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

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

37525095

DOI Digital object identifier for electronic documents.

10.1186/s12866-023-02951-5

URI

https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02951-5

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

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2023/10/18

Curator: Iram jamshed

Revision editor(s): Iram jamshed, Hodan Issah, ChiomaBlessing

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,nasopharyngeal gland

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Microbiome measurement Microbiome measurement,microbiome measurement

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: 44

Group 1 sample size Number of subjects in the case (exposed) group: 43

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None.

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).: relative abundances

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

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2023/10/19

Curator: Iram jamshed

Revision editor(s): Iram jamshed, Hodan Issah, ChiomaBlessing

Source: Additional file 2

Description: Comparison between indoor dust and nasopharyngeal bacteriome

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

NCBI	Quality Control	Links
Bacillota
Corynebacterium
Staphylococcus

Revision editor(s): Iram jamshed, Hodan Issah, ChiomaBlessing

Experiment 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28

Curated date: 2024/01/18

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Nasopharyngeal swab samples collected in the Morning from workplaces (NEO, ENT, RCX)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Nasopharyngeal swab samples collected in the afternoon from workplaces (NEO, ENT, RCX)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Nasopharyngeal swabs collected in the afternoon (after an 8 h exposure to the workplace environment). The participants were working at NEO, ENT, or RCX workplaces.