Top 10 Uses of Microbes in Biotechnology

Biotechnology is the use of biological organisms in technological processes. It is almost as old as the civilization itself, although it wasn’t called “biotechnology” until the 20th century. Far from abandoning it in the 21st century, we are developing new uses for biological organisms.

1. Beer, Bread, and Wine

Biotechnology used for food and drink production is called yellow biotechnology. Simple fungi in yeast forms were likely the first “domesticated” organisms used to make edible products through the process of fermentation. The consumption of glucose by yeast yields a by-product of ethanol and carbon dioxide, which can be exploited for generating bread, beer, and wine. Likewise, the popular hipster drink kombucha and fermented cabbage (kimchi) are made through the fermentation of yeast with lactic acid bacteria and acetic acid bacteria. [1]

The most famous yeast is brewer’s and baker’s yeast Saccharomyces cerevisiae. It was first used by ancient Egyptians to make beer – even the pyramids builders had beer rations. S. cerevisiae are harmless and easy to culture, and its culturing method was eventually refined by Louis Pasteur. In 1996, the genome of baker’s yeast become the first sequenced eukaryotic genome. It is no wonder that it was the first eukaryotic organism used as a model for the production of various metabolites, from isopropanol to menthol.

See our articles about working with yeasts:

• Microscopy.
• Genomic DNA isolation.
• Transformation and transformation troubleshooting.
• Yeast plasmids.

Beyond yeast genetics, yeasts are used as a model to study protein-protein and protein-nucleic acid interactions, both of which are handy in drug discovery, with the help of various hybrid assays:

• One hybrid.
• Two hybrid.
• Three hybrid.

2. Milk Products

Fermenting milk using microorganisms is as old as domesticating herd animals, which began around 14,000 years ago in the Fertile Crescent. Milk is fermented by Lactobacillus; however, some cheeses, like blue cheese are made with a fungi (Penicillium). Similarly, certain dessert wines are made from the “noble rot” of the fungus Botrytis cinerea.

See more about microbes role in food production.

3. Antibiotic Production

Red biotechnology is the use of biotechnology in the medical and pharmaceutical industries.

It is called red because of the association with blood and symbols of medicine – red cross and crescent.

Fungi are most commonly associated with cheese and wine production. However, they have a long history in traditional medicine as moldy bread, overgrown with the fungi Penicillum and Aspegillum, would regularly be applied to wounds for their antimicrobial effect. The jump from antimicrobial compounds to the antibiotics we know now was ushered in by Scottish scientist Alexander Fleming, who accidentally discovered Staphylococcus growth suppression by penicillin mold in 1928. However, it took another 12 years and a world war to start mass-producing penicillin using deep fermentation techniques. [2]

• See our introduction to antibiotics.
• A useful guide on antibiotics used in molecular biology.
• And why you shouldn’t overuse it in cell culture.

4. Restriction Enzymes

It had been known since the 1950s that certain bacteriophages demonstrated poor growth on different bacterial strains, but the reason was unknown. In 1970, US researchers characterized an enzyme from bacteria Haemophilus influenzae that can cut DNA in specific places with the purpose of protecting the bacteria from foreign DNA. [3] The enzyme was HindIII, the first type II restriction endonucleases, or restriction enzymes, that scientists adore. Today we know more than 3000 restriction enzymes recognizing 230 DNA sequences. [4]

• More facts about restriction enzymes.
• Tips about restriction digests.
• Introduction to cloning.
• How to plan your cloning experiment.

5. Protein Production

Protein production in E.coli was the new stage in biotechnology because it used recombinant DNA technology instead of traditional selection techniques. The first human protein produced in E. coli in 1978 was insulin, [5] followed by human growth hormones. [6] But before you jump on to the expressing your protein in E.coli read:

• 8 points to remember.
• Optimize your codons.
• As the code changes can affect the activity of your protein.
• And increase your protein solubility

6. Eukaryotic Viruses

Using E.coli to express eukaryotic proteins has challenges. Firstly, the proteins expressed in bacteria lack post-translational modifications that decorate many of the eukaryotic proteins – from glycosylation, to assembly of protein complexes. Secondly, E. coli reluctantly produce large proteins common in eukaryotic cells. No wonder that the first therapeutic proteins expressed in E. coli were relatively short and simple. For more complex proteins, such as antibodies, the production shifted to eukaryotic cells – Chinese hamster ovary and human cell cultures.

But even in eukaryotic cells, biotechnology cannot work without the help of microbes, e.g. viruses. While the expression vectors in E.coli are based on bacterial plasmids, the vectors for eukaryotic cells are viral vectors.

