FERMENTATION METABOLIC PATHWAYS

We have always looked at fermentation process or the formation of fermentation products by microorganisms as something beneficial to man. While we are deriving the benefits from the activities of the fermentation microorganisms, in reality the action of these microorganisms are really not to serve the human masters but more to their selfish ends. To these microorganisms, the fermentation activities are their mode of survival. Fermentation is their metabolic and physiological method of deriving energy from the substrates for their growth.
The fermentation products during their metabolism are just their metabolic waste products which have served their duty. If however, the human beings get their pleasure by consuming their waste products……well and good for these pathetic humans. Nothing is stopping these humans from drinking their metabolic urine or alcohol !
In fact the cornerstone of human civilization in history has always depend on these fermentation products. There is a rich diversity of fermentat ion products as reflected in the culture of various countries. In essence, the diversity is quite limited in terms of the microorganisms and metabolism involved. The fermentation products are just given different brand names in different languages and by the use of different substrates found in the specific countries
The fermentative microorganisms metabolize the substrate to extract their enegy. This is executed by various metabolic pathways found in the microorganisms. It should be stressed that there is a diversity of metabolic pathways available, depending on the type of microorganisms, substrates and physiological environment. What is important to note are:
1 There are a number of fermentation pathways available in a microorganism
2 TCA cycle is only available in aerobic microorganism, BUT at the same time these aerobic microorganisms too have anaerobic or fermentation pathways . These microorganisms too are carrying fermentation process in their metabolism
Most students, in their early stages of learning microbial metabolism erroneously tend to think that only one or two pathways are involved. Or they only tend to think that in the study of fermentation metabolism only carbohydrate catabolism is important! Nothing could be further than truth in these assumptions. It is like saying lipids and proteins are not used as substrates in fermentation.
The beauty about having many fermentation pathways interlinking allows the fermentation microorganisms adaptability in the uncertain environment....and their survival!!!
The changing of tracks in metabolic pathways are achieved by the presence of branch end compounds. Branch compounds are compounds which interlinked two or more metabolic pathways. On reaching a branch end compound the microorganism will have the choice to go for one or other pathway depending on the circumstances. A very central branch end compound is pyruvate. From pyruvate the metabolism can go almost any where.
Such branch end compound such as pyruvate allows the effective linking of carbohydrate, lipid and protein metabolism. It also linked the various anabolic, catabolic and intermediary metabolism.


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BIONEXUS: COMPANY PROFITABILITY OR NATIONAL INTEREST?

Everyone knows the greatest power in driving any company is profitability. To increase the company profits and to reduce its risks companies are known to cut corners and finding ways to reduce the taxes they have to pay. Even better if there are other parties who are willing to inject capital especially in their high risk projects! Things simply could not go wrong! It is the ultimate formulae for success at least for the companies
Every body knows that setting up companies involve a lot of risks and it is a well known principle that out of the many new companies formed, many will fail. This failure is attributed to many reasons ranging from poor management, technical problems, and marketing and even from oversight to cash flow problems.
Some projects are even doomed to failure even before taking off, or while still on paper. They just don’t learn!!!. The best advice you can get before starting a company is to try obtaining the fundings from the bank or any other private institutions. They will vet your paper to the dot to see if the project is going to be a liability to their investment
And suddenly in the exciting spin of biotechnology, we have people or bodies who are willing to throw caution to the wind and throw “free or easy” capital to these companies in the name of biotechnology! The only problem is the money they are throwing are not theirs but the taxpayers!
As for me I would not be convinced by hype sounding words or terms, nor promises or potentials! To me I want to see track records. I know there are risks involved in any project but at least I will take calculated risks! I am not convinced at all by the sacks of MOUs but rather by the company performance and profitability.
I fear that in the end all these bionexus exercise will only profit the companies and not the nation


