Fecal Metabolome Research Articles

Dysbiosis index and fecal concentrations of sterols, long-chain fatty acids and unconjugated bile acids in dogs with inflammatory protein-losing enteropathy.

Canine protein-losing enteropathy (PLE) is a syndrome characterized by gastrointestinal loss of proteins. While fecal microbiome and metabolome perturbations have been reported in dogs with chronic enteropathy, they have not been widely studied in dogs with PLE. Therefore, the study aims were to investigate gut microbiome and targeted fecal metabolites in dogs with inflammatory PLE (iPLE) and evaluate whether treatment affects these changes at short-term follow-up. Thirty-eight dogs with PLE and histopathological evidence of gastrointestinal inflammation and 47 healthy dogs were enrolled. Fecal samples were collected before endoscopy (T0) and after one month of therapy (T1). Microbiome and metabolome alterations were investigated using qPCR assays (dysbiosis index, DI) and gas chromatography/mass spectrometry (long-chain fatty acids, sterols, unconjugated bile acids), respectively. Median (min-max) DI of iPLE dogs was 0.4 (-5.9 to 7.7) and was significantly higher (p < 0.0001) than median DI in healthy dogs [-2.0 (-6.0 to 5.3)]. No significant associations were found between DI and selected clinicopathological variables. DI did not significantly differ between T0 and T1. In iPLE dogs, at T0, myristic, palmitic, linoleic, oleic, cis-vaccenic, stearic, arachidonic, gondoic, docosanoic, erucic, and nervonic acids were significantly higher (p < 0.0001) than healthy dogs. In iPLE dogs, oleic acid (p = 0.044), stearic acid (p = 0.013), erucic acid (p = 0.018) and nervonic acid (p = 0.002) were significantly decreased at T1. At T0, cholesterol and lathosterol (p < 0.0001) were significantly higher in iPLE dogs compared to healthy dogs, while total measured phytosterols were significantly lower (p = 0.001). No significant differences in total sterols, total phytosterols and total zoosterols content were found at T1, compared to T0. At T0, total primary bile acids and total secondary bile acids did not significantly differ between healthy control dogs and iPLE dogs. No significant differences in fecal bile acid content were found at T1. Dysbiosis and lipid metabolism perturbations were observed in dogs with iPLE. Different therapeutic protocols lead to an improvement of some but not all metabolome perturbations at short-term follow-up.

Effect of host breeds on gut microbiome and fecal metabolome in commercial pigs

BackgroundGut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics.ResultsThere were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea, Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype.ConclusionsThis work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement.

Lactobacillus rhamnosus ameliorates experimental autoimmune neuritis via modulation of gut microbiota and metabolites

BackgroundGuillain-Barre syndrome (GBS), an autoimmune disease of the peripheral nervous system, is hallmarked by demyelination and immune cellular infiltration. Experimental autoimmune neuritis (EAN), considered a GBS prototype model, has been studied for its potential therapeutic benefits from lactobacilli. This study evaluated the protective role of Lactobacillus rhamnosus GG (GG) for treatment in EAN. T cell ratio, inflammation factors, sciatic nerve pathology, intestinal permeability, and gut inflammation were assessed on day 19 post-immunization to evaluate GG's effect on EAN. Fecal metabolomics and 16s rRNA microbiome analysis were conducted to elucidate its mechanism. ResultsGG dynamically balanced CD4+/CD8+T cell ratio, reduced serum IL-1β and TNF-α expression, improved sciatic nerve demyelination and inflammation, and enhanced neurological scores during peak disease period. Intestinal mucosal damage was evident in EAN rats, with downregulated Occludin and ZO-1 and upregulated IL-1β, TNF-α, and Reg3γ. GG treatment restored intestinal mucosal integrity, upregulated Occludin and ZO-1, and downregulated IL-1, TNF-α, and Reg3γ. GG partially rectified the gut microbiota and metabolite imbalance in EAN rats. ConclusionGG mitigates EAN through immune response modulation and inflammation reduction via the gut microbiota and metabolites.

