NCBI BioSample Submission Strategy for PJI and Nasal Microbiota Study

Which database for genome and epidome data

For NCBI submissions, whole genome sequencing (WGS) assemblies of your S. epidermidis PJI isolates should go to GenBank under the Genome database.
The raw sequencing reads for these isolates should go to the Sequence Read Archive (SRA).

Your epidome data (species-specific amplicon sequencing) is also acceptable for SRA submission.
When you upload, choose Library strategy = AMPLICON, and clearly specify the target gene in your metadata.
Both types of datasets should be linked under a single BioProject and corresponding BioSamples.

Do I need BioSamples for each patient and sample type?

Yes — for NCBI submissions, you must create a separate BioSample for each biological sample type you sequenced, even if they come from the same patient.

Key points:

• BioProject: One per overall study (e.g., "Population structure and genomic features of Staphylococcus epidermidis from prosthetic joint infection and nasal microbiota").
• BioSamples: One per distinct biological sample.
• Nasal swab (metagenomics) and PJI isolate from the same patient are two BioSamples.
• Metagenomics and epidome (amplicon) from the same nasal swab can share a BioSample if they are truly from the same physical specimen.
• Why separate?
• Different source material → different metadata (host body site, isolation method, etc.).
• Makes downstream searches, linking, and data reuse much cleaner.
• Data linking:
• Each BioSample can link to multiple datasets: SRA (raw reads), GenBank (assembly), amplicon reads.
• All are tied together under one BioProject.

If needed, a custom NCBI BioSample metadata spreadsheet can be prepared so that nose WGS, nose epidome, and PJI isolate genomes are all neatly linked in one BioProject.

BioSample Submission Guidance

For each patient, you should create separate BioSample records for: - WGS of the nasal metagenomics sample - WGS of the PJI isolates - Amplicon sequencing (Epidome) of the nasal sample

This is because each dataset type (different source material, sequencing method, and library strategy) represents a distinct biological sample in NCBI's schema.
Even if they come from the same patient, they are technically different samples with separate metadata and accession numbers.

Example: - Patient_1_nose_WGS - Patient_1_nose_epidome - Patient_1_PJI_WGS

Database Choice for Submission

• Whole genome sequencing (Illumina + ONT):
  Submit assemblies to GenBank or RefSeq under your BioProject.

• Amplicon sequencing (Epidome method):
  Submit raw reads to SRA under the same BioProject and BioSample, but with library_strategy = AMPLICON.
  You can also link these datasets to relevant BioSample records for nasal microbiome analysis.

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