Bacterial Fermentation

Part of Fermentation and Brewing

Yeast gets most of the attention in fermentation, but bacteria are responsible for a vast range of preserved and transformed foods — from sauerkraut and kimchi to vinegar, tempeh, yogurt, and koji-fermented grain. Understanding the major groups of fermentation bacteria, their requirements, and their products allows a post-collapse community to preserve food, create flavor complexity, and produce ingredients that support other processes such as baking, cheese-making, and medical-grade acetic acid.

The Main Groups of Fermentation Bacteria

Lactic Acid Bacteria (LAB)

Lactic acid bacteria are the workhorses of vegetable, dairy, and grain fermentation. They convert sugars into lactic acid, lowering pH and creating the sour, tangy flavor characteristic of sauerkraut, pickles, sourdough, yogurt, and kimchi.

Key genera:

• Lactobacillus — found on vegetables, grain, skin; produces lactic acid from glucose
• Leuconostoc — initiates many wild ferments; produces CO2 as well as lactic acid
• Pediococcus — salt-tolerant, important in brine ferments and beer souring
• Streptococcus thermophilus — heat-tolerant, used in yogurt alongside Lactobacillus

LAB are anaerobic or facultative anaerobic — they prefer low-oxygen environments and are outcompeted in open air by molds and acetobacter.

LAB Genus	Temperature Range	Key Products	Typical Application
Lactobacillus	15–45 °C	Lactic acid	Vegetables, sourdough, dairy
Leuconostoc	10–30 °C	Lactic acid, CO2	Early-stage sauerkraut, kimchi
Pediococcus	20–45 °C	Lactic acid	Brine pickles, Belgian sour beer
S. thermophilus	35–45 °C	Lactic acid	Yogurt

Acetic Acid Bacteria (AAB)

Acetic acid bacteria — primarily Acetobacter and Gluconobacter — convert ethanol into acetic acid (vinegar) in the presence of oxygen. They are obligate aerobes: they require oxygen and are suppressed in anaerobic ferments.

AAB are responsible for:

• Vinegar production (wine, cider, beer, or sugar wash → acetic acid)
• Kombucha fermentation (in partnership with yeast)
• The scoby (symbiotic culture of bacteria and yeast)

AAB are a contamination risk in alcoholic ferments

If your wine, beer, or mead develops a sharp vinegar smell, acetic acid bacteria have gotten in through oxygen exposure. A ruined alcoholic ferment can be intentionally completed as vinegar — but it cannot be reversed.

Spore-Forming and Other Fermentation Bacteria

Bacillus subtilis is the key organism in natto (Japanese fermented soybean). It is a spore-former, highly heat-resistant, and produces a powerful protease that breaks down protein into amino acids. Natto has a strong smell and stringy texture but is extremely nutritious and shelf-stable at room temperature for several days.

Rhizopus oligosporus is technically a mold but is discussed here alongside bacterial fermenters because of its functional similarity in tempeh. It binds soybean (or other legume) cotyledons together with white mycelium and produces enzymes that pre-digest protein and reduce anti-nutrients.

Lacto-Fermentation in Practice

Lacto-fermentation is the most accessible bacterial fermentation because it requires only salt, vegetables, water, and time. No starter culture is needed — LAB are naturally present on all raw vegetables.

Basic process

1. Shred or chop vegetables
2. Add salt (see Brine Ratios for correct percentages)
3. Pack tightly into a vessel, submerging vegetables under the brine
4. Exclude oxygen with a weight, airlock, or cloth cover
5. Ferment at room temperature (18–24 °C is ideal) for 3–14 days
6. Taste regularly; move to cold storage when desired sourness is reached

pH progression

Stage	Time (at 20 °C)	pH	Dominant Organism
Fresh vegetables	Day 0	6.0–6.5	Mixed surface flora
Early ferment	Days 1–3	5.0–5.5	Leuconostoc spp.
Mid ferment	Days 3–7	4.0–4.5	Lactobacillus spp.
Mature ferment	Days 7–21	3.2–3.8	Lactobacillus spp.

As pH drops below 4.5, most pathogens (including Listeria and E. coli) are killed. A properly acidified lacto-ferment is safe from pathogenic contamination — the acidity itself is the preservation mechanism.

Taste is your best pH meter

A mature, stable lacto-ferment tastes sharply sour, like high-quality sauerkraut or dill pickles. If it tastes mild or flat, it has not acidified enough. If it smells wrong (see Contamination Signs), discard it.

