Microbial Ecology: The Lifecycle of Your Starter (And Why It Smells)
To the naked eye, a sourdough starter is just bubbling paste. But under a microscope, it is a planet.
When you mix flour and water for the first time, you are not just making dough; you are terraforming a new world. You are initiating a biological sequence known as Ecological Succession.
This process is violent, chaotic, and predictable. It involves a war for resources, a "Great Extinction" event, and finally, the establishment of a stable civilization.
Understanding this lifecycle is the key to patience. It explains why your starter smells like vomit on Day 3, why it goes dead on Day 5, and why it suddenly wakes up on Day 10.
Phase 1: The Chaos (Days 1–3)
The Players: Enterobacteriaceae, Leuconostoc, Weissella.
Raw flour is not sterile. It is teeming with bacteria from the soil, the mill, and your hands. When you add water, you wake them all up.
In the first few days, the jar is dominated by "weeds"—opportunistic bacteria that grow fast and produce carbon dioxide rapidly. This leads to the infamous "False Rise."
You might see your jar double in size on Day 2 and think, "I've done it! I have a starter!"
You haven't. This gas is not from yeast; it is from bacterial fermentation.
The Environment: The pH is still relatively neutral (6.0–5.0), allowing these "bad" bugs to thrive.
The Smell: Often unpleasant. Think wet socks, cheese, or even vomit. This is due to the metabolic byproducts of these early colonisers.
Vomit/Parmesan: Caused by Butyric Acid and Isovaleric Acid, produced by bacteria that thrive before the acidity rises.
Phase 2: The Great Extinction (Days 4–6)
The Mechanism: Acidification.
As fermentation continues, the early bacteria produce weak acids. But slowly, the Lactic Acid Bacteria (LAB)—the heroes of our story—begin to wake up. They are slower to reproduce than the weeds, but they have a superpower: they can survive in acid.
As the LAB produce lactic and acetic acid, the pH of the jar drops below 4.5. This creates a hostile environment for the Phase 1 bacteria.
The result is a die-off. The "weeds" (Enterobacteriaceae) cannot survive the acidity, so they perish. They poison themselves with their own waste [1].
The Symptom: Your starter stops rising. It looks dead. The frothy bubbles disappear.
The Panic: This is where most beginners throw their starter away, thinking they killed it.
The Reality: You didn't kill it. You sanitised it. The bad bugs are dead, and the good bugs (LAB and Wild Yeast) are slowly building their numbers in the silence.
Phase 3: The Stabilization (Days 7–14)
The Players: Fructilactobacillus sanfranciscensis, Candida milleri (humilis), Saccharomyces cerevisiae.
Now that the "Acid Firewall" is established (pH ~4.0–3.5), the stage is safe for the climax community to emerge.
The Bacteria (LAB): They dominate the population (typically outnumbering yeast 100:1). They provide the flavour (acid) and the preservation.
The Yeast: Acid-tolerant wild yeasts finally flourish. They provide the leavening ($CO_2$).
Crucially, they establish a Symbiosis.
In many traditional starters, the bacteria (F. sanfranciscensis) consume maltose but release glucose as a byproduct. The yeast (C. milleri) cannot eat maltose, so it happily eats the glucose scraps left by the bacteria. They stop fighting and start feeding each other [2].
Phase 4: The Mature Ecosystem (Day 14+)
Once established, a starter is remarkably resilient. It builds Biofilms—protective structures that shield the colony from stress.
However, the ecosystem is not static. It shifts based on temperature (Warmth = Bacteria/Acid; Cold = Yeast/Gas) and hydration.
Decoding Your Starter By Smell
Once your starter is mature, the smell is no longer a sign of succession, but a Signal of State. It communicates its needs through Volatile Organic Compounds (VOCs) [3].
1. Ripe Fruit / Yogurt
The Signal: Healthy fermentation.
The Chemistry: A balance of lactic acid (creamy), acetic acid (sharp), and ethanol esters (fruity).
Action: Feed as normal. It is happy.
2. Nail Polish Remover (Acetone)
The Signal: Hunger (Starvation Mode).
The Chemistry: When food runs out and acidity is high, ethanol reacts with acetic acid to form Ethyl Acetate, which smells like solvent.
Action: It needs food now. Discard heavily (to remove the acid load) and feed with a higher ratio (1:3:3 or 1:5:5).
3. Alcohol / Hooch
The Signal: Long-term neglect.
The Chemistry: Ethanol production has pooled on the surface. The yeast has gone dormant to survive.
Action: Pour off the liquid (or stir it in for a boozier flavour), discard, and feed.
Summary
A sourdough starter is not "made"; it is evolved.
The transition from a mixture of flour and water to a leavening agent is a biological war. When you see bubbles on Day 2, do not celebrate. When you see stillness on Day 5, do not mourn.
Trust the succession. Feed the jar. The microbes know what they are doing.
References
McKenney, E. A., Nichols, L. M., Alvarado, S., et al. (2023). Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities. PeerJ.
Gobbetti, M., & Gänzle, M. (Eds.). (2012). Handbook on Sourdough Biotechnology. Springer Science & Business Media.
Hansen, A., & Schieberle, P. (2005). Generation of aroma compounds during sourdough fermentation: applied and fundamental aspects. Trends in Food Science & Technology.
De Vuyst, L., & Neysens, P. (2005). The sourdough microflora: biodiversity and metabolic interactions. Trends in Food Science & Technology.
Last updated: 17 January, 2026