Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain

BACKGROUND

The supramolecular structure and composition of milk fat globules in breast milk is complex. Lipid droplets in formula milk are typically smaller compared to human milk and differ in their lipid and protein composition. These droplets play an important role in gut and immune maturation, and their components possess antimicrobial and antiviral properties. Here, the influence of a concept infant formula (IF) containing large milk phospholipid-coated lipid droplets on the maturation of the infant microbiota, metabolome, and weight gain in the first year of life was investigated.

RESULTS

Formula-fed infants were randomized to receive either a standard IF (Control) or a Test formula containing large milk phospholipid-coated lipid droplets (Test) until 17 weeks of age. A breast-fed Reference group was also investigated. At 3 months of age, several taxa identified as opportunistic pathogens (e.g., Enterobacter, Klebsiella, Enterococcus, Streptococcus) were less abundant in the Test stools compared to Control, while an enrichment of the butyrate-producing Ruminococcaceae and Lachnospiraceae was observed. These findings indicate that the Test formula resulted in gut microbiota maturation trajectories more comparable to healthy breast-fed infants. This was accompanied by variation in several fecal and plasma metabolites at 3 months of age related to gut microbial metabolism including bile acids, hippurate, phenylacetylglycine, trimethylamine, and various lipids and fatty acids. At 12 months, measures of subcutaneous fat and body mass index (BMI) were significantly higher in infants receiving standard IF compared to those receiving breast milk. However, this weight gain and adiposity was attenuated in the Test group infants.

CONCLUSIONS

The presence of large phospholipid-coated lipid droplets in formula milk positively influenced the development of the infants' gut microbiota, their metabolomic profiles, and their body composition to more closely resemble breast-fed infants compared to standard IF. These droplets may further enhance the restriction of pathogenic bacteria seen with standard infant formula and suggest a potential impact on infant metabolic programming that may contribute to physiological development. Video Abstract.

Probing and manipulating the gut microbiome with chemistry and chemical tools

The human gut microbiome represents an extended "second genome" harbouring about 1015 microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host-microbial metabolic interplay, and the microbiome composition also underlies the differential responses to chemotherapeutic agents between people. Chemical information will be the key to tackle this complexity and discover specific gut microbiome metabolism for creating more personalised interventions. Additionally, rising antibiotic resistance and growing awareness of gut microbiome effects are creating a need for non-microbicidal therapeutic interventions. We classify chemical interventions for the gut microbiome into categories like molecular decoys, bacterial conjugation inhibitors, colonisation resistance-stimulating molecules, "prebiotics" to promote the growth of beneficial microbes, and inhibitors of specific gut microbial enzymes. Moreover, small molecule probes, including click chemistry probes, artificial substrates for assaying gut bacterial enzymes and receptor agonists/antagonists, which engage host receptors interacting with the microbiome, are some other promising developments in the expanding chemical toolkit for probing and modulating the gut microbiome. This review explicitly excludes "biologics" such as probiotics, bacteriophages, and CRISPR to concentrate on chemistry and chemical tools like chemoproteomics in the gut-microbiome context.

Gut-Microbiota-Driven Lipid Metabolism: Mechanisms and Applications in Swine Production

Background/Objectives: The gut microbiota plays a pivotal role in host physiology through metabolite production, with lipids serving as essential biomolecules for cellular structure, metabolism, and signaling. This review aims to elucidate the interactions between gut microbiota and lipid metabolism and their implications for enhancing swine production. Methods: We systematically analyzed current literature on microbial lipid metabolism, focusing on mechanistic studies on microbiota-lipid interactions, key regulatory pathways in microbial lipid metabolism, and multi-omics evidence (metagenomic/metabolomic) from swine models. Results: This review outlines the structural and functional roles of lipids in bacterial membranes and examines the influence of gut microbiota on the metabolism of key lipid classes, including cholesterol, bile acids, choline, sphingolipids, and fatty acids. Additionally, we explore the potential applications of microbial lipid metabolism in enhancing swine production performance. Conclusions: Our analysis establishes a scientific framework for microbiota-based strategies to optimize lipid metabolism. The findings highlight potential interventions to improve livestock productivity through targeted manipulation of gut microbial communities.

Lipid Metabolism and Immune Function: Chemical Tools for Insights into T-Cell Biology

Lipids are essential biomolecules playing critical roles in cellular processes, including energy storage, membrane structure, and signaling. This review highlights the chemical tools that have been developed to study the role of lipid metabolism in immune function, focusing on T-cell biology. Fatty acids (FAs), as core lipid components, influence immune responses through structural, signaling, and metabolic roles. Recent studies reveal how specific FAs modulate T-cell activation, proliferation, and function, with implications for regulatory and effector subsets. Emerging tools, such as fluorescence-based lipids and click chemistry, enable precise tracking of lipid uptake and metabolism at the single-cell level, addressing limitations of traditional bulk methods. Advances in metabolomics and proteomics offer further insights into lipid-mediated immune regulation. Understanding these mechanisms provides opportunities to target lipid metabolism in therapeutic strategies for cancer and other immune-related diseases. The integration of lipidomic technologies into immunology uncovers novel perspectives on how lipids shape immune responses at cellular and molecular scales.

