Soak em in some hot water with borax and a touch of bleach... a teaspoon in a large pail you should not be able to smell it but it will be enough to kill the bacteria. Rinse well

You can just wash your Merrel shoes in the washing machine. To prevent odour you could also use this: http://www.mcnett.com/Rank-Away-Odor-Eliminator-for-Minimalist-Footwear-P412.aspx.

In Europe, and maybe also in the US a similar producht is available from HG: http://oc.hg.eu/products/show/id/6653/detergent_additive_for_dispelling_unpleasant_odours_in_sports_clothing

i soak my VFFs & Merrell Trails in a bucket of hot water with a couple of denture cleaner tablets. For my leather Merrell Tough Gloves, i spray them occasionally with http://www.2toms.com/stink-free. both work fairly well for me. i definitely have to soak my VFFs & Trails regularly. my wife will let me know when it's time!

I was my vibram 5 fingers and my vivobarefoots by hand. I will let them soak in a bucket of cold water for 10 mins with biokleen bac out mixed in and then will add biokleen laundry detergent (a small dollop and of course mix it in the water) and let that soak from half an hour to over night. I will do any scrubbing on the soles needed with a soft brush after soaking and then rinse really well in cold water and hang up to dry. Never had a problem with smells. Did this every couple of a weeks or if the 5 fingers got muddy or wet when I was outside in wetter weather.

I usually wear socks to help absorb that crud before it builds up. When it does build up, it's a bucket with a very generous dose of detergent, soak overnight. Rinse lots of times, if still grungy, repeat.

I mostly wear moccasins, and I've not harmed the leather doing this. I figure anything that can hold up to slush can be washed with soap. I'd worry about the washing machine agitation stretching the leather in a soft shoe.

I would recommend vinegar and water sprayed in every few days.