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sounds more like the drain line is clogged between the shower and the main stack, and shares venting and drain with your kitchen sink. Have a plumber run a drain snake down from your kitchen drain (after the 'P' trap ) to clear the line. A covered over floor drain should have no effect on the back-up.
The smell is sewer gas coming back in the house from the sewer or septic tank ether from a dried out water trap in a floor or fixture drain, or from the roof vent, or a hole or separation in pipe or fitting. Like wax ring under toilet. First pore water down every drain to fill any trap that might have gone dry, then flush toilet or run washer or drain bath tub.This will displace gas in pipe and will cause the smell to increases if there is no smell then the problem is fixed if not check roof vent it may need a charcoal filter on top, There is no water trap on air vent on roof and is an open hole to the sewer or septic, The heating system in the winter or AC in summer will draw the gas inside from the vent.If it is the vent you should be able to smell it from outside. If all tests fails You will need to have a smoke test done. A smoker is set up outside and the line is filled with smoke and will show where gas is coming from. Also it might be a good ideal to check all gas fittings in case it is a gas leak.
This is likely "sewer gas" and can cause headaches, dizziness, etc. if you remain exposed to it for a prolonged period of time. This originates mostly in the drain openings of fixtures that are seldom used - such as sinks and showers of basements, guest rooms, etc.
When these fixtures do not get used regularly, the relatively small amount of water that is designed to always be present in the "trap" portion of the drain pipe eventually evaporates. This trapped water prevents the the gasses in the sewer / septic system from passing through the trap. Without it, these gasses will rise through the pipes connected to the sewer / septic system and exit into your living space via the drain opening in the floor drain, shower, tub, sink and even toilet if left unused long enough.
It is usually resolved very easily by slowly pouring about a 1/2 gallon of water down the drain. The water now isolates the drain opening from the sewer / septic system and effectively stops odors from escaping. If you find that this is happening regularly (often from floor drains in dry basements) you should slowly pour water 1/2 gallon of water into the drain, and then add 2 to 3 ounces of cooking oil. The oil is lighter than water and will sit on top of the water surface. Oil does not evaporate and blocks the water from evaporating through it. Evaporation of the water in the trap will take place from the sewer / septic side of the trap, but it occurs at a much slower rate.
After filling the traps with water or water & oil, just ventilate and you're done!
Hydrogen sulfide gas. Try pouring a quart (liter) of distilled white vinegar mixed with a quart (liter) of water down the drain. Let it stand for half an hour, then follow it down with several gallons of water.
If that doesn't clear it up, you may not have a trap - that's a health hazard, and you'll need to have one installed.
Suppose you plugged the drain of the sink and filled the basin with water, then removed the plug. I must think that only after the basin empties you would get the sewer smell, and the smell would persist until you slowly ran some more water. If you try this, and this is the result, then the problem is that the sewer vent (that is supposed to prevent the water in the trap under the sink from being sucked down the drain) is not working right. If this is a new problem then you may be able to clear what is probably a blocked vent pipe. If this bathroom has always had this problem, then you have a poorly designed or executed vent pipe setup that you can only fix it with some surgery to your plumbing. However, to clean the vent you can try pouring a good bit of drain cleaner down the vent pipe on the roof, followed by water. But because there may be several vent pipes sharing the same vent stack out the roof, the drain cleaner may not get to your blockage and may simply go down a different path. Good luck.
Sounds like you have an intermittently blocked vent pipe (the one that goes out through your roof). If there is gas pressure in the downstream sewer line and it can't get up through the vent, it could bubble up through your toilet or sinks. I would get up on the roof with a few jugs of powerful drain cleaner and dump them into your vents. You might also run a few dozen gallons of water down those vents after the drain cleaner has had time to work. Good luck!
You will need to remove the cable operator assembly first. Under the sink, unscrew (turn it counterclockwise) the operator with your hand. Then remove the butterly-shaped retainer and use a needle nose pliers to remove the cam assembly...don't get too rough. Pay attention to which way they both fit.
Once the cam is removed, you can remove the pop-up stopper and proceed as required to clean the drain. Re-assemble in reverse order. Do not overtighten the cable operator.