Impact of Sample Storage on the NMR Fecal Water Metabolome

Impact of a legumes diet on the human gut microbiome articulated with fecal and plasma metabolomes: A pilot study

BACKGROUND & AIMS

Legumes intake is known to be associated with several health benefits the origins of which is still a matter of debate. This paper addresses a pilot small cohort to probe for metabolic aspects of the interplay between legumes intake, human metabolism and gut microbiota.

METHODS

Untargeted nuclear magnetic resonance (NMR) metabolomics of blood plasma and fecal extracts was carried out, in tandem with qPCR analysis of feces, to assess the impact of an 8-week pilot legumes diet intervention on the fecal and plasma metabolomes and gut microbiota of 19 subjects.

RESULTS

While the high inter-individual variability hindered the detection of statistically significant changes in the gut microbiome, increased fecal glucose and decreased threonine levels were noted. Correlation analysis between the microbiome and fecal metabolome lead to putative hypotheses regarding the metabolic activities of prevalent bacteria groups (Clostridium leptum subgroup, Roseburia spp., and Faecalibacterium prausnitzii). These included elevated fecal glucose as a preferential energy source, the involvement of valerate/isovalerate and reduced protein degradation in gut microbiota. Plasma metabolomics advanced mannose and betaine as potential markers of legume intake and unveiled a decrease in formate and ketone bodies, the latter suggesting improved energy utilization through legume carbohydrates. Amino acid metabolism was also apparently affected, as suggested by lowered urea, histidine and threonine levels.

CONCLUSIONS

Despite the high inter-individual gut microbiome variability characterizing the small cohort addressed, combination of microbiological measurements and untargeted metabolomics unveiled several metabolic effects putatively related to legumes intake. If confirmed in larger cohorts, our findings will support the inclusion of legumes in diets and contribute valuable new insight into the origins of associated health benefits.

High-Soluble-Fiber Diet Attenuates Hypoxia-Induced Vascular Remodeling and the Development of Hypoxic Pulmonary Hypertension

BACKGROUND

Hypoxic pulmonary hypertension is a difficult disease to manage that is characterized by sustained elevation of pulmonary vascular resistance and pulmonary artery pressure due to vasoconstriction, perivascular inflammation, and vascular remodeling. Consumption of soluble-fiber is associated with lower systemic blood pressure, but little is known about its ability to affect the pulmonary circulation.

METHODS

Mice were fed either a low- or high-soluble-fiber diet (0% or 16.9% inulin) and then exposed to hypoxia (FiO2, 0.10) for 21 days to induce pulmonary hypertension. The impact of diet on right ventricular systolic pressure and pulmonary vascular resistance was determined in vivo or in ex vivo isolated lungs, respectively, and correlated with alterations in the composition of the gut microbiome, plasma metabolome, pulmonary inflammatory cell phenotype, and lung proteome.

RESULTS

High-soluble-fiber diet increased the abundance of short-chain fatty acid-producing bacteria, with parallel increases in plasma propionate levels, and reduced the abundance of disease-related bacterial genera such as Staphylococcus, Clostridioides, and Streptococcus in hypoxic mice with parallel decreases in plasma levels of p-cresol sulfate. High-soluble-fiber diet decreased hypoxia-induced elevations of right ventricular systolic pressure and pulmonary vascular resistance. These changes were associated with reduced proportions of interstitial macrophages, dendritic cells, and nonclassical monocytes. Whole-lung proteomics revealed proteins and molecular pathways that may explain the effect of soluble-fiber supplementation.

CONCLUSIONS

This study demonstrates for the first time that a high-soluble-fiber diet attenuates hypoxia-induced pulmonary vascular remodeling and the development of pulmonary hypertension in a mouse model of hypoxic pulmonary hypertension and highlights diet-derived metabolites that may have an immuno-modulatory role in the lung.

Optimization of fecal sample homogenization for untargeted metabolomics

INTRODUCTION

Fecal samples are highly complex and heterogeneous, containing materials at various stages of digestion. The heterogeneity and complexity of feces make stool metabolomics inherently challenging. The level of homogenization influences the outcome of the study, affecting the metabolite profiles and reproducibility; however, there is no consensus on how fecal samples should be prepared to overcome the topographical discrepancy and obtain data representative of the stool as a whole.

