For Clostridium difficile, you can either use NCBI Datasets command line application or the API. There is a Python library to parse the assembly descriptions and navigate the directory hierarchy that is described in a more detail here as well as Jupyter Notebooks that can be run on binder.
For the purpose of this post, I will use the command-line application. Assuming you have followed the instructions from this page and downloaded the application, follow the commands shown below:
## download assembly descriptors and make a list of assembly accessions
## NCBI Taxonomy ID for Clostridium difficiles is 1496
$ datasets assembly_descriptors tax_id 1496 -l 'ALL' | python -m json.tool > cdiff.json
## make a list of GCF accessions
$ grep -o 'GC[AF]_[0-9]*\.[0-9]*' cdiff.json | sort -u > cdiff.accs
## download data
$ datasets download assembly -i cdiff.accs
This will download a file ncbi_datasets.zip which will have the genome sequences for >3000 Clostridium species in FASTA format. There are additional options to restrict the list to RefSeq assemblies only in datasets assembly_descriptors command and additional file type options in the datasets download command that may be of interest to you. I suggest you take a quick look at the documentation and the help files.