Koji Fermentation

Koji (Aspergillus oryzae) is a mold — not a bacterium — but it is the foundation of East Asian fermentation culture. Koji grown on rice, barley, or soybeans produces powerful amylases and proteases that:

• Convert starch to sugar (enabling sake, mirin, rice wine)
• Break down protein to amino acids (enabling miso, soy sauce, shio koji)
• Pre-digest grain for animal feed

Growing koji from scratch

Without a commercial starter (tane koji), wild Aspergillus oryzae spores must be sourced. Traditional method:

1. Source spores from a functioning koji culture, dried miso, or dried soy sauce with live cultures
2. Steam short-grain white rice until fully cooked but not wet
3. Cool to 30–35 °C
4. Inoculate with 0.1–0.3% dried spores or crumbled mature koji by weight
5. Maintain at 28–32 °C with high humidity (85–95% RH) for 40–50 hours
6. Stir every 12 hours for the first 24 hours, then every 8 hours
7. Finished koji is white and fluffy, smells like chestnuts or mushrooms

Temperature control is critical for koji

Above 40 °C, koji dies and undesirable molds take over. Below 25 °C, growth is too slow and contamination risk rises. A well-insulated box with a water bowl (for humidity) and a small heat source can maintain the required range without electricity.

Koji Substrate	End Product	Fermentation Time
Rice + water	Sake, amazake	2–4 weeks
Soybeans	Miso	3 months–3 years
Wheat + soybeans	Soy sauce (shoyu)	6–24 months
Rice	Shio koji (salt koji)	7–14 days

Tempeh

Tempeh is fermented soybean cake produced by Rhizopus oligosporus. The mold binds cooked, dehulled soybeans together with dense white mycelium, producing a protein-rich, nutty-flavored food that can be sliced and cooked.

Tempeh production

1. Soak dried soybeans 12–24 hours
2. Dehull by rubbing between hands and floating hulls off in water
3. Cook soybeans until soft but not mushy (~40 minutes boiling)
4. Drain and dry surfaces (steam, spread on cloth, or briefly oven-dry)
5. Cool to 30 °C
6. Inoculate with 0.5–1% tempeh starter (dried Rhizopus spores) by weight
7. Pack into perforated bags or containers, 2–3 cm thick
8. Ferment at 28–32 °C for 24–48 hours

Signs of progress

• 12 hours: faint white fuzz visible
• 24 hours: dense white mycelium, cake holds together, gentle warmth from metabolic heat
• 36 hours: fully bound, ready to eat or refrigerate
• 48+ hours: gray-black sporulation begins; still edible but stronger flavor

Manage heat during tempeh fermentation

Rhizopus generates significant metabolic heat once active. At 36+ hours, the internal temperature can exceed 40 °C without ventilation, killing the culture and spoiling the batch. Ensure airflow around fermenting containers.

Vinegar Production via Acetic Acid Bacteria

Any alcoholic liquid (4–8% ABV) can be converted to vinegar by exposing it to air in the presence of acetic acid bacteria.

Surface method

1. Start with wine, cider, or beer at 5–8% ABV
2. Pour into a wide-mouthed vessel (maximum surface area)
3. Cover with cloth to exclude insects but allow airflow
4. Maintain at 25–30 °C
5. A vinegar mother (SCOBY of AAB) will form on the surface in 2–6 weeks
6. Taste weekly; fermentation is complete when sharp acidity is consistent and alcohol smell is gone

Accelerated method using a mother

Once a vinegar mother exists, future batches are much faster:

1. Add 10–20% volume of active mother to new alcoholic liquid
2. Maintain surface exposure and temperature
3. Vinegar typically ready in 1–2 weeks instead of 4–6

Save your vinegar mother

A healthy mother can be kept alive indefinitely by periodically feeding it fresh dilute wine or cider. It can be split and shared as a community resource.

Combining Bacterial Ferments

Many traditional preserved foods involve sequential or simultaneous bacterial and yeast fermentation.

Product	First Organism	Second Organism	Result
Kombucha	Yeast	Acetic acid bacteria	Acidic, lightly fizzy tea
Kvass	LAB	Yeast	Lightly alcoholic fermented bread
Sourdough	LAB	Wild yeast	Acidic, risen bread
Water kefir	LAB + yeast	—	Probiotic carbonated drink

Understanding which organisms are active at each stage allows you to troubleshoot failures and intentionally shift the balance — for example, promoting LAB over yeast in a sourdough by keeping it cool, or promoting yeast over LAB in a bread culture by keeping it warm and well-fed.

Bacterial Fermentation Summary

Lactic acid bacteria drive vegetable and dairy preservation through acidification; they require salt and anaerobic conditions. Acetic acid bacteria require oxygen and convert ethanol to vinegar. Koji (Aspergillus oryzae) is the key enzyme-producing mold for East Asian ferments including miso and sake. Tempeh (Rhizopus oligosporus) creates a dense protein-rich cake from soybeans in 24–48 hours. Each organism has a specific temperature window and oxygen requirement — matching conditions to organism is the core skill of bacterial fermentation.