Bacterial nodules, galls, and endosymbionts A huge diversity of bacterial symbionts colonize plants, animals, and even fungi [53]. Some of these are largely pathogenic, but many provide the host with essential services, including, for example,

cellulose degradation, nitrogen metabolism, and fat metabolism in ruminant animals [54]. The GO currently has many terms that describe aspects of the mutualism between legumes and nitrogen fixing bacteria, including “”GO: 0009877 nodulation”" (Additional file 1, Figure 1, and Figure 2), defined as “”the formation of nitrogen-fixing root nodules R788 clinical trial on plant roots”" [10]. Other terms from the Cellular Component ontology describe the physical components

of this mutualism, including “”GO: 0043663 host bacteroid-containing symbiosome”", defined as “”a symbiosome Temsirolimus containing any of various structurally modified bacteria, such as those occurring on the root nodules of leguminous plants, of a host cell”" [10] (Additional file 1). In contrast to mutualistic root nodulation, “”GO: 0044005 induction by symbiont in host of tumor, nodule, or growth”" is defined as “”the process by which an organism causes the formation of an abnormal mass of cells in its host organism…”" [10] (Figure 2). As a child term of “”GO: 0044003 modification by symbiont of host morphology or physiology”", this term could be used to describe the tumor-inducing activity of Agrobacterium tumefaciens, which results in plant galls [55]. There are many examples of bacterial endophytes, whose nutritional needs are met while supplying hosts with necessary nutrients or other benefits such as bioluminescence. The

free-living, nitrogen-fixing bacterium Acetobacter diazotrophicus, which colonizes sugar cane, benefits from the low O2 levels and high sucrose levels necessary for nitrogenase activity [56]. In the symbiosis of the squid Euprymna scolopes and Vibrio fischeri bacteria, the bioluminescence of the bacteria, housed in a bilobed light organ, acts as an anti-predatory mechanism for the squid [57]. Symbiont-induced host tissue development leads to the formation of the light organ that houses the bacteria [58] and might be described by “”GO: 0052111 modification by symbiont of host structure”", PIK3C2G defined as “”the process by which an organism effects a change in an anatomical part or cellular component of the host organism”" [10] (Figure 2). To describe the growth of V. fischeri within the E. scolopes light organ, “”GO: 0044412 growth or development of symbiont within host”" could be used (see Figure 2 for this and the following examples). In the case of A. diazotrophicus inside sugarcane, it might be appropriate to use a more specific child term such as “”GO: 0075067 growth or development of symbiont in host intercellular space”".