MongoDB performing slow read-queries under load - mongodb

Question

I'm running a MongoDB on my VPS. Two instances of the same python bot are constantly reading and writing documents. Essentially, they continously repeat the following steps infinitely:
Get a document using find_and_modify() (no i cannot use find() here)
process data fetched in step 1 (takes 10-60 seconds)
update document using find_and_modify() (no i cannot use update() here)
This worked flawlessly until I deployed a REST API web server to view the results in the browser etc. Now whenever the bot instances and the web server are running at the same time, the bots slow down by minutes and a request to my web server takes 2 minutes. When either the bots or the web server are/is running, they both query the database within milliseconds.
Before I think about upgrading my VPS' RAM and CPU, I would like to understand what exactly causes this. I assume the problem lies in the database being overwhelmed with the amount of requests from the 3 clients (2 bot instances, 1 web server).
I found the command currentOp(), but I'm having issues understanding its return.
> db.currentOp({"secs_running": {"$gte": 5}})
{
"inprog" : [
{
"type" : "op",
"host" : "localhost:27017",
"desc" : "conn1555",
"connectionId" : 1555,
"client" : "127.0.0.1:37750",
"clientMetadata" : {
"driver" : {
"name" : "PyMongo",
"version" : "3.11.3"
},
"os" : {
"type" : "Linux",
"name" : "Linux",
"architecture" : "x86_64",
"version" : "5.4.0-71-generic"
},
"platform" : "CPython 3.8.5.final.0"
},
"active" : true,
"currentOpTime" : "2021-04-27T13:37:56.261+00:00",
"opid" : 3151480,
"lsid" : {
"id" : UUID("71d36512-c5a3-4fe9-b3f9-31fd23e86413"),
"uid" : BinData(0,"47DEQpj8HBSa+/TImW+5JCeuQeRkm5NMpJWZG3hSuFU=")
},
"secs_running" : NumberLong(123),
"microsecs_running" : NumberLong(123430156),
"op" : "command",
"ns" : "nxmain.websites",
"command" : {
"aggregate" : "websites",
"pipeline" : [
{
"$match" : {
}
},
{
"$group" : {
"_id" : 1,
"n" : {
"$sum" : 1
}
}
}
],
"cursor" : {
},
"lsid" : {
"id" : UUID("71d36512-c5a3-4fe9-b3f9-31fd23e86413")
},
"$db" : "nxmain",
"$readPreference" : {
"mode" : "primaryPreferred"
}
},
"planSummary" : "COLLSCAN",
"numYields" : 934,
"locks" : {
"ReplicationStateTransition" : "w",
"Global" : "r",
"Database" : "r",
"Collection" : "r"
},
"waitingForLock" : false,
"lockStats" : {
"ReplicationStateTransition" : {
"acquireCount" : {
"w" : NumberLong(936)
}
},
"Global" : {
"acquireCount" : {
"r" : NumberLong(936)
}
},
"Database" : {
"acquireCount" : {
"r" : NumberLong(936)
}
},
"Collection" : {
"acquireCount" : {
"r" : NumberLong(936)
}
},
"Mutex" : {
"acquireCount" : {
"r" : NumberLong(2)
}
}
},
"waitingForFlowControl" : false,
"flowControlStats" : {
}
},
{
"type" : "op",
"host" : "localhost:27017",
"desc" : "conn1535",
"connectionId" : 1535,
"client" : "127.0.0.1:36886",
"clientMetadata" : {
"driver" : {
"name" : "PyMongo",
"version" : "3.11.3"
},
"os" : {
"type" : "Linux",
"name" : "Linux",
"architecture" : "x86_64",
"version" : "5.4.0-71-generic"
},
"platform" : "CPython 3.8.5.final.0"
},
"active" : true,
"currentOpTime" : "2021-04-27T13:37:56.261+00:00",
"opid" : 3152992,
"secs_running" : NumberLong(7),
"microsecs_running" : NumberLong(7503765),
"op" : "command",
"ns" : "admin.$cmd",
"command" : {
"ismaster" : 1,
"topologyVersion" : {
"processId" : ObjectId("60845741af792cc59a636f20"),
"counter" : NumberLong(0)
},
"maxAwaitTimeMS" : 10000,
"$db" : "admin",
"$readPreference" : {
"mode" : "primary"
}
},
"numYields" : 0,
"waitingForLatch" : {
"timestamp" : ISODate("2021-04-27T13:37:48.858Z"),
"captureName" : "AnonymousLatch"
},
"locks" : {
},
"waitingForLock" : false,
"lockStats" : {
},
"waitingForFlowControl" : false,
"flowControlStats" : {
}
}
],
"ok" : 1
}
As you can see there are two operations in the pipeline. The one with secs_running: 123 is the web server, the other one is one of the bot instances, which takes about 10-20 seconds when the web server is running in parallel.
What could be the cause for my problem and how can I solve it? Thank you in advance.