Analysis of the microbiota involved in the early changes associated with indigo reduction in the natural fermentation of indigo

  • Zhihao Tu
  • Helena de Fátima Silva Lopes
  • Kikue Hirota
  • Isao YumotoEmail author
Original Paper


Constituents of the seed microbiota and initial changes in the microbiota in fermentations are important in fermentation progression. To identify the origin of indigo-reducing bacteria and understand the initial changes in the microbiota that occur concomitantly with the initiation of indigo reduction during indigo fermentation, we analysed the initial changes in the microbiota. The proportions of the reported indigo-reducing taxa Alkalibacterium, Amphibacillus and Polygonibacillus increased to 24.0% on the 5th day, to 15.2% on the 7th day and to 42.8% at 4.5 months, and the relative abundances of these taxa were 0.048%, 0.14% and 0.02%, respectively, in sukumo (composted Japanese indigo plant material used for fermentation). In the early phase of the microbiota transition, two substantial changes were observed. The first change may be attributed to the substantial environmental changes caused by the introduction of heated wood ash extract (pH ≥ 10.5, temperature ≥ 60 °C). This change increased the proportions of Alkalibacterium and the family Bacillaceae. The second change in microbiota might be initiated by the consumption of oxygen by aerobic microorganisms until the 5th day followed by an increase in the abundance of the obligate anaerobe Anaerobranca and the aerotolerant Amphibacillus and a decrease in the abundance of Bacillaceae. This experiment demonstrated that the 0.048% Alkalibacterium in the original material was augmented to 23.6% of the microbiological community within 5 days. This means that using the appropriate material and performing appropriate pretreatment and adjustment of fermentation conditions are important to increase the abundance of the taxa that reduce indigo.


Indigo-reduction Alkalibacterium Amphibacillus Polygonibacillus Bacillus 



This study was supported by the Japan Society for the Promotion of Science with Grant-in-Aid for Scientific Research (16K07684).

Compliance with ethical standards

Conflict of interest

The authors declare that there are no competing interests.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Zhihao Tu
    • 1
    • 2
  • Helena de Fátima Silva Lopes
    • 1
    • 2
  • Kikue Hirota
    • 1
  • Isao Yumoto
    • 1
    • 2
    Email author
  1. 1.Bioproduction Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)SapporoJapan
  2. 2.Laboratory of Environmental Microbiology, Graduate School of AgricultureHokkaido UniversitySapporoJapan

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