archAIons · MetaBiome Project · Oral · Public research data

SRR33005051

Control12 saliva 16S_full-length

BioSample: SAMN47766367 · Study: PRJNA1243403 · Body site: Saliva

98Reported species

15Reported genera

Taxonomic abundance

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

Species	Genus	Phylum	Abundance
Streptococcus salivarius	Streptococcus	Bacillota	16.46660%
Haemophilus parainfluenzae	Haemophilus	Pseudomonadota	11.99264%
Streptococcus anginosus	Streptococcus	Bacillota	6.21646%
Veillonella parvula	Veillonella	Bacillota	5.54852%
Streptococcus downei	Streptococcus	Bacillota	4.80350%
Haemophilus influenzae	Haemophilus	Pseudomonadota	3.54605%
Streptococcus gordonii	Streptococcus	Bacillota	3.16599%
Veillonella dispar	Veillonella	Bacillota	2.74026%
Neisseria meningitidis	Neisseria	Pseudomonadota	2.43634%
Veillonella rodentium	Veillonella	Bacillota	1.99188%
Streptococcus pneumoniae	Streptococcus	Bacillota	1.91797%
Streptococcus mitis	Streptococcus	Bacillota	1.77950%
Streptococcus sanguinis	Streptococcus	Bacillota	1.71103%
Neisseria gonorrhoeae	Neisseria	Pseudomonadota	1.64883%
Campylobacter concisus	Campylobacter	Pseudomonadota	1.43524%
Haemophilus aegyptius	Haemophilus	Pseudomonadota	1.30424%
Neisseria flavescens	Neisseria	Pseudomonadota	1.19136%
Leptotrichia wadei	Leptotrichia	Fusobacteriota	1.17503%
Streptococcus pyogenes	Streptococcus	Bacillota	1.09081%
Campylobacter curvus	Campylobacter	Pseudomonadota	1.08413%
Leptotrichia hongkongensis	Leptotrichia	Fusobacteriota	1.08121%
Prevotella jejuni	Prevotella	Bacteroidota	1.03014%
Prevotella intermedia	Prevotella	Bacteroidota	1.02886%
Neisseria elongata	Neisseria	Pseudomonadota	0.99427%
Streptococcus oralis	Streptococcus	Bacillota	0.90021%
Haemophilus pittmaniae	Haemophilus	Pseudomonadota	0.81616%
Prevotella melaninogenica	Prevotella	Bacteroidota	0.80328%
Neisseria dentiae	Neisseria	Pseudomonadota	0.70563%
Granulicatella balaenopterae	Granulicatella	Bacillota	0.69733%
Megasphaera elsdenii	Megasphaera	Bacillota	0.62918%
Campylobacter sputorum	Campylobacter	Pseudomonadota	0.62462%
Streptococcus thermophilus	Streptococcus	Bacillota	0.51743%
Haemophilus haemolyticus	Haemophilus	Pseudomonadota	0.50916%
Granulicatella adiacens	Granulicatella	Bacillota	0.45742%
Gemella haemolysans	Gemella	Bacillota	0.44853%
Prevotella nigrescens	Prevotella	Bacteroidota	0.43864%
Streptococcus himalayensis	Streptococcus	Bacillota	0.43560%
Leptotrichia buccalis	Leptotrichia	Fusobacteriota	0.43474%
Gemella palaticanis	Gemella	Bacillota	0.43359%
Veillonella seminalis	Veillonella	Bacillota	0.43039%
Leptotrichia shahii	Leptotrichia	Fusobacteriota	0.42083%
Neisseria polysaccharea	Neisseria	Pseudomonadota	0.40952%
Haemophilus haemoglobinophilus	Haemophilus	Pseudomonadota	0.39500%
Neisseria subflava	Neisseria	Pseudomonadota	0.38280%
Neisseria canis	Neisseria	Pseudomonadota	0.38027%
Granulicatella elegans	Granulicatella	Bacillota	0.37662%
