Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches

Mechanistic study on the alleviation of postmenopausal osteoporosis by Lactobacillus acidophilus through butyrate-mediated inhibition of osteoclast activity

In China, traditional medications for osteoporosis have significant side effects, low compliance, and high costs, making it urgent to explore new treatment options. Probiotics have demonstrated superiority in the treatment of various chronic diseases, and the reduction of bone mass in postmenopausal osteoporosis (PMOP) is closely related to the degradation and metabolism of intestinal probiotics. It is crucial to explore the role and molecular mechanisms of probiotics in alleviating PMOP through their metabolites, as well as their therapeutic effects. We aim to identify key probiotics and their metabolites that affect bone loss in PMOP through 16srDNA sequencing combined with non-targeted metabolomics sequencing, and explore the impact and possible mechanisms of key probiotics and their metabolites on the progression of PMOP in the context of osteoporosis caused by estrogen deficiency. The sequencing results showed a significant decrease in Lactobacillus acidophilus and butyrate in PMOP patients. In vivo experiments confirmed that the intervention of L. acidophilus and butyrate significantly inhibited osteoclast formation and bone resorption activity, improved intestinal barrier permeability, suppressed B cells, and the production of RANKL on B cells, effectively reduced systemic bone loss induced by oophorectomy, with butyric acid levels regulated by L. acidophilus. Consistently, in vitro experiments have confirmed that butyrate can directly inhibit the formation of osteoclasts and bone resorption activity. The above research results indicate that there are various pathways through which L. acidophilus inhibits osteoclast formation and bone resorption activity through butyrate. Intervention with L. acidophilus may be a safe and promising treatment strategy for osteoclast related bone diseases, such as PMOP.

Structural elucidation of derivatives of polyfunctional metabolites after methyl chloroformate derivatization by high-resolution mass spectrometry gas chromatography. Application to microbiota metabolites

Metabolomics has become an essential discipline in the study of microbiome, emerging gas chromatography coupled to mass spectrometry as the most mature, robust, and reproducible analytical technique. Silylation is the most widely used chemical derivatization strategy, although it has some limitations. In this regard, alkylation by alkyl chloroformate offers some advantages, such as a rapid reaction, milder conditions, better reproducibility, and the generation of more stable derivatives. However, commercial spectral libraries do not include many of the alkyl derivatives, mainly for polyfunctional metabolites, which can form multiple derivatives. That introduces a huge bias in untargeted metabolomics leading to common errors such as duplicates, unknowns, misidentifications, wrong assignations, and incomplete results from which non-reliable findings and conclusions will be retrieved. For this reason, the purpose of this study is to overcome these shortcomings and to expand the knowledge of metabolites in general and especially those closely related to the gut microbiota through the thorough study of the reactivity of the different functional groups in real matrix derivatized by methyl chloroformate, a common representative alkylation reagent. To this end, a systematic workflow has been developed based on exhaustive structural elucidation, along with computational simulation, and taking advantage of the high sensitivity and high-resolution gas chromatography-mass spectrometry. Several empirical rules have been established according to chemically different entities (free fatty acids, amino acids, polyols, sugars, amines, and polyfunctional groups, etc.) to predict the number of derivatives formed from a single metabolite, as well as their elution order and structure. In this work, some methyl chloroformate derivatives not previously reported as well as the mechanisms to explain them are given. Extremely important is the interconversion of E- and Z- geometric isomers of unsaturated dicarboxylic acids (case of fumaric-maleic and case of citraconic-mesaconic acids), or the formation of cycled derivatives for amino acids, as well as common metabolites, as in the case of serine and cysteine, and many others.

A simple liquid chromatography method running in dual modes for quantification of short and medium chain fatty acids

Sample preparation is often a rate-limiting step in quantification of short chain and medium chain fatty acids (SFAs and MFAs) in biological samples. A novel liquid chromatography (LC) method with simple sample preparation is introduced in this report. The method is performed on a column packed with polyvinyl alcohol sorbents. In separation of a mixture of bovine serum albumin (BSA) with SFAs and MFAs, the protein is eluted in size-exclusion mode in the first part of the chromatogram. SFAs and MFAs are then eluted in the second part of the chromatogram in reverse-phase mode where fatty acids with longer carbon lengths are eluted at longer retention times. SFAs and MFAs are well resolved from each other without pre-column derivatization. The size-exclusion mode affords good tolerance to macromolecules in sample matrixes. The dual mode separation allows sample injections without complicated sample preparation steps, such as derivatization, extraction, evaporation, and reconstitution.

