Abstract
While research on the sourdough microbiome has primarily focused on lactic acid bacteria (LAB) and yeast, recent studies have found that acetic acid bacteria (AAB) are also common members. However, the ecology, genomic diversity, and functional contributions of AAB in sourdough remain unknown. To address this gap, we sequenced 29 AAB genomes, including three that represent putatively novel species, from a collection of over 500 sourdough starters surveyed globally from community scientists. We found variations in metabolic traits related to carbohydrate utilization, nitrogen metabolism, and alcohol production, as well as in genes related to mobile elements and defense mechanisms. Sourdough AAB genomes did not cluster when compared to AAB isolated from other environments, although a subset of gene functions was enriched in sourdough isolates. The lack of a sourdough-specificgenomic cluster may reflectthe nomadic lifestyle of AAB. To assess the consequences of AAB on the emergent function of sourdough starter microbiomes, we constructed synthetic starter microbiomes, varying only the AAB strain included. All AAB strains increased the acidificationof synthetic sourdough starters relative to yeast and LAB by 18.5% on average. Differentstrains of AAB had distinct effectson the profileof synthetic starter volatiles. Taken together, our results begin to definethe ways in which AAB shape emergent properties of sourdough and suggest that differencesin gene content resulting from intraspecies diversificationcan have community-wide consequences on emergent function. IMPORTANCE This study is a comprehensive genomic and ecological survey of acetic acid bacteria (AAB) isolated from sourdough starters. By combining comparative genomics with manipulative experiments using synthetic microbiomes, we demonstrate that even strains with >97% average nucleotide identity can shift important microbiome functions, underscoring the importance of species and strain diversity in microbial systems. We also demonstrate the utility of sourdough starters as a model system to understand the consequences of genomic diversity at the strain and species level on multispecies communities. These results are also relevant to industrial and home-bakers as we uncover the importance of AAB in shaping properties of sourdough starters that have direct impacts on sensory notes and the quality of sourdough bread.
Original language | English (US) |
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Article number | e00506-24 |
Journal | mSystems |
Volume | 9 |
Issue number | 10 |
DOIs | |
State | Published - Oct 2024 |
Keywords
- acetic acid bacteria
- comparative genomics
- microbiome
- sourdough starter
- strain diversity
- synthetic communities
ASJC Scopus subject areas
- Microbiology
- Physiology
- Biochemistry
- Ecology, Evolution, Behavior and Systematics
- Modeling and Simulation
- Molecular Biology
- Genetics
- Computer Science Applications