Stable indigo-reducing ecosystem occurs via successive marked changes in microbiota during indigo fermentation

Indigo fermentation fluid maintains its indigo reducing state for more than 6 months under the open air, non-sterilized condition. The mechanisms underlying the development of the bacterial flora responsible for the long-lasting indigo reduction remain unclear. To elucidate the mechanism underlying the sustainability of this indigo reduction, three batches of indigo fermentation with different lifetimes were compared. Batch 1 was fermented for 51 days, Batch 2 was 342 days, and Batch 3 was 364 days. The V3-V4 region of the bacterial 16S rRNA gene was PCR-amplified by using the composite pair of primers 341F and 805R. The next-generation sequencing was performed using the Illumina MiSeq platform.