Discovering microbiota functions via chemical probe incorporation for targeted sequencing

Our microbiota plays crucial roles in immune development and homeostasis and has been implicated in virtually all major diseases of the 21st century. Nevertheless, our understanding of the exact microbial functions that underlie these correlations remains extremely limited, due in large part to the difficulty of profiling cellular activities within non-model organisms and complex communities. Over the past decade, new flow cytometric approaches have been developed to distinguish specific microbial populations based on their interactions with metabolite analogs, modified biomolecules, and reactive compounds. By selecting and separating active microbes via fluorescence-activated cell sorting, PRobe INcorporation for Targeted sequencing (PRINT-seq) has inspired innovative approaches to identify and characterize functional members of our microbiota. Here, we provide a broad overview of this evolving technology and summarize how this method has been recently employed as a diagnostic fingerprint for diverse microbial activities.

Don't Be Surprised When These Surprise You: Some Infrequently Studied Sphingoid Bases, Metabolites, and Factors That Should Be Kept in Mind During Sphingolipidomic Studies

Sphingolipidomic mass spectrometry has provided valuable information-and surprises-about sphingolipid structures, metabolism, and functions in normal biological processes and disease. Nonetheless, many noteworthy compounds are not routinely determined, such as the following: most of the sphingoid bases that mammals biosynthesize de novo other than sphingosine (and sometimes sphinganine) or acquire from exogenous sources; infrequently considered metabolites of sphingoid bases, such as N-(methyl)n-derivatives; "ceramides" other than the most common N-acylsphingosines; and complex sphingolipids other than sphingomyelins and simple glycosphingolipids, including glucosyl- and galactosylceramides, which are usually reported as "monohexosylceramides". These and other subspecies are discussed, as well as some of the circumstances when they are likely to be seen (or present and missed) due to experimental conditions that can influence sphingolipid metabolism, uptake from the diet or from the microbiome, or as artifacts produced during extraction and analysis. If these compounds and factors are kept in mind during the design and interpretation of lipidomic studies, investigators are likely to be surprised by how often they appear and thereby advance knowledge about them.

Gut bacterial sphingolipid production modulates dysregulated skin lipid homeostasis

Sphingolipids are an essential lipid component of the skin barrier with alterations in skin sphingolipid composition associated with multiple skin disorders including psoriasis, atopic dermatitis, and ichthyosis. Contributions to skin sphingolipid abundance are not well characterized, thus the main method of modulating skin lipid levels is the topical application of creams rich with sphingolipids at the skin surface. Evidence that diet and gut microbiome function can alter skin biology proposes an intriguing potential for the modulation of skin lipid homeostasis through gut microbial metabolism, but potential mechanisms of action are not well understood. Sphingolipid synthesis by prominent gut microbes has been shown to affect intestinal, hepatic and immune functions with the potential for sphingolipid-producing bacteria to affect skin biology through altering skin sphingolipid levels. To address this question, we used bioorthogonal chemistry to label lipids from the sphingolipid-producing bacteria Bacteroides thetaiotaomicron and trace these lipids to the skin epidermis. Exposing mice to B. thetaiotaomicron strains mutant in the ability to produce sphingolipids resulted in significantly lower transfer of gut microbiome-derived lipids to the skin, while also altering skin biology and altering expression of skin barrier genes. Measurement of skin ceramide levels, a class of sphingolipids involved in skin barrier function, determined that skin sphingolipid levels were altered in the presence of gut sphingolipid-producing bacteria. Together this work demonstrates that gut bacterial lipids can transfer to the skin and provides a compelling avenue for modulating sphingolipid-dominant compartments of the skin using sphingolipid-producing bacteria of the gut microbiome.

Dietary Restriction and Lipid Metabolism: Unveiling Pathways to Extended Healthspan

Dietary restriction (DR) has been reported to be a significant intervention that influences lipid metabolism and potentially modulates the aging process in a wide range of organisms. Lipid metabolism plays a pivotal role in the regulation of aging and longevity. In this review, we summarize studies on the significant role of lipid metabolism in aging in relation to DR. As a potent intervention to slow down aging, DR has demonstrated promising effects on lipid metabolism, influencing the aging processes across various species. The current review focuses on the relationships among DR-related molecular signaling proteins such as the sirtuins, signaling pathways such as the target of rapamycin and the insulin/insulin-like growth factor (IGF)-1, lipid metabolism, and aging. Furthermore, the review presents research results on diet-associated changes in cell membrane lipids and alterations in lipid metabolism caused by commensal bacteria, highlighting the importance of lipid metabolism in aging. Overall, the review explores the interplay between diet, lipid metabolism, and aging, while presenting untapped areas for further understanding of the aging process.

Regulation of cellular and systemic sphingolipid homeostasis

One hundred and fifty years ago, Johann Thudichum described sphingolipids as unusual "Sphinx-like" lipids from the brain. Today, we know that thousands of sphingolipid molecules mediate many essential functions in embryonic development and normal physiology. In addition, sphingolipid metabolism and signalling pathways are dysregulated in a wide range of pathologies, and therapeutic agents that target sphingolipids are now used to treat several human diseases. However, our understanding of sphingolipid regulation at cellular and organismal levels and their functions in developmental, physiological and pathological settings is rudimentary. In this Review, we discuss recent advances in sphingolipid pathways in different organelles, how secreted sphingolipid mediators modulate physiology and disease, progress in sphingolipid-targeted therapeutic and diagnostic research, and the trans-cellular sphingolipid metabolic networks between microbiota and mammals. Advances in sphingolipid biology have led to a deeper understanding of mammalian physiology and may lead to progress in the management of many diseases.

