The Pregnancy and EARly Life study (PEARL) - a longitudinal study to understand how gut microbes contribute to maintaining health during pregnancy and early life

Phillips, Sarah; Watt, Rachel; Atkinson, Thomas G.; Hayhoe, Antonietta; Hall, Lindsay J.; team, Pearl study

doi:10.1186/s12887-021-02835-5

Cited by 4 publications

(6 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Samples were stored in a 4 °C fridge and anonymised with a unique barcode before being collected and tested on the same day swabbing was performed. In addition to the adult volunteers, swabs (using charcoal cotton swabs M40-A2, Technical Service Consultants Ltd.) from the skin of ten babies collected at 4 months of age, as part of the PEARL study, were also included (see Phillips et al ., [17] for study design and inclusion criteria, and Table S1 for baby participant metadata); the PEARL Study selected the use of charcoal cotton swabs due to their suitability for sampling multiple body sites (i.e. vagina, gut and skin) and long-term preservation of microbes in the −80 degrees Celsius freezer.…”

Section: Methodsmentioning

confidence: 99%

“…To address this need we describe here an optimised high-throughput automated DNA extraction method, for recovery of HMW microbial DNA from skin swabs. This was validated using skin swabs from adult volunteers and babies enrolled in the Pregnancy and Early Life (PEARL) study [17]. The method results in DNA with yield and molecular weight suitable for SMS.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2023

Self Cite

View full text Add to dashboard Cite

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-based 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.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…Samples were stored in a 4°C fridge and anonymised with a unique barcode before being collected and tested on the same day swabbing was performed. In addition to the adult volunteers, swabs from the skin of ten babies collected at four months as part of the PEARL study were also included (see Phillips, et al, (2021) for study design and inclusion criteria, and Table S1 for baby participant metadata).…”

Section: Study Design For Adult Volunteer and Pearl Study Baby Skin S...mentioning

confidence: 99%

“…To address this need we describe here an optimised high-throughput automated DNA extraction method, for recovery of HMW microbial DNA from skin swabs. This was validated using skin swabs from adult volunteers and babies enrolled in the Pregnancy and Early Life 4 (PEARL) study (Phillips, et al, 2021). The method results in DNA with yield and molecular weight suitable for SMS.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Serghiou¹,

Baker²,

Evans³

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Kiu,

Darby,

Alcon-Giner

et al. 2024

Preprint

View full text Add to dashboard Cite

Preterm infants (<37 weeks’ gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. However, antibiotics can disrupt the development of early-life microbiota, potentially impairing gut immunity and colonisation resistance. Evidence shows that probiotics (e.g., certainBifidobacteriumstrains) may help restore healthy gut microbiota. In this study, we examined the effects of probiotics and antibiotics on the preterm gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk- fed preterm infants (moderate to very preterm), with one cohort receiving probiotics. Within each group, some infants were treated with antibiotics (benzylpenicillin and/or gentamicin) while others served as non-antibiotic treated controls. We performed shotgun metagenomic sequencing on 93 longitudinal faecal samples from 34 infants, generated >300 metagenome- assembled genomes, and obtained ∼90 isolate genomes through targeted culturomics, enabling analysis of the microbiome/resistome at species and strain levels. Additionally, we investigatedin vitrohorizontal gene transfer (HGT) capacity of preterm infant-derived multidrug-resistant (MDR) pathogenEnterococcusvia neonatal gut models. Overall, probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and helped restore a typical early-life microbiota. However, the persistence of MDR pathogens likeEnterococcus, with high HGT potential, highlights the need for ongoing surveillance in neonatal care. Our findings underscore the complex interactions between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.

show abstract

The Pregnancy and EARly Life study (PEARL) - a longitudinal study to understand how gut microbes contribute to maintaining health during pregnancy and early life

Cited by 4 publications

References 22 publications

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

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

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

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Contact Info

Product

Resources

About