Investigating the mechanism of enhanced medicinal effects of Terminalia chebula fruit after processing based on intestinal flora and metabolomics

Background and objectiveTerminalia chebula is a classical medicine for the treatment of lingering dysentery, and both raw and processed T. chebula can alleviate ulcerative colitis (UC). The therapeutic efficacy of T. chebula is enhanced after processing, but the mechanism that processing improves this efficacy is still unknown. We investigated the medicinal effects of raw and processed T. chebula on dextran sulfate sodium (DSS)-induced UC model rats using intestinal flora and metabolomics analyses, in order to elucidate the mechanism by which processing enhances the therapeutic effect. MethodsThe major constituents of raw and processed T. chebula were detected by high-performance liquid chromatography (HPLC). UC model was replicated using the DSS method, and then UC rats were administered raw and processed T. chebula. The general physical signs, disease activity index (DAI) scores, colon histopathological morphology, and the expressions of inflammatory cytokines were used to evaluate the therapeutic effect of T. chebula. In addition, 16 s rRNA sequencing and gas chromatography-mass spectrometry (GC–MS) were used to characterize the intestinal flora and contents of short-chain fatty acids (SCFAs). Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was utilized to identify the nontargeted fecal metabolites. ResultsRaw and processed T. chebula significantly improved the general physical signs and colon inflammatory symptoms and decreased DAI scores of UC rats. Both raw and processed T. chebula mitigated intestinal flora disorders in UC rats, increasing probiotic bacteria, including Lactobacillus and Romboutsia. However, the effect of processed T. chebula was more pronounced. Moreover, the levels of SCFAs of DSS-induced UC rats were restored after drug administration, and the processed T. chebula had a better regulatory effect than raw T. chebula. In the fecal nontargeted metabolomics analysis, differential metabolites such as lipids and amino acids were identified. The processed T. chebula can regulate purine metabolism and other pathways to improve UC, and the levels of the disordered metabolites gradually approached those of the control group. ConclusionRaw and processed T. chebula had the capacity to mitigate DSS-induced UC by rebalancing the intestinal flora, restoring the contents of SCFAs, and regulating fecal metabolites, while processed T. chebula showed preferable effects.

Quercetin microgels alter gut metabolome and reverse oxidative damage invitro

Colonic delivery of quercetin using encapsulation techniques is an effective approach in maximizing quercetin efficacy against oxidative-stress related diseases such as inflammatory bowel disease. We hypothesized that colon-targeted delivery of quercetin with quercetin loaded alginate-chitosan microgels (ALQ) could alter colonic microbial metabolism regulating microbial metabolites production that may exert biological effects at the cellular level. To demonstrate this, ALQ were subjected to colonic fermentation using human fecal microbiota with empty microgels (AL) as control, and fermented fecal samples were collected at 0, 8, and 24 h. Short chain fatty acid analysis using gas chromatography showed that ALQ increased productions of acetic acid, while decreased isobutyric and isovaleric acid production. Semi-targeted metabolome scanning using Orbitrap mass spectrometer showed that the overall metabolome profile was remarkably different between AL and ALQ treatments at both 8 h and 24 h of fermentation. There were 9 metabolites at 8 h, and 54 metabolites at 24 h that were significantly regulated with more than 2-fold changes between AL and ALQ treatments. The metabolites included quercetin derived metabolites, amino acids and their derivatives, nucleotide derivatives, and organic acids. ALQ significantly modulated tyrosine metabolism, amino acids metabolic pathways, and the tricarboxylic acid cycle. These ALQ modulated metabolites in turn protected the Caco-2 cells from lipopolysaccharides induced injury, increased cellular antioxidant activities, and alleviated lipid oxidation induced by H2O2. Conclusively, ALQ could alter human fecal metabolome in vitro with significant shifts in key metabolites and exert antioxidant effects on cellular level, exhibiting potentials in colonic disease management.

