Bacteria in the Quran Miracle
The Quran doesn't talk about bacteria at all 
1400 years ago nobody believed that there are organisms that are too small to be seen by the naked eye. Today we know this is false; bacteria is microscopic and spreads everywhere.
In 2016, a study by researchers at the University of Arizona set the germophobic world on fire with a report that said the average shoe sole is covered with 421,000 bacteria and that 90 percent of those bacteria transfer directly to a clean tile floor on first contact. A 2017 study on shoe bacteria by the University of Houston showed that more than 26 percent of shoes examined test positive for C. diff, a bacteria that causes a potentially deadly super diarrhea. That's more than triple the amount typically found in kitchens and bathrooms. Vice, How Gross Is it to Wear Your Shoes in the House?, 2018
Bacteria is microscopic and highly concentrated in shoes. Shoes transfer bacteria to clean tile floor on first contact. This was only known recently, however this was portrayed in the Quran 1400 years before it was discovered. God ordered Moses to take off his shoes.
[Quran 20:12] I am your Lord. Take off your shoes. You are in the sacred valley of Tuwa.
God ordered Moses to remove his shoes in order not to desecrate the place. Today we know why; shoes turned out to spread filthy bacteria.
How could an illiterate man who lived 1400 years ago have known that shoes can desecrate the place?
The miracle claim contains quote from an article called "How Gross Is it to Wear Your Shoes in the House?". The article itself debunks their claims:
Your shoes are covered in bacteria, viruses, germs, and parasites. But also, it doesn’t matter. Unless you live in a sterile laboratory, the rest of your home is too—and so are you.
So it doesn't help that Moses took of his shoes, because there are bacteria on his feet too.
The article does not promote taking off shoes. The article quotes an expert on infectious diseases Amesh Adalja saying:
“I mean, there’s lots of pathogenic material on your socks,” Adalja says. “Should you take those off too? And then there’s bacteria on the skin of your feet—what are you going to do, take your skin off? I really think this is a misguided attempt, and not understanding that the planet is dominated by microbial organisms. There’s no reason to oversterilize it.”
The verse says nothing about bacteria. It only says "remove your sandals". The reason for it could have been simply dirt.
Indeed, I am your Lord, so remove your sandals. Indeed, you are in the sacred valley of Tuwa.
Tafsir ibn Kathir mentions this reason:
(So take off your shoes;) `Ali bin Abi Talib, Abu Dharr, Abu Ayyub and others of the Salaf said, "They (his sandals) were from the skin of a donkey that was not slaughtered. It has also been said that he was only commanded to remove his sandals due to respect for the blessed spot.
And the phrase "take off your shoes" was mentioned more than a thousand years before Muhammad, in the Old Testament:
“Do not come any closer,” God said. “Take off your sandals, for the place where you are standing is holy ground.”
So Muhammad said nothing new. And if this is a miracle, then it is a miracle of the Bible and not of the Quran, because the Bible said it first.