Metabolomic and genomic insights into TMA degradation by a novel halotolerant strain - Paracoccus sp. PS1

Trimethylamine N-oxide (TMAO) is a gut metabolite that acts as a biomarker for chronic diseases, and is generated by the oxidation of trimethylamine (TMA) produced by gut microflora. Since, microbial degradation of TMA is predicted to be used to restrict the production of TMAO, we aimed to isolate bacterial strains that could effectively degrade TMA before being oxidized to TMAO. As marine fish is considered to have a rich content of TMAO, we have isolated TMA degrading isolates from fish skin. Out of the fourteen isolates, depending on their rapid TMA utilization capability in mineral salt medium supplemented with TMA as a sole carbon and nitrogen source, isolate PS1 was selected as our desired isolate. Its TMA degrading capacity was further confirmed through spectrophotometric, Electrospray Ionization Time-of-Flight Mass Spectrometry (ESI TOF-MS) and High performance liquid chromatography (HPLC) analysis and in silico analysis of whole genome (WG) gave further insights of protein into its TMA degradation pathways. PS1 was taxonomically identified as Paracoccus sp. based on its 16S rRNA and whole genome sequence analysis. As PS1 possesses the enzymes required for degradation of TMA, clinical use of this isolate has the potential to reduce TMAO generation in the human gut.

The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme (CutD) for gut microbes and comparison with their TMA production levels

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Analyzed the cutC and cutD gene expression and their TMA production levels.

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Bioinformatic analysis of cutC and cutD proteins showed conserved regions.

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Analysis of cutC protein showed conserved choline binding active site residues.

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TMA levels not only depend on cutC and cutD genes other factors are also involved.

Recent studies revealed that some intestinal microorganisms anaerobically convert choline to trimethylamine (TMA) by choline TMA-lyase (cutC). TMA is further oxidized to trimethylamine-N-oxide (TMAO), by the liver enzyme flavin-dependent monooxygenase 3 (FMO3). TMA in the serum is correlated with the risk of cardiovascular disease and some other diseases in human. The objective of this study is to study the expression levels of cutC and its activating enzyme (cutD) gene for these microorganisms and their association with TMA production. In this study, we collected 20 TMA producing bacteria strains representing 20 species, and designed primers to evaluate their gene expression levels by reverse transcription quantitative PCR (RT-qPCR). In addition, TMA production was analyzed by UPLC-MS/MS. Results showed that gene expression levels of most individual strains were different when compared with the gene expression level of their glyceraldehyde-3 phosphate dehydrogenase (GAPDH) gene and the TMA production level of gut bacteria may not correlate with their cutC/cutD gene expression levels. Bioinformatic analysis of the CutC protein showed conserved choline binding site residues; cutD showed conserved S-adenosylmethionine (SAM) and two CX2-CX2-CX3 motifs. The present study reports that the TMA production level may not only depend on cutC/cutD gene expression. Other factors may need to be investigated.

Trimethylamine modulates dauer formation, neurodegeneration, and lifespan through tyra-3/daf-11 signaling in Caenorhabditis elegans

In the nematode Caenorhabditis elegans, signals derived from bacteria in the diet, the animal's major nutrient source, can modulate both behavior and healthspan. Here we describe a dual role for trimethylamine (TMA), a human gut flora metabolite, which acts as a nutrient signal and a neurotoxin. TMA and its associated metabolites are produced by the human gut microbiome and have been suggested to serve as risk biomarkers for diabetes and cardiovascular diseases. We demonstrate that the tyramine receptor TYRA-3, a conserved G protein-coupled receptor (GPCR), is required to sense TMA and mediate its responses. TMA activates guanylyl cyclase DAF-11 signaling through TYRA-3 in amphid neurons (ASK) and ciliated neurons (BAG) to mediate food-sensing behavior. Bacterial mutants deficient in TMA production enhance dauer formation, extend lifespan, and are less preferred as a food source. Increased levels of TMA lead to neural damage in models of Parkinson's disease and shorten lifespan. Our results reveal conserved signaling pathways modulated by TMA in C. elegans that are likely to be relevant for its effects in mammalian systems.

Vascular reactivity stimulated by TMA and TMAO: Are perivascular adipose tissue and endothelium involved?

