gistfile1.py

# maps names to OTU numbers
name_to_OTU = {
    'name_1': 23,
    'RIO12.3_44008': 93,
}

# contrived data to represent what you emailed
# this represents one sample's counts,
# e.g. the "('MID - OLD12.5',..." line
per_sample_counts = Counter({
    'name_1': 1,
    'RIO12.3_44008': 3,
})

# Print out the counts with updated names
for name, count in per_sample_counts:
    print 'OTU({})'.format(name_to_OTU[name]), count
    
# Or, update the counts without printing
updated = {}
for name, count in per_sample_counts:
    x = 'OTU({})'.format(name_to_OUT[name])
    updated[x] = count