Gut Microbe-Derived Trimethylamine Shapes Circadian Rhythms Through the Host Receptor TAAR5

Reviewer #1 (Public review):

Summary:

This study focuses on the bacterial metabolite TMA, generated from dietary choline. These authors and others have previously generated foundational knowledge about the TMA metabolite TMAO, and its role in metabolic disease. This study extends those findings to test whether TMAO's precursor, TMA, and its receptor TAAR5 are also involved and necessary for some of these metabolic phenotypes. They find that mice lacking the host TMA receptor (Taar5-/-) have altered circadian rhythms in gene expression, metabolic hormones, gut microbiome composition, and olfactory and innate behavior. In parallel, mice lacking bacterial TMA production or host TMA oxidation have altered circadian rhythms.

Strengths:

These authors use state-of-the-art bacterial and murine genetics to dissect the roles of TMA, TMAO, and their receptor in various metabolic outcomes (primarily measuring plasma and tissue cytokine/gene expression). They also follow a unique and unexpected behavioral/olfactory phenotype. Statistics are impeccable.

Weaknesses:

Enthusiasm for the manuscript is dampened by some ambiguous writing and the presentation of ideas in the introduction, both of which could easily be improved upon revision.

Reviewer #2 (Public review):

Summary:

In the manuscript by Mahen et al., entitled "Gut Microbe-Derived Trimethylamine Shapes Circadian Rhythms Through the Host Receptor TAAR5," the authors investigate the interplay between a host G protein-coupled receptor (TAAR5), the gut microbiota-derived metabolite trimethylamine (TMA), and the host circadian system. Using a combination of genetically engineered mouse and bacterial models, the study demonstrates a link between microbial signaling and circadian regulation, particularly through effects observed in the olfactory system. Overall, this manuscript presents a novel and valuable contribution to our understanding of host-microbe interactions and circadian biology. However, several sections would benefit from improved clarity, organization, and mechanistic depth to fully support the authors' conclusions.

Strengths:

(1) The manuscript addresses an important and timely topic in host-microbe communication and circadian biology.

(2) The studies employ multiple complementary models, e.g., Taar5 knockout mice, microbial mutants, which enhance the depth of the investigation.

(3) The integration of behavioral, hormonal, microbial, and transcript-level data provides a multifaceted view of the observed phenotype.

(4) The identification of olfactory-linked circadian changes in the context of gut microbes adds a novel perspective to the field.

Weaknesses:

While the manuscript presents compelling data, several weaknesses limit the clarity and strength of the conclusions.

(1) The presentation of hormonal, cytokine, behavioral, and microbiome data would benefit from clearer organization, more detailed descriptions, and functional grouping to aid interpretation.

(2) Some transitions-particularly from behavioral to microbiome data-are abrupt and would benefit from better contextual framing.

(3) The microbial rhythmicity analyses lack detail on methods and visualization, and the sequencing metadata (e.g., sample type, sex, method) are not clearly stated.

(4) Several figures are difficult to interpret due to dense layouts or vague legends, and key metabolites and gene expression comparisons are either underexplained or not consistently assessed across models.

(5) Finally, while the authors suggest a causal role for TAAR5 and its ligand in circadian regulation, the current data remain correlative; mechanistic experiments or stronger disclaimers are needed to support these claims.

Reviewer #3 (Public review):

Summary:

Deletion of the TMA-sensor TAAR5 results in circadian alterations in gene expression, particularly in the olfactory bulb, plasma hormones, and neurobehaviors.

Strengths:

Genetic background was rigorously controlled.

Comprehensive characterization.

Weaknesses:

The weaknesses identified by this reviewer are minor.

Overall, the studies are very nicely done. However, despite careful experimentation, I note that even the controls vary considerably in their gene expression, etc, across time (eg, compare control graphs for Cry 1 in IB, 4B). It makes me wonder how inherently noisy these measurements are. While I think that the overall point that the Taar5 KO shows circadian changes is robust, future studies to dissect which changes are reproducible over the noise would be helpful.

Impact:

These data add to the growing literature pointing to a role for the TMA/TMAO pathway in olfaction and neurobehavioral.