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PRJNA592261 SRP235006

Infant oropharyngeal & gastrointestinal virome, Mexico

Infant virome during the first year of life

211 samples from healthy infants (with some neonate and unknown ages) in a semi-rural population in Morelos, Mexico, studying oropharyngeal and gastrointestinal virome diversity during the first year of life in a longitudinal cohort design. machine-written summary

211 samples · 211 runs · MX · Infant / toddler · 2020 · 1.72 Gbp / sample

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Sources
✓Sequence archive 1,423✓Abstract / description 211✓Full text 1,285✓Supplementary tables 27–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive1,423 sample values (age, collection date, country, family id, family role, subject id, timepoint)
✓ Abstract / description211 sample values (health condition)
✓ Full text1,285 sample values (antibiotic exposure, feeding mode, lifestyle, lifestyle detail, location locality, location region, location site) · PMC7423923, PMC8865552, PMC9845211
✓ Supplementary tables27 sample values (age, subject id)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
infant187
neonate13
adult7
adolescent2
unknown2
Condition
healthy_control211
Country
MX211
Body site
primary115
excluded96
Collected 2015–2017
2015: 85 samples2016: 111 samples2017: 15 samples20152017
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 49 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 101 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 60 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 1.72 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalmother–infant

9 of 16 people sampled more than once (106 samples; median 12, up to 12 per person) · follow-up median 11 mo (max 15 mo) · median interval between samples 31 d (time from age at collection). Schedule stated by the source: “Stool/oropharyngeal samples per infant at multiple ages (e.g. 0.5, 1, 2.5, 3.5, 4.5, 5.5, 7, 8, 10, 11 months)” (time origin: birth).

1111 (child): day 011 (child): day 3111 (child): day 6111 (child): day 13711 (child): day 16811 (child): day 18311 (child): day 22911 (child): day 25911 (child): day 28911 (child): day 32011 (child): day 3501515 (child): day 015 (child): day 1515 (child): day 6115 (child): day 9215 (child): day 12215 (child): day 15215 (child): day 19815 (child): day 25915 (child): day 28915 (child): day 32015 (child): day 38115 (child): day 3961919 (child): day 019 (child): day 6119 (child): day 7719 (child): day 15319 (child): day 21419 (child): day 27419 (child): day 29019 (child): day 32019 (child): day 35019 (child): day 38119 (child): day 41119 (child): day 44222 (child): day 02 (child): day 152 (child): day 612 (child): day 922 (child): day 1222 (child): day 1522 (child): day 1982 (child): day 2292 (child): day 2892 (child): day 3202 (child): day 35044 (child): day 04 (child): day 614 (child): day 924 (child): day 1374 (child): day 1684 (child): day 1684 (child): day 2134 (child): day 2294 (child): day 2594 (child): day 2894 (child): day 3204 (child): day 35055 (child): day 05 (child): day 155 (child): day 465 (child): day 765 (child): day 1225 (child): day 1375 (child): day 1685 (child): day 2135 (child): day 2295 (child): day 2595 (child): day 2895 (child): day 32066 (child): day 06 (child): day 156 (child): day 466 (child): day 766 (child): day 1226 (child): day 1526 (child): day 1686 (child): day 1986 (child): day 2446 (child): day 2896 (child): day 3656 (child): day 38177 (child): day 07 (child): day 157 (child): day 467 (child): day 927 (child): day 1077 (child): day 1687 (child): day 1837 (child): day 1987 (child): day 2447 (child): day 2747 (child): day 3057 (child): day 35099 (child): day 09 (child): day 159 (child): day 619 (child): day 919 (child): day 1219 (child): day 1379 (child): day 1829 (child): day 2139 (child): day 2439 (child): day 3049 (child): day 3659 (child): day 4260 d4 mo7 mo11 mo15 mo

Each row is one person (9 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).

