor example is by using plastic rings or balls to show the mixing pattern generated by mixing. It does not truly reflect the true mixing pattern as that occuring in the fermentor. The choice of the models and mixing regimes must be as close as possible to real conditions in order to show what really happened in the mixing of the broth.

There are many types of water tracers or flow tracers which can be exploited to show the true phenomenon of mixing. We have physical, chemical and even microbiological tracers to choose and many kinds of detectors and sensors to follow the mixing pattern evolving in the fermentor.

What is important in the choice of the tracers, it must reflect the true situation and it does not influence the mixing pattern! Every type of tracer used has its limitations so the correct tracer must be properly chosen with the objective in mind

One of the weakest point in trying to show mixing using tracers is that the time for mixing to show occur rapidly and within a short time all established observations will be lost. This can be avoided by using rapid Polaroid photography and even infra red techniques where situation is required
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The fourth definition of the fermentation is the mass cultivation of microorganisms or single cells in a specially designed vessel called fermentor or bioreactor. It is in these vessels that optimum conditions are provided that can support the growth of high concentrations of microorganisms and/or to carry out the biological transformations.

In this definition which is probably proposed by engineers, there is no requirement for differentiation between aerobic or anaerobic conditions. It only refers to the technology of mass cultivation of single cells and biochemical transformations

In order to provide the optimal growth conditions to support the cultivation of microorganisms there is the need first of all to understand the requirements of growth of the microorganisms.
Then there is the need to understand the behaviour of the microorganisms grown at high concentrations in the fermentor.

It is rather foolish to admit the basic principle that one simply cannot control the process if one first of all do not understand the process involved. In simple statement : if we cannot or do not understand the physiology of the microorganisms in the fermentor environment, there is no point in the first place to build the fermentor or even try to control the process during the growth of the microorganisms in the fermentor. In most cases even if we proceed to carry out the fermentation process we will not be able to control the growth of the microorganisms or the fermentation process optimally.

It is a sad thing to say that the knowledge of microbial physiology in standard microbiology textbooks are too limited or have no connection with the situation in the fermentation technology. An average microbiology textbook is too general to be applied to the field of fermentation technology. Traditional microbiology textbooks are often too taxonomic, too medically inclined or too ecological in content. Try reading the popular textbook on microbiology by Brock and Madigan! There are simply too few pages being allocated to industrial and environmental microbiology.

If this is bad for the microbiology students, its even worst for the engineering students whose knowledge on microbiology is even weaker.

To compound the disaster in teaching microbiology for fermentation technology, the subjects are more often than not taught by biologists or microbiologists who are not inclined or knows nothing about fermentation technology. This will lead to poor input of the relevant part of microbiology needed by fermentation technology students. A lot that will be taught will show no connection or irrelevant to the subject of fermentation technology. I might even say it will be far worst when chemical engineers have to teach the subject of microbiology to their engineering students.

What I have observed in engineers writing books on microbiology for engineering students are either the subjects of microbial physiology become too mathematical or they would teach what a general microbiology is about. It is doubtful they can give in depth understanding to the subject.
( no wonder students sleep in their lectures)

The internal environment for the cultivation of high concentration of microorganisms is far different from those in nature. In industrial fermentation there is the clear intention of cultivating high concentration of microorganisms within a very limited and confined volume. This situation is often not seen in other fields of microbiology. As such the behaviour and growth of microorganisms in reacting to the environment of the fermentor or bioreactor is very different than normally encountered.

The study of microbial physiology of microorganisms in the fermentor is therefore different and more challenging. At the same time understanding of the microbial physiology of microorganisms is essential in trying to obtain optimal growth conditions for the microorganisms and maximum yield of fermentation products and biotransformations.

If engineers or biotechnologists do not understand the physiology of the microorganisms in the bioreactor it will be very difficult for them to design fermentors which optimize microbial growth and fermentation products. The complexity of the microbial physiology of microorganisms in fermentor is further intensified by the two way interactions between the microorganisms and the fermentor. This means that while the environment of the fermentors can affect the microorganisms, the activity of the microorganisms too can affect the function of the fermentor

One example of the challenges facing microbial physiology of microorganisms in the fermentor is the tendency for the microorganisms to form microbial aggregates such as flocs, granules and pellets while growing in the fermentor. These microorganisms in the form of microbial aggregates will affect the physiology of the microorganisms especially with reference mass transfer of nutrients, waste products diffusions and gas exchanges. These aggregates too will affect the general viscosity of the fermentation broth
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Wednesday, March 26, 2008


The last few years have seen dramatic increases in the price of fuel leading to various nations trying to find the alternatives to the fuel addiction. Biofuel in the form of ethanol have been seen as one of the most attractive source of biofuel to replace or supplement existing fuel demands.

