## 3 Results
### Ecosystem Monitoring through Metabarcoding  
A total of 3,977,403 raw reads were obtained after the Illumina sequencing. A total of 1,746,144 reads passed through the FROGS pipeline for an average of 63,270 reads per sample. The number of sequences per sample ranged from 35,626 to 114,681 and the number of reads was normalized via rarefaction upon the lowest number of sequences per sample. The SG, MAP CSS and VP CSS ecosystem compositions over time are shown in Figure 2. Regardless of the product and the three sampling dates, the microbial diversity was quite low. The richness in terms of the number of OTU per sample ranged between 27 and 56. The evenness of the OTU abundance distribution, calculated with the Shannon index, was between 1.1 and 1.5 for almost all samples. The values that were calculated for these two indexes showed an ecosystem that was mainly composed of a small number of highly dominant OTU that were affiliated with nine main bacterial genera: _Photobacterium_, _Lactobacillus_, _Lactococcus_, _Serratia/Yersinia_, _Brochothorax_, _Carnobacterium_, _Vagococcus_, _Escherichia/Shigella_ and _Cobenia_, with a representative number of sequences that was superior to 0.5% of the total reads. At the beginning of storage, the ecosystems were highly similar between the products, as the samples were closely clustered together on the MDS ordination plot shown in Figure 3. _Photobacterium_, _Lactobacillus_ and _Lactococcus_ were the dominant genera, accounting for about 95% of the microbial composition, with 50, 29-34 and 8-11%, respectively (Figure 2). However, some differences were observed between the products. The SG initial microbial diversity was slightly higher than in the smoked products and remained higher until the end of storage. Indeed, twenty OTU that were specific to the gravlax were found, representing the fifteen following bacterial or archaea genera: _Halorubrun_, _Shewanella_, _Bacillus_, _Weissella_, _Hafnia_/_Obesumbacterium_, _Acinetobacter_, _Brachybacterium_, _Duganella_, _Terribacillus_, _Spelaeicoccus_, _Halohasta_, _Staphylococcus_, _Conomonas_, _Splingobacterium_ and _Brevibacterium_. _Staphylococcus_ and _Actinobacter_ were the only shared genera between the three products (genera represented by several OTU). Genera such as _Halohasta_, _Staphylococcus_ and _Conamomas_, which were specific to the SG microbial ecosystem as earlier reported were detected until 28 days of storage. Conversely, a differential abundance analysis using the DESeq2 R package revealed no statistical difference between the MAP and VP CSS microbial compositions at day 0. Figure 3: Multidimensional scaling representation of the SG, MAP and VP CSS samples microbial composition based on Bray–Curtis distances. The sample nomenclature is structured as follows: (1) the type of product (SG, MAP or VP) and (2) the replicate number. Figure 2: SG, MAP and VP CSS ecosystem relative compositions and \(\alpha\)-diversities. Only OTU with a number of sequences representing more than 0.1% of the total number of reads appear in the legend and are ordered from the most abundant to the least abundant. The sample nomenclature is structured as follows: (1) sampling date, (2) type of sample (MAP, VP or SG) and (3) replicate number. For each sampling date, the experiments were done in triplicates. After 14 days of storage, the gravlax microbial ecosystem was the only one that diverged from the first sampling date, with a diversity that decreased significantly over time (ANOVA on the richness index, \(p\)-value = 0.045). Except for the third biological replicate, the ecosystem composition was largely dominated by _Photobacterium_, whose relative abundance increased from 50 to 97.5% (Figure 2). In the third replicate, the microbial composition was more evenly distributed (highest Shannon index of 2.0) between seven genera: _Photobacterium_ (29.0%), _Brochothrix_ (19.6%), _Cobelia_ (14.4%), _Psychroacter_ (13.8%), _Serratia/Yersinia_ (11.9%), _Pseudomonas_ (5.6%) and _Lactococcus_ (1.7%).