Microbial Identification and How to Learn from Microbes

Microbes, or microorganisms, are extremely small, living organisms that are too tiny to be seen with the naked eye. They’re found virtually everywhere on Earth, including in soil, water, air, and within other living beings. 

Microbial identification - the process of determining which microorganisms, such as bacteria, fungi, or viruses, are present in a sample - is widely used in healthcare, food production, pharmaceuticals, and environmental science. 

Scientists rely on microbial identification to diagnose infections and guide treatment, and scientists apply it to discover beneficial microbes for medicine, agriculture, and industry.  

Streptomyces, shown above, is a genus of Actinobacteria, and is responsible for producing about two-thirds of all known antibiotics. Credit: US Centers for Disease Control and Prevention.

And we’ve got some catching up to do with these miniscule guys. Over billions of years, microbes have adapted to every environment on the planet, from the deep sea to the stratosphere, and transformed them in the process. 

Throughout evolutionary time these tiny organisms have had immeasurable impact - turning barren rock into fertile soil, decomposing organic matter, cycling nutrients into life’s flow, shaping the climate, steering the carbon cycle, and fine-tuning the chemistry of ocean, land, and air.

They drive elemental cycles, shape habitats, and enable essential processes of all other organisms. 

🦠 Interested in more about microbes? Come and see what’s possible when we mimic our planet’s most ancient, abundant, and diverse inhabitants at the Biomimicry Confluence event on 22 & 23 October 2025, where we'll have a session on Microbial Biomimicry. Get your tickets here.

The (Very Long) History of Microbes 

Microbes shape everything we know. They are the unseen engines of life on Earth, orchestrating the processes that sustain ecosystems at every scale. That’s why microbial identification plays a vital role in science and the advancement of human innovation.

Emerging roughly 3.8 billion years ago, microbes were the only type of life on Earth for billions of years, making them our planet’s most ancient, abundant, and diverse inhabitants. 

They form the tangled roots and the greatest expanse of the tree of life, spanning every domain. Many microbes live as single cells and some form simple multicellular structures or colonies, what unites them is their typically microscopic scale: organisms too small to be seen without a microscope.

The Process of Microbial Identification

To learn from these ancient microbes, we have to be very sure that we’ve accurately identified them. Microbial identification usually follows a set of systematic steps, moving from general observations to highly specific analyses. 

Here are the main steps usually followed in the process: 

1. Sample Collection

Obtain the specimen (e.g., soil, water, food, clinical sample) while avoiding contamination.

2. Cultivation (if applicable)

Grow microbes on selective or differential media to isolate pure colonies for study. Some identification methods (like metagenomics) can skip this step.

3. Morphological Examination

Look at colony appearance, size, shape, and color on culture plates, and examine cell shape/arrangement under a microscope (e.g., rods, cocci, spirals).

4. Staining Techniques

Apply stains such as Gram stain, acid-fast stain, or spore stain to differentiate structural and chemical characteristics of the cells.

5. Biochemical Testing

Test for metabolic capabilities (e.g., sugar fermentation, enzyme activity, oxygen requirements) that provide functional fingerprints of the microbe.

6. Molecular Methods

Use DNA or RNA analysis (commonly 16S rRNA gene sequencing for bacteria or ITS sequencing for fungi), to determine genetic identity.

7. Proteomic / Mass Spectrometry Analysis

Techniques like MALDI-TOF MS analyze protein fingerprints to rapidly match microbes against reference databases.

8. Immunological / Serological Tests

Use antibodies or antigen detection methods (like ELISA, agglutination tests) for quick identification, especially in clinical settings.

9. Data Comparison with Databases

Compare results (morphology, biochemistry, or genetic sequences) to established microbial databases for accurate identification.

10. Confirmation & Reporting

Cross-check multiple methods, confirm the species/strain, and report findings with clinical or environmental relevance.

Microbial Biomimicry: What Can We Learn From Microbes?

Microbes are the ultimate innovators. So, once we’ve identified them and learned about them, how can we learn from them? Practicing biomimicry, we can draw lessons from microbes’ extraordinary capabilities and apply them to the design of engineered systems. 

