The footprints of gut microbial-mammalian co-metabolism

The effect of PM2.5 exposure on placenta and its associated metabolites: A birth cohort study

The placenta is an important organ for fetal growth. Air pollution during pregnancy may cause adverse effects on offsprings via placental dysfunction. However, the metabolites underlie the effects of PM2.5 on placenta have not been well studied. 329 pregnant women were randomly selected from the Shanghai Maternal-Child Pairs Cohort. Gestational PM2.5 exposure levels were assessed using individual air sampling method and satellite-based exposure assessment mode, respectively. Placental weight, length, width and thickness were measured by obstetrician-gynecologist at the time of delivery. Ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites in serum from the first and third trimester. Associations between PM2.5 and placental characteristics were analyzed by generalized estimating equation and multiple linear regression. The exposure-response relationship was plotted using restricted cubic splines (RCS). Based on the meet-in-the-middle approach, the metabolites underlying the effects of PM2.5 on placenta were explored. The associations between placental width (βTrimester2=-0.497, 95 %CI: -0.801, -0.193), (βTrimester3=-0.279, 95 % CI: -0.543, -0.016) and chorionic disk area (βTrimester2=-12.634,95 %CI: -21.698, -3.570), (βTrimester3=-9.113, 95 %CI: -17.113, -1.112) with PM2.5 exposure at the second and third trimester were found. The associations between placental characteristics with PM2.5 exposure assessed by individual air sampling and satellite-based methods were consistent. L-arginine (L-Arg), caprylic acid (CA), tauroursodeoxycholic acid (TUDCA), glycylproline (Gly-Pro), maltotriose (MT) and N-acetylneuramic acid (NANA) intermediate the effect of PM2.5 exposure on placental chorionic disk area in the third trimester. CONCLUSION: The second and third trimesters may be the sensitive windows of placental abnormalities to PM2.5 exposure. Caprylic acid (CA), glycylproline (Gly-Pro), and N-acetylneuramic acid (NANA) play a key role on the effects of PM2.5 exposure on placenta. This study provides potential biomarkers of placental exposure to PM2.5, providing an opportunity for future research as well as detection.

Differences in utilization and metabolism of Ulva lactuca polysaccharide by human gut Bacteroides species in the in vitro fermentation

Ulva lactuca polysaccharide (ULP), a sulfated polysaccharide, has been widely used in Asia. However, its digestion process and utilization by gut microbiota remain poorly understood. In this study, the in vitro simulated digestion and fermentation were used to analyze the digestibility of ULP. The results showed that ULP was not degraded during simulated digestion, but was utilized by human fecal microbiota. 16S rRNA sequencing revealed that ULP significantly increased the abundance of Bacteroides. Further evaluation of seven Bacteroides species showed that only B. thetaiotaomicron and B. vulgatus could utilize ULP. Interestingly, these two species exhibited different utilization patterns. B. vulgatus preferentially utilized rhamnose of ULP over glucuronic acid to promote growth. Metabolite profiles of B. thetaiotaomicron and B. vulgatus during in vitro fermentation with ULP as the sole carbon source were different. Although both B. thetaiotaomicron and B. vulgatus utilized ULP to produce various metabolites such as acetic acid, propionic acid, cysteic acid and riboflavin, B. thetaiotaomicron accumulated metabolites, such as linoleic acid, that were not accumulated by B. vulgatus. The effects of ULP on the metabolic pathways of B. thetaiotaomicron and B. vulgatus differed. These findings provide a new perspective on the utilization of ULP by human gut microbiota.

ISCAZIM: Integrated statistical correlation analysis for zero-inflated microbiome data

Microbiome-metabolome association analysis is critical to reveal the key pairs of gut microbiota and metabolites for discovery of the microbial biomarkers in chronic diseases. However, the characteristics of microbiome data, such as zero inflation, over dispersion, may impair the confidence of association analysis between microbiome and metabolome data. The objectives of this study are to evaluate the strengths and weaknesses of existing statistical methods and to develop a computational framework tailored to the unique characteristics of microbiome data. We designed a computational framework called Integrated Statistical Correlation Analysis for Zero-Inflated Microbiome data (ISCAZIM) that takes account of complicated microbiome data characteristics, including zero inflation rates (ZIRs), dispersion and correlation patterns. ISCAZIM first benchmarked prevalent statistical correlation methods, Pearson, Spearman, zero inflated negative binomial (ZINB) model, mutual information and Maximal Information Coefficient. ISCAZIM then classifies the correlation pattern to linear or non-linear and applies the correlation method according to the ZIRs status. Applying to multiple real-world microbiome-metabolomics data, ISCAZIM is overall more accurate than using a single method with more truly significant association pairs included. Therefore, ISCAZIM will significantly facilitate the association analysis using zero-inflated microbiome data for multi-omics integration.

Rat Fecal Metabolomics-Based Analysis

The gut's symbiome, a hidden metabolic organ, has gained scientific interest for its crucial role in human health. Acting as a biochemical factory, the gut microbiome produces numerous small molecules that significantly impact host metabolism. Metabolic profiling facilitates the exploration of its influence on human health and disease through the symbiotic relationship. Fecal metabolomics-based analysis is an indisputably valuable tool for elucidating the biochemistry of digestion and absorption in the gastrointestinal system, serving as the most suitable specimen to study the symbiotic relationship between the host and the intestinal microbiota. It is well-established that the balance of the intestinal microbiota changes in response to various stimuli, both physiological, such as gender, age, diet, and exercise, and pathological, such as gastrointestinal and hepatic diseases. Fecal samples have been analyzed using widely adopted analytical techniques, including NMR spectroscopy, GC-MS, and LC-MS/MS. Rat fecal samples are frequently used and particularly useful substrates for metabolomics-based studies in related fields.The complexity and diversity of fecal samples necessitate careful and skillful handling to extract metabolites, while avoiding their deterioration, effectively and quantitatively. Several determinative factors, such as the fecal sample weight to extraction solvent solution volume, the nature and pH value of the extraction solvent, and the homogenization process, play crucial roles in achieving optimal extraction for obtaining high-quality metabolic fingerprints, whether for untargeted or targeted metabolomics.

Integrated global and unique metabolic characteristics to reveal the intervention effect of Yiyi decoction on acute pancreatitis

Yiyi decoction is a Chinese herbal formula for the treatment of acute pancreatitis that has been used in clinical practice for decades. A previous study has suggested that resveratrol, emodin, rhein and their derivatives might be the potential pharmacodynamic components in Yiyi decoction, and researchers have proposed that resveratrol, emodin and rhein are candidate markers for quality control. The present study investigated the intervention effect of Yiyi decoction and its effective components on murine acute pancreatitis using metabolomic approach that integrated global and unique metabolic characteristics. First, serum metabolomics based on the platform of ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was performed to assess metabolic changes in experimental acute pancreatitis. Second, an in-depth analysis of bile acid metabolism was performed based on an in-house database. Finally, an integrated analysis of the intervention effect of Yiyi decoction and its effective components in response to these metabolic perturbations was performed. As a result, 39 potential biomarkers for the pathogenesis of acute pancreatitis, mainly phospholipids, fatty acids, bile acids and lipoylcarnitines, were screened and annotated. Integrated analysis revealed that the metabolic disorders in acute pancreatitis mice were reversed by Yiyi decoction primarily via regulating glycerophospholipid metabolism, bile acid biosynthesis, carnitine synthesis and fatty acid metabolism. Yiyi decoction components may effectively target the migratory metabolome. Histopathological and biochemical analyses suggested that Yiyi decoction maintained the gut barrier function and inhibited inflammatory cytokines, thus exert anti-acute pancreatitis effects. The present study utilized an approach that integrated global and unique metabolic characteristics to elucidate the underlying mechanisms of Chinese herbal formulas from a metabolomics perspective.

