Introduction and objectives Viruses of microbes are major players in various ecosystems, typically affecting the structuration and dynamics of microbial communities [1]. They nevertheless remain poorly explored in anaerobic digestion (AD) plants [2], where biowaste is valorised into methane-rich biogas. The AD process ecosystems are very sensitive to disturbance, leading to inhibition and loss of methane production [3]. We were therefore interested in better understanding the interplay between abiotic disturbance, microbial community composition, including the viromes, and process performance. Material and methods The variations of both viral and prokaryotic populations were followed in batch AD microcosms under abiotic stress. Four types of abiotic disturbances were tested in triplicates. During incubation, either NaCl, NH4Cl or phenol was injected into the reactors, as inhibitors previously reported in full-scale plants. Mitomycin C was also tested, since it can activate the lytic cycle of proviruses. We first confirmed a significant impact of the tested stresses on biogas production. Then we performed 16S rDNA metabarcoding targeting archaea and bacteria, and shotgun metagenomic sequencing of 30 selected metaviromes. Results, discussion and conclusion Metavirome coassembly showed a N50 of 3,886 bases, and yielded more than 105 contigs longer than 1,000 bp. Among them, 45,914 were predicted as putative viral contigs using VIBRANT (including 2,815 complete). After strict quality filtering, thanks to two more tools, CheckV and VirSorter2, 230 selected contigs emerged. Upon those, 110 were differentially abundant when comparing intra-condition variability before and after disturbance. We will soon be able to interpret the observed community dynamics. We also detected auxiliary metabolic genes related to carbohydrate metabolism and the sulphur relay system, which seems relevant to this specific ecosystem. Moreover, there was a good agreement between the prokarotyic community composition and the predicted hosts of the viral contigs, with the dominance of Clostridiales, in both cases. Also, we plan to apply the epicPCR technique [4] to confirm specific virus-host pairs. Keywords: anaerobic digestion, viruses of microbes, methanogens, meta-omics, epic-PCR 1-Sullivan MB, Weitz JS, Wilhelm S. Viral ecology comes of age. Environmental Microbiology Reports 2016, 9(1):33-35. 2-Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environmental Microbiology 2015, 18(4):1162-1175. 3-Chen Y, Cheng JJ, Creamer KS. Inhibition of anaerobic digestion process: A review. Bioresource Technology 2008, 99(10):4044-4064. 4-Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. The Isme Journal 2015, 10:427.