Environmental exposures and child and maternal gut microbiota in rural Malawi

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

32011017

DOI Digital object identifier for electronic documents.

10.1111/ppe.12623

URI

https://pubmed.ncbi.nlm.nih.gov/32011017/

Authors

Kortekangas E, Kamng'ona AW, Fan YM, Cheung YB, Ashorn U, Matchado A, Poelman B, Maleta K, Dewey KG, Ashorn P

Journal

Paediatric and perinatal epidemiology

Year

2020

Keywords:

child health, environment, gut microbiota, seasons, socio-economic factors

BACKGROUND: Gut microbiota composition is associated with child health, but the effect of the environment on microbiota composition is not well understood. Few studies have been conducted in low-income settings where childhood malnutrition is common and possibly related to microbiota composition. OBJECTIVES: To investigate whether gut microbiota composition in young children and their mothers is associated with different environmental exposures in rural Malawi. We hypothesized that more adverse environmental exposures would be associated with lower levels of microbiota maturity and diversity. METHODS: Faecal samples from up to 631 children and mothers participating in a nutrition intervention trial were collected at 1, 6, 12, 18, and 30 months (children) and at 1 month (mothers) after birth and analysed for microbiota composition with 16S rRNA sequencing. Bacterial OTU and genus abundances, measures of microbiota maturity and diversity, and UniFrac distances were compared between participants with different environmental exposures. The exposure variables included socio-economic status, water source, sanitary facility, domestic animals, maternal characteristics, season, antibiotic use, and delivery mode. RESULTS: Measures of microbiota maturity and diversity in children were inversely associated with maternal education at 6, 18, and 30 months and did not otherwise differ consistently between participants with different environmental exposures. Phylogenetic distance was related to season of stool sample collection at all time points. At the level of individual OTUs and genera, season of stool sample collection, type of water source, and maternal education showed most associations with child gut microbiota, while HIV status was the most important predictor of relative OTU and genus abundances in mothers. CONCLUSION: The results do not support the hypothesis that adverse environmental exposures are broadly associated with lower microbiota maturity and diversity but suggest that environmental exposures influence the abundance of several bacterial OTUs and genera and that low maternal education is associated with higher microbiota maturity and diversity.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2022/07/20

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1, WikiWorks

Subjects

Location of subjects: Malawi

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: seasonal gut microbiome measurement seasonal gut microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: samples taken in dry/hot or rainy season
Group 1 name Corresponds to the case (exposed) group for case-control studies: samples taken in dry/cold season
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: samples taken in the dry/cold season
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): NA

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Zero-Inflated Beta Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: antibiotic exposure, delivery procedure, education level, marital status, maternal age, sex

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2022/07/20

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Figure 3

Description: Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season

Abundance in Group 1: increased abundance in samples taken in dry/cold season

NCBI	Quality Control	Links
Prevotella
Streptococcus porcinus
Faecalibacterium prausnitzii
Oscillospiraceae
Clostridium
Clostridiales bacterium
Faecalibacterium

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2022/07/20

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Figure 3

Description: Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season

Abundance in Group 1: decreased abundance in samples taken in dry/cold season

NCBI	Quality Control	Links
Enterobacter
Agathobacter rectalis CAG:36
Clostridiales bacterium
Clostridium
Granulicatella adiacens
Neisseria
Bacteroides fragilis
Ruminococcus
Enterobacteriaceae
Bacteroides thetaiotaomicron

Revision editor(s): Kaluifeanyi101, Claregrieve1