OBJECTIVES

Various combinations of homogenization conditions were compared to investigate the effects of bead size, addition of solvents and the differences between wet-frozen and lyophilized feces.

METHODS

The homogenization parameters were systematically altered to evaluate the solvent usage, bead size, and whether lyophilization is required in homogenization. The metabolic coverage and reproducibility were compared among the different conditions.

RESULTS

The current work revealed that a combination of mechanical and chemical lysis obtained by bead-beating with a mixture of big and small sizes of beads in an organic solvent is an effective way to homogenize fecal samples with adequate reproducibility and metabolic coverage. Lyophilization is required when bead-beating is not available.

CONCLUSIONS

A comprehensive and systematical evaluation of various fecal matter homogenization conditions provides a profound understanding for the effects of different homogenization methods. Our findings would be beneficial to assist with standardization of fecal sample homogenization protocol.

Untargeted Metabolomic Profiling of Aqueous and Lyophilized Pooled Human Feces from Two Diet Cohorts Using Two-Dimensional Gas Chromatography Coupled with Time-of-Flight Mass Spectrometry

The metabolic profiles of human feces are influenced by various genetic and environmental factors, which makes feces an attractive biosample for numerous applications, including the early detection of gut diseases. However, feces is complex, heterogeneous, and dynamic with a significant live bacterial biomass. With such challenges, stool metabolomics has been understudied compared to other biospecimens, and there is a current lack of consensus on methods to collect, prepare, and analyze feces. One of the critical steps required to accelerate the field is having a metabolomics stool reference material available. Fecal samples are generally presented in two major forms: fecal water and lyophilized feces. In this study, two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) was used as an analytical platform to characterize pooled human feces, provided by the National Institute of Standards and Technology (NIST) as Research-Grade Test Materials. The collected fecal samples were derived from eight healthy individuals with two different diets: vegans and omnivores, matched by age, sex, and body mass index (BMI), and stored as fecal water and lyophilized feces. Various data analysis strategies were presented to determine the differences in the fecal metabolomic profiles. The results indicate that the sample storage condition has a major influence on the metabolic profiles of feces such that the impact from storage surpasses the metabolic differences from the diet types. The findings of the current study would contribute towards the development of a stool reference material.

Gut Microbiota and Microbial Metabolism in Early Risk of Cardiometabolic Disease

Cardiometabolic disease comprises cardiovascular and metabolic dysfunction and underlies the leading causes of morbidity and mortality, both within the United States and worldwide. Commensal microbiota are implicated in the development of cardiometabolic disease. Evidence suggests that the microbiome is relatively variable during infancy and early childhood, becoming more fixed in later childhood and adulthood. Effects of microbiota, both during early development, and in later life, may induce changes in host metabolism that modulate risk mechanisms and predispose toward the development of cardiometabolic disease. In this review, we summarize the factors that influence gut microbiome composition and function during early life and explore how changes in microbiota and microbial metabolism influence host metabolism and cardiometabolic risk throughout life. We highlight limitations in current methodology and approaches and outline state-of-the-art advances, which are improving research and building toward refined diagnosis and treatment options in microbiome-targeted therapies.

The effects of ambient temperature exposure on feline fecal metabolome

Introduction

The fecal metabolome provides insight into overall gastrointestinal and microbial health. Methods for fecal sample storage in metabolomics research vary, however, making comparisons within current literature difficult. This study investigated the effect of ambient temperature exposure on microbial-derived metabolites of feline fecal samples.

Methods

Fecal samples were collected from 11 healthy cats from a local boarding facility. Samples were manually homogenized and aliquoted. The first aliquot was frozen at -80°C within 1 hour of defecation, and remaining samples were exposed to ambient temperature for 2, 4, 6, 8, 12, and 24 h prior to freezing at -80°C. Fecal metabolites were quantified using ¹H NMR spectroscopy. Fifty metabolites were grouped into six categories (27 amino acids, 8 fatty acids, 5 sugars, 3 alcohols, 2 nitrogenous bases, 5 miscellaneous).

Results

Concentrations of 20 out of 50 metabolites significantly differed due to ambient temperature exposure (7 amino acids, 6 fatty acids, 2 alcohols, 1 nitrogenous base, 4 miscellaneous). The earliest detected changes occurred 6 h post-defecation for cadaverine and fumaric acid.

