Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
Agroscope, Liebefeld, Switzerland.
Nat Commun. 2024 Oct 5;15(1):8642. doi: 10.1038/s41467-024-52687-7.
Domestication - the artificial selection of wild species to obtain variants with traits of human interest - was integral to the rise of complex societies. The oversupply of food was probably associated with the formalization of food preservation strategies through microbial fermentation. While considerable literature exists on the antiquity of fermented food, only few eukaryotic microbes have been studied so far for signs of domestication, less is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and maintained stable phenotypic traits. Molecular clock dating further suggests that the evolutionary origin of the bacteria approximately coincided with the first archaeological records of cheese making. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.
驯化——通过人工选择野生物种获得具有人类利益特征的变种——是复杂社会兴起的组成部分。食物的供应过剩可能与通过微生物发酵正式化食物保存策略有关。尽管关于发酵食品的古老性有大量文献，但迄今为止，只有少数真核微生物因驯化迹象而被研究，而细菌则知之甚少。在这里，我们通过对来自历史和现代瑞士传统奶酪发酵剂的 100 多个群落样本和 100 多个分离株进行特征分析，测试了奶酪发酵剂是否具有驯化的典型特征。我们发现，奶酪发酵剂在种和株水平上的遗传多样性都很低，并且保持稳定的表型特征。分子钟年代测定进一步表明，细菌的进化起源与奶酪制作的第一个考古记录大致相符。最后，我们发现了与生态位宽度减小有关的转座子插入导致的持续基因组退化和假基因化的证据。未来的工作将记录这些特征在不同发酵食品系统和地理区域的普遍性，这将是揭示人类与发酵食品微生物共同历史的关键。
