archAIons · MetaBiome Project · Oral · Public research data

SRR12522766

Metagenome or environmental sample from human oral metagenome

BioSample: SAMN15887565 · Study: PRJNA658726 · Body site: Subgingival

85Reported species

21Reported genera

Taxonomic abundance

Relative abundance is normalized among reported taxa. No reported taxa does not establish absence of organisms.

Species	Genus	Phylum	Abundance
Fusobacterium nucleatum	Fusobacterium	Fusobacteriota	9.27750%
Streptococcus mitis	Streptococcus	Bacillota	8.02732%
Veillonella parvula	Veillonella	Bacillota	7.48809%
Filifactor alocis	Filifactor	Bacillota	6.56942%
Streptococcus downei	Streptococcus	Bacillota	5.17913%
Fusobacterium perfoetens	Fusobacterium	Fusobacteriota	4.17271%
Selenomonas flueggei	Selenomonas	Bacillota	3.69434%
Eubacterium ramulus	Eubacterium	Bacillota	3.63338%
Porphyromonas gingivalis	Porphyromonas	Bacteroidota	3.52257%
Campylobacter gracilis	Campylobacter	Pseudomonadota	3.30016%
Streptococcus salivarius	Streptococcus	Bacillota	3.22987%
Filifactor villosus	Filifactor	Bacillota	3.00296%
Parvimonas micra	Parvimonas	Bacillota	2.54457%
Campylobacter hyointestinalis	Campylobacter	Pseudomonadota	1.96640%
Fusobacterium russii	Fusobacterium	Fusobacteriota	1.85042%
Streptococcus pneumoniae	Streptococcus	Bacillota	1.62251%
Campylobacter sputorum	Campylobacter	Pseudomonadota	1.16511%
Streptococcus intermedius	Streptococcus	Bacillota	1.15618%
Mogibacterium timidum	Mogibacterium	Bacillota	1.14978%
Peptostreptococcus anaerobius	Peptostreptococcus	Bacillota	1.07727%
Neisseria flavescens	Neisseria	Pseudomonadota	1.03264%
Selenomonas sputigena	Selenomonas	Bacillota	0.99264%
Veillonella infantium	Veillonella	Bacillota	0.96351%
Eubacterium limosum	Eubacterium	Bacillota	0.95175%
Campylobacter showae	Campylobacter	Pseudomonadota	0.94566%
Lachnoanaerobaculum saburreum	Lachnoanaerobaculum	Bacillota	0.86787%
Leptotrichia hongkongensis	Leptotrichia	Fusobacteriota	0.80762%
Selenomonas noxia	Selenomonas	Bacillota	0.77947%
Tannerella forsythia	Tannerella	Bacteroidota	0.71359%
Streptococcus cristatus	Streptococcus	Bacillota	0.66825%
Fusobacterium simiae	Fusobacterium	Fusobacteriota	0.65408%
Capnocytophaga canis	Capnocytophaga	Bacteroidota	0.64273%
Mogibacterium pumilum	Mogibacterium	Bacillota	0.61454%
Selenomonas dianae	Selenomonas	Bacillota	0.59870%
Streptococcus pyogenes	Streptococcus	Bacillota	0.58262%
Desulfobulbus oralis	Desulfobulbus	Thermodesulfobacteriota	0.55674%
Streptococcus oralis	Streptococcus	Bacillota	0.54587%
Streptococcus anginosus	Streptococcus	Bacillota	0.53368%
Prevotella ruminicola	Prevotella	Bacteroidota	0.52195%
