Free fatty acids are important antimicrobial substances regulating the homeostasis of colonizing bacteria on epithelial surfaces. Here, we show that meningococci express a functional farAB efflux pump, which is indispensable for fatty acid resistance. However, other than in Neisseria gonorrhoeae, the transcriptional regulator FarR is not involved in regulation of this operon in Neisseria meningitidis. We tested the susceptibility of 23 meningococcal isolates against saturated and unsaturated long-chain fatty acids, proving that meningococci are generally highly resistant, with the exception of serogroup Y strains belonging to sequence type 23. Using genetically determined lipopolysaccharide (LPS)-truncated mutant strains, we show that addition of the LPS core oligosaccharide and hexa-acylation of its membrane anchor lipid A are imperative for fatty acid resistance of meningococci. The sensitivity of the serogroup Y strains is due to naturally occurring mutations within the lpxL1 gene, which is responsible for addition of the sixth acyl chain on the LPS membrane anchor lipid A. Therefore, fatty acid resistance in meningococci is provided by both the active efflux pump FarAB and by the natural permeability barrier of the Gram-negative outer membrane. The transcriptional regulator FarR is not implicated in fatty acid resistance in meningococci, possibly giving rise to a constitutively active FarAB efflux pump system and thus revealing diverse mechanisms of niche adaptation in the two closely related Neisseria species.Although humans are physiologically colonized by a vast number of microorganisms, invasion of this microflora is efficiently prevented by dermal and mucosal epithelia which form the barriers of the human body. Homeostasis of the colonizing microflora at these barriers is maintained by numerous mechanisms that include the secretion of antimicrobial compounds by the epithelia. Among these compounds are free fatty acids, which act as nonselective antimicrobials against a broad range of microorganisms. Sebaceous glands, producing a mixture of lipids called sebum, are present in the skin, the nasal epithelium, and the oral epithelium of most adults (62, 71). The produced sebum consists mainly of triglycerides which undergo hydrolysis by both host and bacterial lipases to produce free fatty acids (9). In human saliva, lipid content is about 4 to 20 mg/100 ml and includes both saturated (mainly palmitic and stearic acid) and unsaturated (mainly oleic, linoleic, palmitoleic, arachidonic, and docosahexaenoic acid) fatty acids (59, 65). Similarly, fatty acids form a major constituent of vaginal secretions (45). In most cases bacterial susceptibility to free fatty acids depends on organization of the cell wall, with Gram-negative bacteria being more resistant than Grampositive bacteria (72). Enterobacteriaceae are shielded by their lipopolysaccharide (LPS) from the antimicrobial activity of medium-and long-chain fatty acids (58). Neisseria meningitidis and Neisseria gonorrhoeae are closely related Gram-negative s...