For example, microbes naturally degrade plastic, break down pollutants, upcycle materials, and restore nutrient cycles in ecosystems. By emulating these processes, we may create closed-loop systems that reduce waste and optimize resource use.

Bacteria (such as Pseudomonas and Bacillus), fungi (Phanerochaete, Pleurotus), microalgae (Scenedesmus, Chlorella), and yeast (Yarrowia) are commonly used in bioremediation to break down pollutants like hydrocarbons, pesticides, and heavy metals. Above is an image of Antarctic bacterium Pseudomonas sp. YeP6b, at 45,000× magnification. Credit: Jorgevielmasalazar 

By tapping into the power of microbes, emulating their genius, and enabling their flourishing, we can build a regenerative bioeconomy that supports both ecological health and economic growth. 

But just as is true with the larger organisms we support and depend on, the more we understand about the lives of microorganisms, and the more we connect with them as living beings in their own right, the more fruitful, sustainable, and planet-positive our relationship will be.

Although microorganisms are increasingly utilized in fields like bioremediation, medicine, and industry, applying live organisms comes with challenges. Maintaining viability, scaling production, shifting ecosystems, and avoiding unintended ecological impacts can be difficult, especially in complex organisms or sensitive environments.

Biomimicry offers a complementary path. Instead of utilizing live microbes we can emulate their structures, processes, and systems - reducing the risks while unlocking immense opportunities for innovation. 

Biomimicry Examples in Microbiology 

Below are 10 examples of how microbes have inspired innovation or solved human challenges. 

1. Geometric shells of viruses

The intricate shapes of viral shells have inspired strategies for precision drug delivery, helping medicines reach exactly where they are needed in the body.

2. Microalgae behavior models

The way microalgae respond to their environment is being used to model complex systems, improving rainfall prediction and even strengthening smart city security.

3. Cow gut microbiomes

The highly efficient microbial communities in a cow’s gut have informed innovations in wastewater treatment and renewable energy systems, showing us how to manage resources more effectively.

4. CRISPR/Cas9 from the bacterial immune system

By emulating how bacteria defend themselves against viruses, scientists developed CRISPR/Cas9, a breakthrough tool that revolutionized gene editing.

5. Microbial degradation and nutrient cycling

Because microbes can naturally break down plastics, pollutants, and waste, they inspire closed-loop systems that reduce waste while keeping resources in continuous use.

6. Conditions that support microbial thriving

When we mimic the environments that allow microbes to flourish, we can boost bioproduction efficiency and create healthier, more resilient ecosystems.

7. Biofilm-inspired formats and microbial cues

The structures and chemical signals of microbial communities can guide restoration efforts, helping degraded soils, guts, and reefs recover more quickly.

8. Microbial defense strategies

Microbes can inform strategies to design better antimicrobial products, such as Sharklet Technologies’ micropatterned surfaces that inhibit bacteria by mimicking shark skin.

9. Self-healing concrete with bacteria

Certain bacteria, such as the Bacillus species, can precipitate calcium carbonate. Engineers have harnessed this process to create self-healing concrete that automatically seals cracks when exposed to water, extending infrastructure lifespan.

10. Antibiotics from soil microbes

Many of the world’s most important antibiotics, like streptomycin, were inspired by compounds produced by soil-dwelling microbes to defend themselves. These natural strategies guide ongoing efforts to design new antimicrobial drugs.

In Closing 

These examples only scratch the surface of what’s possible through microbial biomimicry. Microbes have spent billions of years refining strategies for resilience, regeneration, and resourcefulness which can help us meet the urgent challenges of our time. 

From the tiniest molecular tools to the largest ecological networks, microbial life offers an expansive design vocabulary. In learning from their ingenuity we gain innumerable tools for innovation, and a deeper understanding of how to design in partnership with living systems. 

All we have to do is pay attention - to the worlds we share, and to what our human systems can learn from the microbial ones already thriving around us.

Inspired by Erin Miller and adapted from AskNature’s The Nature of Life in Its Smallest Forms. Read the full article and see the full list of microbial examples here. 

🦠 Erin Miller is a Keystone Presenter at the next Biomimicry Confluence. Come and see what’s possible when we mimic our planet’s most ancient, abundant, and diverse inhabitants. Grab your ticket to the Biomimicry Confluence for $27 here.