Process stability is a key operational issue when operating dark fermentation with mixed microbial cultures for hydrogen production. This study aimed at mitigating the instability of hydrogen production by separately adding exogenous pure strains suspected to have key roles in fermentative cultures. Among them, Clostridium acetobutylicum, Clostridium pasteurianum and Lactobacillus bulgaris which became predominant within the mixed culture strongly reduced the spectrum of produced metabolites and H-2 production variability. Interestingly, Escherichia coli and Cupriavidus necator, which remained in minor abundance, maintained a high and stable H-2 production while lowering the metabolic variability. 16S rRNA revealed that this could correlate to a simplification of the microbial diversity and the non-emergence of spore-forming competitors such as Sporolactobacillus sp. These results illustrate the potential beneficial role of minor OTUs as keystone species on H-2-producing complex ecosystem and support the possibility of using them to engineer the ecosystem and maintain high and stable performances.