Variability in fecal metabolome depending on age, PFBS pollutant, and fecal transplantation in zebrafish: A non-invasive diagnosis of health

To protect the wellbeing of research animals, certain non-invasive measures are in increasing need to facilitate an early diagnosis of health and toxicity. In this study, feces specimen was collected from adult zebrafish to profile the metabolome fingerprint. Variability in fecal metabolite composition was also distinguished as a result of aging, perfluorobutanesulfonate (PFBS) toxicant, and fecal transplantation. The results showed that zebrafish feces was very rich in a diversity of metabolites that belonged to several major classes, including lipid, amino acid, carbohydrate, vitamin, steroid hormone, and neurotransmitter. Fecal metabolites had functional implications to multiple physiological activities, which were characterized by the enrichment of digestion, absorption, endocrine, and neurotransmission processes. The high richness and functional involvement of fecal metabolites pinpointed feces as an abundant source of diagnostic markers. By comparison between young and aged zebrafish, fundamental modifications of fecal metabolomes were caused by aging progression, centering on the neuroactive ligand-receptor interaction pathway. Exposure of aged zebrafish to PFBS pollutant also significantly disrupted the metabolomic structure in feces. Of special concern were the changes in fecal hormone intermediates after PFBS exposure, which was concordant with the in vivo endocrine disrupting effects of PFBS. Furthermore, it was intriguing that transplantation of young zebrafish feces efficiently mitigated the metabolic perturbation of PFBS in aged recipients, highlighting the health benefits of therapeutic strategies based on gut microbiota manipulation. In summary, the present study provides preliminary clues to evidence the non-invasive advantage of fecal metabolomics in the early diagnosis and prediction of physiology and toxicology.

The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation

Although the microbiota has largely been associated with the pathogenesis of viral infections, most studies using omics techniques are correlational and hypothesis-generating. The mechanisms affecting the immune responses to viral infections are still being fully understood. Here we focus on the two most important sexually transmitted persistent viruses, HPV and HIV. Sophisticated omics techniques are boosting our ability to understand microbiota-pathogen-host interactions from a functional perspective by surveying the host and bacterial protein and metabolite production using systems biology approaches. However, while these strategies have allowed describing interaction networks to identify potential novel microbiota-associated biomarkers or therapeutic targets to prevent or treat infectious diseases, the analyses are typically based on highly dimensional datasets -thousands of features in small cohorts of patients-. As a result, we are far from getting to their clinical use. Here we provide a broad overview of how the microbiota influences the immune responses to HIV and HPV disease. Furthermore, we highlight experimental approaches to understand better the microbiota-host-virus interactions that might increase our potential to identify biomarkers and therapeutic agents with clinical applications.

Gut Microbiota Alterations in Trace Amine-Associated Receptor 9 (TAAR9) Knockout Rats

Trace amine-associated receptors (TAAR1-TAAR9) are a family of G-protein-coupled monoaminergic receptors which might have great pharmacological potential. It has now been well established that TAAR1 plays an important role in the central nervous system. Interestingly, deletion of TAAR9 in rats leads to alterations in the periphery. Previously, we found that knockout of TAAR9 in rats (TAAR9-KO rats) decreased low-density lipoprotein cholesterol levels in the blood. TAAR9 was also identified in intestinal tissues, and it is known that it responds to polyamines. To elucidate the role of TAAR9 in the intestinal epithelium, we analyzed TAAR9-co-expressed gene clusters in public data for cecum samples. As identified by gene ontology enrichment analysis, in the intestine, TAAR9 is co-expressed with genes involved in intestinal mucosa homeostasis and function, including cell organization, differentiation, and death. Additionally, TAAR9 was co-expressed with genes implicated in dopamine signaling, which may suggest a role for this receptor in the regulation of peripheral dopaminergic transmission. To further investigate how TAAR9 might be involved in colonic mucosal homeostasis, we analyzed the fecal microbiome composition in TAAR9-KO rats and their wild-type littermates. We identified a significant difference in the number of observed taxa between the microbiome of TAAR9-KO and wild-type rats. In TAAR9-KO rats, the gut microbial community became more variable compared with the wild-type rats. Furthermore, it was found that the family Saccharimonadaceae, which is one of the top 10 most abundant families in TAAR9-KO rat feces, is almost completely absent in wild-type animal fecal samples. Taken together, these data indicate a role of TAAR9 in intestinal function.

