How to split multifasta based on partial fasta header
The SeqBuddy --pull_records command can grab sequences based on a regular expression against record IDs and/or metadata. Given your example:

$: seqbuddy.py sequences.fa --pull_records "Clostridium botulinum.*BKT028387" full &gt; Clostridium_botulinum_BKT028387.fas
$: seqbuddy.py sequences.fa --pull_records "Peptoanaerobacter stomatis.*OBRC8" full &gt; Peptoanaerobacter_stomatis_OBRC8.fas