The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities

Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.

Patterns of infant fecal metabolite concentrations and social behavioral development in toddlers

BACKGROUND

Gut-derived metabolites, products of microbial and host co-metabolism, may inform mechanisms underlying children's neurodevelopment. We investigated whether infant fecal metabolites were related to toddler social behavior.

METHODS

Stool samples collected from 6-week-olds (n = 86) and 1-year-olds (n = 209) in the New Hampshire Birth Cohort Study (NHBCS) were analyzed using nuclear magnetic resonance spectroscopy metabolomics. Autism-related behavior in 3-year-olds was assessed by caregivers using the Social Responsiveness Scale (SRS-2). To assess the association between metabolites and SRS-2 scores, we used a traditional single-metabolite approach, quantitative metabolite set enrichment (QEA), and self-organizing maps (SOMs).

RESULTS

Using a single-metabolite approach and QEA, no individual fecal metabolite or metabolite set at either age was associated with SRS-2 scores. Using the SOM method, fecal metabolites of six-week-olds organized into four profiles, which were unrelated to SRS-2 scores. In 1-year-olds, one of twelve fecal metabolite profiles was associated with fewer autism-related behaviors, with SRS-2 scores 3.4 (95%CI: -7, 0.2) points lower than the referent group. This profile had higher concentrations of lactate and lower concentrations of short chain fatty acids than the reference.

CONCLUSIONS

We uncovered metabolic profiles in infant stool associated with subsequent social behavior, highlighting one potential mechanism by which gut bacteria may influence neurobehavior.

IMPACT

Differences in host and microbial metabolism may explain variability in neurobehavioral phenotypes, but prior studies do not have consistent results. We applied three statistical techniques to explore fecal metabolite differences related to social behavior, including self-organizing maps (SOMs), a novel machine learning algorithm. A 1-year-old fecal metabolite pattern characterized by high lactate and low short-chain fatty acid concentrations, identified using SOMs, was associated with social behavior less indicative of autism spectrum disorder. Our findings suggest that social behavior may be related to metabolite profiles and that future studies may uncover novel findings by applying the SOM algorithm.

Host microbiome depletion attenuates biofluid metabolite responses following radiation exposure

Development of novel biodosimetry assays and medical countermeasures is needed to obtain a level of radiation preparedness in the event of malicious or accidental mass exposures to ionizing radiation (IR). For biodosimetry, metabolic profiling with mass spectrometry (MS) platforms has identified several small molecules in easily accessible biofluids that are promising for dose reconstruction. As our microbiome has profound effects on biofluid metabolite composition, it is of interest how variation in the host microbiome may affect metabolomics based biodosimetry. Here, we 'knocked out' the microbiome of male and female C57BL/6 mice (Abx mice) using antibiotics and then irradiated (0, 3, or 8 Gy) them to determine the role of the host microbiome on biofluid radiation signatures (1 and 3 d urine, 3 d serum). Biofluid metabolite levels were compared to a sham and irradiated group of mice with a normal microbiome (Abx-con mice). To compare post-irradiation effects in urine, we calculated the Spearman's correlation coefficients of metabolite levels with radiation dose. For selected metabolites of interest, we performed more detailed analyses using linear mixed effect models to determine the effects of radiation dose, time, and microbiome depletion. Serum metabolite levels were compared using an ANOVA. Several metabolites were affected after antibiotic administration in the tryptophan and amino acid pathways, sterol hormone, xenobiotic and bile acid pathways (urine) and lipid metabolism (serum), with a post-irradiation attenuative effect observed for Abx mice. In urine, dose×time interactions were supported for a defined radiation metabolite panel (carnitine, hexosamine-valine-isoleucine [Hex-V-I], creatine, citric acid, and Nε,Nε,Nε-trimethyllysine [TML]) and dose for N1-acetylspermidine, which also provided excellent (AUROC ≥ 0.90) to good (AUROC ≥ 0.80) sensitivity and specificity according to the area under the receiver operator characteristic curve (AUROC) analysis. In serum, a panel consisting of carnitine, citric acid, lysophosphatidylcholine (LysoPC) (14:0), LysoPC (20:3), and LysoPC (22:5) also gave excellent to good sensitivity and specificity for identifying post-irradiated individuals at 3 d. Although the microbiome affected the basal levels and/or post-irradiation levels of these metabolites, their utility in dose reconstruction irrespective of microbiome status is encouraging for the use of metabolomics as a novel biodosimetry assay.

Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium

BACKGROUND

Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors.

METHODS

Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects.

RESULTS

Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use.

LIMITATIONS

The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD.

CONCLUSIONS

Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.

Strategy for Comprehensive Detection and Annotation of Gut Microbiota-Related Metabolites Based on Liquid Chromatography-High-Resolution Mass Spectrometry

Gut microbiota, widely populating the mammalian gastrointestinal tract, plays an important role in regulating diverse pathophysiological processes by producing bioactive molecules. Extensive detection of these molecules contributes to probing microbiota function but is limited by insufficient identification of existing analytical methods. In this study, a systematic strategy was proposed to detect and annotate gut microbiota-related metabolites on a large scale. A pentafluorophenyl (PFP) column-based liquid chromatography-high-resolution mass spectrometry (LC-HRMS) method was first developed for high-coverage analysis of gut microbiota-related metabolites, which was verified to be stable and robust with a wide linearity range, high sensitivity, satisfactory recovery, and repeatability. Then, an informative database integrating 968 knowledge-based microbiota-related metabolites and 282 sample-sourced ones defined by germ-free (GF)/antibiotic-treated (ABX) models was constructed and subsequently used for targeted extraction and annotation in biological samples. Using pooled feces, plasma, and urine of mice for demonstration application, 672 microbiota-related metabolites were annotated, including 21% neglected by routine nontargeted peak detection. This strategy serves as a useful tool for the comprehensive capture of the intestinal flora metabolome, contributing to our deeper understanding of microbe-host interactions.

Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples From Healthy Individuals

Gut microbiota produce tryptophan metabolites (TMs) important to homeostasis. However, measuring TM levels in stool and determining their microbial sources can be difficult. Here, we measured TMs from the indole pathway in fecal samples from 21 healthy adults with the goal to: 1) determine fecal TM concentrations in healthy individuals; 2) link TM levels to bacterial abundance using 16S and whole genome shotgun (WGS) sequencing data; and 3) predict likely bacterial sources of TM production. Within our samples, we identified 151 genera (16S) and 592 bacterial species (WGS). Eight TMs were found in ≥17 fecal samples, including four in all persons. To our knowledge, we are the first to report fecal levels for indole-3-lactate, indole-3-propionate, and 3-indoleacrylate levels in healthy persons. Overall, indole, indole-3-acetate (IAA), and skatole accounted for 86% of the eight TMs measured. Significant correlations were found between seven TMs and 29 bacterial species.  Predicted multiple TM sources support the notion of a complex network of TM production and regulation. Further, the data suggest key roles for Collinsella aerofaciens and IAA, a metabolite reported to maintain intestinal homeostasis through enhanced barrier integrity and anti-inflammatory/antioxidant activities. These findings extend our understanding of TMs and their relationship to the microbial species that act as effectors and/or regulators in the healthy intestine and may lead to novel strategies designed to manipulate tryptophan metabolism to prevent disease and/or restore health to the dysbiotic gut.

MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies

For studies using microbiome data, the ability to robustly combine data from technically and biologically distinct microbiome studies is a crucial means of supporting more robust and clinically relevant inferences. Formidable technical challenges arise when attempting to combine data from technically diverse 16S rRNA gene variable region amplicon sequencing (16S) studies. Closed operational taxonomic units and taxonomy are criticized as being heavily dependent upon reference sets and with limited precision relative to the underlying biology. Phylogenetic placement has been demonstrated to be a promising taxonomy-free manner of harmonizing microbiome data, but it has lacked a validated count-based feature suitable for use in machine learning and association studies. Here we introduce a phylogenetic-placement-based, taxonomy-independent, compositional feature of microbiota: phylotypes. Phylotypes were predictive of clinical outcomes such as obesity or pre-term birth on technically diverse independent validation sets harmonized post hoc. Thus, phylotypes enable the rigorous cross-validation of 16S-based clinical prognostic models and associative microbiome studies.

Fecal metabonomics combined with 16S rDNA sequencing to analyze the changes of gut microbiota in rats fed with different protein source diets

PURPOSE

When blended, animal and plant proteins can complement each other in terms of amino acid composition and release time. In this study, we investigated whether the blended protein diet has a better feeding effect than the single protein diet, and to reveal the differences in growth and intestinal microbiota composition caused by the blended protein diet.

METHODS

Forty Sprague Dawley (SD) rats received diets with different protein sources, including casein (C), whey protein (WP), black soybean protein (BSP), and black soybean-whey blended protein (BS-WP), for eight weeks. To investigate the effects of blended protein supplement on gut microbiota and metabolites, we performed a high throughput 16S rDNA sequencing and fecal metabolomics profiling. In addition, we determined growth and serum biochemical indices, and conducted intestinal morphology analyses.

RESULTS

Compared to those in the BSP and WP groups, the daily body weight gain and feed conversion efficiency increased in the BS-WP group. Serum biochemical indices indicated that the protein utilization efficiency of the WP and BS-WP groups was relatively high, and the BS-WP blended protein diet improved the protein adoption rate. The BS-WP blended protein diet also improved intestinal tissue morphology and promoted intestinal villi development compared to the single protein diets. Furthermore, dietary protein altered the composition of gut microbiota, the gut microbial diversity of rats fed with the BS-WP diet was significantly (P < 0.05) higher than that of the other groups. The difference in dietary protein corresponded with an alteration of fecal amino acids and their metabolites, and tryptophan and tyrosine metabolism were the key mechanisms leading to the changes in fecal microbial composition.

CONCLUSION

Dietary protein sources played an important role in the growth and development of rats by influencing intestinal metabolism and microbial composition. The BS-WP blended protein diet was more conducive to nutrient absorption than the single protein diet. Furthermore, blended protein increased the diversity of intestinal microbes and aided the establishment of intestinal barrier function.

Thyme (Thymus quinquecostatus Celak) Polyphenol-Rich Extract (TPE) Alleviates HFD-Induced Liver Injury in Mice by Inactivating the TLR4/NF-κB Signaling Pathway through the Gut-Liver Axis

Non-alcoholic fatty liver disease (NAFLD) represents a significant and urgent global health concern. Thyme (Thymus quinquecostatus Celak) is a plant commonly used in cuisine and traditional medicine in Asian countries and possesses potential liver-protective properties. This study aimed to assess the hepatoprotective effects of thyme polyphenol-rich extract (TPE) on high-fat diet (HFD)-induced NAFLD and further explore possible mechanisms based on the gut-liver axis. HFD-induced liver injury in C57 mice is markedly ameliorated by TPE supplementation in a dose-dependent manner. TPE also regulates the expression of liver lipid metabolic genes (i.e., Hmgcr, Srebp-1, Fasn, and Cyp7a1), enhancing the production of SCFAs and regulating serum metabolites by modulating gut microbial dysbiosis. Furthermore, TPE enhances the intestinal barrier function and alleviates intestinal inflammation by upregulating tight junction protein expression (i.e., ZO-1 and occluding) and inactivating the intestinal TLR4/NF-κB pathway in HFD-fed mice. Consequently, gut-derived LPS translocation to the circulation was blocked, the liver TLR4/NF-κB signaling pathway was repressed, and subsequent pro-inflammatory cytokine production was restrained. Conclusively, TPE might exert anti-NAFLD effects through the gut-liver axis and has the potential to be used as a dietary supplement for the management of NAFLD.

Short-chain fatty acids, secondary bile acids and indoles: gut microbial metabolites with effects on enteroendocrine cell function and their potential as therapies for metabolic disease

The gastrointestinal tract hosts the largest ecosystem of microorganisms in the body. The metabolism of ingested nutrients by gut bacteria produces novel chemical mediators that can influence chemosensory cells lining the gastrointestinal tract. Specifically, hormone-releasing enteroendocrine cells which express a host of receptors activated by these bacterial metabolites. This review will focus on the activation mechanisms of glucagon-like peptide-1 releasing enteroendocrine cells by the three main bacterial metabolites produced in the gut: short-chain fatty acids, secondary bile acids and indoles. Given the importance of enteroendocrine cells in regulating glucose homeostasis and food intake, we will also discuss therapies based on these bacterial metabolites used in the treatment of metabolic diseases such as diabetes and obesity. Elucidating the mechanisms gut bacteria can influence cellular function in the host will advance our understanding of this fundamental symbiotic relationship and unlock the potential of harnessing these pathways to improve human health.

In vitro fermentation of heparin by the human gut microbiota: Changes in the microbiota community and metabolic functions

Levels of its utilization suggest that the host glycosaminoglycan heparin is an important carbohydrate in the human gut microbiota. However, the interaction between heparin and the gut microbiota is not well understood. In this study, an in vitro fermentation system combined with microbiome and metabolome technologies was used to study the interaction between heparin and the gut microbiota. Interestingly, we found that heparin can be used by the gut microbiota, which produce large amounts of short chain fatty acids leading to a decrease in pH. In addition, the addition of heparin increased the relative abundance of Bacteroides and Bifidobacterium and decreased the relative abundance of Escherichia-Shigella. Correlation analysis of the microbiome and metabolome revealed that the catabolism of heparin was accompanied by the biosynthesis of bile acids and tryptophan metabolism. Overall, this study provides new evidence on the role of heparin as a stable carbon source for the gut microbiota and forms a strong basis for the use of heparin to condition the gut microbiota.

Metabolite interactions between host and microbiota during health and disease: Which feeds the other?

Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.

