Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children
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ABSTRACT:
PROVIDER: PRJEB70876 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12408600_1.fastq.gz | Fastqsanger.gz | |||
| ERR12408600_2.fastq.gz | Fastqsanger.gz | |||
| ERR12408601_1.fastq.gz | Fastqsanger.gz | |||
| ERR12408601_2.fastq.gz | Fastqsanger.gz | |||
| ERR12408602_1.fastq.gz | Fastqsanger.gz |
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Project description:An exposure to diverse microbial population early in life is important for the development of immunity against various non-communicable diseases including asthma, childhood leukaemia and other cancers. Social mixing in daycare settings helps with exposure to a variety of microbes. However, social isolation and a high emphasis on workplace hygiene during the COVID pandemic may have affected children's exposure to diverse microbiota. The structure of microbial communities and their role in developing immunity to various diseases are not well understood. In this study, we investigated the structure of microbial communities in daycare and home settings during the pandemic. Interestingly, microbial diversity was relatively higher in dust samples collected from homes, with human-associated taxa being more prevalent compared to those from daycare settings. Environmental microbes were more abundant in dust samples from daycare providers. These results potentially suggest that cleaning practices during the pandemic may have influenced the diversity and microbial abundance of the daycare samples. Several bacterial taxa detected in both the environments are known to induce anti-inflammatory and immunomodulatory responses, conferring protection from various diseases. Therefore, exposure to diverse microbial population in early childhood may play an important role in developing immunity against various non-communicable and infectious diseases.
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Project description:Lower Respiratory Tract and Home Dust Microbiomes and Traffic Pollution Exposure
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Project description:Background: During gestation, stressors to the fetus, including viral exposure or maternal psychological distress, can fundamentally alter the neonatal epigenome, and may be associated with long-term impaired developmental outcomes. The impact of in utero exposure to the COVID-19 pandemic on the newborn epigenome has yet to be described. Methods: This study aimed to determine whether there are unique epigenetic signatures in newborns who experienced otherwise healthy pregnancies that occurred during the COVID-19 pandemic (Project RESCUE). The pre-pandemic control and pandemic cohorts (Project RESCUE) included in this study are part of a prospective observational and longitudinal cohort study that evaluates the impact of elevated prenatal maternal stress during the COVID-19 pandemic on early childhood neurodevelopment. Using buccal swabs collected at birth, differential DNA methylation analysis was performed using the Infinium MethylationEPIC arrays and linear regression analysis. Pathway analysis and gene ontology enrichment were performed on resultant gene lists. Results: Widespread differential methylation was found between neonates exposed in utero to the pandemic and pre-pandemic neonates. In contrast, there were no apparent epigenetic differences associated with maternal COVID-19 infection during pregnancy. Differential methylation was observed among genomic sites that underpin important neurological pathways that have been previously reported in the literature to be differentially methylated because of prenatal stress, such as NR3C1. Conclusions: The present study reveals that the onset and continuation of the COVID-19 pandemic has fundamentally altered the epigenomes of newborns born during this time, even in otherwise healthy pregnancies, which should be considered in current and future epigenetic studies and may act as a critical biomarker of stress.
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Project description:We previously identified Keratinocyte-associated protein 3, Krtcap3, as an obesity-related gene in female rats where a whole-body Krtcap3 knock-out (KO) led to increased adiposity compared to wild-type (WT) controls when fed a high-fat diet (HFD). We sought to replicate this work to better understand the function of Krtcap3 but were unable to reproduce the adiposity phenotype. In the current work, WT female rats ate more compared to WT in the prior study, with corresponding increases in body weight and fat mass, while there were no changes in these measures in KO females between the studies. The prior study was conducted before the COVID-19 pandemic, while the current study started after initial lock-down orders and was completed during the pandemic with a generally less stressful environment. We hypothesize that the environmental changes impacted stress levels and may explain the failure to replicate our results. Analysis of corticosterone (CORT) at euthanasia showed a significant study by genotype interaction where WT had significantly higher CORT relative to KO in Study 1, with no differences in Study 2. These data suggest that decreasing Krtcap3 expression may alter the environmental stress response to influence adiposity. We also found that KO rats in both studies, but not WT, experienced a dramatic increase in CORT after their cage mate was removed, suggesting a separate connection to social behavioral stress. Future work is necessary to confirm and elucidate the finer mechanisms of these relationships, but these data indicate the possibility of Krtcap3 as a novel stress gene.
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Project description:The aim of this study was to assess the gene expression profil of skin chilblain-like lesions that appeared during the COVID-19 pandemic and to compare it with seasonal chilblain and healthy skin
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Project description:BackgroundThe Covid-19 pandemic necessitated social distancing restrictions, which placed limitations on access to ophthalmic care to only those who had an imminent risk of sight loss. All other face-to-face consultations were converted to telephone consultations or were postponed. We investigated whether parents were able to test their child's vision using available home vision testing applications, with an aim to aid decision making during a telephone consultation.MethodsFamilies with follow-up consultations at Birmingham Children's Hospital were asked to test their child's vision at home. Instructions for the use of Peek acuity, or iSight Pro, were emailed to a parent. Parents chose to use a particular app based on available devices at home. Parents were asked to test uniocular visual acuity twice. Home versus hospital acuity was correlated. Home acuity test-retest reliability was acquired. Parental feedback was obtained through questionnaires.ResultsOne hundred and three families were contacted, 15 families completed home vision testing. Ten families used Peek acuity, five families used iSight Pro. Uniocular visual acuity test-retest reliability was 0.03 LogMAR. Home-hospital acuity testing had a bias of 0.14 LogMAR, hospital acuity yielding a lower LogMAR score. Most families who completed testing found it easy to do; however, some struggled, and 81 families did not undertake home vision testing.ConclusionsUptake of home vision testing was limited by parental engagement, most likely influenced by the current pandemic. Most families who undertook home vision testing were able to generate results that could be used for clinical decision making. Extending the impact of parental vision testing will require education by clinicians and further study to increase sample sizes and to improve confidence.
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Project description:People living with HIV (PWH) often exhibit poor responses to influenza vaccination despite effective combination anti-retroviral (ART) mediated viral suppression. There exists a paucity of data in identifying immune correlates of influenza vaccine response in context of HIV infection that would be useful in improving its efficacy in PWH, especially in younger individuals. Transcriptomic data were obtained by microarray from whole blood isolated from aviremic pediatric and adolescent HIV-infected individuals (4-25 yrs) given two doses of Novartis/H1N1 09 vaccine during the pandemic H1N1 influenza outbreak. Supervised clustering and gene set enrichment identified contrasts between individuals exhibiting high and low antibody responses to vaccination. High responders exhibited hemagglutination inhibition antibody titers >1:40 post-first dose and 4-fold increase over baseline. Baseline molecular profiles indicated increased gene expression in metabolic stress pathways in low responders compared to high responders. Inflammation-related and interferon-inducible gene expression pathways were higher in low responders 3 wks post-vaccination. The broad age range and developmental stage of participants in this study prompted additional analysis by age group (e.g. <13yrs and >13yrs). This analysis revealed differential enrichment of gene pathways before and after vaccination in the two age groups. Notably, CXCR5, a homing marker expressed on T follicular helper (Tfh) cells, was enriched in high responders (>13yrs) following vaccination which was accompanied by peripheral Tfh expansion. Our results comprise a valuable resource of immune correlates of vaccine response to pandemic influenza in HIV infected children that may be used to identify favorable targets for improved vaccine design in different age groups.
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