Eriocalyxin B ameliorated experimental autoimmune prostatitis via modulation of macrophage polarization through gut microbiota-mediated vitamin D3 alteration

BackgroundChronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a often heterogeneous condition in urology. Accumulating evidence suggests that the autoimmune response against prostate antigens is related to CP/CPPS. The gut microbiota may be a possible cause of a number of autoimmune diseases. Eriocalyxin B (EriB) is used as an anti-inflammatory treatment for autoimmune disorders. The underlying mechanism of fecal metabolome involved in CP/CPPS treatment by EriB remains unclear. MethodsThe experimental autoimmune prostatitis (EAP) mouse model was generated by subcutaneous immunization. Macrophages, inflammatory cytokines, intestinal microbiota, and fecal metabolome of the mice were analyzed. The alteration of the fecal metabolome was investigated in detail in EriB-treated EAP mice and confirmed by in vitro experiments. ResultsEriB ameliorated significantly decreased prostate inflammation in EAP mice and promoted macrophage phenotype polarizing from M1 to M2. The gut microbiome was altered, and intestinal barrier damage was improved by EriB treatment. Furthermore, the enrichment of vitamin digestion and absorption pathways in the fecal metabolome revealed that vitamin D3 was altered by EriB. In vitro experiments confirmed that macrophage polarization from M1 to M2 was promoted by vitamin D3. Finally, fecal transplantation from EriB-treated mice markedly reduced inflammatory indicators and the macrophage M1/M2 ratio in pseudogerm-free EAP mice. In our study, the immune state of macrophage regulated by gut microbiota-mediated vitamin D3 alteration was first time revealed in EAP treatment. ConclusionsEriB ameliorated in mice with EAP, the gut microbiota mediates vitamin D3 alterations to modulate macrophage phenotype polarizing from M1 to M2.

Integrating fecal metabolomics and gut microbiome to reveal the mechanism of Schisandra chinensis-Acorus tatarinowii Schott treatment in Alzheimer’s disease rats

BackgroundSchisandra chinensis (Turcz.) Baill (Schisandraceae) and Acorus tatarinowii Schott (Araceae Juss) (Sc-At) are two traditional Chinese medicinal herbs that are widely used in the treatment of neurological disorders such as insomnia. In our previous study, we found that Sc-At could improve the therapeutic efficacy of Alzheimer’s disease by affecting aromatase activity and estrogen levels, among other pathways. Material and methodsIn this study, first, the ameliorative effect of Sc-At on cognitive dysfunction in Alzheimer’s disease model rats was verified by Y-maze test together with Elisa assay. Second, fecal untargeted metabolomics analysis was performed using a UPLC-Q-TOF/MS-based metabolomics approach. 16S rDNA sequencing was utilized to screen the differential flora between groups, and linear discriminantan alysis effect size (LEfSe) was used to find the target flora. Finally, Spearman correlation analysis was combined to find the relationship between differential flora and differential metabolites in feces. Results(1) The results of Y-maze test and Elisa assay indicated that Sc-At could improve the cognitive dysfunction of AD model rats. (2) Metabolomics results showed that fecal metabolite levels were significantly different from those of rats in the blank group, and 18 potential biomarkers in feces were screened, mainly affecting linoleic acid metabolism, steroid hormone biosynthesis, sphingomyelin metabolism, riboflavin metabolism, etc. The 16S rDNA results showed that the abundance and diversity of intestinal flora in AD rats were destroyed, and the Sc-At treatment was able to reverse these changes. (3) Spearman’s correlation analysis showed a significant correlation between differential metabolites in feces and intestinal flora, further suggesting that Sc-At treats Alzheimer’s disease through the gut-brain axis. ConclusionsIn this study, we explored the mechanism of Sc-At in the treatment of Alzheimer’s disease by integrating fecal untargeted metabolomics and 16S rDNA gene sequencing, and the results showed that Sc-At exerts therapeutic effects on Alzheimer’s disease by improving the intestinal flora and related metabolic pathways.