9 mother–infant pairs (infant stool + oropharynx monthly through year 1; mother stool / oropharynx) · 9 families with 43 sampled people (9 with a parent and a child).

motherMchildC
7 × mother + child
motherMmotherMchildCchildCchildCchildCchildCchildCchildCchildCchildCchildCchildCchildC
1 × mother×2 + child×12
motherMmotherMchildCchildCchildCchildCchildCchildCchildCchildCchildCchildCchildCchildCchildC
1 × mother×2 + child×13
family F1111 — child · 22 samplesC11M11 — mother · 1 sampleMM11
family F22 — child · 11 samplesC2nan — mother · 1 sampleMnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnanM2 — mother · 1 sampleMM2
family F44 — child · 12 samplesC4nan — mother · 1 sampleMnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnanM4 — mother · 1 sampleMM4
family F1515 — child · 21 samplesC15M15 — mother · 1 sampleMM15
family F1919 — child · 19 samplesC19M19 — mother · 1 sampleMM19
family F5M5 — mother · 1 sampleMM55 — child · 24 samplesC5
family F66 — child · 23 samplesC6M6 — mother · 1 sampleMM6
family F77 — child · 24 samplesC7M7 — mother · 1 sampleMM7
family F99 — child · 21 samplesC9M9 — mother · 1 sampleMM9

motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 9 families. 16 people in the project overall.

Families (9)
familymemberssamples
F4mother×2 + child×13SAMN13418665 · SAMN13418666 · SAMN13418667 · SAMN13418668 · SAMN13418669 · SAMN13418670 · SAMN13418671 · SAMN13418672 · SAMN13418681 · SAMN13418682 · SAMN13418692 · SAMN13418693
F5mother + childSAMN13418695 · SAMN13418696 · SAMN13418697 · SAMN13418698 · SAMN13418699 · SAMN13418700 · SAMN13418701 · SAMN13418702 · SAMN13418703 · SAMN13418704 · SAMN13418705 · SAMN13418706
F7mother + childSAMN19607255 · SAMN19607256 · SAMN19607257 · SAMN19607258 · SAMN19607259 · SAMN19607260 · SAMN19607261 · SAMN19607262 · SAMN19607263 · SAMN19607264 · SAMN19607265 · SAMN19607266
F2mother×2 + child×12SAMN13293556 · SAMN13417971 · SAMN13418003 · SAMN13418006 · SAMN13418007 · SAMN13418008 · SAMN13418009 · SAMN13418010 · SAMN13418011 · SAMN13418012 · SAMN13418023 · SAMN13418169
F6mother + childSAMN19607242 · SAMN19607243 · SAMN19607244 · SAMN19607245 · SAMN19607246 · SAMN19607247 · SAMN19607248 · SAMN19607249 · SAMN19607250 · SAMN19607251 · SAMN19607252 · SAMN19607253
F11mother + childSAMN19607281 · SAMN19607282 · SAMN19607283 · SAMN19607284 · SAMN19607285 · SAMN19607286 · SAMN19607287 · SAMN19607288 · SAMN19607289 · SAMN19607290 · SAMN19607291 · SAMN19607292
F15mother + childSAMN19607293 · SAMN19607294 · SAMN19607295 · SAMN19607296 · SAMN19607297 · SAMN19607298 · SAMN19607299 · SAMN19607300 · SAMN19607301 · SAMN19607302 · SAMN19607303 · SAMN19607304
F9mother + childSAMN19607268 · SAMN19607269 · SAMN19607270 · SAMN19607271 · SAMN19607272 · SAMN19607273 · SAMN19607274 · SAMN19607275 · SAMN19607276 · SAMN19607277 · SAMN19607278 · SAMN19607279
F19mother + childSAMN19607306 · SAMN19607307 · SAMN19607308 · SAMN19607309 · SAMN19607310 · SAMN19607311 · SAMN19607312 · SAMN19607313 · SAMN19607314 · SAMN19607315 · SAMN19607316 · SAMN19607317

How longitudinal and relatedness information is derived

Community composition
Prevotella 8.6%Aquipseudomonas 7.3%Bifidobacterium 6.0%Clostridioides 4.4%Streptococcus 2.0%Intestinibacter 1.5%Tyzzerella 1.1%Faecalibacterium 0.8%Nanogingivalis 0.8%Butyricicoccus 0.7%Noda2021 0.5%Methylophilus 0.4%not assigned to a genus 64.0%other genera 1.8%

