## 3 Discussion
johnsonii_ (RefSeq ID: EGP12391) (Table S3) exhibited higher substrate specificity for glycine over taurine conjugated bile acids [58]. In a companion study using the dose response and treatment regimen, [PERSON] et al. reported TCDD increased serum DCA levels \(\sim\)80 fold, with only a \(\sim\)two-fold increase in serum GDCA levels [9]. In contrast, hepatic taurolithocholic acid(TLCA) levels were increased \(\sim\)233 fold while serum lithocholic acid increased only four fold following TCDD treatment. Moreover, glycine conjugated bile acids, including GDCA, are more toxic towards Lactobacillus species than taurine conjugated bile acids [33; 59; 60]. Increased levels of BSH with a substrate preference for glycine conjugated bile acid may partially explain select Lactobacillus species enrichment. Further, both TLCA and DCA are potent FXR and GPBAR1 agonists that regulate the lipid, glucose, and bile acid metabolism [61; 62]. Consequently, shifts in microbial secondary bile acids by Lactobacillus species may play a role in TCDD elicited gut dysbiosis impacting host regulation of energy homeostasis. Coincident with increased levels of _bsh_ was the dose-dependent increase in genes from the mevalonate-dependent isoprenoid biosynthesis, the pathway also used in mammals for cholesterol biosynthesis. The MEP pathway is the predominant isoprenoid biosynthesis pathway among gut microbiota while the mevalonate-dependent pathway is only found in select bacteria, including Lactobacillus and Streptococcus species [63]. The output from either pathway is farnesyl diphosphate (FPP) and geranyl diphosphate (GPP), substrates required for polyprenol biosynthesis used in menaquinone and cell wall biosynthesis. Menaquinones are utilized by bacteria for anaerobic/aerobic respiration, providing antioxidant activity with menaquinone supplementation affecting the gut microbiome [64]. In the context of _L. reuteri_, we observed genes annotated to the shikimate pathway, which is responsible for chorismate biosynthesis, a precursor for aromatic amino acids and the naphthoquinone head group of menaquinone, as well as genes involved in de novo menaquinone biosynthesis. While the complete biosynthesis pathway was not present in _L. reuteri_, it is consistent with other metagenomic reports of incomplete menaquinone biosynthesis pathways in gut Lactobacillus species [44]. It has been proposed that Lactobacillus species may participate in later menaquinone biosynthesis steps through the uptake of intermediates, such as o-succinylbenzeneate from other bacteria or dietary sources [44]. In addition, the ability to utilize menaquinones for respiration is typically not associated with Lactobacillus species. However, some lactic acid bacteria, including _L. reuteri_ strains, demonstrate the ability to respire when menaquinone and heme are supplemented [65; 66]. Metagenomic analysis also identified the mevalonate-dependent pathway enrichment in fecal samples from patients with cirrhosis. The mevalonate-dependent pathway is reported to be increased in fibrosis patients with autoimmune pathologies [67]. Isoprenoid biosynthesis pathways are also elevated in the lung microbiome of cystic fibrosis patients, with the MEP pathway enriched rather than the mevalonate route [68]. The association between fibrosis and isoprenoid biosynthesis enrichment warrants further investigation in the context of potential mechanisms contributing to bacterial fitness and/or fibrosis. Increased abundance of the mevalonate-dependent biosynthesis pathway could also be a biomarker of Lactobacillus and Streptococcus proliferation that is often associated with non-alcoholic steatohepatitis (NASH)/fibrosis [21; 45]. We identified enrichment of the mevalonate-dependent pathway in both mouse and human microbiomes, whereas the complete pathway was primarily annotated to Streptococcus and Lactobacillus species (Table S7). Other factors, such as simvastatin and proton pump inhibitors (PPI), that are commonly prescribed for NAFLD patients may also impact these microbial pathways.