Does entry to center-based childcare affect gut microbial colonization in young infants?

Hermes, Gerben D. A.; Eckermann, Henrik; Vos, Willem M. de; Weerth, Carolina de

doi:10.1038/s41598-020-66404-z

Cited by 17 publications

(23 citation statements)

References 64 publications

(69 reference statements)

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“…Source : The redundancy analysis representation was taken from Hermes et al. (2020), the non‐metric multidimensional scaling was taken from Adams et al. (2017), the bar graph of the linear discriminant analysis effect size was taken from Hoffman et al.…”

Section: Advanced Data Analysis and Visualisationmentioning

confidence: 99%

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Regueira‐Iglesias,

Balsa‐Castro,

Blanco‐Pintos

et al. 2023

Molecular Oral Microbiology

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The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision‐making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene‐derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome‐based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome‐specific methods for accounting for or correcting them.

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Section: Advanced Data Analysis and Visualisationmentioning

confidence: 99%

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Regueira‐Iglesias,

Balsa‐Castro,

Blanco‐Pintos

et al. 2023

Molecular Oral Microbiology

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“…Early education and child care programs across the country have reported substantial drops in enrollment attributable to statewide or voluntary center closures throughout the pandemic along with parental preferences not to enroll in daycare in order to limit COVID-19 exposures. 31 While longitudinal studies have suggested that entry into childcare versus continued care at home by parents does not impact an infant's microbial composition, research in this area is nascent and data from existing studies reflect pre-COVID-19 behaviors. 32 Restricted travel either due to state mandates or personal preferences have also occurred over the last 12 months, with a 43% reduction in air travel compared with 2019.…”

Section: Daycare and Travel Exposurementioning

confidence: 99%

COVID-19 and the neonatal microbiome: will the pandemic cost infants their microbes?

2021

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Mortality and morbidity from infections in children remains low, including an exceedingly low rate of horizontal and vertical transmission. However, unforeseen complications to childhood health have emerged secondary to the pandemic. Few studies to date have examined unintended complications of the pandemic in newborns and infants. In this Commentary, we discuss the impact that COVID-19 may have on inheritance of the newborn microbiome and its assembly throughout the first years of life. In the early stages of the pandemic when vertical transmission of COVID-19 was poorly understood, several studies reported increased rates of C-sections in COVID-19 positive women. Initial recommendations discouraged COVID-19 positive mothers from breastfeeding and participating in skin-to-skin care, advising them to isolate during their window of infectivity. These shifts in perinatal care can adversely impact microbial colonization during the first 1000 days of life. While obstetrical and neonatal management have evolved to reflect our current knowledge of perinatal transmission, we are observing other changes in early life exposures of infants, including increased attention to hygiene, fewer social interactions, and decreased global travel, all of which are major drivers of early-life gut colonization. Composition of the gut microbiota in adults directly impacts severity of infection, suggesting a role of microbial communities in modulating immune responses to COVID-19. Conversely, the role of the intestinal microbiome in susceptibility and severity of COVID-19 in newborns and children remains unknown. The onset of adulthood diseases is related to the establishment of a healthy gut microbiome during childhood. As we continue to define COVID-19 biology, further research is necessary to understand how acquisition of the neonatal microbiome is affected by the pandemic. Furthermore, infection control measures must be balanced with strategies that promote microbial diversity to impart optimal health outcomes and potentially modulate susceptibility of children to

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“…The gut microbiota plays a critical role in many fundamental aspects of health, and its normal development at early ages is required to maintain host fitness during childhood and later in life [1,2]. Longitudinal studies have uncovered that the gut microbiota develops in a relatively dynamic pattern in infancy and toddlerhood [3][4][5]. Importantly, this ecological succession may not come to an end within the first 3 years of life as previously believed [6,7], but changes continue at least until middle childhood, likely as a result of external influential factors [8].…”

Section: Introductionmentioning

confidence: 99%

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty

Belzer

Smidt

et al. 2023

Eur Child Adolesc Psychiatry

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Relations between the gut microbiota and host mental health have been suggested by a growing number of case–control and cross-sectional studies, while supporting evidence is limited in large community samples followed during an extended period. Therefore, the current preregistered study (https://osf.io/8ymav, September 7, 2022) described child gut microbiota development in the first 14 years of life and explored its relations to internalizing and externalizing difficulties and social anxiety in puberty, a period of high relevance for the development of mental health problems. Fecal microbiota composition was analysed by 16S ribosomal RNA gene amplicon sequencing in a total of 1003 samples from 193 children. Through a clustering method, four distinct microbial clusters were newly identified in puberty. Most children within three of these clusters remained in the same clusters from the age of 12 to 14 years, suggesting stability in microbial development and transition during this period. These three clusters were compositionally similar to enterotypes (i.e., a robust classification of the gut microbiota based on its composition across different populations) enriched in Bacteroides, Prevotella, and Ruminococcus, respectively. Two Prevotella 9-predominated clusters, including one reported by us earlier in middle childhood and the other one in puberty, were associated with more externalizing behavior at age 14. One Faecalibacterium-depleted pubertal cluster was related to more social anxiety at age 14. This finding was confirmed by a negative cross-sectional relation between Faecalibacterium and social anxiety in the 14-year-olds. The findings of this study continue to map gut microbiota development in a relatively large community sample followed from birth onwards, importantly extending our knowledge to puberty. Results indicate that Prevotella 9 and Faecalibacterium may be relevant microbial taxa in relation to externalizing behavior and social anxiety, respectively. These correlational findings need validations from other similar cohort studies, as well as well-designed mechanistic pre-clinical investigations before inferring cause and effect.

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Does entry to center-based childcare affect gut microbial colonization in young infants?

Cited by 17 publications

References 64 publications

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

COVID-19 and the neonatal microbiome: will the pandemic cost infants their microbes?

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty

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