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  3. The Indoor Microbiome: Sampling, Analysis And Emerging Trends.
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  3. The Indoor Microbiome: Sampling, Analysis And Emerging Trends.

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The Indoor Microbiome: Sampling, Analysis and Emerging Trends.

Iva Šunić1, Jelena Šarac1,2, Dubravka Havaš Auguštin1

  • 1Institute for Anthropological Research, Zagreb, Croatia.

Environmental Microbiology Reports
|April 7, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

Standardizing indoor microbiome research methods is crucial for understanding links between indoor microbes and respiratory health. This review highlights inconsistencies in current approaches, impacting comparability and reproducibility.

Keywords:
dust microbiomeindoor air qualitymethodological harmonisationsampling methodssequencing methods

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Area of Science:

  • Microbiology
  • Environmental Health
  • Bioinformatics

Background:

  • Indoor microbial communities significantly influence human health, particularly respiratory conditions like asthma and allergies.
  • Research on indoor microbial exposures is hindered by methodological inconsistencies, complicating data comparison and conclusion drawing.
  • Understanding the indoor microbiome is vital for public health and environmental science.

Purpose of the Study:

  • To systematically review and analyze methodologies used in indoor microbiome research.
  • To identify trends, inconsistencies, and areas needing standardization in sampling, DNA extraction, sequencing, and bioinformatics.
  • To assess the impact of these methods on cross-study comparability and reproducibility.

Main Methods:

  • Systematic review of 106 studies published between 2000 and 2025 on indoor microbiomes.
  • Assessment of sampling strategies (e.g., passive sampling, dust collection), DNA extraction protocols, sequencing technologies (e.g., 16S rRNA, ITS amplicon sequencing), and bioinformatic pipelines.
  • Analysis of microbial taxa detected and factors influencing microbial diversity.

    • Main Results:

    • Passive dust collection was the most common sampling method; Illumina-based 16S rRNA and ITS sequencing were dominant molecular techniques.
    • Significant variations in gene regions, extraction kits, and analytical tools limited comparability across studies.
    • Consistent detection of key bacterial (Staphylococcus, Streptococcus) and fungal (Cladosporium, Aspergillus) taxa was observed, influenced by environmental factors.

    Conclusions:

    • Standardized protocols are urgently needed in indoor microbiome research to enhance reproducibility and enable robust meta-analyses.
    • Harmonized methods will facilitate the development of evidence-based health guidelines for indoor environments.
    • Addressing methodological inconsistencies is key to advancing our understanding of indoor microbiomes and their health implications.