Šunić, IvaŠarac, JelenaAuguštin, Dubravka HavašPozdniakova, SofyaFerguson, Robert M.Jergović, MatijanaVisentin, DavidBorràs, SilviaArcher, ElizabethHenderson, Drew K.Vitko, SandraAšić, AdnaBošnjaković, AnjaMaglica, ŽeljkaViegas, CarlaNovokmet, NatalijaKarlović, NinaMarjanović, DamirMuszyński, AdamLiu, YuxiKarisola, PiiaAlenius, HarriKrych, LukaszLovrić, Mario2026-04-142026-04-142026-04Šunić I, Šarac J, Auguštin DH, Pozdniakova S, Ferguson RM, Viegas C, et al. The indoor microbiome: sampling, analysis and emerging trends. Environ Microbiol Rep. 2026;18(2):e70272.1758-22291758-2229http://hdl.handle.net/10400.21/22778This work was supported by the European Union's Horizon Europe research and innovation programme, Grant Agreement No. 101057497 and Grant Agreement No. 101057779. The European Union, Grant agreement: 101056883. Swiss State Secretariat for Education, Research and Innovation, SERI grant agreement 22.00324. United Kingdom Research and Innovation, UKRI grant agreement 10040524. Australian National Health and Medical Research Council, NHMRC grant agreements APP2017786, NHMRC grant agreements APP2008813—European Union's Call on Environment and Health (HORIZON-HLTH-2021-ENVHLTH-02), 101057693.Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as Staphylococcus, Streptococcus, and Corynebacterium, and fungal taxa including Cladosporium, Aspergillus, and Penicillium, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.engDust microbiomeIndoor airAir qualityMethodological harmonisationSampling methodsSequencing methodsjournal article10.1111/1758-2229.70272