Bindels, Laure BLaure BBindelsWatts, Joy E MJoy E MWattsTheis, Kevin RKevin RTheisCarrion, Víctor JVíctor JCarrionOssowicki, AdamAdamOssowickiSeifert, JanaJanaSeifertOh, JuliaJuliaOhShao, YongqiYongqiShaoHilty, MarkusMarkusHilty0000-0002-2418-6474Kumar, PurnimaPurnimaKumarHildebrand, FalkFalkHildebrandLovejoy, ConnieConnieLovejoyWigley, PaulPaulWigleyYu, KeKeYuZhang, MeilingMeilingZhangZhang, TongTongZhangWalter, JensJensWalterDesai, Mahesh SMahesh SDesaiHuws, Sharon AnnSharon AnnHuwsSchriml, Lynn MLynn MSchrimlRavel, JacquesJacquesRavelFricke, W FlorianW FlorianFrickeEloe-Fadrosh, Emiley AEmiley AEloe-FadroshLee, Charles KCharles KLeeClavel, ThomasThomasClavel2025-04-292025-04-292025-04-08https://boris-portal.unibe.ch/handle/20.500.12422/209793This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.en600 - Technology::610 - Medicine & healtharticle10.48620/876124020030610.1186/s40168-025-02091-0