Connecting Gut Microbial Diversity with Plasma Metabolome and Fecal Bile Acid Changes Induced by the Antibiotics Tobramycin and Colistin Sulfate

The diversity of microbial species in the gut has a strong influence on health and development of the host. Further, there are indications that the variation in expression of gut bacterial metabolic enzymes is less diverse than the taxonomic profile, underlying the importance of microbiome functionality, particularly from a toxicological perspective. To address these relationships, the gut bacterial composition of Wistar rats was altered by a 28 day oral treatment with the antibiotics tobramycin or colistin sulfate. On the basis of 16S marker gene sequencing data, tobramycin was found to cause a strong reduction in the diversity and relative abundance of the microbiome, whereas colistin sulfate had only a marginal impact. Associated plasma and fecal metabolomes were characterized by targeted mass spectrometry-based profiling. The fecal metabolome of tobramycin-treated animals had a high number of significant alterations in metabolite levels compared to controls, particularly in amino acids, lipids, bile acids (BAs), carbohydrates, and energy metabolites. The accumulation of primary BAs and significant reduction of secondary BAs in the feces indicated that the microbial alterations induced by tobramycin inhibit bacterial deconjugation reactions. The plasma metabolome showed less, but still many alterations in the same metabolite groups, including reductions in indole derivatives and hippuric acid, and furthermore, despite marginal effects of colistin sulfate treatment, there were nonetheless systemic alterations also in BAs. Aside from these treatment-based differences, we also uncovered interindividual differences particularly centering on the loss of Verrucomicrobiaceae in the microbiome, but with no apparent associated metabolite alterations. Finally, by comparing the data set from this study with metabolome alterations in the MetaMapTox database, key metabolite alterations were identified as plasma biomarkers indicative of altered gut microbiomes resulting from a wide activity spectrum of antibiotics.

Microbial Metabolite Dysbiosis and Colorectal Cancer

The global burden of colorectal cancer (CRC) is expected to continuously increase. Through research performed in the past decades, the effects of various environmental factors on CRC development have been well identified. Diet, the gut microbiota and their metabolites are key environmental factors that profoundly affect CRC development. Major microbial metabolites with a relevance for CRC prevention and pathogenesis include dietary fiber-derived short-chain fatty acids, bile acid derivatives, indole metabolites, polyamines, trimethylamine-N-oxide, formate, and hydrogen sulfide. These metabolites regulate various cell types in the intestine, leading to an altered intestinal barrier, immunity, chronic inflammation, and tumorigenesis. The physical, chemical, and metabolic properties of these metabolites along with their distinct functions to trigger host receptors appear to largely determine their effects in regulating CRC development. In this review, we will discuss the current advances in our understanding of the major CRC-regulating microbial metabolites, focusing on their production and interactive effects on immune responses and tumorigenesis in the colon.

Early-life dietary exposures mediate persistent shifts in the gut microbiome and visceral fat metabolism

In utero dietary exposures are linked to the development of metabolic syndrome in adult offspring. These dietary exposures can potentially impact gut microbial composition and offspring metabolic health. Female BALB/c mice were administered a lard, lard + flaxseed oil, high sugar, or control diet 4 wk before mating, throughout mating, pregnancy, and lactation. Female offspring were offered low-fat control diet at weaning. Fecal 16S sequencing was performed. Untargeted metabolomics was performed on visceral adipose tissue (VAT) of adult female offspring. Immunohistochemistry was used to determine adipocyte size, VAT collagen deposition, and macrophage content. Hippurate was administered via weekly intraperitoneal injections to low-fat and high-fat diet-fed female mice and VAT fibrosis and collagen 1A (COL1A) were assessed by immunohistochemistry. Lard diet exposure was associated with elevated body and VAT weight and dysregulated glucose metabolism. Lard + flaxseed oil attenuated these effects. Lard diet exposures were associated with increased adipocyte diameter and VAT macrophage count. Lard + flaxseed oil reduced adipocyte diameter and fibrosis compared with the lard diet. Hippurate-associated bacteria were influenced by lard versus lard + flax exposures that persisted to adulthood. VAT hippurate was increased in lard + flaxseed oil compared with lard diet. Hippurate supplementation mitigated VAT fibrosis pathology. Maternal high-fat lard diet consumption resulted in long-term metabolic and gut microbiome programming in offspring, impacting VAT inflammation and fibrosis, and was associated with reduced VAT hippurate content. These traits were not observed in maternal high-fat lard + flaxseed oil diet-exposed offspring. Hippurate supplementation reduced VAT fibrosis. These data suggest that detrimental effects of early-life high-fat lard diet exposure can be attenuated by dietary omega-3 polyunsaturated fatty acid supplementation.

Urinary Metabolome Analysis Reveals Potential Microbiota Alteration and Electrophilic Burden Induced by High Red Meat Diet: Results from the French NutriNet-Santé Cohort and an In Vivo Intervention Study in Rats

SCOPE

High red and processed meat consumption is associated with several adverse outcomes such as colorectal cancer and overall global mortality. However, the underlying mechanisms remain debated and need to be elucidated.

METHODS AND RESULTS

Urinary untargeted Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics data from 240 subjects from the French cohort NutriNet-Santé are analyzed. Individuals are matched and divided into three groups according to their consumption of red and processed meat: high red and processed meat consumers, non-red and processed meat consumers, and at random group. Results are supported by a preclinical experiment where rats are fed either a high red meat or a control diet. Microbiota derived metabolites, in particular indoxyl sulfate and cinnamoylglycine, are found impacted by the high red meat diet in both studies, suggesting a modification of microbiota by the high red/processed meat diet. Rat microbiota sequencing analysis strengthens this observation. Although not evidenced in the human study, rat mercapturic acid profile concomitantly reveals an increased lipid peroxidation induced by high red meat diet.

CONCLUSION

Novel microbiota metabolites are identified as red meat consumption potential biomarkers, suggesting a deleterious effect, which could partly explain the adverse effects associated with high red and processed meat consumption.

Turning Microbial AhR Agonists into Therapeutic Agents via Drug Delivery Systems

Developing therapeutics for inflammatory diseases is challenging due to physiological mucosal barriers, systemic side effects, and the local microbiota. In the search for novel methods to overcome some of these problems, drug delivery systems that improve tissue-targeted drug delivery and modulate the microbiota are highly desirable. Microbial metabolites are known to regulate immune responses, an observation that has resulted in important conceptual advances in areas such as metabolite pharmacology and metabolite therapeutics. Indeed, the doctrine of "one molecule, one target, one disease" that has dominated the pharmaceutical industry in the 20th century is being replaced by developing therapeutics which simultaneously manipulate multiple targets through novel formulation approaches, including the multitarget-directed ligands. Thus, metabolites may not only represent biomarkers for disease development, but also, being causally linked to human diseases, an unexploited source of therapeutics. We have shown the successful exploitation of this approach: by deciphering how signaling molecules, such as the microbial metabolite, indole-3-aldehyde, and the repurposed drug anakinra, interact with the aryl hydrocarbon receptor may pave the way for novel therapeutics in inflammatory human diseases, for the realization of which drug delivery platforms are instrumental.

Regulation of Physiological Barrier Function by the Commensal Microbiota

A fundamental characteristic of living organisms is their ability to separate the internal and external environments, a function achieved in large part through the different physiological barrier systems and their component junctional molecules. Barrier integrity is subject to multiple influences, but one that has received comparatively little attention to date is the role of the commensal microbiota. These microbes, which represent approximately 50% of the cells in the human body, are increasingly recognized as powerful physiological modulators in other systems, but their role in regulating barrier function is only beginning to be addressed. Through comparison of the impact commensal microbes have on cell-cell junctions in three exemplar physiological barriers-the gut epithelium, the epidermis and the blood-brain barrier-this review will emphasize the important contribution microbes and microbe-derived mediators play in governing barrier function. By extension, this will highlight the critical homeostatic role of commensal microbes, as well as identifying the puzzles and opportunities arising from our steadily increasing knowledge of this aspect of physiology.

Gut Microbiota-Derived Glutamine Attenuates Liver Ischemia/Reperfusion Injury via Macrophage Metabolic Reprogramming

BACKGROUND & AIMS

Many studies have revealed crucial roles of the gut microbiota and its metabolites in liver disease progression. However, the mechanism underlying their effects on liver ischemia/reperfusion (I/R) injury remain largely unknown. Here, we investigate the function of gut microbiota and its metabolites in liver I/R injury.

