Name: growing hidden microbes with ichip
Uploaded: 2026-03-12T13:36:06.000Z
Duration: 1 min 24 s
Channel: JoVE

The iChip, or isolation chip, is a high-throughput tool used to cultivate previously uncultivable microorganisms.It consists of a plate with hundreds of tiny diffusion chambers.Ideally, each chamber contains a single microbial cell from a diluted environmental sample on an agar medium.The plate is sealed with semi-permeable membranes and pressed between two outer plates.This setup enables nutrients to diffuse in while keeping the cells in place.The assembled iChip is then incubated in the original environment of the sample, allowing the microbes to grow in situ.Microbial growth in iChips can take days to months, depending on the organism, after which the device is screened for colony formation.The colonies are transferred to a laboratory medium with optimized nutrients.The culture flask is placed in a shaker incubator to provide controlled temperature and aeration, supporting microbial adaptation to in vitro conditions.Strains that successfully adapt to laboratory conditions can be scaled up to industrial levels in bioreactors to produce enzymes, metabolites, or antibiotics.

ichip

iChip

The cultivation of environmental microorganisms has long been hindered by the inability to replicate complex native conditions in vitro. The isolation chip (iChip) addresses this limitation by facilitating the growth of previously uncultivable microorganisms through in situ incubation. Designed for high-throughput microbial cultivation, the iChip comprises hundreds of microchambers, each capable of housing a single microbial cell. These microchambers are loaded with a mixture of molten agar and a diluted environmental sample, such as soil or sediment, and sealed with semi-permeable membranes that permit molecular exchange while maintaining microbial isolation.Once assembled, the iChip is returned to the environment from which the sample originated. This enables microbial cells to access native chemical signals, nutrients, and community interactions necessary for growth, conditions often absent in standard laboratory media. Over the course of one week, microbial colonies form within the chambers, leveraging environmental diffusion for metabolic support.Post-incubation, individual colonies are recovered and transferred to nutrient-optimized laboratory media, a carefully formulated mixture of nutrients, growth factors, and other essential components that mimic the natural environment of the microorganisms. The transition period, lasting several weeks, is critical for microbial adaptation to artificial conditions. Successfully acclimatized strains can then be cultured at larger scales using bioreactors. Such strains are valuable for their ability to biosynthesize bioactive compounds, including novel antibiotics, secondary metabolites, and industrially relevant enzymes.The iChip has been pivotal in discovering new microbial species and natural products. A notable example includes the isolation of Eleftheria terrae, a previously uncultured bacterium that produces teixobactin, a novel antibiotic active against multidrug-resistant pathogens. The success of the iChip underscores the importance of mimicking natural environments in microbial cultivation, expanding the frontiers of microbiology and biotechnology.

The cultivation of environmental microorganisms has long been hindered by the inability to replicate complex native conditions in vitro. The isolation ...

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Education

JoVE Core

Microbiology

Unit

Industrial Microbiology

KEY TERMS AND CONCEPTS

growing hidden microbes with ichip

The iChip helps scientists grow environmental microbes that are hard to culture in the lab. It solves a long-standing problem in microbiology by giving cells conditions that are closer to their natural habitat. The method uses in situ incubation, which means the sample grows in the environment where it was collected.

The isolation chip, or iChip, is built for high-throughput microbial cultivation. It contains hundreds of tiny microchambers, and each chamber can hold one microbial cell. The chambers are filled with molten agar and a diluted sample from soil or sediment. They are then sealed with semi-permeable membranes, which let small molecules move through while keeping the cells separate.

After assembly, the iChip is returned to the original environment. There, the cells can receive natural chemical signals, nutrients, and community interactions that standard lab media often lack. Over about one week, colonies form inside the chambers as environmental diffusion supports metabolism and growth.

Once colonies are ready, scientists recover individual microbes and move them to nutrient-optimized laboratory media. This medium is carefully mixed to include nutrients, growth factors, and other essential components that resemble the microbes' natural setting. The transition to lab conditions can take several weeks, and this step is important for helping the strains adapt.

After acclimatization, the microbes can be grown at larger scale in bioreactors. These strains are valuable because they can make bioactive compounds, including new antibiotics, secondary metabolites, and industrial enzymes. The iChip has also helped researchers find new microbial species and useful natural products. One key example is Eleftheria terrae, an uncultured bacterium that produces teixobactin, a novel antibiotic active against multidrug-resistant pathogens. The iChip shows how copying natural conditions can expand microbiology and biotechnology.

