This should do what you are looking to do.

#!/usr/bin/perl

use strict;
use warnings;
use DBI;

sub dbConnect{
    my ($database, $username, $password, $hostname) = @_;
    my $db = DBI->connect("DBI:SQLite:$database:$hostname", $username,
    $password) || die "Cannot connect to host database.".$DBI::errstr;
    return $db;
}

sub dbDisconnect{
    my ($db) = @_;
    $db->disconnect;
}

sub dbINSERT{
    my $table  = shift;
    my $set    = shift;
    my @values = @_;

    my($database) = "myDB";
    my($username) = "username";
    my($password) = "password";
    my($hostname) = "myHost.com";

    my $db = dbConnect($database, $username, $password, $hostname);

    my $vals = join',', map { $db->quote($_) } @values;
    my $query = qq|INSERT into $table ($set) VALUES ($vals)|;
    print "$query\n";

    $query = $db->prepare($query); #LINE 31
    $query->execute; #LINE 40
    $query->finish;
    dbDisconnect($db);
}

sub dbUPDATE{
# Do updates here
}

sub dbDELETE{
# Do deletes here
}

dbINSERT('ORGANISM', 'ORG_NAME, GI, NC', "11111111", "some bacteria", 
+"NC_000000");
[download]

Though, I would move the db connection out of the insert/delete/update subs and just do something like this

#!/usr/bin/perl

use strict;
use warnings;
use DBI;

sub dbConnect{
    my ($database, $username, $password, $hostname) = @_;
    my $db = DBI->connect("DBI:SQLite:$database:$hostname", $username,
    $password) || die "Cannot connect to host database.".$DBI::errstr;
    return $db;
}

sub dbINSERT{
    my $db     = shift;
    my $table  = shift;
    my $set    = shift;
    my @values = @_;

    my $vals = join',', map { $db->quote($_) } @values;
    my $query = qq|INSERT into $table ($set) VALUES ($vals)|;
    print "$query\n";

    $query = $db->prepare($query); #LINE 31
    return ( $query->execute ) : 0 : 1;
    
}

sub dbUPDATE{
# Do updates here
}

sub dbDELETE{
# Do deletes here
}

my $db = dbConnect("myDB", "username", "password", "myHost.com");
my $status = ( dbINSERT($db, 'ORGANISM', 'ORG_NAME, GI, NC', "11111111
+", "some bacteria", "NC_000000") == 0 ) ? 0 : 1;

END { $db->disconnect }
[download]

Its untested, but should work fine for you.

Update added return code from insert and removed disconnect sub. After re-reading your original post - you may wish to re-add the disconnect sub ( and remove the END block ) as this looks to be part of a larger program