This is more or less redundant after toastbread's response and quite possibly naive but I've done it now and it seems to do what the OP wanted:

use strict;
use warnings;

my $my_name="Acidovorax JS42";
my $db_name="Acidovorax sp. JS42";

my @names = split " ", $my_name;
my $numel = @names;  #number of words to match

my $count;
foreach (@names) {
  if ($db_name=~/^|\s\Q$_\E$|\s/) {
     $count++;  #count matches
  }
}

print "MATCH" if $count==$numel;  #report match if all words match
[download]

--->Updated to fix regex - thx JavaFan