METHODS

C57BL/6 mice was pretreated with an antibiotic cocktail. Then, we used multi-omics detection methods including 16s rRNA sequencing, ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) to explore the changes of gut microbiota and metabolites in both feces and portal blood to reveal the mechanism of their protective effect in liver I/R injury.

RESULTS

We found that antibiotic pretreatment (ABX) could significantly reduce the severity of I/R-induced hepatic injury, and this effect could be transferred to germ-free mice by fecal microbiota transplantation (FMT), suggesting a protective role of the gut microbiota depletion. During I/R, the rates of serum α-ketoglutarate (αKG) production and glutamate reduction, downstream products of gut microbiota-derived glutamine, were more significant in the ABX mice. Then, we showed that αKG could promote alternative (M2) macrophage activation through oxidative phosphorylation, and oligomycin A could inhibit M2 macrophage polarization and reversed this protective effect.

CONCLUSIONS

These findings show that the gut microbiota and its metabolites play critical roles in hepatic I/R injury by modulating macrophage metabolic reprogramming. Potential therapies that target macrophage metabolism, including antibiotic therapies and novel immunometabolism modulators, can be exploited for the treatment of liver I/R injury.

Defining the Role of the Gut Microbiome in the Pathogenesis and Treatment of Lymphoid Malignancies

The gut microbiome is increasingly being recognized as an important immunologic environment, with direct links to the host immune system. The scale of the gut microbiome's genomic repertoire extends the capacity of its host's genome by providing additional metabolic output, and the close communication between gut microbiota and mucosal immune cells provides a continued opportunity for immune education. The relationship between the gut microbiome and the host immune system has important implications for oncologic disease, including lymphoma, a malignancy derived from within the immune system itself. In this review, we explore past and recent discoveries describing the role that bacterial populations play in lymphomagenesis, diagnosis, and therapy. We highlight key relationships within the gut microbiome-immune-oncology axis that present exciting opportunities for directed interventions intended to shape the microbiome for therapeutic effect. We conclude with a limited summary of active clinical trials targeting the microbiome in hematologic malignancies, along with future directions on gut microbiome investigations within lymphoid malignancies.

Effects of Gabexate Mesylate on the Gut Microbiota and Metabolomics in Rats with Sepsis

Background

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. However, there is still no single drug that could reduce septic mortality. Previous studies have reported gabexate mesylate (GM) significantly reduced serum inflammatory factors, alleviated sepsis-induced lung injury and improved clinical outcomes. This study aimed to combine with microbiome sequencing and metabolomics analysis to explore the effects of GM administration in septic rats.

Methods

Sixty SD rats were randomly divided into the sham control (SC), cecal ligation and puncture (CLP), and GM injection (GM) groups. The mortality was measured and colonic feces were collected to examine the gut microbiota and metabolism 24 h after the procedure. The lung tissues were collected for hematoxylin-eosin staining.

Results

We observed the relative abundance of Pygmaiobacter, which contributed to short-chain fatty acids (SCFAs) promotion, Lactobacillus and Erysipelotrichaceae UCG-003 increased in the GM-treated rats, while Escherichia-Shigella and Akkermansia decreased compared to the sepsis-induced lung injury group. Furthermore, these 3 metabolites including Palmitoylethanolamide, Deoxycholic acid and Chenodeoxycholic acid correlated significantly to CLP- and GM-rich genus (P < 0.05). Besides, the lung tissues of CLP group showed more severe inflammatory infiltration and edema, and the mortality rate in the CLP group (10/20) was significantly higher than in the SC group (0/20) (P < 0.001) and GM group (4/20) (P < 0.05).

Conclusion

Our findings showed that GM attenuated sepsis-induced lung injury rats and regulated metabolites related to gut microbiota, which may provide an effective treatment for sepsis patients.

Alterations in Microbial-Associated Fecal Metabolites in Relation to Arsenic Exposure Among Infants

In utero and early life exposure to inorganic arsenic (iAs) alters immune response in experimental animals and is associated with an increased risk of infant infections. iAs exposure is related to differences in the gut microbiota diversity, community structure, and the relative abundance of individual microbial taxa both in laboratory and human studies. Metabolomics permits a direct measure of molecular products of microbial and host metabolic processes. We conducted NMR metabolomics analysis on infant stool samples and quantified the relative concentrations of 34 known microbial-related metabolites. We examined these metabolites in relation to both in utero and infant log2 urinary total arsenic concentrations (utAs, the sum of iAs and iAs metabolites) collected at approximately 6 weeks of age using linear regression models, adjusted for infant sex, age at sample collection, type of delivery (vaginal vs. cesarean section), feeding mode (breast milk vs. any formula), and specific gravity. Increased fecal butyrate (b = 214.24), propionate (b = 518.33), cholate (b = 8.79), tryptophan (b= 14.23), asparagine (b = 28.80), isoleucine (b = 65.58), leucine (b = 95.91), malonate (b = 50.43), and uracil (b = 36.13), concentrations were associated with a doubling of infant utAs concentrations (p< 0.05). These associations were largely among infants who were formula fed. No clear associations were observed with maternal utAs and infant fecal metabolites. Metabolomic analyses of infant stool samples lend further evidence that the infant gut microbiota is sensitive to As exposure, and these effects may have functional consequences.

Polyphenol-Rich Liupao Tea Extract Prevents High-Fat Diet-Induced MAFLD by Modulating the Gut Microbiota

The modulation of gut microbiota dysbiosis might regulate the progression of metabolic-associated fatty liver disease (MAFLD). Here, we found that polyphenol-rich Liupao tea extract (PLE) prevents high-fat diet (HFD)-induced MAFLD in ApoE^-/- male mice accompanied by protection of the intestinal barrier and downregulation of lipopolysaccharide (LPS)-related Toll-like receptor 4 (TLR4)-myeloid differentiation primary response 88 (MyD88) signaling in the liver. Fecal microbiome transplantation (FMT) from PLE-and-HFD-treated mice delayed MAFLD development significantly compared with FMT from HFD-treated mice. In this case, 16S rRNA gene sequencing revealed that Rikenellaceae and Odoribacter were significantly enriched and that Helicobacter was significantly decreased in not only the HFD+PLE group but also the HFD+PLE-FMT group. Furthermore, the level of 3-sulfodeoxycholic acid was significantly decreased in the HFD+PLE-FMT group compared with the HFD-FMT group. In conclusion, our data demonstrate that PLE could modulate the MAFLD phenotype in mice and that this effect is partly mediated through modulation of the gut microbiota.

How to employ metabolomic analysis to research on functions of prebiotics and probiotics in poultry gut health?

Gut health can be considered one of the major, manageable constituents of the animal immunity and performance. The fast spread of intestinal diseases, and increase of antimicrobial resistance have been observed, therefore the intestinal health has become not only economically relevant, but also highly important subject addressing the interest of public health. It is expected, that the strategies to control infections should be based on development of natural immunity in animals and producing resilient flocks using natural solutions, whilst eliminating antibiotics and veterinary medicinal products from action. Probiotics and prebiotics have been favored, because they have potential to directly or indirectly optimize intestinal health by manipulating the metabolism of the intestinal tract, including the microbiota. Studying the metabolome of probiotics and gut environment, both in vivo, or using the in vitro models, is required to attain the scientific understanding about the functions of bioactive compounds in development of gut health and life lasting immunity. There is a practical need to identify new metabolites being the key bioactive agents regulating biochemical pathways of systems associated with gut (gut-associated axes). Technological advancement in metabolomics studies, and increasing access to the powerful analytical platforms have paved a way to implement metabolomics in exploration of the effects of prebiotics and probiotics on the intestinal health of poultry. In this article, the basic principles of metabolomics in research involving probiotics and probiotics are introduced, together with the overview of existing strategies and suggestions of their use to study metabolome in poultry.

