070-oral_microbiome

Oral microbiome dataset

Description

The collection of buccal swabs for human genetic sequencing presents an advantageous opportunity to simultaneously explore the oral microbiome using the non-human DNA sequences found. This metagenomic analysis provides insight into the diverse microbial community within the buccal mucosa. The obtained data not only enriches our genetic understanding but also broadens our knowledge on the microorganisms residing in the oral cavity, their interactions, and potential implications for oral and systemic health. This dual analysis underscores the utility of buccal swabs as a resourceful means for both genetic and microbial investigations.

Introduction

The primary intent behind collecting buccal swabs was to explore human genetics. Concurrently, it yielded metagenomic data, unveiling the microbial community within the oral cavity.

This data illuminates the diversity and interactions of microorganisms, specifically in the buccal mucosa. Delving into the oral microbiome presents an opportunity to understand its linkage to health conditions. For instance, an imbalanced oral microbiome can lead to periodontal disease, associated with an increased risk of cardiovascular diseases. Moreover, alterations in the oral microbiome have been observed in oral cancers, hinting at its potential role in their onset and progression​ The oral microbiome: diversity, biogeography and human health​.

Through this data, the exploration into possible connections between oral microbial composition and various health conditions is facilitated, marking a step towards understanding the broader health implications.

Measurement protocol

This dataset is a derivative of the human genome dataset (that has been collected via buccal swabs) - ergo the measurement protocol can be found at the Human genetics dataset.

Data availability

The information is stored in multiple parquet files:

  • oral_microbiome.parquet: Sequencing and QC statistics.
  • metaphlan_*: 8 tables with MetaPhlAn 4 vJan21 relative abundances, separated by taxonomic levels.
  • humann_aggregated_*: arrow files of either gene level abundances or pathway level abundances+coverage from HumanN 3.6 given MetaPhlAn 4 vJan21 outputs

graph LR;
    A(Human Aligned<br>BAM) --> |Filter and convert| B(Non Human Reads<br>FASTQ)
    B --> |Trimmomatic| C(Clean FASTQ File)
    C --> |MetaPhlAn| D(MetaPhlAn 4 /<br>vJan21 Abundances<br>Tabular)
    C --> |HumanN| E(HumanN 3.6 genes abundance)
    C --> |HumanN| F(HumanN 3.6 Pathways abundance)
    C --> |HumanN| G(HumanN 3.6 Pathways coverage)
    C --> |FastQC| H(Reads QC report - after)
    B ---> |FastQC| I(Reads QC report - before)