Veillonella dispar	Veillonella	Bacillota	0.51846%
Aggregatibacter actinomycetemcomitans	Aggregatibacter	Pseudomonadota	0.51639%
Lachnoanaerobaculum orale	Lachnoanaerobaculum	Bacillota	0.50430%
Streptococcus gordonii	Streptococcus	Bacillota	0.47870%
Streptococcus sanguinis	Streptococcus	Bacillota	0.45091%
Selenomonas infelix	Selenomonas	Bacillota	0.44493%
Streptococcus infantis	Streptococcus	Bacillota	0.41770%
Aggregatibacter segnis	Aggregatibacter	Pseudomonadota	0.41333%
Fusobacterium periodonticum	Fusobacterium	Fusobacteriota	0.41145%
Granulicatella adiacens	Granulicatella	Bacillota	0.39449%
Mogibacterium diversum	Mogibacterium	Bacillota	0.36784%
Peptostreptococcus stomatis	Peptostreptococcus	Bacillota	0.34565%
Lachnoanaerobaculum umeaense	Lachnoanaerobaculum	Bacillota	0.32648%
Neisseria macacae	Neisseria	Pseudomonadota	0.31144%
Eubacterium xylanophilum	Eubacterium	Bacillota	0.30866%
Porphyromonas circumdentaria	Porphyromonas	Bacteroidota	0.30429%
Treponema pectinovorum	Treponema	Spirochaetota	0.29173%
Mogibacterium vescum	Mogibacterium	Bacillota	0.27527%
Porphyromonas endodontalis	Porphyromonas	Bacteroidota	0.27505%
Selenomonas ruminantium	Selenomonas	Bacillota	0.26705%
Streptococcus constellatus	Streptococcus	Bacillota	0.22793%
Leptotrichia wadei	Leptotrichia	Fusobacteriota	0.22694%
Porphyromonas macacae	Porphyromonas	Bacteroidota	0.22267%
Eubacterium pyruvativorans	Eubacterium	Bacillota	0.22178%
Streptococcus dysgalactiae	Streptococcus	Bacillota	0.21443%
Neisseria meningitidis	Neisseria	Pseudomonadota	0.21291%
Prevotella oris	Prevotella	Bacteroidota	0.21078%
Prevotella melaninogenica	Prevotella	Bacteroidota	0.20941%
Streptococcus parasanguinis	Streptococcus	Bacillota	0.20115%
Mogibacterium neglectum	Mogibacterium	Bacillota	0.20013%
Neisseria gonorrhoeae	Neisseria	Pseudomonadota	0.19886%
Prevotella intermedia	Prevotella	Bacteroidota	0.19839%
Neisseria mucosa	Neisseria	Pseudomonadota	0.19551%
Eubacterium barkeri	Eubacterium	Bacillota	0.19343%
Veillonella rodentium	Veillonella	Bacillota	0.17548%
Streptococcus australis	Streptococcus	Bacillota	0.17469%
Veillonella atypica	Veillonella	Bacillota	0.17338%
Capnocytophaga granulosa	Capnocytophaga	Bacteroidota	0.17288%
Capnocytophaga gingivalis	Capnocytophaga	Bacteroidota	0.16784%
Streptococcus suis	Streptococcus	Bacillota	0.16306%
Campylobacter concisus	Campylobacter	Pseudomonadota	0.14665%
Eubacterium ventriosum	Eubacterium	Bacillota	0.14614%
Eubacterium callanderi	Eubacterium	Bacillota	0.13636%
Streptococcus periodonticum	Streptococcus	Bacillota	0.12979%
Eubacterium multiforme	Eubacterium	Bacillota	0.12961%
Streptococcus gallolyticus	Streptococcus	Bacillota	0.12207%

