I have two bacterial srains - one is wild type and the other has one gene deleted. In my experiment, I calculate some phenotype for both of these strains. I repeat this experiment 5 times. Now I want to see if there is a difference in this phenotype between the two strains, so I perform a t-test (assuming the data is normally distributed for now). My question is - should I perform a paired t-test or unpaired? I am a bit confused about it since I feel I have some rationale for doing it either ways - 

Why I think its **paired** : in every replicate, I compare the same two strains and I repeat this 5 times

Why I think its **unpaired** : Its not like I am subjecting the same strain to two different conditions (which often happens in paired tests). Rather, I have two different strains being subjected to the same condition.

Any help would be appreciated!
Assuming your use of the t-test is valid, you should use the unpaired version.  Your question is getting at the difference between biological and technical replicates, which is different than paired vs. unpaired measurements.  

A paired measurement would be taken across conditions or time (the groups being compared), so for example measuring 5 individuals at two time points and testing the distributions of time1 vs. time2.  This is different than what you're doing, which is doing technical replication within each group but comparing those to independent observations in another group (5 replicates in group1 versus 5 replicates in group2).

I think you reasoned through this already in your statement "I think its unpaired."

You would, however, expect there to be less variation under your technically replicated experimental design than if you had used 5 biological replicates.  You might mention this in your limitations.