Host-pathogen interactions from a metabolic perspective: methods of investigation

Metabolism shapes immune homeostasis in health and disease. This review presents the range of methods that are currently available to investigate the dialog between metabolism and immunity at the systemic, tissue and cellular levels, particularly during infection.

Gut microbiota-derived metabolites tune host homeostasis fate

The gut microbiota, housing trillions of microorganisms within the gastrointestinal tract, has emerged as a critical regulator of host health and homeostasis. Through complex metabolic interactions, these microorganisms produce a diverse range of metabolites that substantially impact various physiological processes within the host. This review aims to delve into the intricate relationships of gut microbiota-derived metabolites and their influence on the host homeostasis. We will explore how these metabolites affect crucial aspects of host physiology, including metabolism, mucosal integrity, and communication among gut tissues. Moreover, we will spotlight the potential therapeutic applications of targeting these metabolites to restore and sustain host equilibrium. Understanding the intricate interplay between gut microbiota and their metabolites is crucial for developing innovative strategies to promote wellbeing and improve outcomes of chronic diseases.

Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization

Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide the stability of the fecal metabolome and microbiome at room temperature (RT). Here, we investigated the stability of various metabolites and the microbiome (16S rRNA) in feces collected in 95% ethanol (EtOH) and commercially available sample collection kits with specific preservatives OMNImet•GUT/OMNIgene•GUT. To simulate field-collection scenarios, the samples were stored at different temperatures at varying durations (24 h + 4 °C, 24 h RT, 36 h RT, 48 h RT, and 7 days RT) and compared to aliquots immediately frozen at -80 °C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar metabolites, endocannabinoids, short-chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the nonstabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet•GUT. When comparing the metabolite levels between aliquots stored at room temperature and at +4 °C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing samples at RT and stabilizing them in 95% EtOH yielded metabolomic results comparable to those from flash freezing. We also found that the overall composition of the microbiome did not vary significantly between different storage types. However, notable differences were observed in the α diversity. Altogether, the stability of the metabolome and microbiome in 95% EtOH provided results similar to those of the validated commercial collection kits OMNImet•GUT and OMNIgene•GUT, respectively.

Effect of 1-year lifestyle intervention with energy-reduced Mediterranean diet and physical activity promotion on the gut metabolome and microbiota: a randomized clinical trial

BACKGROUND

The health benefits of the Mediterranean diet (MedDiet) have been linked to the presence of beneficial gut microbes and related metabolites. However, its impact on the fecal metabolome remains poorly understood.

OBJECTIVES

Our goal was to investigate the weight-loss effects of a 1-y lifestyle intervention based on an energy-reduced MedDiet coupled with physical activity (intervention group), compared with an ad libitum MedDiet (control group), on fecal metabolites, fecal microbiota, and their potential association with cardiovascular disease risk factors.

METHODS

A total of 400 participants (200 from each study group), aged 55-75 y, and at high cardiovascular disease risk, were included. Dietary and lifestyle information, anthropometric measurements, blood biochemical parameters, and stool samples were collected at baseline and after 1 y of follow-up. Liquid chromatography-tandem mass spectrometry was used to profile endogenous fecal metabolites, and 16S amplicon sequencing was employed to profile the fecal microbiota.

RESULTS

Compared with the control group, the intervention group exhibited greater weight loss and improvement in various cardiovascular disease risk factors. We identified intervention effects on 4 stool metabolites and subnetworks primarily composed of bile acids, ceramides, and sphingosines, fatty acids, carnitines, nucleotides, and metabolites of purine and the Krebs cycle. Some of these were associated with changes in several cardiovascular disease risk factors. In addition, we observed a reduction in the abundance of the genera Eubacterium hallii group and Dorea, and an increase in alpha diversity in the intervention group after 1 y of follow-up. Changes in the intervention-related microbiota profiles were also associated with alterations in different fecal metabolite subnetworks and some cardiovascular disease risk factors.

CONCLUSIONS

An intervention based on an energy-reduced MedDiet and physical activity promotion, compared with an ad libitum MedDiet, was associated with improvements in cardiometabolic risk factors, potentially through modulation of the fecal microbiota and metabolome. This trial was registered at https://www.isrctn.com/ as ISRCTN89898870 (https://doi.org/10.1186/ISRCTN89898870).

