Hi. There is no way on earth you would see bacteria, or shadows of bacteria with the naked eye. If you're unsure then get checked, but trust me, you didn't 'see' bacteria
So first, bacteria that causes infections are microscopic, meaning you can't see them with your naked eye. You'd need a microscope.
Urine can be dark if you aren't hydrated.
However, sediment can appear in your urine. This can be skin tissue, blood cells, crystals and protein. https://www.healthline.com/health/sediment-in-urine#1
That can be normal, or if it's new, or there's a lot, it can be a sign of infection. It could be a UTI, kidney stones, dehydration, an STD/STI, diabetes, and a host of other things.
If you're concerned, see your doctor. Since you don't have other symptoms, you might try drinking extra water, and see if that helps over the next day or two. If it doesn't, see your doctor then.
If your urine is very dark and you are seeing particulate matter in the toilet bowl this could be a myriad of things, and not necessarily an STI
At 4 Days, the likelihood of any STI making an appearance is low... it would normally take about a week to become symptomatic for Chlamydia/Gonorrhoea/NSU
What you are probably experiencing is Dehydration ( Dark Pee is normally a giveaway). The particulates could also be proteins more evident from the dehydration ( foamy patches in the water).
Questions you need to eliminate first.
1. Is there any pain/burning of the urethra/tip of the penis
2. If so, is there any noticeable discharge first thing in the morning ( milking the penis gently or looking in your underwear is a way to be sure).
3. Is there testicular pain?
4. Do you have any itching/redness
For men, Chlamydia normally is quite a silent infection & its common to be asymptomatic (carrier but no symptoms).
Gonorrhoea on the other hand is pretty noticeable and you tend to feel it when you pee.
To allay any of your fears, if by 2 weeks you are not experiencing the above, then the likelihood you have contracted an STI is very very low..
However regular testing every 6 months (just like a dental check-up, is always recommended)