Early life stress may contribute to depression vulnerability, possibly through immune system development and gut microbial colonization patterns. Increased pro-inflammatory cytokines and differences in gut microbiota composition have been seen in depressed individuals. The current study investigated inflammatory and bacterial profiles of 39 individuals with a current major depressive episode and 43 healthy volunteers with varying severity of childhood trauma. Plasma interleukin (IL)-6/IL-10 ratios was positively correlated with depression severity, and childhood trauma explained variance in severity of symptoms above and beyond that accounted for by the IL-6/IL-10 ratios. Expression of Faecalibacterium prausnitzi (F. prausnitzi) in stool was decreased in depressed participants compared to healthy controls. Importantly, this relationship was significant only in participants who had experienced moderate-to-severe physical neglect. These findings suggest a relationship between particular gut bacteria and depressive symptoms that is dependent on the presence of specific types of early life trauma.