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LAMINAR AIR FLOWS IN FERMENTATION ACTIVITIES

It is very difficult to imagine running a fermentation plant without a good air supply. Air in various forms and quality are needed to carry out the various activities in the fermentation right from upstream to downstream activities.
Today, we will be discussing about the use of laminar air flows in fermentation activities. Laminar air flow is the term we use to describe the flow of air which occur in parallel layers or sheets just like a laminated sheet in cross section. The easiest way to visualize occurs air flow is to observe the laminar flow in liquid during primary mixing.
Conditions of generating laminar air flows occur under low energy power. High power usage will generate turbulence. Laminar air flow may further be enhanced by the type of nozzle used and by using laminar devices.
Laminar air flow are used more in the belief that such air flow do not create turbulence that might result in increased loading of microparticles in the air.
What is often not appreciated there is turbulence associated with laminar air flows by mechanically disturbing the immediate environment. Second turbulence is created as the laminar flows get mixed and merge. Points of energy cancellations will result in fast sedimentation particles
Laminar air flows do effectively transport microparticles at the zone separating the various layers of air.
The use of laminar flow is usually only effective in small space confinement such as in the inoculation chambers where the positive pressure exerted within the chamber tend to repel any intrusion of particles from the outside.
There is the trend nowadays to incorporate gentle laminar flow on the top surface of the fermentation floor to sweep away the microparticles.
It is regretful despite the understanding of the properties of laminar air flow its incorporation in the architectural design of aseptic areas in sensitive fermentation areas or even in the design of surgical operating theatres are still poorly understood

It is therefore not surprising in surgical operating theatres higher infections are often associated with the use of laminar airflow?


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RHEOLOGY PART THREE: DISCUSSIONS

One of my students used to ask me this question,
“What is the point of trying to understand the complexities of fermentation rheology, when rheology itself is not one of the common parameters used in monitoring the fermentation process?”
I threw this question to the class for deeper discussions..
The general consensus is that:
1 Rheology is an important and relevant parameter of understanding and controlling the fermentation process.
2The use of rheology part could contribute significantly in understanding the changes that occur during the fermentation process.
3 Rheological data could be used in trying to optimize the conditions towards optimum fermentation process.
4 Rheological data could be used to extrapolate the likely event of impending fermentation failure
5 The use of rheology data such as the type of non Newtonian fluid could indicate the right opportunity to change the mixing regime and save energy
6 Operating parameters could be adapted such as mode of feeding to control the rheology of the fermentation broth
7 The failure to use rheology as the online parameter is because there are no sensors that can measure rheology on lines for now, and not because rheology is not an important parameter!


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PROBLEMS OF VOLATILE FERMENTATION PRODUCTS

In the true tradition and history of fermentation, the reference to fermentation products has always been associated to fermented drinks and foods. These fermentation products are products excreted by various fermentative microorganisms in the absence of oxygen.
These diverse fermentation products have always been characterized by their unique chemical and physical characteristics which give them their own unique taste and odours.
The fermentation products are simple organic compounds usually with carbon skeleton between one and three carbon. The short chain compounds are characterized by their volatility at room or ambient temperature.
The aromatic nature of these fermented products are attributed to their own unique chemical groups such as volatile fatty acids, ketones, aldehydes and even the presence of sulphur containing compounds. It is the interactions of these various volatile which give the unique odour and taste to butter, fish sauce and wine among others.
The problem is that in the age of industrial fermentations there is the need to produce large volumes of these compounds. Some of these fermentation products need to undergo various processing treatments to make the product safe and acceptable. Some of these products need to be modified and repackaged to fulfill the needs of the modern consumers.
What are the effects of these processings and treatments to the quality of the fermentation products? This would not be a problem if the fermentation products are simple compounds produced by single cultures and using modern fermentation technology such as beers. This would however be a problem when the fermentation products are a mixture of volatile organic compounds produced by mixed culture fermentation such as in fish sauce or budu fermentation
Definitely such processing treatments using high temperature will affect the composition and quality of fermented products. The powdered fermentation products when reconstituted will definitely taste different or lost that characteristic bouquet!
Maybe it is for that reason certain fermentation products will always remain traditional…..and tasted better





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MIXED CULTURE VERSUS PURE CULTURE FERMENTATIONS: WHICH IS EASIER?

Traditionally in microbiology and biotechnology lectures and practicals, there seemed to be a slant towards pure culture practicals. In real life, microorganisms in nature do not often occur in pure culture communities. Microbial ecology generally involves the interactions of mixed cultures and their environment.
No amount of pure culture data studies will give the accurate picture what really happened to microorganisms in nature! At best, pure culture will perhaps help in giving understanding as to what really happened in nature
Mixed culture studies seem to be avoided by most microbiologists especially those involved in the studying of microbial physiology and biochemistry of microorganisms. Don’t believe me? Just read a few popular microbiological or biochemical textbooks!
Although the study of pure culture has its own strength especially in the production of fermentation products by single pure microorganism, its success is more attributed to the ability of microbiologists to generate pure cultures or aseptic techniques. To these microbiologists the presence of other microorganisms in the industrial process is more a minus minus factor and regarded as a microbial contaminant which will complicate the fermentation process and affect its productivity
In my personal experience it is far more difficult to understand and control a mixed culture fermentation compared to doing a pure culture fermentation!
There are many parameters which affect the mixed culture fermentation process and slight change in one operating parameter will result in the change in the components of the mixed culture population dynamics….. To put it simply, the process may easily run out of control.
In pure culture fermentation this is not the problem. Pure culture fermentation are more stable and the only goal is to obtain the optimum fermentation process to produce the best yield possible!
The principles of mixed culture fermentation are often complicated by:
1 Selection of steady environment
2 Ensuring stable substrate composition and delivery
Most that involve complex substrate will often see the formation of microbial succession which could be good or bad depending on the purpose of fermentation
Mixed culture metabolism too tend to change the environment that lead to microbial succession
This is one of the main reason in traditional mixed culture fermentation becomes further complicated when the scaling up is exercised!
Merry Christmas!