Multi-omics analysis reveals neuroinflammation, activated glial signaling, and dysregulated synaptic signaling and metabolism in the hippocampus of aged mice

Aging is an intricate biological event that occurs in both vertebrates and invertebrates. During the aging process, the brain, a vulnerable organ, undergoes structural and functional alterations, resulting in behavioral changes. The hippocampus has long been known to be critically associated with cognitive impairment, dementia, and Alzheimer’s disease during aging; however, the underlying mechanisms remain largely unknown. In this study, we hypothesized that altered metabolic and gene expression profiles promote the aging process in the hippocampus. Behavioral tests showed that exploration, locomotion, learning, and memory activities were reduced in aged mice. Metabolomics analysis identified 69 differentially abundant metabolites and showed that the abundance of amino acids, lipids, and microbiota-derived metabolites (MDMs) was significantly altered in hippocampal tissue of aged animals. Furthermore, transcriptomic analysis identified 376 differentially expressed genes in the aged hippocampus. A total of 35 differentially abundant metabolites and 119 differentially expressed genes, constituting the top 200 correlations, were employed for the co-expression network. The multi-omics analysis showed that pathways related to inflammation, microglial activation, synapse, cell death, cellular/tissue homeostasis, and metabolism were dysregulated in the aging hippocampus. Our data revealed that metabolic perturbations and gene expression alterations in the aged hippocampus were possibly linked to their behavioral changes in aged mice; we also provide evidence that altered MDMs might mediate the interaction between gut and brain during the aging process.

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample

Voluntary caloric restriction (e.g., eating disorders) often results in alterations in the gut microbiota composition and function. However, these findings may not translate to food insecurity, where an individual experiences inconsistent access to healthy food options. In this study we compared the fecal microbiome and metabolome of racially and ethnically diverse first year college students (n = 60) experiencing different levels of food access. Students were dichotomized into food secure (FS) and food insecure (FI) groups using a validated, 2-question screener assessing food security status over the previous 30 days. Fecal samples were collected up to 5 days post survey-completion. Gut microbiome and metabolome were established using 16S rRNA amplicon sequencing, targeted liquid chromatography-tandem mass spectrometry, and gas chromatography-mass spectrometry. FI students experienced significantly greater microbial diversity with increased abundance of Enterobacteriaceae and Eisenbergiella, while FS students had greater abundance of Megasphaera and Holdemanella. Metabolites related to energy transfer and gut–brain-axis communication (picolinic acid, phosphocreatine, 2-pyrrolidinone) were elevated in FI students (q < 0.05). These findings suggest that food insecurity is associated with differential gut microbial and metabolite composition for which the future implications are unknown. Further work is needed to elucidate the longitudinal metabolic effects of food insecurity and how gut microbes influence metabolic outcomes.

The Role of Intestinal Microbial Metabolites in the Immunity of Equine Animals Infected With Horse Botflies

The microbiota and its metabolites play an important role in regulating the host metabolism and immunity. However, the underlying mechanism is still not well studied. Thus, we conducted the LC-MS/MS analysis and RNA-seq analysis on Equus przewalskii with and without horse botfly infestation to determine the metabolites produced by intestinal microbiota in feces and differentially expressed genes (DEGs) related to the immune response in blood and attempted to link them together. The results showed that parasite infection could change the composition of microbial metabolites. These identified metabolites could be divided into six categories, including compounds with biological roles, bioactive peptides, endocrine-disrupting compounds, pesticides, phytochemical compounds, and lipids. The three pathways involving most metabolites were lipid metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. The significant differences between the host with and without parasites were shown in 31 metabolites with known functions, which were related to physiological activities of the host. For the gene analysis, we found that parasite infection could alarm the host immune response. The gene of “cathepsin W” involved in innate and adaptive immune responses was upregulated. The two genes of the following functions were downregulated: “protein S100-A8” and “protein S100-A9-like isoform X2” involved in chemokine and cytokine production, the toll-like receptor signaling pathway, and immune and inflammatory responses. GO and KEGG analyses showed that immune-related functions of defense response and Th17 cell differentiation had significant differences between the host with and without parasites, respectively. Last, the relationship between metabolites and genes was determined in this study. The purine metabolism and pyrimidine metabolism contained the most altered metabolites and DEGs, which mainly influenced the conversion of ATP, ADP, AMP, GTP, GMP, GDP, UTP, UDP, UMP, dTTP, dTDP, dTMP, and RNA. Thus, it could be concluded that parasitic infection can change the intestinal microbial metabolic activity and enhance immune response of the host through the pathway of purine and pyrimidine metabolism. This results will be a valuable contribution to understanding the bidirectional association of the parasite, intestinal microbiota, and host.

The microbial metabolite trimethylamine N-oxide promotes antitumor immunity in triple-negative breast cancer

Immunotherapy has achieved limited success in patients with triple-negative breast cancer (TNBC), an aggressive disease with a poor prognosis. Commensal microbiota have been proven to colonize the mammary gland, but whether and how they modulate the tumor microenvironment remains elusive. We performed a multiomics analysis of a cohort of patients with TNBC (n = 360) and found genera under Clostridiales, and the related metabolite trimethylamine N-oxide (TMAO) was more abundant in tumors with an activated immune microenvironment. Patients with higher plasma TMAO achieved better responses to immunotherapy. Mechanistically, TMAO induced pyroptosis in tumor cells by activating the endoplasmic reticulum stress kinase PERK and thus enhanced CD8⁺ T cell-mediated antitumor immunity in TNBC in vivo. Collectively, our findings offer new insights into microbiota-metabolite-immune crosstalk and indicate that microbial metabolites, such as TMAO or its precursor choline, may represent a novel therapeutic strategy to promote the efficacy of immunotherapy in TNBC.

Metabolomic Workflow for the Accurate and High-Throughput Exploration of the Pathways of Tryptophan, Tyrosine, Phenylalanine, and Branched-Chain Amino Acids in Human Biofluids

The modulation of host and dietary metabolites by gut microbiota (GM) is important for maintaining correct host physiology and in the onset of various pathologies. An ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry method was developed for the targeted quantitation in human plasma, serum, and urine of 89 metabolites resulting from human-GM cometabolism of dietary essential amino acids tryptophan, tyrosine, and phenylalanine as well as branched-chain amino acids. Ninety-six-well plate hybrid-SPE enables fast clean-up of plasma and serum. Urine was diluted and filtered. A 15 min cycle enabled the acquisition of 96 samples per day, with most of the metabolites stable in aqueous solution for up to 72 h. Calibration curves were specifically optimized to cover expected concentrations in biological fluids, and limits of detection were at the order of ppb. Matrix effects were in acceptable ranges, and analytical recoveries were in general greater than 80%. Inter and intraday precision and accuracy were satisfactory. We demonstrated its application in plasma and urine samples obtained from the same individual in the frame of an interventional study, allowing the quantitation of 51 metabolites. The method could be considered the reference for deciphering changes in human-gut microbial cometabolism in health and disease. Data are available via Metabolights with the identifier MTBLS4399.