Multi-omics and bioinformatics for the investigation of therapeutic mechanism of roucongrong pill against postmenopausal osteoporosis

Ethnopharmacological relevanceThe Roucongrong Pill (RCRP), originating from the historical General Medical Collection of Royal Benevolence, is frequently used to treat postmenopausal osteoporosis (PMOP). Despite its prevalent application, the specific anti-osteoporotic mechanisms of RCRP remain to be elucidated. Aim of the studyThis study aims to elucidate the therapeutic mechanism of RCRP in the context of ovariectomy (OVX)-induced PMOP in rats. By employing an integrative approach, the research combines medicinal chemistry, gut microbiota (GM) profiling, metabolomics, MetOrigin traceability, network pharmacology, molecular docking, and molecular dynamics simulations to deliver a comprehensive analysis. Materials and methodsSprague-Dawley (SD) rats underwent bilateral OVX to establish a PMOP model. The therapeutic efficacy of RCRP was evaluated through bone metrics (BMD, bone strength, BV/TV, Tb.Sp), hematoxylin and eosin (H&E) histological assessment, and bone metabolism markers (OPG, BALP, TRACP-5b, β-CTX, RANKL). Fecal metabolomics and 16S rDNA sequencing were employed to assess the influence of RCRP on GM and metabolite profiles. Furthermore, MetOrigin facilitated the traceability analysis of relevant metabolites. Molecular docking identified potential RCRP compounds with anti-PMOP activity, while their stability and protein interactions were assessed through molecular dynamics simulations. Network pharmacology further confirms the targets of action. ResultsRCRP alleviated PMOP in rats, enhancing bone strength, cortical and trabecular BMD, BV/TV, and serum OPG levels, while reducing Tb.Sp, serum BALP, TRACP-5b, β-CTX, and RANKL concentrations. A total of twenty-six distinct metabolites were identified, of which ten—tribufos, sulfoacetic acid, betamethasone dipropionate, 9-oxooctadeca-10,12,15-trienoic acid, menatetrenone, piperlongumine, maltopentaose, enol-phenylpyruvate, catechol, pentaacetate, and (+)-2-methylpropanoic acid—exhibited correlations with six GM species: Turicibacter, Roseburia, Colidextribacter, Helicobacter, Odoribacter, and Lachnoclostridium, as determined by Spearman's correlation analysis. Notably, MetOrigin revealed the microbial metabolism of taurine and hypotaurine, along with host-specific steroid hormone synthesis. Computational docking studies demonstrated robust interactions between five RCRP-derived steroids (hydroxyecdysone, corticosterone, trilostane, 5α-androstan-3,6,17-trione, and cortisol) and key enzymes (estradiol 17α-dehydrogenase and UDP-glucuronosyltransferase), suggesting a potential enhancement of therapeutic efficacy against PMOP. Furthermore, molecular dynamics simulations indicated stable interactions between hydroxyecdysone and two proteins, with binding free energies of −67.427 kJ/mol and −156.948 kJ/mol, respectively. Through network pharmacology and molecular docking approaches, potential targets of these metabolites were identified, including estrogen receptors ESR1 and ESR2, dual specificity phosphatase 6 (DUSP6), sex hormone-binding globulin (SHBG), prostaglandin E receptor 4 (PTGER4), cannabinoid receptor 2 (CNR2), cathepsin K (CTSK), and androgen receptor (AR). ConclusionsRCRP effectively mitigates OVX-induced bone loss in PMOP rats by modulating GM and associated metabolites, along with their potential targets and key metabolic pathways, including taurine and hypotaurine metabolism, as well as steroid hormone biosynthesis. These findings offer new insights into the therapeutic mechanisms by which RCRP may alleviate PMOP.

Campylobacter infection of young children in Colombia and its impact on the gastrointestinal environment.