The first proof-of-principle was a vector-based on SV40 (simian vacuolating virus 40) that infected a cell culture of monkey kidney cells. [7]

• Explore common misconceptions about viral vectors.
• How to improve your (lenti)virus titre.
• And in more details about using adeno-associated virus – popular vector for creating coronavirus vaccine.

7. Phage Display Libraries

It would be fair to say that molecular biology started with bacteriophages. Aside from the discovery of restriction enzymes, the enzyme that joins the ends of recombinant DNA molecules, T4 ligase, also comes from a bacteriophage. But maybe the biggest phage contribution to biotechnology are phage display libraries (PDLs), developed in 1985. [7]

In PDL, a gene encoding a protein of interest is inserted into a phage coat protein gene, causing the phage to “display” the protein on its outside. [8] PDLs are used in the studies of protein-protein, protein-peptide, and protein–DNA interactions. PDLs are useful in vaccine and drug discovery. [9]

• Learn how to handle bacteriophages.
• Count the phage titre.
• And work with phage display libraries.

8. Microalgae

Blue biotechnology uses sea resources to create products and industrial applications.

The leading application of blue biotechnology is producing renewable bio-oils with photosynthetic microalgae to replace oil extraction. Working with algae is not much different working with other microorganisms.

To genetically modify your microalgae, use the familiar method of DNA introduction into a cell- transformation.

9. Agrobacterium Tumefaciens

Green biotechnology is biotechnology involving the genetic engineering of plants. It’s based on a neat trick by the microbe Agrobacterium tumefaciens. It has a plasmid, Ti, that transfers some of its genes into the plant genome. The transfer requires only T-DNA border sequences, and you can insert foreign DNA between them that will be integrated and expressed in a plant genome. Several cereal crop plants were modified using this method, as well as HeLa cells. [10]

• How to work with Ti-plasmids.
• And how to increase protein expression in plants.

10. CRISPR

Last, but not least, in the history of biotechnology is the use of CRISPR. Of course, it’s not a microbe but rather a bacterial mechanism that is used to engineer organisms.

CRISPR was discovered in 1987 but has gained considerable traction in the last decade. In short, bacteria have no immune system, so they evolved a mechanism to recognize and fight off bacteriophages should the bacteria encounter the bacteriophage a second time. Each time a bacteria is infected with a bacteriophage, the bacteria stores a bit of DNA from the bacteriophage genome. Using the bacteriophage DNA sequences as a guide, the Cas9 enzyme (encoded by the bacteria) recognizes similar DNA sequences (i.e. a second infection by the same type of bacteriophage) and destroys them. Scientists recognized that this same mechanism could be used to introduce stable changes into the genetic material of eukaryotic cells as well.

• Where to use CRISPR.
• How to start with CRISPR.
• How to validate CRISPR experiment.

And particular CRISPR applications in more details:

• CRISPRa and CRISPRi
• Use in immuno-oncology
• In drug screening

Hopefully, having read this article and some of the others you will be able to see that answer to the question “What have microbes ever done for us?” is “A LOT”!

Sources:

1. Villarreal-Soto, SA, et al. (2018). Understanding Kombucha Tea Fermentation: A Review: Understanding Kombucha tea fermentation. Journal of Food Science. 83 (3): 580–588. doi:10.1111/1750-3841.14068
2. American Chemical Society (2008). Penicillin Production through Deep-tank Fermentation. (Accessed 13/07/20)
3. Smith HO, Wilcox KW (1970). A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. Journal of Molecular Biology. 51 (2): 379–91. doi:10.1016/0022-2836(70)90149-X.
4. Promega. Restriction Enzyme Resource. (Accessed 13/07/20)
5. Human Insulin: Seizing the Golden Plasmid. Science News. 114 (12): 195. 1978-09-16. doi:10.2307/3963132.
6. Goeddel DV,  et al. (1979). Direct expression in Escherichia coli of a DNA sequence coding for human growth hormone. Nature. 281 (5732): 544–8. doi:10.1038/281544a0.
7. Goff SP, Berg P (1976). Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells. Cell. 9 (4 PT 2): 695–705. doi:10.1016/0092-8674(76)90133-1.
8. Smith GP (1985). Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 228 (4705): 1315–7. doi:10.1126/science.4001944.
9. Rahbarnia L. et al. (2017). Evolution of Phage Display Technology: From Discovery to Application. Review J Drug Target. 25 (3):216-224. doi: 10.1080/1061186X.2016.1258570.
10. Kunik, T., et al. (2001). Genetic transformation of HeLa cells by Agrobacterium. PNAS. 98 (4): 1871–1876.. doi:10.1073/pnas.98.4.1871.