Streptococcus parasanguinis	Streptococcus	Bacillota	0.37045%
Streptococcus periodonticum	Streptococcus	Bacillota	0.36992%
Lachnoanaerobaculum orale	Lachnoanaerobaculum	Bacillota	0.36779%
Neisseria animaloris	Neisseria	Pseudomonadota	0.36447%
Veillonella infantium	Veillonella	Bacillota	0.36310%
Streptococcus marmotae	Streptococcus	Bacillota	0.35784%
Haemophilus parahaemolyticus	Haemophilus	Pseudomonadota	0.33451%
Neisseria lactamica	Neisseria	Pseudomonadota	0.32228%
Neisseria animalis	Neisseria	Pseudomonadota	0.31045%
Prevotella oris	Prevotella	Bacteroidota	0.30462%
Neisseria zoodegmatis	Neisseria	Pseudomonadota	0.29985%
Rothia aeria	Rothia	Actinomycetota	0.29900%
Prevotella veroralis	Prevotella	Bacteroidota	0.29868%
Lachnoanaerobaculum umeaense	Lachnoanaerobaculum	Bacillota	0.27870%
Streptococcus intermedius	Streptococcus	Bacillota	0.27215%
Streptococcus vestibularis	Streptococcus	Bacillota	0.23787%
Porphyromonas gingivalis	Porphyromonas	Bacteroidota	0.23435%
Streptococcus equinus	Streptococcus	Bacillota	0.22394%
Megasphaera sueciensis	Megasphaera	Bacillota	0.22046%
Selenomonas sputigena	Selenomonas	Bacillota	0.21558%
Campylobacter hyointestinalis	Campylobacter	Pseudomonadota	0.20969%
Prevotella ruminicola	Prevotella	Bacteroidota	0.20969%
Streptococcus pluranimalium	Streptococcus	Bacillota	0.20747%
Streptococcus koreensis	Streptococcus	Bacillota	0.20600%
Schaalia cardiffensis	Schaalia	Actinomycetota	0.20413%
Streptococcus cristatus	Streptococcus	Bacillota	0.19236%
Schaalia funkei	Schaalia	Actinomycetota	0.18775%
Selenomonas ruminantium	Selenomonas	Bacillota	0.18316%
Megasphaera paucivorans	Megasphaera	Bacillota	0.16764%
Gemella parahaemolysans	Gemella	Bacillota	0.16715%
Haemophilus paraphrohaemolyticus	Haemophilus	Pseudomonadota	0.16573%
Prevotella corporis	Prevotella	Bacteroidota	0.16558%
Streptococcus constellatus	Streptococcus	Bacillota	0.16542%
Streptococcus sobrinus	Streptococcus	Bacillota	0.16542%
Streptococcus sinensis	Streptococcus	Bacillota	0.16256%
Haemophilus sputorum	Haemophilus	Pseudomonadota	0.15749%
Neisseria cinerea	Neisseria	Pseudomonadota	0.15230%
Neisseria macacae	Neisseria	Pseudomonadota	0.15225%
Schaalia odontolytica	Schaalia	Actinomycetota	0.14955%
Streptococcus alactolyticus	Streptococcus	Bacillota	0.14887%
Megasphaera stantonii	Megasphaera	Bacillota	0.14392%
Gemella asaccharolytica	Gemella	Bacillota	0.13894%
Streptococcus mutans	Streptococcus	Bacillota	0.13574%
Leptotrichia hofstadii	Leptotrichia	Fusobacteriota	0.12065%
Neisseria iguanae	Neisseria	Pseudomonadota	0.11710%
Neisseria arctica	Neisseria	Pseudomonadota	0.11652%
Gemella morbillorum	Gemella	Bacillota	0.11286%
Veillonella atypica	Veillonella	Bacillota	0.10992%
Prevotella bryantii	Prevotella	Bacteroidota	0.10856%
Streptococcus gallolyticus	Streptococcus	Bacillota	0.10193%
Streptococcus troglodytidis	Streptococcus	Bacillota	0.09997%
Streptococcus acidominimus	Streptococcus	Bacillota	0.09987%