Discussion

This study shows ambient temperature exposure alters the composition of the feline fecal metabolome, but short-term (up to 4 h) exposure prior to storage in the freezer seems to be acceptable.

Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus

Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.

Clinical Application Value of Lactobacillus Plantarum PS128 in Patients with Anxiety Disorders

Objective

PS128 is a novel psycho biotic strain, it has been reported to play an important role in neuropsychiatric disorders. This study investigated the clinical effect of PS128 supplementation on patients with anxiety.

Methods

A total of 200 patients with anxiety were recruited, and divided into two groups (n = 100/group). The control group received oral treatment with citalopram, and the PS128 group received PS128 capsules based on citalopram treatment. Hamilton Anxiety Scale (HAMA) and Self-Rating Anxiety Scale (SAS) were used to evaluate the anxiety levels. After 2 months of continuous administration, clinical efficacy was evaluated according to HAMA score.

Results

There was no significant difference in HAMA and SAS scores between the two groups before treatment. With the treatment prolonged, the HAMA and SAS score decreased gradually in both control and PS128 groups, and the decrease rate of PS128 group was significantly greater than that of the control group. The clinical effective rates of PS128 group were higher than those in the control group, high levels of clinical cure rate were also detected in the PS128 group. Compared with the control group (22%), the incidence of adverse reactions was significantly reduced for patients in the PS128 group (4%).

Conclusion

The treatment effect of citalopram combined with PS128 against anxiety is satisfactory clinically. It can greatly improve the anxiety symptoms of patients, increase the cure rate, reduce adverse reactions.

Fecal amine metabolite analysis before onset of severe necrotizing enterocolitis in preterm infants: a prospective case-control study

Infants developing necrotizing enterocolitis (NEC) have a different metabolomic profile compared to controls. The potential of specific metabolomics, i.e. amino acids and amino alcohols (AAA), as early diagnostic biomarkers for NEC is largely unexplored. In this multicenter prospective case-control study, longitudinally collected fecal samples from preterm infants (born <30 weeks of gestation) from 1-3 days before diagnosis of severe NEC (Bell's stage IIIA/IIIB), were analyzed by targeted high-performance liquid chromatography (HPLC). Control samples were collected from gestational and postnatal age-matched infants. Thirty-one NEC cases (15 NEC IIIA;16 NEC IIIB) with 1:1 matched controls were included. Preclinical samples of infants with NEC were characterized by five increased essential amino acids-isoleucine, leucine, methionine, phenylalanine and valine. Lysine and ethanolamine ratios were lower prior to NEC, compared to control samples. A multivariate model was rendered based on isoleucine, lysine, ethanolamine, tryptophan and ornithine, modestly discriminating cases from controls (AUC 0.67; p < 0.001). Targeted HPLC pointed to several specific AAA alterations in samples collected 1-3 days before NEC onset, compared to controls. Whether this reflects metabolic alterations and has a role in early biomarker development for NEC, has yet to be elucidated.

Dominant Components of the Giant Panda Seminal Plasma Metabolome, Characterized by 1H-NMR Spectroscopy

Simple Summary

As China’s flagship animal, the giant panda (Ailuropoda melanoleuca) attracts much attention due to its small population and low natural reproductive rate. Therefore, artificial insemination has become the leading practical approach in the captive breeding programs of giant pandas worldwide. Seminal plasma acts as a medium between spermatozoa and the external stimuli, and its characteristics have been directly linked to fertility in both artificial insemination and natural fertilization. The current work, for the first time, attempts to characterize, by proton magnetic resonance spectroscopy (¹H-NMR), the metabolome of healthy giant panda seminal plasma. A total of 35 molecules were quantified, with distinct age-related trends highlighted by a multivariate analysis, and the concentrations of 2,3-butanediol were significantly different between individuals younger than 8 years and older than 13 years. In addition, isopropanol’s concentration was significantly linked to estrus stages. Besides, the variations in the metabolome’s profile with storage time were also evaluated. This study may serve as a reference for research wishing to shed light on the biological mechanisms affecting giant panda sperm’s overall quality and may ultimately lead to novel approaches to giant panda artificial insemination.

