# Metabolism of bile salts in the estrogen degrading bacterium Caenibius tardaugens

## TL;DR

This paper explores how the bacterium Caenibius tardaugens breaks down bile salts, revealing specific genes and metabolic pathways involved.

## Contribution

The study identifies gene clusters and metabolic pathways in Caenibius tardaugens for bile salt degradation, including the Δ4,6 variant pathway.

## Key findings

- Two gene clusters, bsd I and bsd II, are induced during cholate metabolism in C. tardaugens.
- C. tardaugens uses the Δ4,6 variant pathway for cholate metabolism, indicated by homologs of 7α-hydroxy steroid dehydratase.
- Mutation of the igr-like operon does not affect bile salt degradation in C. tardaugens.

## Abstract

Bile salts are conjugated steroids with digestive functions in vertebrates that reach the ecosystem upon excretion. Their environmental degradation by bacteria resembles the steroid nucleus catabolism that uses the 9,10-seco pathway, although there are two variants depending on whether the hydroxyl group at C-7 is eliminated (variant Δ4,6) or not (variant Δ1,4). Caenibius tardaugens, formerly known as Novosphingobium tardaugens, is a steroid-degrading bacterium used as a model to study the genetic and metabolic traits of steroidal sex-hormones catabolism. In this work, we investigated the bacterium ability to grow on bile salts such as cholate and deoxycholate and we performed directed mutagenesis along with transcriptomic analysis to shed light on the genes involved in bile salt metabolism. The mutation of the igr-like operon (EGO55_03105-EGO55_03125), similar to the cholesterol-degrading operon igr from Rhodococcus jostii RHA1, did not affect the ability to grow on bile salts. The transcriptomic analysis in the presence of cholate showed the induction of two gene clusters named bsd I (bile-salts degradation) (EGO55_16295 to EGO55_16335) and bsd II (EGO55_11460–EGO55_11480), containing genes that, according to their sequence identity to other bile salt-degrading bacteria, might participate in the side chain degradation and the HIP pathway of cholate catabolism, respectively. Moreover, the presence of other proteins homologous to the 7α-hydroxy steroid dehydratase Hsh2, such as EGO55_02245, EGO55_12965, or EGO55_06935, indicates that C. tardaugens cholate metabolism proceeds via the Δ4,6 variant, as it is conserved in several bacteria from the genera Sphingobium, Novosphingobium, and Sphingomonas.

The online version contains supplementary material available at 10.1007/s10532-026-10252-7.