Learning from Fermentation Failures: The Microbial Science Behind Why We Fail and How to Prevent It

“Failure is the mother of success”—this saying applies to making fermented foods as well. Miso that’s become too sour, nukadoko that smells bad, bread that won’t rise—these are failures everyone experiences. However, behind these failures lie the ecology of microorganisms and the mechanisms of fermentation.

In this article, we’ll delve into the science of microorganisms through fermentation failure examples. Let’s view failure as a “learning opportunity” and understand the profundity of fermentation.

What is Fermentation?

Microbial Metabolic Activity

Fermentation is the metabolic activity by which microorganisms (bacteria, yeast, mold, etc.) break down organic matter (sugars, proteins, fats, etc.) to obtain energy. In this process, various compounds are produced, giving food distinctive flavors, aromas, and textures.

As explained in yogurt fermentation science, lactic acid bacteria break down lactose to produce lactic acid. As explained in the mystery of yeast: good in the lab, bad at baking, yeast breaks down sugar to produce alcohol and carbon dioxide.

The Difference Between Beneficial Fermentation and Harmful Spoilage

Both fermentation and spoilage involve microbial decomposition of organic matter, but they’re distinguished by whether they’re beneficial to humans.

The boundary between fermentation and spoilage is determined by the type of microorganisms and the environment. By creating the right environment, beneficial microorganisms can be made dominant while harmful microorganisms are suppressed.

Failure Example 1: Too Sour

Symptoms

• Miso, nukadoko, or bread tastes sour
• Sourness is too strong to eat comfortably

Cause: Excessive Lactic Acid Fermentation

Lactic acid bacteria break down sugars to produce lactic acid. Lactic acid is the cause of sour taste. When lactic acid bacteria multiply excessively, lactic acid accumulates and the food becomes sour.

pH Changes and Microbial Activity

As fermentation progresses, lactic acid accumulates and pH decreases (becomes acidic). When pH drops, lactic acid bacteria activity is suppressed, but other microorganisms that prefer acidic environments (such as acetic acid bacteria) may multiply.

As explained in kimchi fermentation science, kimchi fermentation involves a lactic acid bacteria relay. Initially, Leuconostoc mesenteroides is dominant, but as pH drops, Lactobacillus plantarum becomes dominant.

Scientific Solutions

1. Add salt: Salt suppresses lactic acid bacteria activity. Increasing salt concentration can slow lactic acid bacteria growth.
2. Switch to refrigeration: At low temperatures (5-10°C/41-50°F), lactic acid bacteria activity slows. Switching to refrigeration can slow fermentation.
3. Add fresh nuka or koji: Adding new nuka or koji dilutes lactic acid bacteria concentration and rebalances the microbial community.
4. Measure pH: Use pH test strips or a pH meter. When pH falls below 4, it’s quite sour.

Prevention

• Temperature control: Keep fermentation temperature low (15-20°C/59-68°F)
• Salt concentration: Follow recipe salt concentration
• Regular observation: Monitor fermentation progress regularly and address issues early

Failure Example 2: Mold Growth

Symptoms

• Mold grows on the surface of miso, nukadoko, or cheese
• White film, black spots, green mold, etc.

Cause: Mold Growth Conditions

Mold is a type of fungus that multiplies by releasing spores. Mold requires the following conditions to proliferate:

• Temperature: 20-30°C (68-86°F) is optimal
• Humidity: 60% or higher
• Oxygen: Aerobic (requires oxygen)
• Nutrients: Sugars, proteins, fats

The Difference Between Aerobic and Anaerobic

Microorganisms are classified as aerobic or anaerobic based on oxygen requirements.

Aerobic microorganisms: Require oxygen (e.g., mold, some yeast, aerobic bacteria)

Anaerobic microorganisms: Don’t require oxygen, or can’t multiply with oxygen (e.g., lactic acid bacteria, butyric acid bacteria, anaerobic bacteria)

Because mold is aerobic, it tends to grow on surfaces (parts in contact with air). Conversely, lactic acid bacteria are anaerobic, so they multiply internally (parts not in contact with air).

As explained in the nukadoko microbial ecosystem, yeast is distributed in the surface layer, lactic acid bacteria in the middle layer, and butyric acid bacteria in the deep layer of nukadoko. This is because microbial distribution is determined by oxygen availability.

Scientific Solutions

1. Remove moldy portions: Remove the moldy area and surroundings (about 5 cm radius) deeply. Mold hyphae may have extended internally.
2. Sprinkle salt on surface: Salt suppresses mold growth. Lightly sprinkling salt on the surface prevents mold recurrence.
3. Cover tightly with plastic wrap: Reducing air contact suppresses aerobic mold growth.
4. Switch to refrigeration: At low temperatures, mold growth slows.
5. Stir daily (for nukadoko): Supplying oxygen throughout the nukadoko activates surface yeast and suppresses mold growth.