Growing Hidden Microbes with iChip

bioreactor design and operational system

Bioreactor Types and Key Features

Bioreactors are engineered vessels that grow microorganisms under controlled conditions for bioprocessing. They keep the system sterile and let operators control pH, temperature, oxygen, and nutrient levels. These settings help support microbial growth and the production of useful metabolites. Bioreactors come in a wide size range. Some are small laboratory units that hold 1 liter, while industrial systems can hold up to 500,000 liters. In many systems, only about 75% of the vessel volume is...

bioreactor controls-i

Fermenter Monitoring and Control

Fermenter monitoring and control keeps microbial growth conditions stable in fermentation systems. Temperature, foam, pH, carbon dioxide, oxygen, and pressure all need careful measurement. These settings help improve productivity and process efficiency. Temperature control is especially important because many fermentation reactions release heat. Small laboratory fermenters may use mercury-in-glass thermometers, resistance thermometers, or thermistors. Mercury thermometers are often used for...

bioreactor controls-ii

Oxygen Transfer in Stirred Fermentors

Oxygen transfer in stirred fermentors is essential for aerobic fermentation. Microbes need oxygen for growth and for making useful products. This can be difficult because air contains only about 20% oxygen, and oxygen dissolves poorly in water. At 20°C, its solubility is only about 9 ppm. In some high-demand processes, such as yeast growth or citric acid production, even a saturated broth may supply oxygen for only a few seconds. To improve oxygen delivery, sterile or scrubbed air is fed into...

bioreactor controls-iii

Engineering Yeast for Higher Product Yields

Strain improvement helps industrial microbiology make more product from microbes such as Saccharomyces cerevisiae. Natural isolates often produce useful compounds in very low amounts. Medium changes and growth condition changes can help, but their effect is limited by the organism’s genes. Because of that limit, scientists often improve the strain first and then adjust the culture conditions again. This cycle can repeat several times and lead to better overall output. S. cerevisiae is a common...

designing growth media for bioreactors

Key Ingredients in Bioreactor Growth Media

Growth media for bioreactors supply the nutrients cells need for growth and metabolism. A well-balanced medium can improve the yield of useful products such as enzymes, antibiotics, and biomass. If nutrients are too low or too high, cell growth and product output can drop. A typical growth medium includes a carbon source, a nitrogen source, salts, vitamins, trace elements, and water. Carbon sources such as glucose or glycerol provide energy and building blocks for biomass. Nitrogen sources...

methods of medium optimization

Screening Variables in Medium Optimization

Microbial growth media can be improved by testing which ingredients most affect growth and product yield. Statistical experimental design gives a structured way to do this. It also makes the process more reproducible and efficient. The One-Factor-at-a-Time, or OFAT, method changes one variable while all others stay the same. This approach is simple, but it cannot show interactions between variables. When two factors work together, OFAT may miss that effect and lead to a less effective result. <br...

batch vs continuous culture

Fermentation Methods for Industrial Production

Fermentation methods for industrial production use microbes to make pharmaceuticals, biofuels, enzymes, and food additives. The two main approaches are batch fermentation and continuous fermentation. Both depend on microbial conversion of a substrate into a desired product, but they differ in how the culture is run and how the product is collected. Batch fermentation is a closed system. Nutrient medium and inoculum are added at the start, and no more material is fed in except for gas exchange...

fed-batch culture

Fed-Batch Feeding Strategies

Fed-batch culture uses controlled feeding to guide cell growth and product formation in bioprocessing. It combines features of batch culture with nutrient additions during fermentation. In this semi-closed system, fresh substrate is added while the biomass and products stay in the bioreactor until the run ends. This feeding control helps manage growth rate, nutrient limits, and the buildup of metabolites. By adjusting when and how substrate is added, the process can support longer production...

scale-up processes

Fermenter Materials and Contamination Control

Microbial fermentation scale-up depends on fermenter materials and contamination control as production moves from the lab to the factory. The goal is to keep yield and product quality stable while the culture volume gets larger. That requires changes in equipment design, process settings, and cleaning methods. At the laboratory scale, cultures are usually grown in 1 to 10 liter glass or autoclavable plastic fermenters. These materials make sterilization easier and allow careful control of...

upstream processing

Bioreactor Growth in Biomanufacturing

Bioreactor growth is a key part of biomanufacturing. It uses microorganisms, mammalian cells, or insect cells to make therapeutic proteins, vaccines, enzymes, and other biologically derived products. The process includes choosing and preparing the production organism and then growing it under tightly controlled conditions. The first step is host selection and genetic optimization. A host can be a natural strain, a cell line, or a genetically modified organism designed to make the target...

downstream processing

Purifying Products After Fermentation

Purifying products after fermentation starts once the growth stage is finished. The goal is to recover useful products such as acids, vitamins, antibiotics, or proteins and remove the unwanted material around them. The first step is often cell harvesting. For intracellular protein-based products, the cells are separated from the liquid phase by centrifugation or filtration. If the target product is inside the cells, those cells must then be broken open. Cell disruption releases the contents...

production of alcohol

Continuous Ethanol Fermentation

Continuous ethanol fermentation is the process used to make alcohol in a steady, nonstop flow. It is valued in industry because it supports efficiency, scale, and high ethanol output. The feedstock is corn starch, which must first be broken down into sugars before microbes can ferment it. Corn starch undergoes enzymatic hydrolysis, which means enzymes split starch into smaller sugar molecules. The enzymes used are α-amylase and glucoamylase. They convert the starch into fermentable sugars such...

