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Dalby, Matthew J., Kiu, Raymond, Serghiou, Iliana R., Miyazaki, Asuka, Acford-Palmer, Holly, Tung, Rathavy, Caim, Shabhonam, Phillips, Sarah, Kujawska, Magdalena, Matsui, Mitsuaki, Iwamoto, Azusa, Taking, Bunsreng, Cox, Sharon E. and Hall, Lindsay J. 
ORCID: https://orcid.org/0000-0001-8938-5709
(2024)
Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes.
npj Biofilms and Microbiomes, 10.
ISSN 2055-5008
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Abstract
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.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability statement: Bacterial pure genome assemblies are now deposited at NCBI GenBank under project accession PRJNA958097, while 16S rRNA amplicon sequencing raw reads are deposited in NCBI SRA under project PRJNA958098. Code availability statement: Bacterial pure genome assemblies are now deposited at NCBI GenBank under project accession PRJNA958097, while 16S rRNA amplicon sequencing raw reads are deposited in NCBI SRA under project PRJNA958098. Funding Information: We thank the families for participating in the study. L.J.H. is supported by Wellcome Trust Investigator Awards 100974/C/13/Z and 220876/Z/20/Z; the Biotechnology and Biological Sciences Research Council (BBSRC), Institute Strategic Programme Gut Microbes and Health BB/R012490/1, and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. |
| Uncontrolled Keywords: | biotechnology,microbiology,applied microbiology and biotechnology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences Faculty of Medicine and Health Sciences > Norwich Medical School |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 09:30 |
| Last Modified: | 28 Oct 2024 00:53 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97127 |
| DOI: | 10.1038/s41522-024-00562-0 |
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