Prevention

• Clean environment: Keep tools and hands clean to prevent contamination
• Sealed storage: Reduce air contact
• Refrigerated storage: Suppress mold growth at low temperatures
• Maintain salt concentration: Salt suppresses mold

Failure Example 3: Strong Odor

Symptoms

• Unpleasant odor from nukadoko or miso
• Ammonia smell, putrid smell, butyric acid smell, etc.

Cause: Growth of Butyric Acid Bacteria or Acetic Acid Bacteria

Unpleasant odors are caused by compounds produced by microorganisms such as butyric acid bacteria and acetic acid bacteria.

Butyric Acid Bacteria

Butyric acid bacteria (such as Clostridium genus) are anaerobic bacteria that break down sugars and proteins to produce butyric acid. Butyric acid produces various odors from butter-like to putrid.

Butyric acid bacteria multiply in oxygen-free environments (such as the bottom of nukadoko).

Acetic Acid Bacteria

Acetic acid bacteria (such as Acetobacter genus) are aerobic bacteria that break down alcohol to produce acetic acid. Acetic acid produces a pungent vinegar-like smell.

Acetic acid bacteria multiply in oxygen-rich environments (such as surfaces).

Why Microbial Balance Collapses

Fermented foods are ecosystems where multiple microorganisms coexist. In the right environment, beneficial microorganisms (lactic acid bacteria, yeast, etc.) become dominant and harmful microorganisms (butyric acid bacteria, acetic acid bacteria, etc.) are suppressed.

However, when microbial balance collapses for the following reasons, harmful microorganisms multiply:

1. Insufficient stirring (for nukadoko): Oxygen isn’t supplied to the bottom, allowing butyric acid bacteria to multiply
2. Insufficient salt: When salt is lacking, harmful microorganisms multiply more easily
3. High temperature: At high temperatures, harmful microorganisms multiply more easily
4. Over-pickling vegetables (for nukadoko): Vegetable proteins break down, producing ammonia

Scientific Solutions

1. Stir the entire nukadoko well: Supply oxygen and suppress butyric acid bacteria growth
2. Remove strongly odorous portions: Remove areas with many butyric acid bacteria
3. Add fresh nuka: Add new nuka to rebalance microorganisms
4. Add salt: Salt suppresses harmful microorganism growth
5. Switch to refrigeration: Suppress microbial activity at low temperatures

Failure Example 4: Won’t Set or Rise

Symptoms

• Yogurt won’t set
• Bread won’t rise

Cause: Insufficient Microbial Activity

Microbial activity is essential for fermented food production. When microbial activity is insufficient, fermentation doesn’t progress, resulting in failures like not setting or not rising.

Temperature and Microbial Growth Rate

Microbial growth rate depends heavily on temperature.

• Low temperature (5-15°C/41-59°F): Microbial activity slows
• Optimal temperature (20-40°C/68-104°F): Microorganisms multiply most actively
• High temperature (above 50°C/122°F): Microorganisms die

As explained in yogurt fermentation science, 40-45°C (104-113°F) is optimal for yogurt fermentation. If temperature is too low, lactic acid bacteria activity slows and it won’t set.

Scientific Solutions

1. Maintain optimal temperature range:
   • Yogurt: 40-45°C (104-113°F)
   • Bread: 25-30°C (77-86°F)
2. Extend fermentation time: If temperature is low, extend fermentation time
3. Use fresh starter culture: Old starter cultures may have reduced activity
4. Use a thermometer: Measure temperature accurately

Fundamentals of Microbiology to Prevent Failure

Key Factors in Fermentation Control

1. Temperature: Each microorganism has an optimal temperature
2. pH: Acidic environments favor lactic acid bacteria and yeast
3. Salt concentration: Medium salt (5-10%) favors lactic acid bacteria and yeast
4. Oxygen availability: Controls whether aerobic or anaerobic microorganisms dominate

Failure is a Learning Opportunity

A Researcher’s Perspective on Fermentation Failure

During my doctoral studies researching yeast, failure was routine even in the lab. The culture medium’s pH would change and kill the yeast, or contamination would force me to restart experiments—from these failures, I learned the importance of microbial ecology and environment.

Home fermented food making is the same. Failure is an excellent opportunity to understand microbial ecology. By asking “Why did it become sour?” or “Why did mold grow?”, the mechanisms of fermentation become visible.

Insights Gained from Failure

Insights gained from failure cannot be obtained from success alone.

• Too sour → Understanding excessive lactic acid fermentation
• Mold growth → Understanding the difference between aerobic and anaerobic
• Strong odor → Understanding the importance of microbial balance
• Won’t set or rise → Understanding the importance of temperature control

Don’t fear failure—embrace troubles as “learning opportunities.”

Conclusion

Fermentation failures always have scientific causes. And when you understand the causes, solutions become clear.

• Too sour → Excessive lactic acid fermentation → Add salt, refrigerate
• Mold growth → Aerobic mold proliferation → Seal, refrigerate
• Strong odor → Butyric acid bacteria growth → Stir, add salt
• Won’t set or rise → Insufficient microbial activity → Temperature control, fresh starter

By viewing failure as a “learning opportunity” and understanding the science of microorganisms, making fermented foods becomes more enjoyable and profound.