New Insights into Vitamin K-From Its Natural Sources through Biological Properties and Chemical Methods of Quantitative Determination

Vitamin K is one of the many health-promoting substances whose impact on the human body has been underestimated until recently. However, recently published research results have changed this situation, prompting some researchers to consider it a new panacea for diseases of old age. The result is a significant increase in interest in the accurate analysis of vitamin K in various types of samples, ranging from food, through dietary supplements, to biological matrices and clinical trials, both observational and interventional. This review summarizes the current state of knowledge about the proven and speculated biological activity of vitamin K and its importance for the world's aging societies, including the methods used for its isolation and analysis in various matrices types. Of all the analytical methods, the currently preferred methods of choice for the direct analysis of vitamin K are chromatographic methods, in particular liquid chromatography-tandem mass spectrometry. This technique, despite its sensitivity and selectivity, requires an appropriate stage of sample preparation. As there is still room for improvement in the efficiency of these methods, especially at the sample preparation stage, this review shows the directions that need to be taken to make these methods faster, more efficient and more environmentally friendly.

Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials

Ingested nanomaterials are exposed to many metabolites that are produced, modified, or regulated by members of the enteric microbiota. The adsorption of these metabolites potentially affects the identity, fate, and biodistribution of nanomaterials passing the gastrointestinal tract. Here, we explore these interactions using in silico methods, focusing on a concise overview of 170 unique enteric microbial metabolites which we compiled from the literature. First, we construct quantitative structure–activity relationship (QSAR) models to predict their adsorption affinity to 13 metal nanomaterials, 5 carbon nanotubes, and 1 fullerene. The models could be applied to predict log k values for 60 metabolites and were particularly applicable to ‘phenolic, benzoyl and phenyl derivatives’, ‘tryptophan precursors and metabolites’, ‘short-chain fatty acids’, and ‘choline metabolites’. The correlations of these predictions to biological surface adsorption index descriptors indicated that hydrophobicity-driven interactions contribute most to the overall adsorption affinity, while hydrogen-bond interactions and polarity/polarizability-driven interactions differentiate the affinity to metal and carbon nanomaterials. Next, we use molecular dynamics (MD) simulations to obtain direct molecular information for a selection of vitamins that could not be assessed quantitatively using QSAR models. This showed how large and flexible metabolites can gain stability on the nanomaterial surface via conformational changes. Additionally, unconstrained MD simulations provided excellent support for the main interaction types identified by QSAR analysis. Combined, these results enable assessing the adsorption affinity for many enteric microbial metabolites quantitatively and support the qualitative assessment of an even larger set of complex and biologically relevant microbial metabolites to carbon and metal nanomaterials.

Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes

Advances in technology and software have radically expanded the scope of metabolomics studies and allow us to monitor a broad transect of central carbon metabolism in routine studies. These increasingly sophisticated tools have shown that many human diseases are modulated by microbial metabolism. Despite this, it remains surprisingly difficult to move beyond these statistical associations and identify the specific molecular mechanisms that link dysbiosis to the progression of human disease. This difficulty stems from both the biological intricacies of host-microbiome dynamics as well as the analytical complexities inherent to microbiome metabolism research. The primary objective of this review is to examine the experimental and computational tools that can provide insights into the molecular mechanisms at work in host-microbiome interactions and to highlight the undeveloped frontiers that are currently holding back microbiome research from fully leveraging the benefits of modern metabolomics.