Reference-based 16S phylogeny

84 of 85 reported species have an eligible reference. MAFFT alignment and FastTree GTR+CAT tree, pruned to this sample. This is not a phylogeny inferred from sample reads or ASVs. Root placement is arbitrary; branch lengths are substitutions per site.

Public raw read files

Files contain the original full run. Downloads are hosted by ENA.

File	Type / bytes	MD5
SRR12522766_1.fastq.gz	FASTQ / 242538091	`c1ff5910aafd015151ca979fa6dd14f1`

Analysis provenance

marker	16S
pipeline	Archaions v18.8
read_sampling	First available reads, not random subsampling
input_sha256	062fa6bba0577090ce874413537a287357306664b9a0a780c84a27e3f5743835
median_read_length	1423.0
reads_in_length_window	27633
length_window_bp	[1200, 2000]
quality_scores	Unavailable in fetched FASTA; no measured quality filtering
classifier_stats	{"marker": "16s", "pipeline": "v18.8", "gpu": "RTX-PRO-6000", "input_path": "volume-fastq-gz", "reads_in": 30000, "reads_skipped": 11253, "elapsed_seconds": 2.5857151339999973, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 1, "fraction": 0.005, "adapters_found": {"BC_FLANK": 1}, "should_trim": false}, "porechop_ran": false, "porechop_reason": "fast-path: no adapter trimming required"}

Full public metadata

All retrieved values are included. Blank source values are displayed as “Not reported”. Expand the sections below to inspect the full record.

ENA run fields (195)

run_accession	SRR12522766
age	Not reported
aligned	Not reported
altitude	Not reported
assembly_quality	Not reported
assembly_software	Not reported
bam_aspera	Not reported
bam_bytes	Not reported
bam_file_role	Not reported
bam_ftp	Not reported
bam_galaxy	Not reported
bam_md5	Not reported
base_count	230503660
binning_software	Not reported
bio_material	Not reported
bisulfite_protocol	Not reported
broad_scale_environmental_context	Not reported
broker_name	Not reported
cage_protocol	Not reported
cell_line	Not reported
cell_type	Not reported
center_name	SUB7951364
checklist	Not reported
chip_ab_provider	Not reported
chip_protocol	Not reported
chip_target	Not reported
collected_by	Not reported
collection_date	not applicable
collection_date_end	Not reported
collection_date_start	Not reported
completeness_score	Not reported
contamination_score	Not reported
control_experiment	Not reported
country	United Arab Emirates
cultivar	Not reported
culture_collection	Not reported
datahub	dcc_metagenome
depth	Not reported
description	MinION sequencing: metagenomic
dev_stage	Not reported
disease	Not reported
dnase_protocol	Not reported
ecotype	Not reported
elevation	Not reported
environment_biome	Not reported
environment_feature	Not reported
environment_material	Not reported
environmental_medium	Not reported
environmental_sample	Not reported
experiment_accession	SRX9012848
experiment_alias	C12-P
experiment_target	Not reported
experiment_title	MinION sequencing: metagenomic
experimental_factor	Not reported
experimental_protocol	Not reported
extraction_protocol	Not reported
faang_library_selection	Not reported
fastq_aspera	fasp.sra.ebi.ac.uk:/vol1/fastq/SRR125/066/SRR12522766/SRR12522766_1.fastq.gz
fastq_bytes	242538091
fastq_file_role	GENERATED_FILE
fastq_ftp	ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/066/SRR12522766/SRR12522766_1.fastq.gz
fastq_galaxy	ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/066/SRR12522766/SRR12522766_1.fastq.gz
fastq_md5	c1ff5910aafd015151ca979fa6dd14f1
file_location	Not reported
first_created	2021-10-01
first_public	2021-10-01
germline	Not reported
hi_c_protocol	Not reported
host	Homo sapiens
host_body_site	Not reported
host_genotype	Not reported
host_gravidity	Not reported
host_growth_conditions	Not reported
host_phenotype	Not reported
host_scientific_name	Homo sapiens
host_sex	Not reported
host_status	Not reported
host_tax_id	9606
identified_by	Not reported
instrument_model	MinION
instrument_platform	OXFORD_NANOPORE
investigation_type	Not reported
isolate	mixed1
isolation_source	oral
last_updated	2021-10-01
lat	Not reported
library_construction_protocol	Not reported
library_gen_protocol	Not reported
library_layout	SINGLE
library_max_fragment_size	Not reported
library_min_fragment_size	Not reported
library_name	C12-P