Campylobacter infections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low- and middle-income countries. It remains unclear how Campylobacter impacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well-characterized clinical cohorts in diverse settings. In this study, we analyzed the fecal microbiota and the metabolomic and micronutrient profiles of asymptomatic and symptomatic pediatric patients in Colombia who were either infected or uninfected with Campylobacter during a case-controlled study on acute diarrheal disease. Here, we report that the microbiome of Campylobacter-infected children only changed in their abundance of Campylobacter spp. despite the inclusion of children with or without diarrhea. In addition to increased Campylobacter, computational models were used to identify fecal metabolites that were associated with Campylobacter infection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggests that colonocyte metabolism is impacted during infection. Despite changes to the fecal metabolome, the concentrations of intestinal minerals and trace elements were not significantly impacted by Campylobacter infection but were elevated in uninfected children with diarrhea.IMPORTANCEGastrointestinal infection with pathogenic Campylobacter species has long been recognized as a significant cause of human morbidity. Recently, it has been observed that pediatric populations in low- and middle-income countries are uniquely impacted by these organisms in that infected children can be persistently colonized, develop enteric dysfunction, and exhibit reduced development and growth. While the association of Campylobacter species with these long-term effects continues to emerge, the impact of infection on the gastrointestinal environment of these children remains uncharacterized. To address this knowledge gap, our group leveraged clinical samples collected during a previous study on gastrointestinal infections in pediatric patients to examine the fecal microbiota, metabolome, and micronutrient profiles of those infected with Campylobacter species and found that the metabolome was impacted in a way that suggests gastrointestinal cell metabolism is affected during infection, which is some of the first data indicating how gastrointestinal health in these patients may be affected.

233 Exploring the impact of intrauterine growth restriction on fecal microbiota and metabolome in pigs

Abstract Intrauterine growth restriction (IUGR) poses a significant challenge in swine production, affecting approximately 20% of piglets and resulting in increased mortality rates, metabolic disturbances, compromised intestinal development, and altered microbial colonization. This phenomenon arises as the IUGR fetus adapts to limited oxygen and nutrient supply in utero by reallocating blood flow towards vital organs, particularly the brain, consequently leading to a greater brain-to-liver weight ratio (BrW/LW) at birth. Our study aimed to comprehensively investigate the repercussions of IUGR on fecal microbiota composition and plasma metabolome profiles in pigs from birth through to slaughter. To elucidate these effects, we conducted computed tomography scans on piglets within 24 h of birth to assess brain and liver weights accurately. Subsequently, we selected two groups of piglets based on the BrW/LW. Specifically, 12 piglets with the greatest BrW/LW (IUGR; BrW/LW: 1.00 ± 0.09) and 12 with the least BrW/LW (NORM; BrW/LW: 0.36 ± 0.04). From these piglets we collected fecal and blood samples at specific time points: during lactation (T1: d 16 ± 0.6), after the starter period (T2: d 63 ± 8.6), and at the onset (T3: d 119 ± 11.4) and conclusion (T4: d 162 ± 14.3) of the finisher period. Throughout the study, all pigs received identical diets to eliminate dietary confounders. In the lactation, starter and grower but not finisher period, IUGR piglets grew 47, 19 and 14% slower, respectively compared with their NORM littermates. Our findings revealed that fecal microbial α-diversity remained unaffected by IUGR across all time points examined, indicating a stable microbial richness within the gut microbiota of IUGR and NORM pigs. However, β-diversity, reflecting inter-group microbial community variation, exhibited significant differences at T1 (P = 0.002), T2 (P = 0.079), and T3 (P = 0.027), suggesting distinct microbial compositions between IUGR and NORM pigs at these stages. Specifically, IUGR pigs displayed a greater abundance of Clostridium sensu stricto 1 and Romboutsia at T1, Prevotellaceae NK3B31 group, Rikenellaceae RC9 gut group, and Alloprevotella at T2, and p-2534-18B5 gut group at T3. Conversely, the NORM group exhibited increased concentrations of Ruminococcus at T1, HT002 at T2, and Prevotella_9 at T3. Furthermore, while plasma metabolite analysis revealed no significant differences between IUGR and NORM pigs at T1, decreased arginine levels were observed in the IUGR group compared with NORM at T2 (P &amp;lt; 0.05). In conclusion, our study underscores the profound and persistent impact of IUGR on fecal microbiota composition in pigs from birth to the initial stages of the finisher period, while suggesting minimal alterations in the blood metabolome profile throughout various growth stages. These findings provide valuable insights into the long-term consequences of IUGR on swine health and production. This research received funding from the European Union’s Horizon 2020 research and innovation program under a Marie Sklodowska-Curie grant (agreement no. 955374).

Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.

Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with ( qCD+S ) vs. without persistent GI symptoms ( qCD-S ). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur-metabolic pathways in qCD+S. We performed a multi-center observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD ( aCD ) and non-IBD diarrhea-predominant irritable bowel syndrome ( IBS-D ) were included as controls. Thirty-nine patients with qCD+S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD+S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD+S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD+S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H 2 S signaling. Multi-omic integration demonstrated that enriched microbes in qCD+S were associated with important sulfur-metabolic pathways. Bacterial sulfur-metabolic genes, including CTH , isfD , sarD , and asrC , were dysregulated in qCD+S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting presence of qCD+S. Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD+S, which implicate H 2 S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H 2 S pathways results in improved quality of life in qCD+S. What is Already Known Even in the absence of inflammation, persistent gastrointestinal symptoms are common in Crohn's disease.The microbiome is altered in quiescent Crohn's disease patients with persistent symptoms, but the functional significance of these changes is unknown. What is New Here Sulfur metabolites and sulfur metabolic pathways were enriched in stool in quiescent Crohn's disease patients with persistent symptoms.Multi-omic integration showed enriched microbes were associated with important sulfur metabolic pathways in quiescent Crohn's disease patients with persistent symptoms. How Can This Study Help Patient Care Strategies to decrease sulfidogenic microbes and associated sulfur metabolic pathways could represent a novel strategy to improve quality of life in quiescent Crohn's disease with persistent GI symptoms.

Gut microbiota‐directed dietary factors enhance exercise performance in mice

AbstractThis study investigated the effect of dietary interventions targeting gut microbiota on exercise performance in mice. Analysis of the gut microbiota of individuals with varying levels of physical activity revealed enrichment of Eubacterium rectale and Faecalibacterium prausnitzii in the active population. Through in vitro fecal fermentation experiments, dietary factor combinations that promote the abundance of these bacteria were identified. Dietary interventions, including E. rectale supplementation, FAG combination (gavage of Fructus Arctii extract, Agaricus blazei Murrill polysaccharides, and galactooligosaccharides mixture), and CFG combination (gavage of curcumin, Fructus Arctii extract, and galactooligosaccharides mixture), significantly improved mouse exercise performance, increased glycogen accumulation, regulated serum biochemical parameters, and increased short‐chain fatty acid and fatty acid amide levels in feces. Metagenomic sequencing revealed alterations in the composition of the gut microbiota. Fecal metabolome analysis highlighted changes in metabolites related to lipids, organic acids, nucleic acids, and carbohydrates. These findings suggest that E. rectale and dietary interventions positively affect exercise performance by modulating the gut microbiota and associated metabolites.

