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Teaching Resources

How we study microorganism?

Scientific studies aim to explain phenomena through hypotheses, which generate predictions that can be tested with experimental data. While both observation and experimental testing involve data collection and analysis, quantitative data offer more thorough, accurate, and complete insights than qualitative data. For example, knowing pasteurization reduces bacterial abundance to a specific percentage (e.g., 50% or 0.0001%) is more valuable than just observing a reduction. Quantitative data are crucial in microbiology, with statistics providing the tools for organizing, presenting, analyzing, and interpreting this data. Statistics can be descriptive, summarizing data visually or numerically, or inferential, drawing conclusions from the data. While some studies may only require qualitative analysis, most generate quantitative data needing statistical analysis. Therefore, microbiologists must understand statistical principles and methods for data collection and analysis. The following discussion covers basic statistical principles for continuous data in simple situations, though the full range of microbiological data and experimental design is broader. Statistical software now handles most calculations, but it’s important to understand the underlying principles to avoid misinterpretation.

The Importance of Statistics and Replication in Microbiology

Granda: I play much better if I have an energy drink at half-time!

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Photo by Kelly L from Pexels

Microbial life is closely linked to the transformation of substrates into products and the generation of metabolic energy. Analyzing these processes requires a precise quantification of substrates and products to derive a balanced process equation, which also measures the energy released and the cell material formed. Examples include aerobic glucose oxidation and fermentations used in yogurt, sauerkraut, silage, beer, wine, and bread. The formation of gaseous products highlights the energy released in microbial metabolism. Quantitative analysis is crucial in commercial microbiological applications, such as the production of organic acids, yeast biomass, and pharmaceuticals, where controlled processes rely on accurate substrate predictions and calculations.

The Importance of Quantitation: Mass Balances, Bioenergetics, and the Money of Life

Mum, why does the bread dough flow over and cause a mess, even before it is in the oven?

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Copyright: Thomas Grasberger, with permission

When you look in the mirror, you may think you're the same person as yesterday, but in terms of your composition, that's not entirely true. Life on Earth is made up of elements constantly cycled between the environment and living organisms. Microbes play a crucial role in these cycles, such as the carbon and nitrogen cycles, and their activities can be measured using isotopes.

How we use isotopes to study microbes and their activities

We cannot even see microbes – how can we possibly understand what they do!?

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Image Philippe Laissue of the University of Essex

Soil contains thousands of microbe types, each using different foods (substrates) to grow. When observed under a microscope, they appear similar, making it hard to identify them and understand their diets. While laboratory cultivation has helped microbiologists for over 150 years, many microbes cannot yet be grown due to unknown requirements. To study them in their natural habitats, scientists use a "toolkit" of techniques to analyze key molecules in cells, revealing which microbes are present and what they consume. Understanding these microbes is crucial for maintaining Earth's nutrient cycles and ecosystem health.

Who does what: how do we figure out what microbes do in the environment?

Miss: there are thousands of different microbes in the soil, so how do we know who does what in the environment?

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Courtesy of Dr Nasmille Larke-Mejia, University of East Anglia, UK

The environment is diverse: fields grow wheat for humans, corn for livestock, and hay for horses, each supporting different plant populations. However, microbes are invisible, so to understand which ones are present and their activities, we need tools like microsensors. These instruments allow us to measure processes at the microscopic level.

Microsensors: A look into the microbial environment

Miss: we can see microbes with a microscope but how can we see what they are doing?

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Graphics by Fabian Steininger, photo by Niels Peter Revsbech.

Microfluidics is the manipulation of fluids at the sub-millimeter scale, enabling the analysis and control of individual microbial cells. Traditional methods are insufficient for studying single-cell behavior and discovering new natural products. Microfluidics offers advantages such as smaller sample volumes, faster experiments, and the ability to perform complex tests on a single chip. Techniques like continuous-flow and droplet microfluidics provide precise control and high parallelization of microbial cultures. This technology is used in studying microbial growth, behavior, and interactions, screening for new products, optimizing biotechnological processes, and advancing personalized medicine, diagnostics, and antibiotic resistance detection. Future developments promise significant impacts in healthcare, environmental monitoring, and sustainable industries.

Microfluidics: taking experimentation to the scale and diversity of microorganism

We can’t see microbes. How can we find the ones that are special among millions of others?

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Microbes were unknown to humans until a few centuries ago due to their small size. Studying them has been challenging because they are hard to observe in their natural habitats. Initially, scientists used microscopes and lab cultivation to study microbes, revealing how they look, move, and interact with chemicals. However, much of their natural behavior remained unknown. Today, scientists study microbial DNA to understand their functions, relationships, and evolution. Since microbes are abundant, with billions of species in a gram of soil, processing this genetic data requires advanced computing power. As a result, microbiologists now use data science, combining computer technology, math, and programming to analyze and interpret genetic information, providing new insights into how microbes thrive in diverse environments.

Maths and computer science in the study of microbes – bioinformatics, statistics, modelling

Mum! How can you be so certain that an apple a day keeps the doctor away?

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During a family vacation in 1964, Drs. Thomas and Louise Brock visited Yellowstone National Park and discovered the hot springs' colorful microbial life. Unknowingly, their successful cultivation of *Thermus aquaticus* from Mushroom Pool would change the world. This heat-loving organism became crucial in developing the polymerase chain reaction (PCR), a technique now essential in labs. PCR has since driven life-changing discoveries, advanced forensic science, and contributed to the development of vaccines, antibiotics, and other medicines.

PCR: The Polymerase Chain Reaction – A Molecular Biology Revolution

My friend at school has COVID. Do I have it, too?

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Credit Jawahar Swaminathan and staff at the European Bioinformatics Institute.

Microbes are all around us, even on us, though we often only notice them when food spoils, meat develops a sheen, or water bottles grow a green film. But how do we know microbes are responsible? How do they thrive in these conditions? Can we reproduce their growth in the lab, and how can we study their properties?

How do we study microbes?

Hey, the cake I saved from last week is covered in spots of different shapes and colours. Are these microbes? How can we analyse them?

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Bacteria, fungi, and viruses are tiny organisms living around us. Most are beneficial, but some are not. Microbiology is the study of these organisms, but how can we see them given their tiny size? Microorganisms are around 1 micrometer in size, too small to be seen by the naked eye. The microscope, invented in 1590 by Zaccharias Janssen and later used by Antoine van Leeuwenhoek to observe microbes, allows us to magnify them. Microscopy is crucial in microbiology as it helps us understand microbial processes and identify beneficial or harmful organisms. Modern microscopes can even observe bacteria in real-time, swimming and forming biofilms. While these instruments are expensive, it's possible to build a low-cost version with everyday materials.

I can make my own microscope!

Miss: can we also show our families microbes?

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Image by Maria José González & Paola Scavone.

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