Home sampling is a feasible method for oral microbiota analysis for infants and mothers

Collaborating to Improve Neonatal Care: ParentAl Participation on the NEonatal Ward-Study Protocol of the neoPARTNER Study

Parents are often appointed a passive role in the care for their hospitalised child. In the family-integrated care (FICare) model, parental involvement in neonatal care is emulated. Parental participation in medical rounds, or family-centred rounds (FCR), forms a key element. A paucity remains of randomised trials assessing the outcomes of FCR (embedded in FICare) in families and neonates, and outcomes on an organisational level are relatively unexplored. Likewise, biological mechanisms through which a potential effect may be exerted are lacking robust evidence. Ten level two Dutch neonatal wards are involved in this stepped-wedge cluster-randomised trial FCR (embedded in FICare) by one common implementation strategy. Parents of infants hospitalised for at least 7 days are eligible for inclusion. The primary outcome is parental stress (PSS:NICU) at discharge. Secondary outcomes include parental, neonatal, healthcare professional and organisational outcomes. Biomarkers of stress will be analysed in parent-infant dyads. With a practical approach and broad outcome set, this study aims to obtain evidence on the possible (mechanistic) effect of FCR (as part of FICare) on parents, infants, healthcare professionals and organisations. The practical approach provides (experiences of) FICare material adjusted to the Dutch setting, available for other hospitals after the study.

The Highly Leukotoxic JP2 Genotype of Aggregatibacter actinomycetemcomitans Is Present in the Population of the West African Island, Sal in Cape Verde: A Pilot Study

Aggregatibacter actinomycetemcomitans is strongly associated with severe periodontitis, possibly due to its production of a potent leukotoxin. A genetic variant, the JP2 genotype, was found to produce more leukotoxin than the wild type because of a mutation in the leukotoxin gene, and this genotype is frequently found in African populations. The aim of this study was to investigate whether this JP2 genotype can be found in a randomly selected group of inhabitants of Sal, Cape Verde. Twenty-nine adults between 20 and 59 years of age (58.6% female) participated, and information on their oral health and living standards was collected. An oral examination was performed for each participant, including DMF-T and CPI scores. Plaque and saliva samples were collected and transported to Europe, where DNA was isolated, and the concentration of A. actinomycetemcomitans and its JP2 genotype was determined using dedicated PCR analyses. All 29 plaque and 31% of the saliva samples harboured A. actinomycetemcomitans, and two participants were positive for the JP2 genotype. The presence of this JP2 genotype was not associated with either CPI or DMF-T. This pilot study is the first to describe the presence of the A. actinomycetemcomitans JP2 genotype in a Cape Verdean population living in the Cape Verde Islands, and the findings warrant further research.

Comparability of microbiota of swabbed and spit saliva

In general, saliva is used for microbiota analysis in longitudinal studies, and several collection methods are being used. Using a robust sample collection procedure is important, as it may influence salivary composition. This study explored the comparability of the microbiota of swabbed and spit saliva. Twenty‐two females participated in this cross‐sectional study. The bacterial composition of the three saliva samples (swab collected by the participant (SW‐P), swab collected by the researcher (SW‐R), and spit (SP) was assessed by 16S rRNA gene amplicon sequencing. The bacterial composition of the swabbed and the spit saliva was significantly different irrespective of the operator, and Shannon diversity was significantly higher in spit saliva than in SW‐P and SW‐R. The salivary microbiota of spit and swabbed adult saliva differs significantly. Research on microbial composition therefore requires collection of similar saliva sample types in all study participants.

Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples

Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition.

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Lysis buffer keeps the microbial composition stable during various storage conditions

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Host DNA depletion introduces a larger bias toward Gram-negative taxa

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The HostZERO Microbial DNA kit performed best in human DNA depletion for metagenomics

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Body site-specific approach based on microbial composition is needed to minimize bias