Trimethylamine (TMA), formed by intestinal microbiota, and its Flavin-Monooxygenase 3 (FMO3) product Trimethylamine-N-Oxide (TMAO), are potential modulators of host cardiometabolic phenotypes. High circulating levels of TMAO are associated with increased risk for cardiovascular diseases. We hypothesized that TMA/TMAO could directly change the vascular tone. Perivascular adipose tissue (PVAT) helps to regulate vascular homeostasis and may also possess FMO3. Thoracic aorta with(+) or without(-) PVAT, also + or - the endothelium (E), of male Sprague Dawley rats were isolated for measurement of isometric tone in response to TMA/TMAO (1nM-0.5 M). Immunohistochemistry (IHC) studies were done to identify the presence of FMO3. TMA and TMAO elicited concentration-dependent arterial contraction. However, at a maximally achievable concentration (0.2 M), contraction stimulated by TMA was of a greater magnitude (141.5 ± 16% of maximum phenylephrine contraction) than that elicited by TMAO (19.1 ± 4.03%) with PVAT and endothelium intact. When PVAT was preserved, TMAO-induced contraction was extensively reduced the presence (19.1 ± 4.03%) versus absence of E (147.2 ± 20.5%), indicating that the endothelium plays a protective role against TMAO-induced contraction. FMO3 enzyme was present in aortic PVAT, but the FMO3 inhibitor methimazole did not affect contraction stimulated by TMA in aorta + PVAT. However, the l-type calcium channel blocker nifedipine reduced TMA-induced contraction by ∼50% compared to the vehicle. Though a high concentration of these compounds was needed to achieve contraction, the findings that TMA-induced contraction was independent of PVAT and E and mediated by nifedipine-sensitive calcium channels suggest metabolite-induced contraction may be physiologically important.

Lignin and holocellulose from coir pith involved in trimethylamine (fishy odor) adsorption

Coir pith is a highly potential adsorbent for adsorbing trimethylamine (TMA). It harbors a higher adsorption capacity for TMA compared to commercial activated carbon (CAC). It was found that lignin and holocellulose extracted from coir pith played an important role in TMA adsorption. Lignin itself had the highest TMA adsorption capacity (269.01 mg/g) followed by holocellulose (75.43 mg/g), coir pith (14.3 mg/g) and CAC (10.26 mg/g), respectively. The pseudo-first- and second orders were applied to the kinetic data. For the adsorption of TMA by coir pith, the best fit was achieved by the pseudo-second order. Thermodynamic studies showed an endothermic and physico-chemical adsorption process between TMA and the coir pith. TMA desorption study suggested that only 14%-47% of TMA was desorbed with distilled water. In addition, Fourier transform-infrared (FT-IR) spectra showed that C-H bond (methyl group), C-O bond from phenolic alcohol and C-O bond from tertiary alcohol in lignin and holocellulose were involved in TMA adsorption. Coir pith-based filter showed high TMA adsorption efficiency (98%) and kept constant for more than 48 days in a continuous system. Pilot scale experiment, coir pith beads filter could be succesfully applied as a packing material for TMA removal. Therefore, coir pith can be used as a promising packing material for TMA treatment at contaminated site.

A simple dilute and shoot approach incorporated with pentafluorophenyl (PFP) column based LC-MS/MS assay for the simultaneous determination of trimethylamine N-oxide and trimethylamine in spot urine samples with high throughput

Determination of trimethylamine N-oxide (TMAO) and trimethylamine (TMA) in biological and environmental samples has drawn great attention recently due to their increasing association with human health and disease. It remains a challenge to simultaneously quantify TMAO and TMA in a simple, fast and cost-effective manner due to pre-analytical and analytical constraints. For the first time, we describe a dilute and shoot approach combined with LC-MS/MS detection for the simultaneous measurement of the analytes in spot urine samples with high throughput. Compared to the existing methods, the merits of the proposed assay include the use of a simple dilute and shoot approach (100-fold), small sample volume (10μL), short LC run on a PFP column (4.0min) and multi-analyte MS detection without sample cleanup, derivatization, evaporation and a HILIC column. Dilution, LC and MS parameters were optimized in detail. Method validation yielded a wide linearity for TMAO (1.0-400μg/mL) and TMA (0.025-10μg/mL) with a respective limit of quantitation of 1.0 and 0.025μg/mL. The quantitation was not affected by 41 major urinary components, structurally-related drugs and metabolites. The intra- and inter-day assay precisions were ≤3.6% and recoveries were 93.3%-103.3% for spiked quality control samples. The clinical utility of the alternative spot urine sampling approach compared to conventional 24h urine collection was supported by a significant correlation between the two sampling strategies (n=20, p<0.0001, r=0.757-0.862; slope=0.687-1.170) and no statistical difference in day-to-day biological variability (n=20). The applicability and reliability of the assay was verified by the assessment of reference intervals in a cohort of 118 healthy people. The proposed assay would be beneficial for the rapid and accurate determination of the increasingly important TMAO and TMA demanded in clinical, environmental, pharmaceutical and nutritional fields.