Laser-assisted microbial culturomics

Metagenomics have revolutionized the characterization of the human microbiome, but the lack of robust culture collections prevents detailed mechanistic studies. Here we describe the development and application of a laser-assisted culturomics platform, which consistsincorporating the elements of a bioprinter, the culture conditions, the methods to charactereization methods forthe microorganisms and a biobank. Laser-assisted bioprinting facilitates rapid and precise transfer of microorganisms from clinical biofilms to highly organized biofilm arrays, which are suitable for co-culturing and molecular analyses. The presented technique propagated 99 of 100 microbial species and recovered 80% of abundant species from dental plaque in accordance with according to full 16S gene profiling encompassing 691,199 sequences. Microscopy, spectroscopy and enzyme assays were used to guide isolations. Processing of oral biofilms from four individuals yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting indicated commensals that can potentially contribute to diseases development. Isolates from peri-implantitis covered 85.4% of the transcriptionally active clinical biofilms at the genus level. Collectivel Taken togethery, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.