Optimization and validation of direct gas chromatography-mass spectrometry method for simultaneous quantification of ten short-chain fatty acids in rat feces

Short-chain fatty acids (SCFAs) play key roles in maintaining health and treating disease. Quantification of important fecal SCFAs is necessary to facilitate the clarification of their biological roles. However, the existing quantifying methods mainly depend on complicated precolumn derivatization, and/or are unable to determine formic acid, a SCFA commonly associated with toxicity. In this study, a direct gas chromatography-mass spectrometry (GC-MS) method for simultaneous quantification of ten SCFAs including formic acid in rat feces was developed. The approach was optimized in terms of chromatographic and spectrometric conditions as well as sample preparation. DB-FFAP capillary column with temperature programming was used to get baseline separation and symmetrical peak shape of SCFAs without precolumn derivatization in a relatively short running time (8 min). Multiple reaction monitoring (MRM) scan mode was employed to enhance the sensitivity and selectivity of SCFAs. Acidification with 50% HCl and immediate extraction with diethyl ether were utilized to achieve sample preparation of ten SCFAs from feces. Furthermore, the developed method was validated with wide linear range, high sensitivity and precision, low matrix effect and acceptable accuracy. The established method was successfully applied to compare the contents of fecal SCFAs between normal and immunosuppressed animal models.

Separation of short and medium-chain fatty acids using capillary electrophoresis with indirect photometric detection: Part I: Identification of fatty acids in rat feces

Short and medium-chain fatty acids (SMCFAs) are known as essential metabolites found in gut microbiota that function as modulators in the development and progression of many inflammatory conditions as well as in the regulation of cell metabolism. Currently, there are few simple and low-cost analytical methods available for the determination of SMCFA. This report focuses on SMCFA analysis utilizing CE with indirect photometric detection (CE-IPD). A ribonucleotide electrolyte, 5'-adenosine mono-phosphate (5'-AMP), is investigated as an IPD reagent due to its high molar absorptivity and dynamic reserve compatible with separation and detection of SMCFA. The operating parameters like the composition of organic solvent, millimolar concentrations of the complexing agent (alpha-cyclodextrin), 5'-AMP and non-absorbing electrolyte (boric acid), as well as the applied voltage, are optimized for resolution, efficiency, and signal-to-noise ratio. A baseline resolution of all nine SMCFAs is achieved in less than 15 min. Additionally, the developed CE-IPD method shows promising potential to identifying SMCFA in rat fecal supernatant. The presented analytical assay is simple, economical, and has considerably good repeatability. The intraday and interday RSD of less than 1 and 2% for relative migration time, as well as less than 14 and 15% for peak area, respectively, were obtained for SMCFA in fecal solution.

Modern Analytical Techniques for Detection of Bacteria in Surface and Wastewaters

Contamination of surface waters with pathogens as well as all diseases associated with such events are a significant concern worldwide. In recent decades, there has been a growing interest in developing analytical methods with good performance for the detection of this category of contaminants. The most important analytical methods applied for the determination of bacteria in waters are traditional ones (such as bacterial culturing methods, enzyme-linked immunoassay, polymerase chain reaction, and loop-mediated isothermal amplification) and advanced alternative methods (such as spectrometry, chromatography, capillary electrophoresis, surface-enhanced Raman scattering, and magnetic field-assisted and hyphenated techniques). In addition, optical and electrochemical sensors have gained much attention as essential alternatives for the conventional detection of bacteria. The large number of available methods have been materialized by many publications in this field aimed to ensure the control of water quality in water resources. This study represents a critical synthesis of the literature regarding the latest analytical methods covering comparative aspects of pathogen contamination of water resources. All these aspects are presented as representative examples, focusing on two important bacteria with essential implications on the health of the population, namely Pseudomonas aeruginosa and Escherichia coli.

Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies

Gut microbiota and their metabolic products are increasingly being recognized as important modulators of human health. The fecal metabolome provides a functional readout of the interactions between human metabolism and the gut microbiota in health and disease. Due to the high complexity of the fecal matrix, sample preparation often introduces technical variation, which must be minimized to accurately detect and quantify gut bacterial metabolites. Here, we tested six different representative extraction methods (single-phase and liquid–liquid extractions) and compared differences due to fecal amount, extraction solvent type and solvent pH. Our results indicate that a minimum fecal (wet) amount of 0.50 g is needed to accurately represent the complex texture of feces. The MTBE method (MTBE/methanol/water, 3.6/2.8/3.5, v/v/v) outperformed the other extraction methods, reflected by the highest extraction efficiency for 11 different classes of compounds, the highest number of extracted features (97% of the total identified features in different extracts), repeatability (CV < 35%) and extraction recovery (≥70%). Importantly, optimization of the solvent volume of each step to the initial dried fecal material (µL/mg feces) offers a major step towards standardization, which enables confident assessment of the contributions of gut bacterial metabolites to human health.

An insight into the exploration of proliferation of antibiotic resistance genes in high-fat diet induced obesity mice

Using mice as an animal model, we first demonstrated the significant proliferation of ARGs and the change of mobile genetic elements (MGEs) in high-fat diet induced obesity (DIO) mice, which the ermB and tnpA-03 genes mostly increased, illuminating that DIO could enrich the abundance of ARGs. Additionally, Lactobacillus sharply increased in the DIO mice and might contribute to the proliferation of ARGs and dramatical change of MGEs in the HFD groups. Finally, procrustes analysis showed the explanatory variables of the MGEs, the metabolites, and the microbial communities for the ARGs accounted for 94.3%, 53.4%, and 68.1%, respectively, and implying that MGEs might be the most direct factor affecting ARGs, and microbiota could be the main driver of the proliferation of ARGs in the DIO mice.

Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review

Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.

Effect of Probiotic Administration on Serum Tryptophan Metabolites in Pediatric Type 1 Diabetes Patients

Type 1 diabetes (T1D) is characterized by anomalous functioning of the immuno regulatory, tryptophan-catabolic enzyme indoleamine 2,3 dioxygenase 1 (IDO1). In T1D, the levels of kynurenine-the first byproduct of tryptophan degradation via IDO1-are significantly lower than in nondiabetic controls, such that defective immune regulation by IDO1 has been recognized as potentially contributing to autoimmunity in T1D. Because tryptophan catabolism-and the production of immune regulatory catabolites-also occurs via the gut microbiota, we measured serum levels of tryptophan, and metabolites thereof, in pediatric, diabetic patients after a 3-month oral course of Lactobacillus rhamnosus GG. Daily administration of the probiotic significantly affected circulating levels of tryptophan as well as the qualitative pattern of metabolite formation in the diabetic patients, while it decreased inflammatory cytokine production by the patients. This study suggests for the first time that a probiotic treatment may affect systemic tryptophan metabolism and restrain proinflammatory profile in pediatric T1D.

The role of gut microbiota (GM) and GM-related metabolites in diabetes and obesity. A review of analytical methods used to measure GM-related metabolites in fecal samples with a focus on metabolites' derivatization step

Disruption of gut microbiota (GM) composition is increasingly related to the pathogenesis of various metabolic diseases. Additionally, GM is responsible for the production and transformation of metabolites involved in the development of metabolic disorders, such as obesity and type 2 diabetes mellitus (T2DM). The current state of knowledge regarding the composition of GM and GM-related metabolites in relation to the progress and development of obesity and T2DM is presented in this review. To understand the relationships between GM-related metabolites and the development of metabolic disorders, their accurate qualitative and quantitative measurement in biological samples is needed. Feces represent a valuable biological matrix which composition may reflect the health status of the lower gastrointestinal tract and the whole organism. Mass spectrometry (MS), mainly in combination with gas chromatography (GC) or liquid chromatography (LC), is commonly used to measure fecal metabolites. However, profiling metabolites in such a complex matrix as feces is challenging from both analytical chemistry and biochemistry standpoints. Chemical derivatization is one of the most effective methods used to overcome these problems. In this review, we provide a comprehensive summary of the derivatization methods of GM-related metabolites prior to GC-MS or LC-MS analysis, which have been published in the last five years (2015-2020). Additionally, analytical methods used for the analysis of GM-related metabolites without the derivatization step are also presented.