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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
Summary
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.
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.
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