The use of click chemistry in sphingolipid research

Sphingolipid dysregulation is involved in a range of rare and fatal diseases as well as common pathologies including cancer, infectious diseases or neurodegeneration. Gaining insights into how sphingolipids are involved in these diseases would contribute much to our understanding of human physiology, as well as the pathology mechanisms. However, scientific progress is hampered by a lack of suitable tools that can be used in intact systems. To overcome this, efforts have turned to engineering modified lipids with small clickable tags and to harnessing the power of click chemistry to localize and follow these minimally modified lipid probes in cells. We hope to inspire the readers of this Review to consider applying existing click chemistry tools for their own aspects of sphingolipid research. To this end, we focus here on different biological applications of clickable lipids, mainly to follow metabolic conversions, their visualization by confocal or superresolution microscopy or the identification of their protein interaction partners. Finally, we describe recent approaches employing organelle-targeted and clickable lipid probes to accurately follow intracellular sphingolipid transport with organellar precision.

Exposure of Helicobacter pylori to clarithromycin in vitro resulting in the development of resistance and triggers metabolic reprogramming associated with virulence and pathogenicity

In H. pylori infection, antibiotic-resistance is one of the most common causes of treatment failure. Bacterial metabolic activities, such as energy production, bacterial growth, cell wall construction, and cell-cell communication, all play important roles in antimicrobial resistance mechanisms. Identification of microbial metabolites may result in the discovery of novel antimicrobial therapeutic targets and treatments. The purpose of this work is to assess H. pylori metabolomic reprogramming in order to reveal the underlying mechanisms associated with the development of clarithromycin resistance. Previously, four H. pylori isolates were induced to become resistant to clarithromycin in vitro by incrementally increasing the concentrations of clarithromycin. Bacterial metabolites were extracted using the Bligh and Dyer technique and analyzed using metabolomic fingerprinting based on Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (LC-Q-ToF-MS). The data was processed and analyzed using the MassHunter Qualitative Analysis and Mass Profiler Professional software. In parental sensitivity (S), breakpoint isolates (B), and induced resistance isolates (R) H. pylori isolates, 982 metabolites were found. Furthermore, based on accurate mass, isotope ratios, abundances, and spacing, 292 metabolites matched the metabolites in the Agilent METLIN precise Mass-Personal Metabolite Database and Library (AM-PCDL). Several metabolites associated with bacterial virulence, pathogenicity, survival, and proliferation (L-leucine, Pyridoxone [Vitamine B6], D-Mannitol, Sphingolipids, Indoleacrylic acid, Dulcitol, and D-Proline) were found to be elevated in generated resistant H. pylori isolates when compared to parental sensitive isolates. The elevated metabolites could be part of antibiotics resistance mechanisms. Understanding the fundamental metabolome changes in the course of progressing from clarithromycin-sensitive to breakpoint to resistant in H. pylori clinical isolates may be a promising strategy for discovering novel alternatives therapeutic targets.

Prevotella copri variants among a single host diverge in sphingolipid production

Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, Bacteroides species have been identified as major producers of sphingolipids, and Bacteroides-produced sphingolipids have been shown to be modulators of host immune and metabolic functions. While Bacteroides species are a prominent feature of the gut microbiomes of populations living in industrialized countries, Prevotella copri, a member of the same phyla, albeit a different family, is the dominant feature across the remainder of the global population, although their sphingolipid-producing capabilities have not been as thoroughly investigated. To fill this gap, we examined the genomes of over 60 diverse isolates of P. copri and identified several key enzymes involved in sphingolipid synthesis in P. copri. Combining bioorthogonal labeling and liquid chromatography-mass spectrometry (LC-MS) based lipidomics, we functionally characterized the first step in P. copri de novo sphingolipid synthesis in addition to profiling the sphingolipidomes of P. copri strains, identifying key enzymes that may play roles in producing a diverse set of P. copri sphingolipids. Given the limited genetic engineering tools amenable for use in P. copri, our approach takes advantage of comparative genomics and phenotypic profiling to explore sphingolipid production in these understudied, yet highly prevalent, organisms.IMPORTANCESphingolipids are important signaling molecules for maintaining metabolic and immune homeostasis in the host. These lipids are also produced by gut commensals, most notably by Bacteroides species. Despite the global prevalence of Prevotella copri in gut microbiomes of individuals, little is known about the types of sphingolipids they produce and whether they are similar in composition and structure to those produced by Bacteroides. Given the varied associations of P. copri with diverse sphingolipid-related health outcomes, such as rheumatoid arthritis and glucose intolerance, it is important to first characterize the specific sphingolipids produced by individual strains of P. copri and to identify the genes involved in their pathways of production. This characterization of P. copri-derived sphingolipids provides further insight into how bacterial sphingolipid production can serve as a mechanism for microbial modulation of host phenotypes.

Role and interaction of bacterial sphingolipids in human health

Sphingolipids, present in both higher animals and prokaryotes, involving in cell differentiation, pathogenesis and apoptosis in human physiological health. With increasing attention on the gut microbiome and its impact on wellbeing, there is a renewed focus on exploring bacterial sphingolipids. This review aims to consolidate the current understanding of bacterial sphingolipids and their impact on host health. Compared to mammalian sphingolipids, bacterial sphingolipids are characterized by odd chain lengths due to the presence of branched alkyl chains. Additionally, intestinal microbial sphingolipids can migrate from the gut to various host organs, affecting the immune system and metabolism. Furthermore, the intricate interplay between dietary sphingolipids and the gut microbiota is explored, shedding light on their complex relationship. Despite limited knowledge in this area, this review aims to raise awareness about the importance of bacterial sphingolipids and further our understanding of more uncharacterized bacterial sphingolipids and their significant role in maintaining host health.

Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria

Malaria is caused by Plasmodium species and remains a significant cause of morbidity and mortality globally. Gut bacteria can influence the severity of malaria, but the contribution of specific bacteria to the risk of severe malaria is unknown. Here, multiomics approaches demonstrate that specific species of Bacteroides are causally linked to the risk of severe malaria. Plasmodium yoelii hyperparasitemia-resistant mice gavaged with murine-isolated Bacteroides fragilis develop P. yoelii hyperparasitemia. Moreover, Bacteroides are significantly more abundant in Ugandan children with severe malarial anemia than with asymptomatic P. falciparum infection. Human isolates of Bacteroides caccae, Bacteroides uniformis, and Bacteroides ovatus were able to cause susceptibility to severe malaria in mice. While monocolonization of germ-free mice with Bacteroides alone is insufficient to cause susceptibility to hyperparasitemia, meta-analysis across multiple studies support a main role for Bacteroides in susceptibility to severe malaria. Approaches that target gut Bacteroides present an opportunity to prevent severe malaria and associated deaths.

Untargeted GC-MS and FT-NIR study of the effect of 14 processing methods on the volatile components of Polygonatum kingianum

Introduction

Polygonatum kingianum is a traditional medicinal plant, and processing has significantly impacts its quality.

Methods

Therefore, untargeted gas chromatography-mass spectrometry (GC-MS) and Fourier transform-near-infrared spectroscopy (FT-NIR) were used to analyze the 14 processing methods commonly used in the Chinese market.It is dedicated to analyzing the causes of major volatile metabolite changes and identifying signature volatile components for each processing method.

Results

The untargeted GC-MS technique identified a total of 333 metabolites. The relative content accounted for sugars (43%), acids (20%), amino acids (18%), nucleotides (6%), and esters (3%). The multiple steaming and roasting samples contained more sugars, nucleotides, esters and flavonoids but fewer amino acids. The sugars are predominantly monosaccharides or small molecular sugars, mainly due to polysaccharides depolymerization. The heat treatment reduces the amino acid content significantly, and the multiple steaming and roasting methods are not conducive to accumulating amino acids. The multiple steaming and roasting samples showed significant differences, as seen from principal component analysis (PCA) and hierarchical cluster analysis (HCA) based on GC-MS and FT-NIR. The partial least squares discriminant analysis (PLS-DA) based on FT-NIR can achieve 96.43% identification rate for the processed samples.

Discussion

This study can provide some references and options for consumers, producers, and researchers.

Gut microbiome lipid metabolism and its impact on host physiology

Metabolites produced by commensal gut microbes impact host health through their recognition by the immune system and their influence on numerous metabolic pathways. Notably, the gut microbiota can both transform and synthesize lipids as well as break down dietary lipids to generate secondary metabolites with host modulatory properties. Although lipids have largely been consigned to structural roles, particularly in cell membranes, recent research has led to an increased appreciation of their signaling activities, with potential impacts on host health and physiology. This review focuses on studies that highlight the functions of bioactive lipids in mammalian physiology, with a special emphasis on immunity and metabolism.

Untargeted metabolite profiling of Enterococcus villorum SB2, isolated from the vagina of pregnant women, by HR-LCMS

Enterococcus bacteria are studied in various sectors including fermentation, food and dairy industries,as well as studied for their probiotic properties but have limited use due to their possible pathogenic behavior. The present report talks about the metabolites produced, by the previously isolated Enterococcus strain, E.villorum SB2 (accession number KX830968), from the vaginal source. The growth of the bacteria in three types of media (M17, MRS and LAPTg) was compared, where the M17 media gave better bacterial colonies, also maximum growth rate was observed in M17 media (T_d = 1.6 h & k = 0.4 h^-1), and thus was selected as the metabolite production media. Further, the studied bacteria did not show any hemolytic activity, making it safe for industrial applications. The HR-LCMS results showed the production of various amino acids, organic acids, peptides, and other metabolites like flavonoids (Quercetin 3-O-Manoglucoside), terpenoids (7',8',Dihydro-8'-hydroxycitraniaxanthin, O-Methylganoderic acid O, Thalicsessine, Austinol, Valdiate), indole derivatives produced by tryptophan metabolism (5-hydroxykynurenamine, 2S,4R)-4-(9H-Pyrido[3,4-b]indol-1-yl)-1,2,4-butanetriol, Indoleacrylic acid), antimicrobial compounds (Fortimicin A) and fatty acids (Stearic acid, Myristic acid), which were earlier unreported form Enterococcus species opening new scope for discovering new industrial applications of the strain. As the studied bacteria has been reported to be a potential probiotic, the detection of these industrially important metabolites can be studied further in future studies to reveal the potential industrial applications of the strain.

