Table 2. Relative abundance and number of OTUs of selected bacterial taxa present in initial and either cold-stored or cold-stored N2-flushed raw milk (n = 3, standard deviation in parentheses).
The taxa listed below correspond to the most abundant bacterial groups in the initial raw-milk samples, together with taxa hosting human pathogens, dairy starters, dairy secondary cultures, milk spoilage bacteria and groups for which this study highlighted changes subsequent to the applied treatments (either cold storage at 6°C, or cold storage combined with N2 flushing). The complete list of bacterial taxa found in all samples is shown in S1 Table. Data of the 773138 reads of sequences with the corresponding 2448 OTUs are available under the accession numbers SRR2481188, SRR2481213, SRR2481233, SRR2481257, SRR2481271, SRR2481286, SRR2481304, SRR2481319, SRR2481331, SRR2481345, SRR2481360, SRR2481370, SRR2481383, SRR2481397 and SRR2481507.
| CONDITIONS | Initial raw milk | cold-stored | cold-stored+N2-flushed | cold-stored | cold-stored+N2-flushed | OTU no. | |
|---|---|---|---|---|---|---|---|
| Time | 0 day | 3 to 4 days | 3 to 4 days | 6 to 7 days | 6 to 7 days | ||
| reads = 134076 | reads = 155564 | reads = 156150 | reads = 170269 | reads = 157079 | |||
| Phylum | Genus | ||||||
| Actinobacteria | Brevibacterium | 0.010 (0.006) | 0.011 (0.006) | 0.012 (0.009) | 0.011 (0.005) | 0.010 (0.001) | 15 |
| Corynebacterium | 0.026 (0.001) | 0.018 (0.010) | 0.021 (0.013) | 0.011 (0.005) | 0.017 (0.005) | 46 | |
| Kocuria | 0.011 (0.011) | 0.014 (0.004) | 0.014 (0.005) | 0.009 (0.004) | 0.010 (0.004) | 16 | |
| Micrococcus | 0.005 (0.002) | 0.013 (0.009) | 0.009 (0.003) | 0.006 (0.002) | 0.009 (0.002) | 7 | |
| Propionibacterium | 0.004 (0.001) | 0.007 (0.004) | 0.004 (0.001) | 0.005 (0.005) | 0.006 (0.002) | 4 | |
| Bacteroidetes | Alistipes | 0.023 (0.009) | 0.004 (0.007) | 0.010 (0.015) | 0.000 (0.000) | 0.005 (0.006) | 45 |
| Bacteroidales_u a | 0.049 (0.003) | 0.012 (0.010) | 0.018 (0.023) | 0.002 (0.003) | 0.007 (0.003) | 75 | |
| Bacteroidetes_u | 0.098 (0.010) | 0.034 (0.032) | 0.049 (0.064) | 0.009 (0.008) | 0.013 (0.005) | 166 | |
| Chryseobacterium | 0.009 (0.002) | 0.016 (0.011) | 0.011 (0.007) | 0.014 (0.010) | 0.016 (0.008) | 14 | |
| Firmicutes | Bacillus | 0.001 (0.001) | 0.000 (0.000) | 0.002 (0.002) | 0.002 (0.003) | 0.002 (0.003) | 4 |
| Clostridiales_u | 0.059 (0.021) | 0.004 (0.007) | 0.018 (0.027) | 0.002 (0.003) | 0.006 (0.008) | 124 | |
| Clostridium (sum) b | 0.014 (0.005) | 0.009 (0.012) | 0.004 (0.006) | 0.000 (0.000) | 0.008 (0.006) | 17 | |
| Enterococcus | 0.005 (0.002) | 0.006 (0.002) | 0.009 (0.003) | 0.008 (0.003) | 0.014 (0.001) | 11 | |
| Jeotgalicoccus | 0.010 (0.009) | 0.000 (0.000) | 0.000 (0.000) | 0.000 (0.000) | 0.000 (0.000) | 14 | |
| Lachnospiraceae_u | 0.028 (0.005) | 0.001 (0.002) | 0.006 (0.006) | 0.000 (0.000) | 0.009 (0.008) | 55 | |
| Lactobacillus | 0.005 (0.002) | 0.000 (0.000) | 0.004 (0.004) | 0.000 (0.000) | 0.002 (0.003) | 10 | |
| Lactococcus | 0.004 (0.002) | 0.015 (0.009) | 0.004 (0.003) | 0.014 (0.013) | 0.007 (0.008) | 7 | |
| Leuconostoc | 0.003 (0.001) | 0.000 (0.000) | 0.005 (0.003) | 0.005 (0.004) | 0.007 (0.008) | 3 | |
| Oscillibacter | 0.008 (0.002) | 0.000 (0.000) | 0.003 (0.005) | 0.000 (0.000) | 0.000 (0.000) | 18 | |
| Ruminococcaceae_u | 0.050 (0.015) | 0.003 (0.003) | 0.022 (0.026) | 0.000 (0.000) | 0.005 (0.002) | 127 | |
| Staphylococcus | 0.013 (0.004) | 0.007 (0.009) | 0.014 (0.009) | 0.003 (0.003) | 0.014 (0.006) | 15 | |
| Streptococcus | 0.009 (0.005) | 0.001 (0.002) | 0.007 (0.007) | 0.000 (0.000) | 0.007 (0.004) | 14 | |
| Proteobacteria | Acinetobacter | 0.042 (0.011) | 0.124 (0.056) | 0.069 (0.010) | 0.128 (0.053) | 0.079 (0.026) | 111 |
| Campylobacter | 0.004 (0.004) | 0.002 (0.003) | 0.002 (0.004) | 0.000 (0.000) | 0.001 (0.002) | 6 | |
| Delftia | 0.002 (0.001) | 0.005 (0.001) | 0.007 (0.005) | 0.003 (0.003) | 0.007 (0.001) | 8 | |
| Enterobacteriaceae_u | 0.040 (0.048) | 0.091 (0.076) | 0.090 (0.088) | 0.121 (0.031) | 0.168 (0.092) | 163 | |
| Escherichia_Shigella | 0.001 (0.001) | 0.000 (0.000) | 0.000 (0.000) | 0.000 (0.000) | 0.000 (0.000) | 1 | |
| Hafnia | 0.002 (0.000) | 0.003 (0.002) | 0.003 (0.002) | 0.006 (0.002) | 0.013 (0.004) | 8 | |
| Pseudomonadales_u | 0.000 (0.001) | 0.048 (0.041) | 0.005 (0.001) | 0.026 (0.032) | 0.005 (0.005) | 32 | |
| Pseudomonas | 0.037 (0.010) | 0.297 (0.051) | 0.214 (0.148) | 0.401 (0.071) | 0.176 (0.110) | 257 | |
| Psychrobacter | 0.009 (0.004) | 0.009 (0.008) | 0.012 (0.007) | 0.005 (0.004) | 0.007 (0.004) | 18 | |
| Serratia | 0.006 (0.009) | 0.014 (0.013) | 0.009 (0.007) | 0.018 (0.004) | 0.027 (0.017) | 16 | |
| Yersinia | 0.005 (0.007) | 0.016 (0.015) | 0.013 (0.015) | 0.024 (0.014) | 0.025 (0.009) | 17 |
au, unclassified
bsum, sum of Clostridium sensu stricto groups (IV, XI, XIVa and XIVb)