## 2 Results and Discussion
### Cysteine and Methionine Metabolism  
The _luxS_ gene encodes for _S_-ribosylhomocysteine (_luxS_), which is also involved in the amino acid metabolic pathway. It was downregulated by 2.4-3.0-fold when treated with \begin{table}
\begin{tabular}{c c c c c} \hline \multirow{2}{*}{**Gene**} & \multicolumn{2}{c}{**qPCR**} & \multicolumn{2}{c}{**Microarray**} & \multirow{2}{*}{**Match with Microarray**} \\ \cline{2-2} \cline{4-5}  & **Fold Change (Abs)** & & & & \\ \hline _rplF_ & \(-1.6\) & Down & 2.3 & Up & ✗ \\ _rplI_ & \(-1.2\) & Down & 1.2 & Up & ✗ \\ _luxS_ & \(-2.4\) & Down & \(-2.0\) & Down & ✓ \\ _argC_ & \(2.5\) & Up & 1.3 & Up & ✓ \\ _rpsK_ & \(-1.1\) & Down & 2.2 & Up & ✗ \\ \hline \end{tabular}
\end{table} 
Table 4: A comparison between microarray and qPCR results for E (eugenol) versus C (control) for the genes, _rplF_, _rplI_, _luxS_, _argC_, and _rpsK_, using the _gmk_ gene for normalisation. \begin{table}
\begin{tabular}{c c c c} \hline \hline \multicolumn{1}{c}{**Functional Classes**} & \multicolumn{1}{c}{**Gene(s) Symbol**} & \multicolumn{1}{c}{**Upregulated**} & \multicolumn{1}{c}{**Downregulated**} \\ \hline Translation & _rplI_, _rplF_, _rpsK_ & _rplI_, _rplF_, _rpsK_ & \\ Amino acid transportation metabolism & _luxS_, _argC_ & _argC_ & _luxS_ \\ Translational, ribosomal, and biogenesis & _Obg_, _rplI_, _rplF_, _rpsK_ & _Obg_, _rplI_, _rpsK_ & \\ Argin and proline metabolism & _argC_ & _argC_ & _luxS_ \\ Cysteine and methionine metabolism & _luxS_ & & \\ \hline \end{tabular}
\end{table} 
Table 2: Functional classes with associated upregulated and downregulated genes in control (C) vs. eugenol (E). \begin{table}
\begin{tabular}{c c c c c} \hline \hline \multirow{2}{*}{**Gene**} & \multicolumn{2}{c}{**qPCR**} & \multicolumn{2}{c}{**Microarray**} & \multirow{2}{*}{**Match with Microarray**} \\ \cline{2-2} \cline{4-5}  & **Fold Change (Abs)** & & & & \\ \hline _rplF_ & \(-1.9\) & Down & 2.3 & Up & ✗ \\ _RplI_ & \(-1.4\) & Down & 1.2 & Up & ✗ \\ _luxS_ & \(-3.0\) & Down & \(-2.0\) & Down & ✓ \\ _argC_ & \(2.0\) & Up & 1.3 & Up & ✓ \\ _Rpsk_ & \(-1.3\) & Down & 2.2 & Up & ✗ \\ \hline \end{tabular}
\end{table} 
Table 5: RT-qPCR percentage of correlation with microarray data. e eugenol. _luxS_, as an Fe\({}^{2+}\)-dependent metalloenzyme, plays a catalytic role in _S_-ribosylhomocysteine (SRH)-thioether bond cleavage to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD) [15]. The enzyme _S_-(5-deoxy-D-ribos-5-yl)-L-homocysteine _l_-homocysteine-ly [(4S)-4,5-dihydroxypentan-2,3-dione-forming] belongs to the class of carbon-sulphur lyases and the family of lyases [16], and is also commonly referred to as _S_-ribosylhomocysteine and _luxS_[17]. The enzymes are involved in methionine metabolism [17], which is a key step in the biosynthetic pathway of the type II autoinducer (AI-2), which plays a vital role in the quorum-sensing mechanisms of both Gram-positive and Gram-negative bacteria [18]. AI-2 functions as a signalling molecule in interspecies communication through regulation of niche-specific genes that have diverse functions in various bacterial species, which is often in response to a change in the population density [17]. This response serves a dual purpose, i.e., for detoxification via elimination/metabolism of _S_-adenosylhomocysteine, and also for the production of a type II quorum-sensing molecule [19]. Cell-population-density-dependent regulation of gene expression is a key contributing factor to bacterial pathogenesis. There are two quorum-sensing (QS) systems in the staphylococci [20], namely, the accessory gene regulator (_agr_), and _luxS_. In staphylococci, upregulation of _luxS_ reduces biofilm formation and virulence rather than inducing it, especially during biofilm-associated infection. The _agr_ gene has been shown to enhance biofilm detachment through upregulation of detergent-like peptides, whilst _luxS_ decreases cell-cell adhesion through downregulation of biofilm exopolysaccharideacharide expression [20].