Characterization of interactions of dietary cholesterol with the murine and human gut microbiome

Consumption of dietary lipids, such as cholesterol, modulates the gut microbiome with consequences for host health through the production of microbiome-derived metabolites. Despite the implications for host metabolism, a limited number of specific interactions of the gut microbiome with diet-derived lipids have been characterized. This is partially because obtaining species-level resolution of the responsible taxa can be challenging and additional approaches are needed to identify health-relevant metabolites produced from cholesterol-microbiome interactions. Here we performed bio-orthogonal labelling sort sequence spectrometry, a click chemistry based workflow, to profile cholesterol-specific host-microbe interactions. Mice were exposed to an alkyne-functionalized variant of cholesterol and 16S ribosomal RNA gene amplicon sequencing of faecal samples identified diet-derived cholesterol-interacting microbes from the genera Bacteroides, Bifidobacterium, Enterococcus and Parabacteroides. Shotgun metagenomic analysis provided species-level resolution of diet-derived cholesterol-interacting microbes with enrichment of bile acid-like and sulfotransferase-like activities. Using untargeted metabolomics, we identify that cholesterol is converted to cholesterol sulfate in a Bacteroides-specific manner via the enzyme BT_0416. Mice monocolonized with Bacteroides thetaiotaomicron lacking Bt_0416 showed altered host cholesterol and cholesterol sulfate compared with wild-type mice, identifying a previously uncharacterized microbiome-transformation of cholesterol and a mechanism for microbiome-dependent contributions to host phenotype. Moreover, identification of a cholesterol-responsive sulfotransferase in Bacteroides suggests diet-dependent mechanisms for altering microbiome-specific cholesterol metabolism. Overall, our work identifies numerous cholesterol-interacting microbes with implications for more precise microbiome-conscious regulation of host cholesterol homeostasis.

The Lard Works in Mysterious Ways: Ceramides in Nutrition-Linked Chronic Disease

Diet influences onset, progression, and severity of several chronic diseases, including heart failure, diabetes, steatohepatitis, and a subset of cancers. The prevalence and clinical burden of these obesity-linked diseases has risen over the past two decades. These metabolic disorders are driven by ectopic lipid deposition in tissues not suited for fat storage, leading to lipotoxic disruption of cell function and survival. Sphingolipids such as ceramides are among the most deleterious and bioactive metabolites that accrue, as they participate in selective insulin resistance, dyslipidemia, oxidative stress and apoptosis. This review discusses our current understanding of biochemical pathways controlling ceramide synthesis, production and action; influences of diet on ceramide levels; application of circulating ceramides as clinical biomarkers of metabolic disease; and molecular mechanisms linking ceramides to altered metabolism and survival of cells. Development of nutritional or pharmacological strategies to lower ceramides could have therapeutic value in a wide range of prevalent diseases.

Fatty liver? Microbiome sphingolipids to the rescue

In this issue of Cell Host & Microbe, Le et al. discover that addition of exogenous Bacteroides sphingolipids can reverse lipid accumulation in the liver in a mouse model of hepatic steatosis. An elegant labeling strategy also revealed a unique microbially produced sphingolipid that was able to transit to the liver.

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids

Microbially-derived gut metabolites are important contributors to host phenotypes, many of which may link microbiome composition to metabolic disease. However, relatively few metabolites with known bioactivity have been traced from specific microbes to host tissues. Here, we use a labeling strategy to characterize and trace bacterial sphingolipids from the gut symbiont Bacteroides thetaiotaomicron to mouse colons and livers. We find that bacterial sphingolipid synthesis rescues excess lipid accumulation in a mouse model of hepatic steatosis and observe the transit of a previously uncharacterized bacterial sphingolipid to the liver. The addition of this sphingolipid to hepatocytes improves respiration in response to fatty-acid overload, suggesting that sphingolipid transfer to the liver could potentially contribute to microbiota-mediated liver function. This work establishes a role for bacterial sphingolipids in modulating hepatic phenotypes and defines a workflow that permits the characterization of other microbial metabolites with undefined functions in host health.

Mammalian gut metabolomes mirror microbiome composition and host phylogeny

In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics

Approximately 2.8 million people worldwide are infected with bacteria that are deemed resistant to clinically relevant antibiotics. This accounts for 700,000 deaths every year and represents a major public health threat that has been on the rise for the past two decades. In contrast, the pace of antibiotic discovery to treat these resistant pathogens has significantly decreased. Most antibiotics are complex natural products that were isolated from soil microorganisms during the golden era of antibiotic discovery (1940s to 1960s) employing the “Waksman platform”. After the collapse of this discovery platform, other strategies and approaches emerged, including phenotype- or target-based screenings of large synthetic compound libraries. However, these methods have not resulted in the discovery and/or development of new drugs for clinical use in over 30 years. A better understanding of the structure and function of the molecular components that constitute the bacterial system is of paramount importance to design new strategies to tackle drug-resistant pathogens. Herein, we review the traditional approaches as well as novel strategies to facilitate antibiotic discovery that are chemical biology-focused. These include the design and application of chemical probes that can undergo bioorthogonal reactions, such as copper (I)-catalyzed azide-alkyne cycloadditions (CuAAC). By specifically interacting with bacterial proteins or being incorporated in the microorganism’s metabolism, chemical probes are powerful tools in drug discovery that can help uncover new drug targets and investigate the mechanisms of action and resistance of new antibacterial leads.

