Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study

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Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Konecna E, Videnska P, Buresova L, Urik M, Smetanova S, Smatana S, Prokes R, Lanickova B, Budinska E, Klanova J, Borilova Linhartova P
Journal
BMC microbiology
Year
2023
Keywords:
16S rRNA, Bacteriome, Dust, Exposure, Hospital, Household, Indoor environment, Nasopharynx, Sequencing
BACKGROUND: Indoor dust particles are an everyday source of human exposure to microorganisms and their inhalation may directly affect the microbiota of the respiratory tract. We aimed to characterize the changes in human nasopharyngeal bacteriome after short-term exposure to indoor (workplace) environments. METHODS: In this pilot study, nasopharyngeal swabs were taken from 22 participants in the morning and after 8 h of their presence at the workplace. At the same time points, indoor dust samples were collected from the participants' households (16 from flats and 6 from houses) and workplaces (8 from a maternity hospital - NEO, 6 from a pediatric hospital - ENT, and 8 from a research center - RCX). 16S rRNA sequencing analysis was performed on these human and environmental matrices. RESULTS: Staphylococcus and Corynebacterium were the most abundant genera in both indoor dust and nasopharyngeal samples. The analysis indicated lower bacterial diversity in indoor dust samples from flats compared to houses, NEO, ENT, and RCX (p < 0.05). Participants working in the NEO had the highest nasopharyngeal bacterial diversity of all groups (p < 0.05). After 8 h of exposure to the workplace environment, enrichment of the nasopharynx with several new bacterial genera present in the indoor dust was observed in 76% of study participants; however, no significant changes were observed at the level of the nasopharyngeal bacterial diversity (p > 0.05, Shannon index). These "enriching" bacterial genera overlapped between the hospital workplaces - NEO and ENT but differed from those in the research center - RCX. CONCLUSIONS: The results suggest that although the composition of nasopharyngeal bacteriome is relatively stable during the day. Short-term exposure to the indoor environment can result in the enrichment of the nasopharynx with bacterial DNA from indoor dust; the bacterial composition, however, varies by the indoor workplace environment.

Experiment 1


Needs review

Curated date: 2023/10/18

Curator: Iram jamshed

Revision editor(s): Iram jamshed, Hodan Issah

Subjects

Location of subjects
Czechia
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
Nasopharyngeal gland Nasopharyngeal gland
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
nasopharyngitis chronic nasopharyngitis,inflammation of nasopharynx,nasopharynx inflammation,nasopharyngitis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Indoor dust samples
Group 1 name Corresponds to the case (exposed) group for case-control studies
Nasopharyngeal swab samples from workplaces
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The workplaces in the study were commercially used buildings characterized by higher levels of human occupancy and usage of HVAC (heating, ventilation, air conditioning) systems, both contributing to the higher abundance of microorganisms and their spread in the building . The participants working at NEO, ENT, or RCX workplaces were included in the study
Group 0 sample size Number of subjects in the control (unexposed) group
22
Group 1 sample size Number of subjects in the case (exposed) group
21

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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).
centered log-ratio
Statistical test
Mann-Whitney (Wilcoxon)
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
2.0

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2023/10/19

Curator: Iram jamshed

Revision editor(s): Iram jamshed, Hodan Issah

Source: Additional file 2

Description: Abundant bacteria in Nasopharyngeal samples

Abundance in Group 1: increased abundance in Nasopharyngeal swab samples from workplaces

NCBI Quality ControlLinks
Actinomycetota
Bacillota
Corynebacterium
Staphylococcus

Revision editor(s): Iram jamshed, Hodan Issah