Genera, mean relative abundance over 35 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category209 99%
country211 100%211
health_condition211 100%211
subject_id186 88%16026
collection_date211 100%211
detailed_location211 100%
family_id211 100%211
family_role211 100%211
lifestyle211 100%211
lifestyle_detail211 100%211
location_locality211 100%211
location_region211 100%211
location_site211 100%211
timepoint_label211 100%211
age_at_collection_days209 99%2081
antibiotic_exposure115 55%115
feeding_mode115 55%115
Papers (3)
  • Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life. PMID 32788688 PMC7423923 curated
  • High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach. PMID 35196791 PMC8865552 curated
  • The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal. PMID 36650178 PMC9845211 curated
Details
Archive description

In this study, we set to determine the diversity and dynamic of the oropharyngeal and gastrointestinal virome in children under one year of age, in a semi-rural population in Mexico, by next-generation sequencing.

How this project entered the registry

Classified as human gut / stool / oral cavity shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.description · “oropharyngeal and gastrointestinal virome”
  • life stage study.description · “children under one year of age”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN13293556age_at_collection_days15R10.85sample.title0.5 month
SAMN13418169age_at_collection_days5479.0R10.85biosample.attribute:isolation_sourceisolation_source: Stools of a 15 year old woman
SAMN13418703age_at_collection_days228R20.85paper.supp.tableAge (months)=7.5
SAMN13293556antibiotic_exposurenoR30.80paper.fulltext.resultsNone of the children received antibiotics during the study period
SAMN13293556collection_date2015-03-19R10.85biosample.attribute:collection_datecollection_date: 2015-03-19
SAMN13293556countryMXR10.90biosample_attrMexico:Morelos,Xoxocotla
SAMN13293556family_idF2R10.70run.library_namelibrary_name=I2_05
SAMN13293556family_rolechildR10.70run.library_namelibrary_name=I2_05; Human virome isolated from stool of healthy infant of 0.5 mo
SAMN13293556feeding_modeexclusive_breastR30.40paper.fulltext.resultsAll the children were breastfed
SAMN13293556health_conditionhealthy_controlR40.50paper.abstractthree apparently healthy children in a semi-rural
SAMN13293556lifestylerural_non_industrializedR30.70paper.fulltext.methodssemi-rural community of Xoxocotla, Morelos
SAMN13293556lifestyle_detailsemi-rural community of Xoxocotla, MorelosR30.60paper.fulltext.methodssemi-rural community of Xoxocotla, Morelos
SAMN13293556location_localityXoxocotlaR30.70paper.fulltext.methodssemi-rural community of Xoxocotla, Morelos
SAMN13293556location_regionMorelosR30.70paper.fulltext.methodssemi-rural community of Xoxocotla, Morelos
SAMN13293556location_siteXoxocotla community Health CenterR30.70paper.fulltext.methodsXoxocotla community Health Center were voluntarily enrolled
SAMN13417971subject_id2R10.70sample.name_rule:library_nameI2_1
SAMN13418696subject_id5R10.70sample.name_rule:sample_aliasI5_05
SAMN13293556subject_id2R20.80archive
SAMN13418006subject_id2R20.80paper.supp.spectrum01853-21_supp_1_seq6.xlsx[S1!Sample information / Child]Child 2; Sample ID G2_4.5_JUL15
SAMN13293556timepoint_label0.5 monthR10.70sample.titleHuman virome isolated from stool of healthy infant of 0.5 month old
SAMN13418667timepoint_label1.5R10.70sample.name_rule:sample_aliasI4_1.5
Sequencing

211 runs over 211 samples · mean 2.38 Gbp per run (median 1.72 Gbp, total 501.67 Gbp; 211 runs with a base count) · layout PAIRED 143, SINGLE 68 · platform ILLUMINA 211 · models Illumina MiSeq (211) · 55% of runs with a Sandpiper profile · first public 2020-02-29 – 2022-06-23

Authors (12)

Aguado-García Y first · Taboada B · Morán P · Rivera-Gutiérrez X · Serrano-Vázquez A · Iša P · Rojas-Velázquez L · Pérez-Juárez H · López S · Torres J · Ximénez C · Arias CF last

Downloads

PRJNA592261.csv.gz (9.1 KB) · parquet (82.3 KB) — all 211 samples, every field with route and confidence · PRJNA592261_determinations.csv.gz (28.4 KB) — 2,946 evidence rows

Samples (211 · every field this project has values for · hover a cell for its source)
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