Convergent evolution of bacterial ceramide synthesis

The bacterial domain produces numerous types of sphingolipids with various physiological functions. In the human microbiome, commensal and pathogenic bacteria use these lipids to modulate the host inflammatory system. Despite their growing importance, their biosynthetic pathway remains undefined since several key eukaryotic ceramide synthesis enzymes have no bacterial homolog. Here we used genomic and biochemical approaches to identify six proteins comprising the complete pathway for bacterial ceramide synthesis. Bioinformatic analyses revealed the widespread potential for bacterial ceramide synthesis leading to our discovery of a Gram-positive species that produces ceramides. Biochemical evidence demonstrated that the bacterial pathway operates in a different order from that in eukaryotes. Furthermore, phylogenetic analyses support the hypothesis that the bacterial and eukaryotic ceramide pathways evolved independently.

Targeted Analysis of Sphingolipids in Turkeys Fed Fusariotoxins: First Evidence of Key Changes That Could Help Explain Their Relative Resistance to Fumonisin Toxicity

The effects of fumonisins on sphingolipids in turkeys are unknown, except for the increased sphinganine to sphingosine ratio (Sa:So) used as a biomarker. Fumonisins fed at 20.2 mg/kg for 14 days were responsible for a 4.4 fold increase in the Sa:So ratio and a decrease of 33% and 36% in C14-C16 ceramides and C14-C16 sphingomyelins, respectively, whereas C18-C26 ceramides and C18-C26 sphingomyelins remained unaffected or were increased. Glucosyl- and lactosyl-ceramides paralleled the concentrations of ceramides. Fumonisins also increased dihydroceramides but had no effect on deoxysphinganine. A partial least squfares discriminant analysis revealed that all changes in sphingolipids were important in explaining the effect of fumonisins. Because deoxynivalenol and zearalenone are often found in feed, their effects on sphingolipids alone and in combination with fumonisins were investigated. Feeding 5.12 mg deoxynivalenol/kg reduced dihydroceramides in the liver. Zearalenone fed at 0.47 mg/kg had no effect on sphingolipids. When fusariotoxins were fed simultaneously, the effects on sphingolipids were similar to those observed in turkeys fed fumonisins alone. The concentration of fumonisin B1 in the liver of turkeys fed fumonisins was 0.06 µmol/kg. Changes in sphingolipid concentrations differed but were consistent with the IC50 of fumonisin B1 measured in mammals; these changes could explain the relative resistance of turkeys to fumonisins.

Chewing the Fat with Microbes: Lipid Crosstalk in the Gut

It is becoming increasingly important for any project aimed at understanding the effects of diet on human health, to also consider the combined effect of the trillions of microbes within the gut which modify and are modified by dietary nutrients. A healthy microbiome is diverse and contributes to host health, partly via the production and subsequent host absorption of secondary metabolites. Many of the beneficial bacteria in the gut rely on specific nutrients, such as dietary fiber, to survive and thrive. In the absence of those nutrients, the relative proportion of good commensal bacteria dwindles while communities of opportunistic, and potentially pathogenic, bacteria expand. Therefore, it is unsurprising that both diet and the gut microbiome have been associated with numerous human diseases. Inflammatory bowel diseases and colorectal cancer are associated with the presence of certain pathogenic bacteria and risk increases with consumption of a Western diet, which is typically high in fat, protein, and refined carbohydrates, but low in plant-based fibers. Indeed, despite increased screening and better care, colorectal cancer is still the 2nd leading cause of cancer death in the US and is the 3rd most diagnosed cancer among US men and women. Rates are rising worldwide as diets are becoming more westernized, alongside rising rates of metabolic diseases like obesity and diabetes. Understanding how a modern diet influences the microbiota and how subsequent microbial alterations effect human health will become essential in guiding personalized nutrition and healthcare in the future. Herein, we will summarize some of the latest advances in understanding of the three-way interaction between the human host, the gut microbiome, and the specific class of dietary nutrients, lipids.

Dietary Sphingolipids Contribute to Health via Intestinal Maintenance

As sphingolipids are constituents of the cell and vacuole membranes of eukaryotic cells, they are a critical component acquired from our daily diets. In the present review, we highlight the knowledge regarding how dietary sphingolipids affect our health, particularly our intestinal health. Animal- and plant-derived foods contain, respectively, sphingomyelin (SM) and glucosylceramide (GlcCer) as their representative sphingolipids, and the sphingoid base as a specific structure of sphingolipids also differs depending upon the source and class. For example, sphingosine is predominant among animal sphingolipids, and tri-hydroxy bases are present in free ceramide (Cer) from plants and fungi. Dietary sphingolipids exhibit low absorption ratios; however, they possess various functions. GlcCer facilitates improvements in intestinal impairments, lipid metabolisms, and skin disorders, and SM can exert both similar and different effects compared to those elicited by GlcCer. We discuss the digestion, absorption, metabolism, and function of sphingolipids while focused on the structure. Additionally, we also review old and new classes in the context of current advancements in analytical instruments.

Milk polar lipids favorably alter circulating and intestinal ceramide and sphingomyelin species in postmenopausal women

BACKGROUND

High circulating levels of ceramides (Cer) and sphingomyelins (SM) are associated with cardiometabolic diseases. The consumption of whole fat dairy products, naturally containing such polar lipids (PL), is associated with health benefits, but the impact on sphingolipidome remains unknown.