Preclinical modeling of metabolic syndrome to study the pleiotropic effects of novel antidiabetic therapy independent of obesity

Cardiovascular-kidney-metabolic health reflects the interactions between metabolic risk factors, chronic kidney disease, and the cardiovascular system. A growing body of literature suggests that metabolic syndrome (MetS) in individuals of normal weight is associated with a high prevalence of cardiovascular diseases and an increased mortality. The aim of this study was to establish a non-invasive preclinical model of MetS in support of future research focusing on the effects of novel antidiabetic therapies beyond glucose reduction, independent of obesity. Eighteen healthy adult Beagle dogs were fed an isocaloric Western diet (WD) for ten weeks. Biospecimens were collected at baseline (BAS1) and after ten weeks of WD feeding (BAS2) for measurement of blood pressure (BP), serum chemistry, lipoprotein profiling, blood glucose, glucagon, insulin secretion, NT-proBNP, angiotensins, oxidative stress biomarkers, serum, urine, and fecal metabolomics. Differences between BAS1 and BAS2 were analyzed using non-parametric Wilcoxon signed-rank testing. The isocaloric WD model induced significant variations in several markers of MetS, including elevated BP, increased glucose concentrations, and reduced HDL-cholesterol. It also caused an increase in circulating NT-proBNP levels, a decrease in serum bicarbonate, and significant changes in general metabolism, lipids, and biogenic amines. Short-term, isocaloric feeding with a WD in dogs replicated key biological features of MetS while also causing low-grade metabolic acidosis and elevating natriuretic peptides. These findings support the use of the WD canine model for studying the metabolic effects of new antidiabetic therapies independent of obesity.

The Impact of Milk on Gut Permeability, Fecal 16S rRNA Gene Microbiota Profiling, and Fecal Metabolomics in Children with Moderate Malnutrition in Sierra Leone: A Double-Blind, Randomized Controlled Trial

Background. ObjectivesOur objectives were to determine the effect of dietary milk protein and milk carbohydrate on the intestinal permeability, fecal 16S rRNA gene configuration, and fecal metabolomics of children with moderate malnutrition. MethodsThis was a randomized, double-blind, controlled trial among 413 children with wasting in rural Sierra Leone who received 1 of the following 4 supplementary foods, which differed in sources of protein and carbohydrate: milk protein and milk carbohydrate (MPMC), milk protein and vegetable carbohydrate (MPVC), vegetable protein and milk carbohydrate (VPMC), or a control group consuming entirely vegetable-based food (VPVC). After 4 wk, urine and stool were collected from participants enrolled with mid-upper arm circumference of <12.1 cm. Urine was analyzed for lactulose excretion (%L). Stool samples were subjected to both 16S rRNA gene analysis to assess β-diversity and untargeted metabolomic abundance. ResultsAmong the 386 children who completed permeability testing, the mean difference (95% CI) in %L excretion as compared with VPVC was 0.01 (−0.05, 0.07) for MPMC, 0.05 (−0.01, 0.11) for MPVC, and 0.01 (−0.05, 0.07) for VPMC. Of the 374 children who provided a stool sample that was analyzed, the β-diversity among bacterial taxa was similar between dietary groups (P > 0.05 for all comparisons). No significant differences between dietary groups were seen among the 20 most abundant bacterial taxa. Among the 5769 unique metabolomic features identified, greater flavonoid levels in VPVC were seen. ConclusionsAbnormal intestinal permeability do not improve with 4 wk of supplementary feeding. Fecal rRNA do not differ with consumption of different diets.This trial was registered at clinicaltrials.gov as NCT04216043.

Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease

ABSTRACT Emerging evidence suggests the gut microbiome’s potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome’s impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.

Early Life Air Pollution Exposure is Associated with the Infant Gut Microbiome and Fecal Metabolome

Early Life Air Pollution Exposure is Associated with the Infant Gut Microbiome and Fecal Metabolome

GC×GC-TOFMS Analysis of Fecal Metabolome Stabilized Using an At-Home Stool Collection Device