Reference-based 16S phylogeny

98 of 98 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
SRR33005051_1.fastq.gz	FASTQ / 130892115	`9fa44661c1066fb9352868d2c2c1317d`

Analysis provenance

marker	16S
pipeline	Archaions v18.8
read_sampling	First available reads, not random subsampling
input_sha256	904ecf5fb9229334c9143c4cf38749d30e9f8abbf85b687c171e7d7a81e1d7f0
median_read_length	1573.0
reads_in_length_window	28850
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": 5047, "elapsed_seconds": 2.636431808999987, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 14, "fraction": 0.07, "adapters_found": {"27F": 14}, "should_trim": true}, "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	SRR33005051
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	143991593
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	SUB15232072
checklist	Not reported
chip_ab_provider	Not reported
chip_protocol	Not reported
chip_target	Not reported
collected_by	Not reported
collection_date	Not reported
collection_date_end	Not reported
collection_date_start	Not reported
completeness_score	Not reported
contamination_score	Not reported
control_experiment	Not reported
country	Not reported
cultivar	Not reported
culture_collection	Not reported
datahub	dcc_metagenome
depth	Not reported
description	MinION sequencing: Full-Length 16S sequencing of saliva from Alzheimer patients and healthy controls
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	SRX28271073
experiment_alias	ct12 sa 16S full-length
experiment_target	Not reported
experiment_title	MinION sequencing: Full-Length 16S sequencing of saliva from Alzheimer patients and healthy controls
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/SRR330/051/SRR33005051/SRR33005051_1.fastq.gz
fastq_bytes	130892115
fastq_file_role	GENERATED_FILE
fastq_ftp	ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/051/SRR33005051/SRR33005051_1.fastq.gz
fastq_galaxy	ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/051/SRR33005051/SRR33005051_1.fastq.gz
fastq_md5	9fa44661c1066fb9352868d2c2c1317d
file_location	Not reported
first_created	2025-04-08
first_public	2025-04-08
germline	Not reported
hi_c_protocol	Not reported
host	Not reported
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	Not reported
host_sex	Not reported
host_status	Not reported
host_tax_id	Not reported
identified_by	Not reported
instrument_model	MinION
instrument_platform	OXFORD_NANOPORE
investigation_type	Not reported
isolate	Not reported
isolation_source	Not reported
last_updated	2025-04-08
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	ct12 sa 16S full-length
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	Not reported
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	93545
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	control12.fastq.gz
run_date	Not reported
salinity	Not reported
sample_accession	SAMN47766367
sample_alias	Not reported
sample_capture_status	Not reported
sample_collection	Not reported
sample_description	Not reported
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	Not reported
sampling_campaign	Not reported
sampling_platform	Not reported
sampling_site	Not reported
scientific_name	Not reported
secondary_project	Not reported
secondary_sample_accession	SRS24617203
secondary_study_accession	SRP573912
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	Not reported
study_accession	PRJNA1243403
study_alias	PRJNA1243403
study_title	Oral microbiota of patients with Alzheimer's disease and healthy controls
sub_species	Not reported
sub_strain	Not reported
submission_accession	SRA2107592
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	Not reported
tax_lineage	Not reported
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	Control12 saliva 16S_full-length
title	MIMARKS Survey related sample from human oral metagenome
description	Not reported
source	NCBI BioSample

collection_date	2021
env_broad_scale	Human unstimulated saliva control12
env_local_scale	Department of Psychiatry of the LVR-Klinikum Dsseldorf
env_medium	Unstimulated saliva
geo_loc_name	Germany: Dsseldorf
host	Homo sapiens
lat_lon	51.227700 N 6.77350 E

Curated cohort annotations and QC

run	SRR33005051
sample	SAMN47766367
study	PRJNA1243403
title	Not reported
alias	Control12 saliva 16S_full-length
site	Saliva
subject	Control12
phenotype	Control
sex	Not reported
smoking	Not reported
periodontitis	Not reported
time_point	Not reported
negative_control	False
lab_model	False
state	complete
reads_input	30000
species_reported	98
human_primary	True

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