Additional file 1

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Feed composition:

27.97% corn
30% wheat
34.2% soybeans
4% soybean oil
0.94% calcium carbonate
1.8% dicalcium phosphate
0.17% methionine
0.4% salt
0.4% Prémix VHT791NE  (Techna France) containing several additives including oligo-elements, vitamins, etc

(INRAE, UE PEAT Centre Val de Loire, 37380 Nouzilly, France)

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Supplemental Primer/Adapter Sequences:


Primers used for the amplification of the region specific to Salmonella Enteritidis in the invA gene (102-bp, 5’-> 3’)

Sal-TM (probe) : [FAM]TGGCGGTGGGTTTTGTTGTCTTCT[TAM] , Tm = 62°C
Sal-F (Forward) : GCGTTCTGAACCTTTGGT, Tm = 57 °C
Sal- R (Reverse) : CGTTCGGGCAATTCGTTA, Tm = 53 °C



Primers used for the amplification of the V3-V4 hyper-variable region of the 16S rRNA gene

Primer 1F 
CTTTCCCTACACGACGCTCTTCCGATCT-TCCTACGGGAGGCAGCAGT (partial P5 adapter–primer)
Primer 1R 
GGAGTTCAGACGTGTGCTCTTCCGATCT-GGACTACCAGGGTATCTAATCCTGTT (partial P7 adapter–primer )
Primer 2F 
AATGATACGGCGACCACCGAGATCTACACT-CTTTCCCTACACGAC (partial P5 adapter–primer targeting primer 1F)
Primer 2R 
CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACT-GGAGTTCAGACGTGT (partial P7 adapter including index–primer targeting primer 1R)