Gut microbiome in HIV-exposed mother-infant pairs, Kenya/USA
Impact of SARS-CoV-2 in stool sample from women living with HIV and HIV-negative women and their infants.
Longitudinal cohort of 655 stool samples from mothers (some living with HIV) and infants in Nairobi, Kenya and Arizona, USA, examining SARS-CoV-2 seroconversion and its influence on gut bacterial and viral microbiomes. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalmother–infant
139 of 150 people sampled more than once (644 samples; median 4, up to 22 per person) · follow-up median 7 mo (max 10 mo) · median interval between samples 3 mo(time from collection dates).
Each row is one person (36 shown of 139); 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).
63 mother–infant dyads plus 9 infants without a maternal sample (72 families; ptnum links mother and infant) · 63 families with 126 sampled people (63 with a parent and a child).
63 × mother + child
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: 24 of 63 families (one per family structure, then more). 150 people in the project overall.
Bifidobacterium 18.7%Prevotella 10.1%Faecalibacterium 7.6%Ruminococcoides 3.8%Collinsella 3.1%Streptococcus 2.5%Blautia_A 2.3%Roseburia 1.8%Dialister 1.3%Gemmiger 1.2%Bacteroides 0.9%Mediterraneibacter 0.9%not assigned to a genus 15.7%other genera 29.9%
Genera, mean relative abundance over 396 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants. PMID 39185682PMC11352790curated
Details
Archive description
SARS-CoV-2 infection is known to alter the gut virome and bacterial microbiome of individuals, even those with mild severity. However, the impact of SARS-CoV-2 on the gut microbiome of women living with HIV (WLHIV) and their children is poorly understood. In this study, metagenomic sequencing was used to analyze the stool samples of 63 mother and 72 infants that seroconverted to SARS-CoV-2 with mild disease and found SARS-CoV-2 to influence their bacterial and viral microbiomes. Overall, our study provides valuable insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status on these populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and infant / toddler by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
hostrun.host_tax_id · “9606”
body siterun.scientific_name · “human gut metagenome”
life stagestudy.title · “living with HIV and HIV-negative women and their infants”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN39242275
collection_date
2020-01-14
R1
0.85
biosample.attribute:collection_date
2020-01-14
SAMN39242275
country
KE
R1
0.90
biosample_attr
Kenya:Nairobi
SAMN39242275
family_id
PRJNA1045584:fam166
R1
0.85
biosample.attribute:ptnum
ptnum: 166; patient: 44110166B1
SAMN39242275
family_role
child
R1
0.85
biosample.attribute:personcode
personcode: Infant
SAMN39242275
location_locality
Nairobi
R3
0.70
paper.fulltext.methods
Mathare North Health Center in Kenya, Narobi
SAMN39242275
location_site
Mathare North Health Center
R3
0.70
paper.fulltext.methods
enrolled in their third trimester
SAMN39242275
subject_id
44110166B1
R1
0.85
biosample_attr
44110166B1
Sequencing
655 runs over 655 samples · mean 3.10 Gbp per run (median 2.43 Gbp, total 2,027.66 Gbp; 655 runs with a base count) · layout PAIRED 655 · platform ILLUMINA 655 · models NextSeq 2000 (655) · 65% of runs with a Sandpiper profile · first public 2024-09-11