Data dictionary

pl.dict
folder_id feature_set field_type field_string description_string relative_location data_coding stability units sampling_rate bulk_file_extension bulk_dictionary strata sexed array debut completed transformation list_of_tags pandas_dtype
tabular_field_name
collection_date NaN oral_microbiome Datetime Sampled date Date sample was given oral_microbiome/oral_microbiome.parquet NaN Complete Time NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome datetime64[ns]
metaphlan_abundance_kingdom_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (kingdom) Aggregated abundance (MetaPhlAn 4) at the king... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_phylum_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (phylum) Aggregated abundance (MetaPhlAn 4) at the phyl... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_class_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (class) Aggregated abundance (MetaPhlAn 4) at the clas... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_order_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (order) Aggregated abundance (MetaPhlAn 4) at the orde... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_family_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (famiily) Aggregated abundance (MetaPhlAn 4) at the fami... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_genus_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (genus) Aggregated abundance (MetaPhlAn 4) at the genu... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_species_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (species) Aggregated abundance (MetaPhlAn 4) at the spec... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan_abundance_strain_parquet NaN metaphlan_aggregated Mapping table (group) MetaPhlAn 4 abundance (strain) Aggregated abundance (MetaPhlAn 4) at the stra... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
raw_fastq NaN raw_fastq Fastq file (individual) Raw FASTQ path (Post human removal) The original FASTQ file oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN fastq.gz NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
trimmed_fastq NaN trimmed_fastq Fastq file (individual) Post QC FASTQ path FASTQ file post Trimmomatic (removing adaptors... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN fastq.gz NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
fastqc_raw_html NaN fastqc Bulk file (individual) FASTQC HTML path Raw data FASTQC Output for Raw FASTQ - HTML oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN html NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
fastqc_raw_zip NaN fastqc Bulk file (individual) FASTQC zip path Raw data FASTQC Output for Raw FASTQ - Zip oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN zip NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
fastqc_trimmed_html NaN fastqc Bulk file (individual) FASTQC HTML path Trimmed data FASTQC Output for Post QC FASTQ - HTML oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN html NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
fastqc_trimmed_zip NaN fastqc Bulk file (individual) FASTQC zip path Trimmed data FASTQC Output for Post QC FASTQ - Zip oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN zip NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
metaphlan4_results_tsv NaN metaphlan Bulk file (individual) MetaPhlAn 4 abundance path MetaPhlAn4 relative abundances oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN tsv NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
raw_read_count NaN oral_microbiome Integer Raw reads count # Reads in the original bam file from gencove oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome int
non_human_read_count NaN oral_microbiome Integer Non-human reads count # Reads with no alignment to the human genome oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome int
trimmed_non_human_read_count NaN oral_microbiome Integer Post QC Non-human reads count # Non human Reads After QC oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome int
metaphlan4_aligned_read_count NaN oral_microbiome Integer Jan21 MetaPhlAn4 unique aligned reads count # Reads after QC aligned to bacteria genomes oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome int
gene_aligned_read_count NaN oral_microbiome Integer HumanN 3.6 diamond aligned unique read count # Reads after QC aligned to Uniref90 oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN NaN NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome int
humann_gene_families_tsv NaN humann Bulk file (individual) HumanN 3.6 - Gene families in original .tsv HumanN 3.6 output of Microbial reads protein a... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN tsv NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_gene_familites_gene_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Gene families, in gene only level... HumanN 3.6 output of Microbial reads protein a... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_gene_familites_microbe_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Gene families, microbiome level, ... HumanN 3.6 + MetaPhlAn 4 output of Microbial r... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_abundance_tsv NaN humann Bulk file (individual) HumanN 3.6 - Pathway abundance in original .tsv HumanN 3.6 output of Oral microbime metaboliti... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN tsv NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_abundance_pathway_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Pathway abundance, in gene only l... HumanN 3.6 output of Oral microbime metaboliti... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_abundance_microbe_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Pathway abundance, microbiome lev... HumanN 3.6 + MetaPhlAn 4 output of Oral microb... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_coverage_tsv NaN humann Bulk file (individual) HumanN 3.6 - Pathway coverage in original .tsv HumanN 3.6 output of Oral microbime metaboliti... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN tsv NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_coverage_pathway_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Pathway coverage, in gene only le... HumanN 3.6 output of Oral microbime metaboliti... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_pathway_coverage_microbe_level_parquet NaN humann Bulk file (individual) HumanN 3.6 - Pathway coverage, microbiome leve... HumanN 3.6 + MetaPhlAn 4 output of Oral microb... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN parquet NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_intermediate_files_tar NaN humann Bulk file (individual) HumanN 3.6 - Intermidiate files All of the HumanN 3.6 + MetaPhlAn 4 intermidia... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN tar.gz NaN Supporting Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_gene_familites_gene_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Gene families (gene le... Aggregated HumanN 3.6 output of Microbial read... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_gene_familites_microbiome_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Gene families (microbe... Aggregated HumanN 3.6 output of Microbial read... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_pathway_abundance_pathway_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Pathways abundances (p... Aggregated HumanN 3.6 output of Oral microbime... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_pathway_abundance_microbiome_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Pathways abundances (m... Aggregated HumanN 3.6 output of Oral microbime... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_pathway_coverage_pathway_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Pathways coverage (pat... Aggregated HumanN 3.6 output of Oral microbime... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string
humann_aggregated_pathway_coverage_microbiome_level_arrow NaN humann_aggregated Mapping table (group) Aggregated HumanN 3.6 - Pathways coverage (mic... Aggregated HumanN 3.6 output of Oral microbime... oral_microbiome/oral_microbiome.parquet NaN Complete NaN NaN arrow NaN Primary Both sexes Single NaN NaN NaN Oral Microbiome string

Plot histogram and ecdf for raw_read_count at baseline visit

from pheno_utils.basic_plots import hist_ecdf_plots

col = "raw_read_count"
df = pl[[col] + ["age", "sex", "collection_date"]].loc[:,:,"00_00_visit",0,:]

# plot histogram and ecdf
hist_ecdf_plots(df.dropna(subset=[col,"sex", "age"]), col, gender_col="sex")

# stats
display(df[col].describe().to_frame().T)

count mean std min 25% 50% 75% max
raw_read_count 8294.0 19529470.245479 7338498.393217 8805038.0 15039265.5 18221025.5 21923790.0 127497332.0