diff --git a/humann2/search/nucleotide.py b/humann2/search/nucleotide.py
index 552a523c..9ea46823 100644
--- a/humann2/search/nucleotide.py
+++ b/humann2/search/nucleotide.py
@@ -90,6 +90,10 @@ def index(custom_database):
 
     args=["-f",custom_database,index_name]
 
+    #add threads
+    if config.threads > 1:
+        args+=["--threads",config.threads]
+    
     outfiles=[index_name + ext for ext in config.bowtie2_index_ext_list] 
 
     # if custom_database is large (>4G) then use the --large-index flag