Bifidobacterium strains in UK twins by LCT genotype
94 gut metagenome samples from adults in the United Kingdom, including monozygotic twin pairs sampled longitudinally, examining Bifidobacterium species and strains across lactase persistence (LCT) genotypes in a cross-sectional design. machine-written summary
94 samples · 94 runs · GB · Adult · 2020 · 3.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 774 sample values (collection date, country, family id, family role, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7527142 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinaltwins
22 of 22 people sampled more than once (92 samples; median 4, up to 6 per person) · follow-up median 3.3 y (max 3.9 y) · median interval between samples 2.1 y (time from collection dates).
Each row is one person (21 shown of 22); 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).
TwinsUK adults: 7 monozygotic twin pairs with both twins sampled (+8 singletons, incl. F2-T1/F3-T2 label mismatch with Table S1) · 7 families with 14 sampled people, 14 twin sets.
twin · 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: 7 linked groups from explicit relations. 22 people in the project overall.
Families (7)
Genera, mean relative abundance over 72 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 94 | 100% | ||||
| country | 94 | 100% | 94 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 92 | 98% | 92 | |||
| collection_date | 94 | 100% | 94 | |||
| detailed_location | 94 | 100% | ||||
| latitude | 94 | 100% | 94 | |||
| location_region | 94 | 100% | 94 | |||
| longitude | 94 | 100% | 94 | |||
| timepoint_label | 92 | 98% | 92 | |||
| family_id | 60 | 64% | 60 | |||
| family_role | 60 | 64% | 60 |
- Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes. 2020 PMID 32994293 PMC7527142 own_data
Archive description
BackgroundOne of the strongest signals of human genetic effects on the gut microbiome is the association between the relative abundance of Bifidobacterium and host genotype at the locus for the lactase gene (LCT), which is associated with lactase persistence. In several populations of European descent, individuals with lactase non-persistence have been shown to harbor a greater proportion of Bifidobacterium in stool compared to those with lactase persistence. These associations are based on 16S rRNA gene data that do not discriminate between species of Bifidobacterium. Given the wide functional and taxonomic diversity of this genus, a species-level resolution of the LCT-Bifidobacterium association would allow better understanding of the underlying relationship. Here, we further interrogated the LCT-Bifidobacterium in adult monozygotic twins that were concordant for either lactase persistence (AA/AG) or non-persistence (GG). We used metagenomics on (1) bulk DNA extracts and (2) post genome-capture with a Bifidobacterium-specific probe array.ResultsWe observed specific Bifidobacteria are proportionally enriched in GG versus AG/AA individuals, which are both dominated by B. adolescentis and B. longum. We found no discriminant Bifidobacterium species between GG and AG/AA genotypes, nor any genotypic signal on Bifidobacterium community structure. Our genome capture data revealed strong intra-individual longitudinal stability of B. longum, B. adolescentis, and B. bifidum strains, and increased intra-twin strain similarities compared to unrelated individuals, but did not reveal an effect of host lactase persistence genotype on strain stability or strain composition. ConclusionsThe Bifidobacteria are often considered specialists in human gut communities. Yet our study suggests a wide niche space across all human associated Bifidobacteria, which would enable them to exploit the greater availability of intact lactose reaching the large intestine of lactase non-persistent people.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “spp. from human gut metagenomes of individuals”
- body site study.description · “effects on the gut microbiome is the”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “the LCT-Bifidobacterium in adult monozygotic twins that”
- life stage study.description · “dominated by B. adolescentis and B. longum.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6801812 | collection_date | 2010-11-08 | R1 | 0.90 | biosample.attribute:collection_date | 2010-11-08 |
| SAMEA6801812 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA6801814 | family_id | PRJEB38000:F9 | R1 | 0.70 | biosample.attribute:alias | alias: F9-T1-S2_pre |
| SAMEA6801814 | family_role | twin | R1 | 0.70 | biosample.attribute:alias | alias: F9-T1-S2_pre |
| SAMEA6801812 | latitude | 51.5107 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.5107 -0.1158 |
| SAMEA6801812 | location_region | England | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.5107 -0.1158 |
| SAMEA6801812 | longitude | -0.1158 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.5107 -0.1158 |
| SAMEA6801812 | subject_id | F5-TX | R1 | 0.70 | sample.name_rule:alias | F5-TX-S2_pre |
| SAMEA6801812 | timepoint_label | S2 | R1 | 0.70 | sample.name_rule:alias | F5-TX-S2_pre |
Sequencing
94 runs over 94 samples · mean 4.37 Gbp per run (median 3.52 Gbp, total 411.05 Gbp; 94 runs with a base count) · layout PAIRED 94 · platform ILLUMINA 94 · models Illumina HiSeq 3000 (94) · 77% of runs with a Sandpiper profile · first public 2020-05-01
Authors (5)
Schmidt V first · Enav H · Spector TD · Youngblut ND · Ley RE last
Downloads
PRJEB38000.csv.gz (3.6 KB) · parquet (74.5 KB) — all 94 samples, every field with route and confidence · PRJEB38000_determinations.csv.gz (8.5 KB) — 774 evidence rows