We shall progressively know and understand better the gut microbiota, its modulation by the diet and its relationship with the host health status. The last decade has seen the emergence of a broad range of applications for microarray-based DNA and RNA oligonucleotide libraries. In synthetic biology, DNA oligonucleotides are the building blocks for the assembly of single genes to whole genomes. Targeted next-generation sequencing relies heavily on oligonucleotide libraries as a source of baits to capture, either in the form of DNA padlock probes for the circularization of targeted sequences or in the form of RNA baits for the direct capture of sequencing genomic DNA library fragments. Millykangas et al. pushed the application of oligonucleotide libraries for targeted sequencing even further by integrating the target capture into the sequencing device, using a DNA oligonucleotide library to customize the primer lawn on a sequencing flowcell. Similarly, oligonucleotide libraries are used for sequence-specific priming of molecular reactions such as reverse transcription. Oligonucleotides libraries are also widely used to encode active RNA such as shRNA, or peptides after cloning in appropriate vectors. Recently, fluorescently labeled oligonucleotide libraries as molecular detection probes in fluorescent in situ hybridization techniques such as OligoPaint. While it is technically possible to separately synthesize each oligonucleotide of a library in a column, this process becomes cost prohibitive as the number of sequences increases. Synthesis prices can be greatly reduced by using massively parallel synthesis technologies primarily developed for manufacturing DNA microarrays. This has been achieved by using various methods including photodeprotection electrochemical acid generation, inkjet printing of synthesis reagents and photo-generated acid deprotection. However, the major drawback of all massively parallel DNA synthesis technologies is the relatively small amount of oligonucleotides produced on planar substrates. The yield of synthesized oligonucleotides released from a microarray can be increased by an initial PCR amplification step. This leads to the formation of double-stranded DNA flanked by PCR primer sequences, hence the need for a robust procedure to remove the complementary strand and both primer sequences. Massively parallel oligonucleotide synthesis on microarrays has the advantage to produce hundreds of thousand different sequences on a single planar substrate. However, one drawback of this technology is the limited spot size where the synthesis occurs, which is usually well below 100 microns diameters. This results in very small synthesis scale. In order to produce workable amount of oligonucleotides, it is necessary and more economical to go through a molecular amplification procedure, PCR being the easiest one, but also comes with its own limitations.