Biology subjects

Serghiou, I. R.

Publications and source records attributed to Serghiou, I. R..

2 recordsLinked to original sources

bioRxiv2023

Gut microbiota and faecal cytokine profiles of rural Cambodian infants and links to early life nutrition and diarrhoeal episodes.

The gut microbiota of infants in low-middle income countries like Cambodia remain underrepresented in microbiome research. This study aimed to explore the faecal gut microbiota composition and faecal cytokine profiles in a cohort of infants living in a rural province of Cambodia and explore the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants (96 samples in total) after 7 months of age were analysed using 16S rRNA amplicon sequencing to determine the composition of the microbiota. Bacterial strains were isolated and subjected to whole genome sequencing and genomic analysis and concentrations of faecal cytokines were also measured. Initially, we compared the effects of two sample collection methods due to the challenges of faecal sample collection and storage in a rural location. Storage of faecal samples in a DNA preservation solution retained a greater abundance of Bacteroides. Analyses of microbiota composition of samples stored in DNA preservation solution indicated that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, particularly in breastfed infants. Most infants had detectable pathogenic taxa indicating frequent pathogen exposure, with Shigella and Klebsiella more abundant in infants with recent diarrheal illness. We did not detect antibiotic-associated perturbations in the gut microbiota, and no associations were found between the gut microbiota and infant growth. Genomic analysis of isolated strains indicated the presence of gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and Bifidobacterium breve isolates. The presence of antibiotic-resistant genes was also identified in potentially pathogenic species, as well as in beneficial genera including Bifidobacterium. Faecal cytokine analysis showed higher concentrations of Interlukin-1alpha and vascular endothelial growth factor in breastfed infants, which may influence the infant gut mucosal immune system. This study provides insights into an underrepresented population of rural Cambodian infants, emphasising the impact of pathogen exposure and breastfeeding on gut microbiota composition and faecal immune profiles.

microbiology↗

bioRxiv2023

An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs

The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome. Impact StatementDetermining the functional capabilities of microbial communities within different human microbiomes is important to understand their impacts on health. Extraction of sufficient DNA is challenging, especially from low biomass samples, such as skin swabs suitable for shotgun metagenomics, which is needed for taxonomic resolution and functional information. Here we describe an optimised DNA extraction method that produces enough DNA from skin swabs, suitable for shotgun metagenomics, and demonstrate it can be used to effectively characterise the skin microbiota. This method will allow future studies to identify taxonomic and functional changes in the skin microbiota which is needed to develop interventions to improve and maintain skin health. Data SummaryAll sequence data and codes can be accessed at: NCBI Bio Project ID: PRJNA937622 DOI: https://github.com/quadram-institute-bioscience/coronahit_guppy DOI: https://github.com/ilianaserghiou/Serghiou-et-al.-2023-Codes

genomics↗