Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

40778780

DOI Digital object identifier for electronic documents.

10.1128/msystems.00467-25

URI Uniform resource identifier for web resources.

https://doi.org/10.1128/msystems.00467-25

Authors

Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H., Saavedra C.P.

Journal

mSystems

Year

2025

Keywords:

nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition

The "School MicroBE" initiative explores how the built environment impacts microbial communities in school-aged children by examining temporal dynamics and shifts in nasopharyngeal and oral microbiomes. This longitudinal study involved 119 children aged 4 to 13 at a public school, with nasopharyngeal and oral samples collected in autumn, winter, and spring of 2023. Using 16S rRNA gene sequencing, we assessed microbial composition through alpha and beta diversity analyses, characterized microbial assemblages, and evaluated the relative abundance of key taxa. Significant seasonal variations were observed, with an increase in alpha diversity from autumn to spring in nasopharyngeal samples. Beta diversity analyses did not reveal distinct clustering patterns based on collection months. Hierarchical clustering identified four major microbiome groups with characteristic taxonomic distribution, and co-occurrence network analysis suggested both synergistic and competitive interactions among taxa. Longitudinal transition analysis between microbiome clusters revealed dynamic changes over time, providing a baseline of microbiome states in the tested children. These findings highlight the importance of microbial community shifts in the environment by providing direct measures on microbiome stability and diversity in children, providing insights into how microbial communities respond to environmental fluctuations, including potential pathogen exposures. Understanding these temporal changes will improve the development of targeted public health strategies to assess and manage potential infectious disease outbreaks and the emergence of antimicrobial resistance in school settings.IMPORTANCEThe "School MicroBE" initiative enhances our understanding of pediatric microbiome dynamics by revealing temporal and compositional shifts, thus establishing basal studies on a sentinel school contributing to the understanding of pediatric microbiome and its associated health issues.

Experiment 1

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Curated date: 2025/10/15

Curator: Addanma

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Subjects

Location of subjects: Chile

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oral cavity , Nasopharynx Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,Epipharynx,Nasal part of pharynx,Nasenrachenraum,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Autumn

Group 1 name Corresponds to the case (exposed) group for case-control studies: Spring

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Microbial samples collected from children during Spring.

Group 0 sample size Number of subjects in the control (unexposed) group: 119

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Signature 1

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Source: Castro-Severyn J, Pacheco N, Valdivia G, et al. "Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative." mSystems, Vol. 10, No. 9, 2025. https://doi.org/10.1128/msystems.00467-25

Description: Streptococcus was the most abundant genus detected in both oral and nasopharyngeal samples of school-aged children. Its relative abundance increased from autumn to spring, reaching up to 40% in oral samples and 30% in nasopharyngeal samples in spring. It played a key role as a hub genus in the transition network analysis, associated with microbial community stability.

Abundance in Group 1: increased abundance in Spring

NCBI	Quality Control	Links
Streptococcus
NCBI Taxonomy: Streptococcus.NCBI Taxonomy: Streptococcus.

Revision editor(s): Addanma

Experiment 2

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Healthspan health span,health-span,Healthspan,healthspan

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: School-aged children sampled in spring. Samples collected from school-aged children (4–13 years) during spring (October) at “Rebeca Matte” public school, Renca, Santiago de Chile, Chile.

Group 0 sample size Number of subjects in the control (unexposed) group: 74

Group 1 sample size Number of subjects in the case (exposed) group: 153

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Children undergoing antibiotic treatment within 3 months prior to sample collection were excluded.

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: PERMANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 0

Matched on Factors on which subjects have been matched on in a case-control study: age, Matched on: "GENDER" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.GENDER

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, Confounders controlled for: "GENDER" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.GENDER

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: increased

Richness Number of species: increased

Signature 1

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Curated date: 2025/10/15

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Source: https://doi.org/10.1128/msystems.00467-25

Description: Streptococcus was identified as the most abundant and dominant genus in both oral and nasopharyngeal microbiomes of school-aged children. Its relative abundance increased from autumn to spring, reaching 40% in oral samples and 30% in nasopharyngeal samples in spring. Streptococcus was also a central hub in transition network analyses, contributing to community stability and resilience.

Abundance in Group 1: increased abundance in Spring

NCBI	Quality Control	Links
Streptococcus

Revision editor(s): Addanma