METHODS

In a 4-week randomized controlled trial, 58 postmenopausal women daily consumed milk PL-enriched cream cheese (0, 3, or 5 g of milk PL). Postprandial metabolic explorations were performed before and after supplementation. Analyses included SM and Cer species in serum, chylomicrons, and feces. The ileal contents of 4 ileostomy patients were also explored after acute milk PL intake.

RESULTS

Milk PL decreased serum atherogenic C24:1 Cer, C16:1 SM, and C18:1 SM species (P_group < 0.05). Changes in serum C16+18 SM species were positively correlated with the reduction of cholesterol (r = 0.706), LDL-C (r = 0.666), and ApoB (r = 0.705) (P < 0.001). Milk PL decreased chylomicron content in total SM and C24:1 Cer (P_group < 0.001), parallel to a marked increase in total Cer in feces (P_group < 0.001). Milk PL modulated some specific SM and Cer species in both ileal efflux and feces, suggesting differential absorption and metabolization processes in the gut.

CONCLUSION

Milk PL supplementation decreased atherogenic SM and Cer species associated with the improvement of cardiovascular risk markers. Our findings bring insights on sphingolipid metabolism in the gut, especially Cer, as signaling molecules potentially participating in the beneficial effects of milk PL.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT02099032, NCT02146339.

FUNDING

ANR-11-ALID-007-01; PHRCI-2014: VALOBAB, no. 14-007; CNIEL; GLN 2018-11-07; HCL (sponsor).

The Impact of Dietary Sphingolipids on Intestinal Microbiota and Gastrointestinal Immune Homeostasis

The large surfaces of gastrointestinal (GI) organs are well adapted to their diverse tasks of selective nutritional uptake and defense against the external environment. To maintain a functional balance, a vast number of immune cells is located within the mucosa. A strictly regulated immune response is required to impede constant inflammation and to maintain barrier function. An increasing prevalence of GI diseases has been reported in Western societies over the past decades. This surge in GI disorders has been linked to dietary changes followed by an imbalance of the gut microbiome, leading to a chronic, low grade inflammation of the gut epithelium. To counteract the increasing health care costs associated with diseases, it is paramount to understand the mechanisms driving immuno-nutrition, the associations between nutritional compounds, the commensal gut microbiota, and the host immune response. Dietary compounds such as lipids, play a central role in GI barrier function. Bioactive sphingolipids (SLs), e.g. sphingomyelin (SM), sphingosine (Sph), ceramide (Cer), sphingosine-1- phosphate (S1P) and ceramide-1-phosphate (C1P) may derive from dietary SLs ingested through the diet. They are not only integral components of cell membranes, they additionally modulate cell trafficking and are precursors for mediators and second messenger molecules. By regulating intracellular calcium levels, cell motility, cell proliferation and apoptosis, SL metabolites have been described to influence GI immune homeostasis positively and detrimentally. Furthermore, dietary SLs are suggested to induce a shift in the gut microbiota. Modes of action range from competing with the commensal bacteria for intestinal cell attachment to prevention from pathogen invasion by regulating innate and immediate defense mechanisms. SL metabolites can also be produced by gut microorganisms, directly impacting host metabolic pathways. This review aims to summarize recent findings on SL signaling and functional variations of dietary SLs. We highlight novel insights in SL homeostasis and SL impact on GI barrier function, which is directly linked to changes of the intestinal microbiota. Knowledge gaps in current literature will be discussed to address questions relevant for understanding the pivotal role of dietary SLs on chronic, low grade inflammation and to define a balanced and healthy diet for disease prevention and treatment.

In vitro gastrointestinal digestion and simulated colonic fermentation of pistachio nuts determine the bioaccessibility and biosynthesis of chronobiotics

Chronodisruption leads to obesity and other metabolic disorders that can be alleviated by food-derived potential chronobiotics, such as phytomelatonin (PMT), phenolic compounds (PCs) and dietary fiber rich pistachios. Pistachios with (PN + SC) or without (PN) the seed coat were investigated for their in vitro chronobiotic potential since they are one of the main reported PMT sources. Consequently we evaluated the bioaccessibility, permeability, and biosynthesis of pistachio chronobiotics, particularly PMT, during gastrointestinal and colonic fermentation. The maximum in vitro bioaccessibility and apparent permeability (efflux-prone) of PCs, flavonoids and PMT were sample-specific [∼1.3% (both), 27 and 3.4% (PN + SC)], but additional amounts (flavonoids > PCs > PMT) were released under simulated colonic conditions. Short-chain fatty acids (SCFAs; 38 mM; >50% butyrate, PN + SC > PN) and some metabolites (e.g., indole, benzaldehyde, phenolic acids, and aliphatic/aromatic hydrocarbons) were detected depending on the sample. The predominant pistachio butyrate production during in vitro colonic fermentation can improve chronodisruption and benefit obese individuals. Pistachio's digestion increases the bioaccessibility and intestinal permeability of potential chronobiotics (PMT and PCs) and the biosynthesis of colonic metabolites (SCFAs, among others) also with chronobiotic potential.

Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.