The functions of more than half of the genes present in Escherichia coli
and Salmonella enterica
serovar Typhimurium (hereafter referred to as S.
Typhimurium) have never been determined, despite decades of genetic screens and selections. This failure is hypothesized to result from a lack of gene expression or gene function in the laboratory environment. A major component of the natural environment missing from most laboratory experiments is the presence of other microbial species. E. coli
Typhimurium colonize and propagate in the intestines of animals in the presence of large numbers of other microbial species. We have previously identified genes of S.
Typhimurium that are expressed specifically in the presence of signaling molecules produced by other microbes 
. These seven genes (two loci) are activated by SdiA, a member of the LuxR family of transcription factors, in response to N
-acylhomoserine lactones (AHLs) produced by other species.
The use of LuxR homologs to detect the AHL production of other species is unusual. The typical function of LuxR homologs is “quorum sensing”, a phenomenon by which bacteria sense their own population density 
. Many Gram-negative bacteria use this information to regulate the production of host colonization factors. For instance, Vibrio fischeri
uses this information to regulate genes that play a role in colonization of the squid, Euprymna scolopes 
. Numerous plant and animal pathogens use quorum sensing to regulate host interaction genes 
. Presumably, this prevents the bacteria from alerting host immune responses before a population sufficient to overcome host defenses has been assembled.
AHLs are synthesized using enzymes of the LuxI or LuxM family 
. AHLs vary widely in the length of their acyl chain (from four to 18 carbons) and can be modified at the 3-carbon position to have a carbonyl or hydroxyl group. Each LuxI homolog produces predominantly a single AHL variant, along with smaller quantities of closely related variants 
. The LuxR family member of a species can detect nanomolar concentrations of the AHL produced by that species, providing some species specificity to the system. However, LuxR homologs can often detect other related AHLs with lower sensitivity 
encodes a LuxR homolog, SdiA, but does not encode an AHL synthase 
. Instead, SdiA responds to AHLs produced by other microbial species 
. SdiA detects a much wider range of AHLs than other LuxR homologs, although with varying sensitivities. The most potent AHL is 3-oxo-octanoyl-homoserine lactone (oxoC8) and SdiA responds to this molecule at concentrations of 1 nM or higher 
. The closely related AHL, 3-oxo-hexanoyl-homoserine lactone (oxoC6) can be detected at concentrations above 5 nM, and at 50 nM SdiA responds to oxoC4, oxoC10, oxoC12, and the unmodified AHLs C6 and C8. At concentrations above 1 µM SdiA responds to C4, C10, and C12 
. The three-dimensional structure of the N-terminus of E. coli
SdiA bound to C8 has been determined using NMR, confirming that detection of AHLs by SdiA is direct 
Upon detection of AHL, SdiA activates the expression of two srg
ene) loci: the rck
operon located on the S.
Typhimurium virulence plasmid, pSLT, and the srgE
gene located in the chromosome at 33.6 centisomes 
. The rck
operon is directly downstream of the pef
operon that encodes plasmid-encoded fimbriae 
. These fimbriae play a role in adhesion to the small intestine of mice 
. The rck
operon contains six genes: pefI
, and srgC 
. PefI is a regulator of the upstream pef
. SrgD is a putative transcription factor with a helix-turn-helix motif of the LuxR family, but its target genes have not been identified 
. SrgA is a DsbA homolog that catalyzes disulfide bond formation of the Pef fimbrial subunit and other periplasmic proteins 
. SrgB is a lipoprotein of unknown function 
. Rck is an 8-stranded β-barrel protein localized to the outer membrane 
. This protein has dual functions. The first function provided its name: resistance to complement killing 
. More specifically, Rck prevents the polymerization of complement component C9 on the bacterial surface 
. Second, Rck serves as an adhesin to fibronectin and laminin 
. The last gene in the rck
, is a regulator of the AraC-family of transcription factors whose target genes are unknown 
. The second srg
locus consists of a single gene, srgE
, which is predicted to encode a protein containing a coiled-coil domain 
. As with the rck
is not present in E. coli
and was probably acquired horizontally by Salmonella
. Despite the regulation of putative virulence genes by SdiA, we have previously reported that an sdiA
mutant of S.
Typhimurium is not attenuated in mouse, chicken, or cow models of infection 
The mammalian intestinal community is comprised of approximately 800 microbial species 
. We hypothesized that members of this community utilize AHL-type quorum sensing and that the presence of these AHLs would provide an effective way for S.
Typhimurium to detect the intestinal environment 
. In this report we have tested this hypothesis. S.
Typhimurium did not detect AHLs during transit through the intestinal tract of several species of animals, indicating that the normal microbiota of these hosts did not produce AHLs of the correct type or at a sufficient concentration to activate SdiA. However, SdiA was active during transit through turtles colonized by the AHL-producing organism, Aeromonas hydrophila