BackOnlyBriefly surely your argument about what the man knew or did not know in relation to the room is trying to put the emphasis back on the man. The real emphasis is on what is true. It was true (that there were microorganisms) but he did not know it, it is true now, and we know it. The real issue is - it being true.
Being able to prove it is true or not does not make it true. I totally get where you are coming from but I think as humans we worry a lot about what we can prove when really the most important things in life are things we can't really always prove or not prove, just experience.
headinhands that's a very good question, how do we know it is the real deal. For me the fact that God took the initiative. He came down to earth to seek us out. Yes, before we get back into the old proof was Jesus real and all that circle, can I just say it how I see it and you can question as much as you like? 
Because I know everything I say as a Christian will be contentious or will be in tension for an atheist or agnostic so I value your even being interested in it.
For me it is the fact God looks on the heart, and is concerned for the poor, the broken hearted etc (it says it in the Bible but I also feel it in my spirit). The church is full of ritual and I think people like ritual and maybe that is why God allows a lot of it in there but at his heart (and I say his meaning his or hers rather than its) I believe God just wants to know us and love us, and to be known and loved by us. Which is why the imagery of the Bible is of a father and a mother. There are also images of a king, Prince of Peace etc and these are all facets of God. God is matchless, someone beyond our comprehension, and yet also knowable! How weird and wonderful is that!
I am petty and angry at times and if I had made God in my own image I would have made him like me, yet he is not like me, he is utterly bigger and better - yet he draws me in and makes me part of what he is doing in the world.
I believe God puts things on my heart and that is why I know he has a compassion for the poor. I could go on and on but I won?t now. So for me The Lord (Father, Son and Holy Spirit) is the real deal. Thank you for asking, headinhands.