diff --git a/bakta/config.py b/bakta/config.py
index be07c5c4..75d05acc 100644
--- a/bakta/config.py
+++ b/bakta/config.py
@@ -148,6 +148,7 @@ def setup(args):
     global genus, species, strain, plasmid, taxon
     genus = args.genus
     if(genus is not None):
+        genus = genus.trim()
         if(genus == ''):
             log.error("Empty 'genus' parameter! genus=%s", genus)
             sys.exit(f"ERROR: empty 'genus' parameter!")
@@ -156,6 +157,7 @@ def setup(args):
     log.info('genus=%s', genus)
     species = args.species
     if(species is not None):
+        species = species.trim()
         if(species == ''):
             log.error("Empty 'species' parameter! species=%s", species)
             sys.exit(f"ERROR: empty 'species' parameter!")
@@ -164,6 +166,7 @@ def setup(args):
     log.info('species=%s', species)
     strain = args.strain
     if(strain is not None):
+        strain = strain.trim()
         if(strain == ''):
             log.error("Empty 'strain' parameter! strain=%s", species)
             sys.exit(f"ERROR: empty 'strain' parameter!")