Autochthonous fungi in addition to starter cultures are central components of the microbial ecosystem in raw fermented sausages

Raw meat represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. During raw meat sausage production heat is not applied to render the final product microbiologically safe. Instead, starter cultures are applied to improve product stability and safety as well as flavor characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not been explored so far. Here we evaluate the microbiological status of four different raw meat sausages using high-throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to Lactobacillus sakei and the genera Acinetobacter, Pseudomonas, and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.

生肉为微生物增殖提供了营养丰富的独特生态位，使其极易受到微生物腐败的侵袭。在生鲜肉香肠的生产过程中，并不会通过加热手段使最终产品达到微生物学安全标准，取而代之的是，人们通过添加发酵剂（starter cultures）来提升产品的稳定性、安全性与风味特性。然而，发酵剂在整个发酵过程中对微生物群落组装与演替的影响，目前仍知之甚少，尤其是其对真菌群落的影响，至今尚未得到研究。本研究采用高通量16S rRNA基因与ITS2基因测序技术，对四款不同的生鲜肉香肠的微生物学状态进行了评估。本研究的目标为解析发酵过程中微生物群落组成的时序变化，并筛选出在微生物群落中发挥关键作用的潜在关键物种（keystone species）。本研究结果显示，隶属于汉逊德巴利酵母（Debaryomyces hansenii）与链格孢霉（Alternaria alternata）的真菌，在发酵过程中的微生物群落动态中扮演着核心角色。此外，与清酒乳杆菌（Lactobacillus sakei）、不动杆菌属（Acinetobacter）、假单胞菌属（Pseudomonas）以及嗜冷杆菌属（Psychrobacter）相关的细菌，是生鲜发酵香肠微生物生态系统的核心组成部分。阐明这些微生物的确切功能与相互作用机制，有望直接提升发酵食品的品质与安全性。