Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

39277573

DOI Digital object identifier for electronic documents.

https://doi.org/10.1038/s41522-024-00562-0

URI

Authors

Dalby MJ, Kiu R, Serghiou IR, Miyazaki A, Acford-Palmer H, Tung R, Caim S, Phillips S, Kujawska M, Matsui M, Iwamoto A, Taking B, Cox SE, Hall LJ

Journal

NPJ biofilms and microbiomes

Year

2024

The gut microbiota of infants in low- to middle-income countries is underrepresented in microbiome research. This study explored the faecal microbiota composition and faecal cytokine profiles in a cohort of infants in a rural province of Cambodia and investigated the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants were analysed for microbiota composition using 16S rRNA amplicon sequencing and concentrations of faecal cytokines. Faecal bacterial isolates were subjected to whole genome sequencing and genomic analysis. We compared the effects of two sample collection methods due to the challenges of faecal sample collection in a rural location. Storage of faecal samples in a DNA preservation solution preserved Bacteroides abundance. Microbiota analysis of preserved samples showed that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, with higher abundance in breast-fed infants. Most infants had detectable pathogenic taxa, with Shigella and Klebsiella more abundant in infants with recent diarrhoeal illness. Neither antibiotics nor infant growth were associated with gut microbiota composition. Genomic analysis of isolates showed gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and B. breve isolates. Antibiotic-resistant genes were present in both potentially pathogenic species and in Bifidobacterium. Faecal concentrations of Interlukin-1alpha and vascular endothelial growth factor were higher in breast-fed infants. This study provides insights into an underrepresented population of rural Cambodian infants, showing pathogen exposure and breastfeeding impact gut microbiota composition and faecal immune profiles.

Experiment 1

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Curated date: 2024/10/16

Curator: Aishat

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Subjects

Location of subjects: Cambodia

Host species Species from which microbiome was sampled. Contact us to have more species added.: 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,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Diarrhea , Diarrhea, Infantile , Malnutrition Diarrhea,Diarrhoea,Watery stool,diarrhea,Diarrhea, Infantile,diarrhea, Infantile,Lack of food,Malnutrition,malnutrition

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Infants who are not breast-fed

Group 1 name Corresponds to the case (exposed) group for case-control studies: Infants who are breast-fed

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants that are being breastfed at the time of the research/sample collection

Group 0 sample size Number of subjects in the control (unexposed) group: 9

Group 1 sample size Number of subjects in the case (exposed) group: 23

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V9

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

Statistical Analysis

Statistical test: PERMANOVA; MaAsLin2; Pearson Correlation

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: time

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Richness Number of species: decreased

Signature 1

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Source: Figure 2C

Description: Bacterial genera differentially abundant between breastfed infants and infants who were not breastfed.

Abundance in Group 1: increased abundance in Infants who are breast-fed

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Bifidobacterium
Streptococcus

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Signature 2

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Source: Figure 3c

Description: Bacterial species differentially abundant between breastfed infants and infants who were not breastfed.

Abundance in Group 1: increased abundance in Infants who are breast-fed

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Bifidobacterium longum

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Signature 3

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Source: Figure 3c

Description: Bacterial species difference between breastfed infants and infants who were not breastfed

Abundance in Group 1: decreased abundance in Infants who are breast-fed

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Klebsiella pneumoniae

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Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Infants without diarrhea

Group 1 name Corresponds to the case (exposed) group for case-control studies: Infants with diarrhea

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants who experienced diarrhea within the 7 days prior to sample collection.