I have mounted 3 Gateway devices (Rak7248 868 MHz) with 5.8 dBi high-gain antennas (mounted on the roof at the same level as the building) in different locations in a rural area. The purpose is to collect temperature values from industrial poultry houses, which are sealed with sandwich panels.
The main problem is that the RSSI values are lower than -100, but the SNR values range between 5 and 9. What could be the reason for the low RSSI, and how can I improve it?
Those are reasonable values for a LoRaWAN system! Are there any signs of missing messages? If not dont worry about it 
If you see RSSI dropping below -115-118 range then more marginal depending on SF used. Without much more detail wrt distance, SF values, built environment etc. not much more we can comment on. Generally however if you see values in the range -65 → -115 as reported at the GW you are good to go. Remember also if you have multiple GW’s only one needs a good signal for the message to get through to the NS…more obviously add redundance/resiliance to your deployment and is to be commended…
Construction/materials info? - Forum is largely RF/LoRaWAN/Electronics/Systems types vs poultry farmers so not widely known in this context? 
Perhaps obvious: make sure that the antennas are all pointing in the same direction (up). The gain of high-gain antennas is in the sideways direction, like a donut on a stick. Put the antennas in a high place, clear of obstructions.
The construction is sandwich panel(5-6 cm foam between metal plate) as you can see from the image, the farms looks like this.
DR is 0 and SF12. Some devices never connects the gateways some messages are lost.
There is only one gateway each a farm but there are 3 different farm on different cities and have same problem on all.
LoRa Alliance requires network operators to restrict the habitual use of SF11 or 12.
One gateway to cover all those faraday cages is rather ambitious bordering on never going to work and that it is clearly a commercial farm, not really a TTN community application.
So perhaps @rish1 can advise on a more suitable setup for your backend.