production of organic acids

Microbial Fermentation for Lactic Acid

Microbial fermentation is used to produce lactic acid from starch-based raw materials. This organic acid is important in food, pharmaceutical, and biodegradable polymer industries. It is often preferred over chemical synthesis because it is more sustainable and can produce an enantiomerically pure product. The process starts with starch hydrolysis. Starch-rich feedstocks such as corn and potatoes are broken down to release fermentable sugars. This can be done with amylase enzymes or with...

production of antibiotics

Industrial Penicillin Fermentation Process

Industrial penicillin is made by growing the fungus Penicillium chrysogenum in large stirred-tank bioreactors. These tanks can range from tens to hundreds of thousands of liters. The process depends on close control of temperature, pH, and dissolved oxygen so the fungus can keep making the antibiotic efficiently. Penicillin is a secondary metabolite, which means the fungus makes it mainly during the stationary phase of growth. To support this shift, the feed strategy must limit rapid cell...

production of pharmaceuticals

Making Human Insulin in Bacteria

Industrial insulin production uses genetically engineered E. coli to make human insulin at large scale. The bacteria carry a proinsulin gene under a tryptophan promoter, and the gene includes a methionine linker so the product can be cut later. The cells also contain ampicillin resistance, which helps with selective growth during culture. Production starts with seed cultures stored at −80 °C. A small amount is thawed to begin starter cultures, and the culture is expanded step by step until it...

production of biopesticides

Bt Biopesticides and Crop Protection

Bt biopesticides use Bacillus thuringiensis to help protect crops from insect pests. Bt is a bacterium that is valued for its strong insect-killing activity, its specificity to target insects, and its natural breakdown in the environment. Because of these traits, it offers a more sustainable option than many chemical pesticides. Bt makes insecticidal crystal proteins, also called Cry proteins, during sporulation. Sporulation is the stage when the bacterium forms spores. The Cry proteins form...

The iChip helps scientists grow environmental microbes that are hard to culture in the lab. It solves a long-standing problem in microbiology by giving cells conditions that are closer to their natural habitat. The method uses in situ incubation, which means the sample grows in the environment where it was collected. The isolation chip, or iChip, is built for high-throughput microbial cultivation. It contains hundreds of tiny microchambers, and each chamber can hold one microbial cell. The...

vaccine production

Vaccine Manufacturing: Purification to Packaging

Vaccine manufacturing turns cultured microorganisms into a safe immunological product. The process starts with growing viruses or bacteria to collect antigenic material, which is the part of the pathogen that helps trigger an immune response. For viral vaccines, mammalian host cells are first grown in bioreactors. The target virus is then added so it can replicate inside the cells. After the cells lyse, or break open, the viral particles are released. The mixture is clarified by filtration or...

bioplastics

Microbial PHAs for Sustainable Plastics

Microbial PHAs are a sustainable option for making plastics from bacteria instead of petroleum. These bioplastics are known as polyhydroxyalkanoates, or PHAs, and one important example is polyhydroxybutyrate, or PHB. They are valued because they can break down in the environment and are also compatible with living tissue. Bacteria such as Cupriavidus necator and Pseudomonas putida make PHAs inside their cells. They store these polymers as carbon and energy reserves. PHA buildup is especially...

microbial biosensors

Microbes as Sensors for Chemical Detection

Microbes can be used as sensors to detect specific chemicals by producing a measurable signal. These microbial biosensors are analytical devices that combine living cells with a signal-transducing element. The biosensing organisms are often Escherichia coli or Saccharomyces cerevisiae, and they are commonly placed in multiwell plates for rapid, real-time detection of target analytes. When a target analyte, such as sucrose, interacts with the microbes, the cells respond biochemically. That...

biological treatment of effluent and waste water 

biological-treatment-of-effluent-and-waste-water

Steps in Wastewater Cleanup by Microbes

Wastewater cleanup often uses microbes to remove pollutants from sewage. Modern treatment systems do this in stages. Each stage lowers solid waste, dissolved organic matter, and microbial contamination. The treated water is then prepared for safe discharge or reuse. Primary treatment is the first physical step. Screening removes large debris, and sedimentation lets suspended particles settle out of the wastewater. This lowers the amount of material that later treatment steps must handle. <br...

biofuels

Microalgae Biodiesel Production

Microalgae can be used to make biodiesel, a renewable fuel made from biological material. These photosynthetic microorganisms grow quickly and turn sunlight and carbon dioxide into biomass. They can also grow in freshwater, marine water, and wastewater, which makes them flexible feedstocks for fuel production. Microalgae are especially useful because they can build up large amounts of lipids, or fats, in their cells. When growth conditions are good, they multiply rapidly. When nutrients become...

key terms and concepts

Learn how the iChip grows hard-to-culture environmental microbes in natural conditions, helping scientists isolate new species and discover antibiotics.

Growing Hidden Microbes with iChip | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

Growing Hidden Microbes with iChip

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