Responses of the gut microbiota and metabolite profiles to sulfated polysaccharides from sea cucumber in humanized microbiota mice

Sea cucumber Stichopus japonicus has been consumed as functional food traditionally in Asia, and its sulfated polysaccharide (SCSPsj) demonstrates health-promoting effects in rodents which are related to the regulation of the gut microbiota. However, little is known about the response of the human gut microbiota to SCSPsj. Therefore, the present study aimed to study the response of the donor microbiota to SCSPsj in vivo through a humanized microbiota mice model, which was constructed by antibiotic treatment combined with fecal microbiota transplant. The results revealed that the SCSPsj supplement could positively interact with the specific donor microbiota. It could significantly regulate the gut microbiota community, especially the abundance of Lactobacillus. In addition, SCSPsj could modulate the metabolites in serum and cecal contents of mice, including short-chain fatty acids (SCFAs) and lactic acid, and the changes of some bioactive metabolites were associated with the gut microbiota enriched by SCSPsj. Furthermore, in vitro experiments demonstrated that the Lactobacillus strains isolated could not be proliferated directly by SCSPsj, but SCSPsj significantly promoted biofilm formation and mucus binding of Lactobacillus spp., which contributed to the enrichment of Lactobacillus in vivo. The present study could provide insight into the application of SCSPsj as microbiota-directed food.

Rapid and simultaneous determination of histidine metabolism intermediates in human and mouse microbiota and biomatrices

Histidine metabolism is a key pathway physiologically involved in satiety, recognition memory, skin, and neural protection and allergic diseases. Microbiologically-produced imidazole propionate induces type II diabetes and interferes with glucose lowering drugs. Despite their determinant health implications, no single method simultaneously assesses histidine metabolites in urine, feces, and microbiota. The aim of this study was to develop a simple, rapid, and sensitive method for the determination of histidine and its major bioactive metabolites histamine, N-acetylhistamine, imidazole-4-acetate, cis-urocanate, trans-urocanate, glutamate and imidazole propionate, using ultrahigh-performance liquid chromatography with electrospray ionization tandem mass spectrometry. An innovative simple extraction method from small aliquots of human and mice urine, feces and microbial cell extracts was coupled to separation in a 6.5 min chromatographic run. The successful performance allowed accurate and precise quantification of all metabolites in mouse feces, suggesting broad exchange of histidine metabolites between the gut and mice. Higher urine histamine, histamine to histidine ratio, and imidazole-4-acetate pointed to an underlying inflammatory or allergic process in mice compared to human subjects. N-acetylhistamine and imidazole propionate were detected in human and mouse feces, confirming its origin from gut microbial metabolism. Our novel and robust analytical method captured histidine metabolism in a single assay that will facilitate broad and deep histidine metabolic phenotyping assessing the impact of microbiota on host health in large-scale human observational and interventional studies.

Gut Microbiome and the Role of Metabolites in the Study of Graves’ Disease

Graves’ disease (GD) is an autoimmune thyroid disease (AITD), which is one of the most common organ-specific autoimmune disorders with an increasing prevalence worldwide. But the etiology of GD is still unclear. A growing number of studies show correlations between gut microbiota and GD. The dysbiosis of gut microbiota may be the reason for the development of GD by modulating the immune system. Metabolites act as mediators or modulators between gut microbiota and thyroid. The purpose of this review is to summarize the correlations between gut microbiota, microbial metabolites and GD. Challenges in the future study are also discussed. The combination of microbiome and metabolome may provide new insight for the study and put forward the diagnosis, treatment, prevention of GD in the future.

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis

MOTIVATION

The metabolome and microbiome disorders are highly associated with human health, and there are great demands for dual-omics interaction analysis. Here, we designed and developed an integrative platform, 3MCor, for metabolome and microbiome correlation analysis under the instruction of phenotype and with the consideration of confounders.

RESULTS

Many traditional and novel correlation analysis methods were integrated for intra- and inter-correlation analysis. Three inter-correlation pipelines are provided for global, hierarchical and pairwise analysis. The incorporated network analysis function is conducive to rapid identification of network clusters and key nodes from a complicated correlation network. Complete numerical results (csv files) and rich figures (pdf files) will be generated in minutes. To our knowledge, 3MCor is the first platform developed specifically for the correlation analysis of metabolome and microbiome. Its functions were compared with corresponding modules of existing omics data analysis platforms. A real-world dataset was used to demonstrate its simple and flexible operation, comprehensive outputs and distinctive contribution to dual-omics studies.

AVAILABILITYAND IMPLEMENTATION

3MCor is available at http://3mcor.cn and the backend R script is available at https://github.com/chentianlu/3MCorServer.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Gut microbiota and gut tissue metabolites involved in development and prevention of depression

Depression is a prevalent, life-threatening, and highly recurrent psychiatric illness. Several studies have shown that depression is associated with endogenous metabolites and the gut microbiota. However, it is unclear whether metabolites in different gut tissues play a role in the pathogenesis of depression and whether the gut microbiota has an impact on depression. Here, we investigated the metabolic signatures in the jejunum, ileum, and colorectum using metabolomics and explored the influence of the gut microbiota on both the development of chronic variable stress (CVS)-induced depression rat model and variations in gut tissue metabolites using a gnotobiotic rat model. The results showed that CVS induced disturbances in gut metabolites (29 differential metabolites) and had different effects on the different segments. When CVS rats were treated with antibiotics, depression-like ethological disorders disappeared, and the decreased catecholamine levels almost normalized. The depression recovery was attributed to the influence of antibiotics on the gut microbiota, especially inhibiting Clostridiaceae (F1), Candidatus arthromitus (G2), Lactobacillus (G6), and elevating Pseudomonadaceae (F6). Moreover, 16 of 29 varied metabolites in CVS rats were reversed with antibiotic treatment. Among them, 12 increased metabolites were decreased, suggesting a trigger for depression. However, four decreased metabolites were increased, indicating a potential therapeutic effect on depression. Based on the Pearson's correlation analysis, hypoxanthine, 3-hydroxypristanic acid, threonic acid, and L-carnitine were strongly associated with F6, F1, G2, and G6, which are involved in the development and prevention of depression. These findings provide a possibility for further exploration of the pathogenesis and prevention of depression.

Metabolomic Biomarkers to Predict and Diagnose Cystic Fibrosis Pulmonary Exacerbations: A Systematic Review

INTRODUCTION

Metabolomics is an emerging area of research and has the potential to identify clinical biomarkers for predicting or diagnosing cystic fibrosis (CF) pulmonary exacerbations (PEx).

OBJECTIVE

To identify clinically promising metabolites across different sample sources that can be used to predict or diagnose PEx in CF.

EVIDENCE REVIEW

Searches for original literature were completed through EMBASE, MEDLINE, and all databases on the Web of Science with no restrictions on language or publication date. Gray literature was collected through Google Scholar. Additional studies were obtained by contacting authors and searching reference lists of candidate papers. The patient population included individuals with CF. Studies involving patients who underwent lung transplantation were excluded. The outcome was the prediction or diagnosis of pulmonary exacerbations from metabolites directly measured from biological samples. Search results were downloaded and imported into Covidence and duplicates were removed automatically. Any remaining duplicates were manually tagged and excluded. Two independent reviewers screened each abstract for eligibility and repeated this process for full texts. Risk of bias was conducted using QUADAS-2 by two independent reviewers. A third author resolved any remaining conflicts.