Abstract

As an assisted breeding technique, artificial insemination has become the main effective practical approach in the captive breeding programs of giant panda worldwide. The composition of seminal plasma plays an important role in the success of breeding. The present work is the first attempt to characterize, by proton magnetic resonance spectroscopy (¹H-NMR), the metabolome of healthy giant panda seminal plasma. A total of 35 molecules were quantified, with the concentration of 2,3-butanediol being significantly different between individuals younger than 8 years and older than 13 years, and other distinct age-related trends were highlighted by a multivariate analysis. Isopropanol’s concentration was significantly linked to estrus stages. Besides, the variations in the metabolome’s profile during storage were also evaluated. This study may serve as a reference for further research wishing to shed light on the biological mechanisms affecting giant panda sperm’s overall quality and may ultimately lead to novel approaches to giant panda artificial insemination.

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.

Evaluation of fresh, frozen, and lyophilized fecal samples by SPME and derivatization methods using GC×GC-TOFMS

INTRODUCTION

Feces is a highly complex matrix containing thousands of metabolites. It also contains live bacteria and enzymes, and does not have a static chemistry. Consequently, proper control of pre-analytical parameters is critical to minimize unwanted variations in the samples. However, no consensus currently exists on how fecal samples should be stored/processed prior to analysis.

OBJECTIVE

The effects of sample handling conditions on fecal metabolite profiles and abundances were examined using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS).

METHODS

Solid-phase microextraction (SPME) and derivatization via trimethylsilylation (TMS) were employed as complementary techniques to evaluate fresh, frozen, and lyophilized fecal samples with expanded coverage of the fecal metabolome. The total number of detected peaks and the signal intensities were compared among the different handling conditions.

RESULTS

Our analysis revealed that the metabolic profiles of fecal samples depend greatly on sample handling and processing conditions, which had a more pronounced effect on results obtained by SPME than by TMS derivatization. Overall, lyophilization resulted in a greater amount of total and class-specific metabolites, which may be attributed to cell lysis and/or membrane disintegration.

CONCLUSIONS

A comprehensive comparison of the sample handling conditions provides a deeper understanding of the physicochemical changes that occur within the samples during freezing and lyophilization. Based on our results, snap-freezing at -80 °C would be preferred over lyophilization for handling samples in the field of fecal metabolomics as this imparts the least change from the fresh condition.

A Multiomic Approach to Investigate the Effects of a Weight Loss Program on the Intestinal Health of Overweight Horses

Obesity is endemic in human populations in the western society, and with mounting evidence that the intestinal ecological environment plays a major role in its pathogenesis, identification of therapies based on intestinal microbiota modulation are gaining attention. Obesity in companion animals is also a common clinical problem. We set out using a multidimensional approach, to determine the effectiveness and safety of a weight loss program for horses incorporating diet restriction and exercise. In addition, we aimed to investigate the effect of this program on the overall intestinal health of overweight sedentary horses. The investigation comprised of a randomized, controlled, 6-week study of 14 overweight sedentary horses and ponies who were blocked for age, gender, and breed (controls n = 7, treatment n = 7). The treatment group were fed a restricted diet (1.4% of body weight dry matter intake) and the control group a maintenance diet (2% of body weight as dry matter intake) over the study period. The treatment group were subjected to a prescribed exercise regime, while the control group were exercised to mimic foraging conditions. Several clinical measurements were taken at the start and end of the study, including morphological parameters, ultrasound measurements of subcutaneous fat, and blood pressure. Fecal microbiota analysis was performed using 16S rRNA gene sequence analysis, and fecal metabolome was analyzed using NMR spectroscopy, on samples taken at weeks 1, 3, and 6 of the study. All horses completed the study period successfully. However, two of the treatment group had to have modified exercise regimes. The treatment group showed significant weight loss (p < 0.00001) and an associated decrease in waste circumference (p < 0.0001) when compared with the control group. The alpha-diversity of the fecal microbiota in the treatment group showed a significant increase from the start to the end of the study period (p < 0.05); however, there was no significant difference between groups at any sampling point. There were significant changes (p < 0.05) in the metabolome in both groups between the start and end of the study, but not between groups at any sampling point. Finally, the resting blood pressure of all horses was significantly lower by the end of the study.