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THINGS THEY DON’T TELL YOU ABOUT FISH SAUCE (BUDU) FERMENTATION

In the first place let us get a few things straight. Fish sauce fermentation is the traditional fermentation of many countries, especially those in South East Asian countries. It is a grave error to regard the fish fermentation as the traditional right or heritage of a particular country or state.
According to Wikipedia the Romans have been known to produce fish sauce called garum as part of their Greco Roman cuisine!!. The famous Lea Perrin sauce in typical British culinary is a fish sauce. The ingredients of a traditional bottle of Worcestershire sauce sold in the UK as "The Original & Genuine Lea & Perrins Worcestershire Sauce" are malt vinegar (from barley), spirit vinegar, molasses, sugar, salt, anchovies tamarind extract, onions, garlic, spice, and flavouring. The "spice, and flavouring" is believed to include cloves soy sauce, lemons, pickles and peppers.
I just can’t help laughing how emotional some readers are in claiming the “rights” to the fish sauce without doing research into the origin and diversity of fish sauce. Sometimes blind ignorance can have its place in this country!
While the use of fish sauce or budu is quite limited in Malaysia, this is not the case in Thailand or Vietnam where the fish sauce is almost in everything and regarded as the Magic elixir in their cooking. Fish sauce made in Thailand is easily available on the supermarket shelves that cater for Asian cooking. The bottled fish sauce looked very attractive especially with their golden brown colour, beautifully labeled and subjected to perfect advertising and marketing strategies that make the product successful.
When you buy a bottle of fish sauce in the market, the sauce looks golden brown and appealing. Everything is so hygienic and sanitary that you would not be able to appreciate how the fish sauce was manufactured. Gladly you will buy the bottle and use it frequently in cooking dishes to your family delight at the dinner table.
Little do you suspect that what you are enjoying is merely a rotting broth of decomposing fish with the added nutritional values contributed by flies and maggots!
There are certain things they will not tell or show you about fish sauce fermentation. Zimmerman of Bizarre Foods would probably faint or go into prolonged coma if he witness up close and personal how fish sauce are produced.
Coupled to this bottled product advertising approach the fish sauce companies make great effort to prove the sanitary quality of the production facilities especially in stressing:
1 The use of fresh fish or anchovies to be used as the fermentation substrate
2 Clean and hygienic bottling facilities
3 Use of scientific quality control such as GMP and HACCP and the use of advance analytical laboratories to monitor the production especially in downstream activities
What is not shown is the true facts of how the fish sauce is really fermented. They only show you the nice sanitized end products. They don’t show you the dirt and the grime of the fish sauce fermentation! (This is akin to the presentable chicken all clean and wrapped in the butchery area of the supermarket. You don’t see the slaughter! You don’t see the blood!)
Let us get the facts straight! Let us visit the “ground zero” of fish sauce fermentation!
1Fish sauce fermentation is a mixed culture fermentation which involves the action of multitudes of microorganisms
2 Fish sauce fermentation is still basically traditional fermentation even though it might be industrialized
3 The fermentation vats for fish sauce fermentation are often ceramic vats cement vats or even PVC vats operated in batch operations
4 The fermentation is natural and septic and occur over periods of months
5 There is poor quality or hygienic control during the fish sauce fermentation in the vats
6 The fish are left to rot and decompose over long periods of times under high concentrations of salts. At the end of the period the salt would have sucked out the water from the fish entrails or tissues
7 Periodically the vats are left open to expose it to air and sunlight to enhance fermentation or decomposition
8 Its not uncommon to see flies and maggots or larvae breeding in the vat while the fish sauce is fermenting. Urgghhh! It stinks! Its visually repulsive!
I often wonder how some of these fish sauce are GMP or HACCP compliance ?





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