DOI: 10.5061/dryad.bk3j9kdh3
title: Data for: Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities

description: The microbial fermentation behind sourdough bread is among our oldest
 technologies, yet there are many opportunities for sourdough science to
 learn from traditional bakers. We analyzed the microbiome structure and
 function of 40 starters (grown from 10 types of flour) over 14 days and
 identified 6 distinct stages of succession. At each stage, bacterial taxa
 correlate with key functions that determine bread quality, including pH,
 rise, and aromatic profile. Day 1 starter cultures were dominated by
 microorganisms commonly associated with plants and flour and by aromas
 similar to toasted grain/cereal. Bacterial diversity peaked from days 2-6
 as taxa shifted from opportunistic/generalist bacteria associated with
 flour inputs, toward specialized climax bacterial communities (days 10–14)
 characterized by acid-tolerant taxa and fruity (p&lt;3.03e-03), sour
 (p&lt;1.60e-01), and fermented (p&lt;1.47e-05) aromas. This
 collection of traits changes predictably through time, regardless of flour
 type, highlighting patterns of bacterial constraints and dynamics that are
 conserved across systems and scales. Yet, while sourdough climax
 communities exhibit similar markers of maturity (i.e., pH ≤4 and enriched
 in Lactobacillus [mean abundance 48.1%], Pediococcus [mean abundance
 22.7%], and/or Gluconobacter [mean abundance 19.1%],), we also detected
 specific taxa and aromas associated with each type of flour. Our results
 address important ecological questions about the relationship between
 community structure and function and may enable bakers to deliberately
 select for specific sourdough starter and bread characteristics.
description: Five researchers grew a total of 40 starters from 10 different
 flour types: 4 replicates each of five flours containing gluten–unbleached
 all-purpose flour (processed from <em>Triticum</em>
 <em>aestivum</em>), red turkey wheat
 (<em>Triticum</em> <em>aestivum</em>), rye
 <em>(Secale</em> <em>cereale</em>), emmer
 (<em>Triticum dicoccon</em>), and einkorn
 (<em>Triticum</em> <em>monococcum</em>) – and five
 gluten-free flours – teff (<em>Eragostis</em>
 <em>tef</em>), millet (<em>Eleusine</em>
 <em>coracana</em>), sorghum (<em>Sorghum</em>
 spp.), buckwheat (<em>Fagopyrum</em>
 <em>esculentum</em>), and amaranth
 (<em>Aramanthus</em> <em>caudatus</em>). The
 all-purpose, red turkey wheat, emmer, einkorn, rye, and millet flours were
 milled at Boulted Bread Bakery (Raleigh, NC), while the teff, sorghum,
 buckwheat, and amaranth flours were purchased from commercial vendors
 online. On day 0, two level tablespoons of flour and
 two tablespoons of distilled water were mixed in a half-pint wide-mouth
 glass jar with a sterilized spoon. All spoons were washed with soap and
 water and wiped with 70% ethanol immediately before mixing. A paper towel
 was fastened over the mouth of the jar with a rubber band to prevent large
 particles or insects from settling into the jar while still allowing
 environmental microbes to colonize the flour-water mixture. After 24
 hours, we measured the maximum height of the starter in cm, described the
 smell(s) of the starter using free association, then mixed the starter and
 measured pH using short-range (0–6, 0.5 interval) Hydrion Brilliant Paper
 (MicroEssential Laboratory, Brooklyn, NY). Next, we and transferred 1 mL
 starter to a sterile, labeled 2-mL microcentrifuge tube, which was stored
 at -20°C for DNA sequencing. Then we removed 1 tablespoon of sourdough to
 discard. Finally, we added 1 tablespoon fresh flour and 1 tablespoon water
 to the remaining starter and mixed thoroughly with the spoon. These
 measuring and refreshing steps were repeated once a day (at 24-hour
 intervals) for 14 days.  We collected three 1-mL
 samples of each flour type (n=30) and three 1-mL samples of distilled
 water to represent the resource inputs to each starter on day zero. We
 also collected a daily 1-mL aliquot from each starter on days 1, 2, 3, 6,
 10, and 14 (n=240), as part of the discard. All aliquots were transferred
 to a sterile, labeled 2-mL microcentrifuge tube, which was stored at -20C
 for DNA sequencing. Together with the flour and water aliquots, a total of
 273 samples were shipped on dry ice for DNA extraction, PCR amplification,
 and Illumina multiplexed sequencing of the bacterial 16S v4 region using
 the 515f/806r for bacteria at the Fierer Microbial Community Sequencing
 Lab (Boulder, CO).
description:  The Fierer Microbial Community Sequencing Lab demultiplexed raw
 sequences to produce fastq files with the DADA2 pipeline, as described at
 (https://github.com/fiererlab/dada2_fiererlab/tree/626a1aff9abe1fcdcac7fdf57ba51f3cf1db1e8e).