Well, if you go by 2013 NIH funding levels for Microbiology (
http://www.brimr.org/NIH_Awards/2013/Microbiology_2013.xls), the list looks like this:
1 OREGON HEALTH & SCIENCE UNIVERSITY $23,258,618
2 HARVARD UNIVERSITY (MEDICAL SCHOOL) $22,589,861
3 UNIVERSITY OF WASHINGTON $21,438,417
4 UNIVERSITY OF PENNSYLVANIA $18,811,514
5 UNIVERSITY OF TEXAS MEDICAL BR GALVESTON $18,674,919
6 YALE UNIVERSITY $18,220,662
7 EMORY UNIVERSITY $14,414,302
8 UNIV OF NORTH CAROLINA CHAPEL HILL $14,115,266
9 ALBERT EINSTEIN COLLEGE OF MEDICINE $13,411,713
10 THOMAS JEFFERSON UNIVERSITY $13,029,821
11 UNIVERSITY OF MICHIGAN $12,921,972
12 DARTMOUTH COLLEGE $12,751,449
13 OHIO STATE UNIVERSITY $12,619,102
14 UNIVERSITY OF CALIFORNIA LOS ANGELES $12,615,318
15 UNIVERSITY OF CALIFORNIA SAN FRANCISCO $12,560,002
16 UNIVERSITY OF CALIFORNIA IRVINE $12,352,267
17 MOUNT SINAI SCHOOL OF MEDICINE $11,356,362
18 UNIVERSITY OF SOUTHERN CALIFORNIA $10,495,064
19 STANFORD UNIVERSITY $10,251,974
20 UNIVERSITY OF CALIFORNIA DAVIS $9,937,620
21 UNIVERSITY OF CONNECTICUT SCH OF MED/DNT $9,815,048
22 UNIVERSITY OF CHICAGO $9,774,908
23 UNIVERSITY OF MARYLAND BALTIMORE $8,940,262
24 WEILL MEDICAL COLL OF CORNELL UNIV $8,927,643
25 WASHINGTON UNIVERSITY $8,833,641
I might disagree with the order of some of these though. OHSU, for example, likely is at the top because of the funding it gets for the Oregon National Primate Center but not necessarily for R01's. Same thing for UTMB and the biocontainment center there.