library_pcr_isolation_protocol	Not reported
library_prep_date	Not reported
library_prep_date_format	Not reported
library_prep_latitude	Not reported
library_prep_location	Not reported
library_prep_longitude	Not reported
library_selection	PCR
library_source	GENOMIC
library_strategy	AMPLICON
local_environmental_context	Not reported
location	Not reported
location_end	Not reported
location_start	Not reported
lon	Not reported
marine_region	Not reported
mating_type	Not reported
ncbi_reporting_standard	Metagenome or environmental
nominal_length	Not reported
nominal_sdev	Not reported
pcr_isolation_protocol	Not reported
ph	Not reported
project_name	Not reported
protocol_label	Not reported
read_count	166526
read_strand	Not reported
restriction_enzyme	Not reported
restriction_enzyme_target_sequence	Not reported
restriction_site	Not reported
rna_integrity_num	Not reported
rna_prep_3_protocol	Not reported
rna_prep_5_protocol	Not reported
rna_purity_230_ratio	Not reported
rna_purity_280_ratio	Not reported
rt_prep_protocol	Not reported
run_alias	C12.fastq
run_date	Not reported
salinity	Not reported
sample_accession	SAMN15887565
sample_alias	C12
sample_capture_status	Not reported
sample_collection	Not reported
sample_description	Metagenome or environmental sample from human oral metagenome
sample_material	Not reported
sample_prep_interval	Not reported
sample_prep_interval_units	Not reported
sample_storage	Not reported
sample_storage_processing	Not reported
sample_title	Metagenome or environmental sample from human oral metagenome
sampling_campaign	Not reported
sampling_platform	Not reported
sampling_site	Not reported
scientific_name	human oral metagenome
secondary_project	Not reported
secondary_sample_accession	SRS7263860
secondary_study_accession	SRP278853
sequencing_date	Not reported
sequencing_date_format	Not reported
sequencing_location	Not reported
sequencing_longitude	Not reported
sequencing_method	Not reported
sequencing_primer_catalog	Not reported
sequencing_primer_lot	Not reported
sequencing_primer_provider	Not reported
serotype	Not reported
serovar	Not reported
sex	Not reported
specimen_voucher	Not reported
sra_aspera	Not reported
sra_bytes	Not reported
sra_file_role	Not reported
sra_ftp	Not reported
sra_galaxy	Not reported
sra_md5	Not reported
status	public
strain	mixed
study_accession	PRJNA658726
study_alias	PRJNA658726
study_title	The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study
sub_species	Not reported
sub_strain	Not reported
submission_accession	SRA1117712
submission_tool	Not reported
submitted_aspera	Not reported
submitted_bytes	Not reported
submitted_file_role	Not reported
submitted_format	Not reported
submitted_ftp	Not reported
submitted_galaxy	Not reported
submitted_host_sex	Not reported
submitted_md5	Not reported
submitted_read_type	Not reported
surveillance_target	Not reported
tag	Not reported
target_gene	Not reported
tax_id	447426
tax_lineage	1;2787823;12908;408169;410656;447426
taxonomic_classification	Not reported
taxonomic_identity_marker	Not reported
temperature	Not reported
tissue_lib	Not reported
tissue_type	Not reported
transposase_protocol	Not reported
variety	Not reported

BioSample record and attributes

alias	C12
title	Metagenome or environmental sample from human oral metagenome
description	Not reported

strain	mixed
collection_date	not applicable
INSDC secondary accession	SRS7263860
aliquot	cig2
organism	human oral metagenome
sample_type	Subgingival
isolate	mixed1
NCBI submission package	Metagenome.environmental.1.0
periodontitis	no-mild
smoking	S-Cigarettes
host	Homo sapiens
geo_loc_name	United Arab Emirates
lat_lon	missing
isolation_source	oral
BioSampleModel	Metagenome or environmental
ENA-FIRST-PUBLIC	2021-09-30
ENA-LAST-UPDATE	2021-09-30

Curated cohort annotations and QC

run	SRR12522766
sample	SAMN15887565
study	PRJNA658726
title	Metagenome or environmental sample from human oral metagenome
alias	C12
site	Subgingival
subject	Not reported
phenotype	Not reported
sex	Not reported
smoking	S-Cigarettes
periodontitis	no-mild
time_point	Not reported
negative_control	False
lab_model	False
state	complete
reads_input	30000
species_reported	85
human_primary	True

Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.