Using alcohol as “gasohol” for automobiles is not really a new idea as Brazil has always been exploiting this technology for decades. This is not surprising as Brazil have enormous tracts of lands that can be used to grow sugar canes from where the sugar for the fermentation of alcohol is derived.

The technology to produce alcohol from sugars is through the process of fermentation, whereby microorganisms such as yeasts and certain species of bacteria have the ability to convert sugar through their metabolism to form alcohol as their main fermentation products.

In the fermentation of sugar to alcohol, economic factors play the most crucial roles. No industry will survive if it cannot make profits.

Analyzing the fermentation of alcohol from sugar raw materials, the two main constraints are:

1 High cost of substrates or raw materials for fermentation

2 High costs of product recovery

Now let us look closely at these two factors.


The main source of alcohol fermentation is sugar. There are many plants that can be the source of sugars such as sugar canes, sugar beets and others. However, the supply of these sugars is also required for human consumption. It is not wise to use substrates used by human for foods to be used as raw materials for fermentation as the increase in demand for the substrates will affect the prices of sugar in the market or would make the fermentation process costly.

It is the usual practice in industrial fermentation to choose a source of carbohydrates which are cheap to make the process economically viable. This is the reason why in most industrial fermentations the industries either opt for agricultural waste residues such as pineapple skins or they go for substrates which are not in high demand as food for the population such as starch from sago or tapioca.


Alcohol is a short chain fermentation product produced by microbial metabolism. It is only produced at very low concentrations and dissolved in the fermentation broth. Recovery of the alcohol is energy intensive and expensive and requires complex distillation.


There are many attempts to improve the alcohol fermentation process ranging from:

1 Improving the fermentation environment through optimal

temperature and ph range

2 Improving the nutrients required for the growth of microorganisms

3 Using the proper microorganisms

4 Improving fermentation operation parameters such as mixings,loading rate


In this blog we will be looking into improving the fermentation through microbial component.

Let us look at the simple equation of producing alcohol by microorganisms using sugars:


From the above simple model we see that the sugar substrate is being utilized by the microorganisms to form alcohol by fermentation

The microorganism that produce the alcohol from sugar are usually yeasts such as the common Saccharomyces cerevisiae which are normally used in the fermentation of alcoholic beverages. There are other bacteria such as Zymomonas mobilis which could offer better fermentation yield.

If we want to improve the alcohol fermentation process we do have a choice of other yeasts and bacteria. The choice of the microorganism to run the fermentation must fulfil certain criteria:

1 Are we producing alcohol for industrial purposes and not for beverages?

2 Are the microorganism chosen show high alcohol productivity?

3 Are the microorganisms pathogenic or non pathogenic?

4 Are the microorganisms chosen capable of using cheaper source of substrates?

5 What are their optimal range of temperature and ph?

6 Are the microorganism chosen capable of tolerating high alcohol concentration?

7 If we use certain microorganisms such as yeasts will we be facing strains of 'killer yeasts' that can kill normal yeasts?

That is why feasibility studies need to be done initially in choosing the right strain or microorganism before we decide to go ahead with any fermentation process. If the project fails on paper or in the preliminary studies it is wiser to abandon the project and not to incur financial loses at the end of the day after large amount of capital has been pumped

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The concept of gradient microbiology in the study of microbiology is not new as Beijerinck had earlier pioneered the idea in his soil column enrichment studies. However, it was in the early seventies that an eminent microbial physiologist, Professor JWT Wimpenny, from University College Cardiff (now known as University Cardiff, Wales) pioneered and revitalize the concept of “Gradient Microbiology” through the use of a system of bioreactors or fermentors in creating a steady state or dynamic gradient which allows for various types of microorganisms to establish themselves at certain physical, chemical gradients.

In his studies he has pioneered the use of fermentors in creating a dynamic state of microbial equilibrium that can be controlled through the use of gradients established in a linear one way gradient.

The fermentors are linked to one another by tubes through which nutrients and other parameters are controlled by the use of pumps that feed the linear axes either from top to bottom or vice versa.

Each fermentor is just made up of a simple Quickfit culture vessel controlled by a heater stirrer module which is magnetically stirred.

He studied the distribution and growth dynamics of microorganisms using models from simple linear gradient of one parameter to more complex bidirectional gradients on the Gradostat bioreactor model.

Prof JWT Wimpenny believes that the occurrence and distribution of various types of microorganisms are in a steady state under the influence of the interactions of various parameter gradients. With this simple Gradostat bioreactor system using fermentors, he has managed to put some light on the complex interactions of microorganisms in nature and to establish various models to understand the behaviour of microorganisms

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