Stool is a mixture of excrement, microbiota, enzymes, undigested material, and small molecules. Fecal metabolomics has gained interest recently, owing to advances in metabolomics and growing research into both the host’s physiology and the gut microbiome. One challenge with fecal metabolomics is preserving the sample integrity from collection until analysis, as the microbiota and enzymes continue to alter the metabolome following defecation. Currently, flash-freezing or lyophilization are utilized to minimize post-collection metabolome changes; however, this requires complex equipment and immediate processing, precluding the possibility for at-home sampling. Commercial devices containing stabilizing solvents have been developed to facilitate at-home collection, ambient transport, and sample storage. Here, we explore the efficacy of a commercially available stool collection device with a stabilization reagent tailored to fecal metabolomics. Stool samples from six donors were either processed shortly post-collection or stored at room temperature for seven days in the tube, with and without the stabilization reagent. Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS)-based untargeted metabolomics was utilized for analyzing extracted metabolites. Chemometric analysis was used to evaluate the performance of the device. We found that the device with the stabilization reagent minimized changes in the metabolite profile relative to unstabilized stool left at room temperature for one week.

Prenatal and Early Life Exposure to Ambient Air Pollutants Is Associated with the Fecal Metabolome in the First Two Years of Life.

Prenatal and early life air pollution exposure has been linked with several adverse health outcomes. However, the mechanisms underlying these relationships are not yet fully understood. Therefore, this study utilizes fecal metabolomics to determine if pre- and postnatal exposure to ambient air pollutants (i.e., PM10, PM2.5, and NO2) is associated with the fecal metabolome in the first 2 years of life in a Latino cohort from Southern California. The aims of this analysis were to estimate associations between (1) prenatal air pollution exposure with fecal metabolic features at 1-month of age, (2) prior month postnatal air pollution exposure with fecal metabolites from 1-month to 2 years of age, and (3) how postnatal air pollution exposure impacts the change over time of fecal metabolites in the first 2 years of life. Prenatal exposure to air pollutants was associated with several Level-1 metabolites, including those involved in vitamin B6 and tyrosine metabolism. Prior month air pollution exposure in the postnatal period was associated with Level-1 metabolites involved in histidine metabolism. Lastly, we found that pre- and postnatal ambient air pollution exposure was associated with changes in metabolic features involved in metabolic pathways including amino acid metabolism, histidine metabolism, and fatty acid metabolism.

Physiological Function of Gut Microbiota and Metabolome on Successful Pregnancy and Lactation in the Captive Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).

The gestation period in captive Yangtze finless porpoise (YFP) is a well-coordinated and dynamic process that involves both systemic and local alterations. The gut microbiota and its connection to fecal metabolites are crucial in supporting fetal development and ensuring maternal health during reproductive stages. This study evaluates changes in the gut microbiota and their correlation with fecal metabolites in captive YFPs during different reproductive stages. The results reveal that microbial community structure changed significantly during reproductive stages, while gut microbial diversity remained stable. The genus unclassified Peptostrptococcaceae, Corynebacterium, and norank KD4-96 were significantly greater in non-pregnancy (NP), Terrisporobacter was significantly greater in lactating (LL), and Clostridium was significantly higher in early-pregnancy (EP) compared to the other groups. The host fecal metabolome exhibited significant alterations during the reproductive stages. Indoxyl sulfate, octadecatrienoic acid, and methionyl-methionine were significantly higher in the NP; galactosylglycerol, chondroitin 6-sulfate, and lumichrome were significantly higher in the EP and mid-pregnancy (MP); and valylleucine and butyryl-l-carnitine were significantly higher in the LL. The altered metabolites were mostly concentrated in pathways associated with arachidonic acid metabolism (significantly altered in NP), leucine, valine, and isoleucine biosynthesis (significantly altered in EP and MP), and glycerophospholipid metabolism (significantly altered in LL compared to others stages). Additionally, we found a strong link between variations in the host metabolism and alterations in the fecal bacteria of captive YFP. In conclusion, this study provides detailed insights into host metabolic and fecal bacterial changes in captive YFP during reproduction stages, providing important knowledge for improving the reproductive management in the captive YFP.

Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients

Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n = 38) and fecal samples (n = 179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (≥ 3 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.