Lactate can be produced by many gut bacteria, but its accumulation in the colon is often an indicator of microbiota perturbation and disease. Here, we investigated the impact of continuous lactate infusions (up to 20 mM) at two pH values (6.5 and 5.5) on human gut microbiota and metabolites in anaerobic fermentor systems. Lactate concentrations remained low in communities of human colonic bacteria maintained at pH 6.5, while pH 5.5 often led to lactate accumulation and greatly reduced butyrate and propionate production. This occurred concomitantly with major shifts in microbiota composition. Microbial communities with lower abundances of lactate-utilizing bacteria were inherently less stable and more prone to lactate-induced perturbations. Mathematical modelling reproduced the chaotic behavior of the system, including the potential for lactate infusion both to promote and to rescue the perturbed system. These investigations provide clear evidence of the important role lactate-utilizers may play in health maintenance, and suggest that these should be considered as therapeutic probiotics to combat microbiota perturbations.