Cryptosporidiosis Modulates the Gut Microbiome and Metabolism in a Murine Infection Model

Cryptosporidiosis is a major human health concern globally. Despite well-established methods, misdiagnosis remains common. Our understanding of the cryptosporidiosis biochemical mechanism remains limited, compounding the difficulty of clinical diagnosis. Here, we used a systems biology approach to investigate the underlying biochemical interactions in C57BL/6J mice infected with Cryptosporidium parvum. Faecal samples were collected daily following infection. Blood, liver tissues and luminal contents were collected 10 days post infection. High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of these samples. Faeces and luminal contents were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis of the acquired data illustrated altered host and microbial energy pathways during infection. Glycolysis/citrate cycle metabolites were depleted, while short-chain fatty acids and D-amino acids accumulated. An increased abundance of bacteria associated with a stressed gut environment was seen. Host proteins involved in energy pathways and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase were upregulated during cryptosporidiosis. Liver oxalate also increased during infection. Microbiome–parasite relationships were observed to be more influential than the host–parasite association in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite–microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model towards biomarker discovery, and rapid and accurate diagnostics.

Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics

The connection between gut microbiota and human health is becoming increasingly relevant and the number of groups working in this field is constantly growing. In this context, from high-throughput gene sequencing to metabolomics analysis, the omics technologies have contributed enormously to unveil the secret crosstalk between us and our microbes. All the omics technologies produce a great amount of information, and processing this information is time-consuming and expensive. For this reason, a correct experimental design and a careful pre-analytical planning are crucial. To study the human gut microbiota, faeces are the sample of choice. Faecal material is complex, and procedures for collecting and preserving faeces are not well-established. Furthermore, increasing evidence suggests that multiple confounding factors, such as antibiotics consumption, mode of delivery, diet, aging and several diseases and disorders can alter the composition and functionality of the microbiota. This review is focused on the discussion of critical general issues during the pre-analytical planning, from patient handling to faeces sampling, including collection procedures, transport, storage conditions and possible pre-treatments, which are critical for a successful research in omics with a special attention to metabolomics and gene sequencing. We also point out that the adoption of standard operating procedures in the field is needed to guarantee accuracy and reproducibility of results.

Lyophilized fecal short-chain fatty acid and electrolyte determination by capillary electrophoresis with indirect UV detection for assessment of pediatric inflammatory bowel disease

Short-chain fatty acids (SCFAs) and electrolytes are major constituents of human feces involved in maintaining gastrointestinal homeostasis that underlie complex diet, host and microbiome interactions. Reliable quantification of SCFAs and electrolytes is challenging given the heterogeneity of stool specimens from pediatric patients with diarrhea-predominate inflammatory bowel disease (IBD). Herein, we introduce two validated methods for determination of 3 SCFAs and 5 electrolytes consistently quantified from fecal extracts when using capillary electrophoresis with indirect UV detection (CE-iUV), where concentrations are normalized to total dried weight (mmol/kg d.w.). Lyophilization facilitates sample handling and extraction of heterogeneous stool specimens (∼ 15 mg) from a cohort of children with Crohn's disease (CD, n = 12) and ulcerative colitis (UC, n = 10) treated with exclusive enteral nutrition (EEN) or corticosteroid (CS) therapy to induce remission, respectively. Good technical precision (mean CV = 13 %, n = 14) and accuracy (recovery from 84 to 116%) is demonstrated for SCFAs and electrolytes from freeze dried stool extracts using a modified Bligh-Dyer protocol with low micromolar detection limits (∼ 2-15 μM). Fecal butyrate is 2.6-fold higher in CD as compared to UC patients (effect size = 1.51; p = 0.00291), and there is a strong co-linearity between fecal butyrate and acetate (r = 0.835) unlike propionate, which is correlated with fecal calprotectin (r = 0.517), a protein biomarker of intestinal inflammation. Also, a longitudinal study of matching stool samples collected from a sub-set of IBD patients revealed about a 7-fold enrichment in magnesium and calcium following 4 weeks of EEN as compared to baseline (F > 4.1 ; p < 0.05) unlike the CS treatment arm with no changes in other fecal SCFAs and electrolytes, including sodium, potassium, and ammonium. CE-iUV enables rapid fecal SCFA and electrolyte determination as required for new insights into the role of gut dysbiosis in IBD, as well as treatment monitoring of nutritional interventions that stabilize the disease course in affected children.