RESULTS

A combined 3974 relevant abstracts were identified and 115 full texts were assessed for eligibility. The final 25 studies underwent data extraction for study design, patient demographics, studied metabolites, concentration values, and diagnostic accuracy values. Included studies differed considerably in methodologies, sample specimen types (exhaled breath condensate [EBC], sputum, saliva, plasma, urine), and disease states. We identified 19 unique metabolites that were measured by two or more studies of which 2 have the potential to predict PEx (EBC 4-hydroxycyclohexylcarboxylic acid [4-HCHC] and lactic acid) and 6 to diagnose PEx (EBC 4-HCHC and lactic acid, sputum lactic acid and nitrate, and plasma arginine and methionine).

CONCLUSION AND RELEVANCE

This systematic review has identified promising metabolites for further study in CF. Certain metabolites may provide clinical potential in predicting or diagnosing PEx, but further validation studies are required. With better tools to aid in the earlier identification of PEx, clinicians can implement preventative measures to mitigate airway damage.Systematic Review Registration: https://www.crd.york.ac.uk/prospero/.

Fecal metabolomics reveals products of dysregulated proteolysis and altered microbial metabolism in obesity-related osteoarthritis

OBJECTIVE

The objective of this exploratory study was to determine if perturbations in gut microbial composition and the gut metabolome could be linked to individuals with obesity and osteoarthritis (OA).

METHODS

Fecal samples were collected from obese individuals diagnosed with radiographic hand plus knee OA (n = 59), defined as involvement of at least 3 joints across both hands, and a Kellgren-Lawrence (KL) grade 2-4 (or total knee replacement) in at least one knee. Controls (n = 33) were without hand OA and with KL grade 0-1 knees. Fecal metabolomes were analyzed by a UHPLC/Q Exactive HFx mass spectrometer. Microbiome composition was determined in fecal samples by 16 S ribosomal RNA amplicon sequencing (rRNA-seq). Stepwise logistic regression models were built to determine microbiome and/or metabolic characteristics of OA.

RESULTS

Untargeted metabolomics analysis indicated that OA cases had significantly higher levels of di- and tripeptides and significant perturbations in microbial metabolites including propionic acid, indoles, and other tryptophan metabolites. Pathway analysis revealed several significantly perturbed pathways associated with OA including leukotriene metabolism, amino acid metabolism and fatty acid utilization. Logistic regression models selected metabolites associated with the gut microbiota and leaky gut syndrome as significant predictors of OA status, particularly when combined with the rRNA-seq data.

CONCLUSIONS

Adults with obesity and knee plus hand OA have distinct fecal metabolomes characterized by increased products of proteolysis, perturbations in leukotriene metabolism, and changes in microbial metabolites compared with controls. These metabolic perturbations indicate a possible role of dysregulated proteolysis in OA.

Green Alga Enteromorpha prolifera Oligosaccharide Ameliorates Ageing and Hyperglycemia through Gut-Brain Axis in Age-Matched Diabetic Mice

SCOPE

To investigate the anti-ageing and anti-diabetic effects of Enteromorpha prolifera oligosaccharide (EPO) in age-matched streptozocin-induced diabetic mice.

METHODS AND RESULTS

LC-MS metabolomics and 16S rRNA sequencing is used to identify the brain metabolites and gut microbiota, respectively. EPO could significantly improve glucose metabolism and activity of total superoxide dismutase in serum. It also could regulate the tricarboxylic acid cycle, arginine, and inosine-related metabolic pathways in the brain of aged diabetic mice. Inosine is found to enhance the relative expressions of daf-2, daf-16, and skn-1 in insulin-resistant Caenorhabditis elegans. Additionally, EPO could alter the composition and diversity of gut microbiota in mice. It could upregulate the Signal Transducer and Activator of Transcription 3/Forkhead Box O1 (FOXO1)/B cell lymphoma 6 (Bcl-6) pathways in the brain and the c-Jun N-terminal Kinase (JNK)/FOXO1/Bcl-6 signaling axis in the intestine to regulate glucose metabolite status and ageing in mice. EPO could also improve the levels of glucagon-like peptide type 1 (GLP1) expression in the gut, thereby inducing high expression of GLP1 receptor in the brain to control glucose metabolites through the brain-gut axis. Enterococcus is negatively correlated with AMP in the brain and could be a potential hallmark species in age-related diabetes.

CONCLUSIONS

These results suggest that EPO could be a potential novel natural drug for the treatment of diabetes in the elderly.

Intrauterine antibiotic exposure affected neonatal gut bacteria and infant growth speed

Although abundant evidence has suggested that early-life antibiotic exposure was associated with adipogenesis later in life, limited data were available on the effect of intrauterine antibiotic exposure on infant growth and growth speed. Additionally, few studies have investigated the role of the neonatal gut microbiota in the above association. In this study, we examined the association between intrauterine cumulative antibiotic exposure and infant growth and explored the potential role of the neonatal gut microbiota in the association. 295 mother-child pairs from the Shanghai Maternal-Child Pairs Cohort (MCPC) study were included, and meconium samples and infant growth measurements were assessed. Z-scores of length-for-age, weight-for-age (weight-for-age), and body mass index (BMI)-for-age (BMI-for-age) were calculated. Eighteen common antibiotics were measured in meconium. Multivariable linear regression models were applied to test the interrelationships between antibiotic exposure, diversity indicators, and the relative abundance of selected bacterial taxa from phylum to genus levels from least absolute shrinkage and selection operator (LASSO) and infant growth indicators. The detection rates of the 18 antibiotics, except for chlortetracycline, penicillin, and chloramphenicol, were below 10 %. Penicillin was found to be positively associated with infant growth at birth and with growth speed from 2 to 6 months. The Pielou and Simpson indexes were negatively associated with meconium penicillin. Nominally significant associations between penicillin and the relative abundances of several bacterial taxa from the phyla Proteobacteria, Bacteroidetes, and Firmicutes were found. The Pielou and Simpson indexes were also found to be negatively associated with infant growth. Among taxa selected from LASSO regression, the relative abundances of the phyla Actinobacteria and Firmicutes and order Bifidobacteriales were found to be significantly associated with weight and BMI growth speeds from 2 to 6 months. In conclusion, intrauterine antibiotic exposure can affect infant growth. The neonatal gut microbiota might play a role in the abovementioned association.

Gut Microbiota-Derived Metabolites in Colorectal Cancer: The Bad and the Challenges

Accumulating evidence from studies in humans and animal models has elucidated that gut microbiota, acting as a complex ecosystem, contributes critically to colorectal cancer (CRC). The potential mechanisms often reported emphasize the vital role of carcinogenic activities of specific pathogens, but in fact, a series of metabolites produced from exogenous dietary substrates or endogenous host compounds occupy a decisive position similarly. Detrimental gut microbiota-derived metabolites such as trimethylamine-N-oxide, secondary bile acids, hydrogen sulfide and N-nitroso compounds could reconstruct the ecological composition and metabolic activity of intestinal microorganisms and formulate a microenvironment that opens susceptibility to carcinogenic stimuli. They are implicated in the occurrence, progression and metastasis of CRC through different mechanisms, including inducing inflammation and DNA damage, activating tumorigenic signaling pathways and regulating tumor immunity. In this review, we mainly summarized the intimate relationship between detrimental gut microbiota-derived metabolites and CRC, and updated the current knowledge about detrimental metabolites in CRC pathogenesis. Then, multiple interventions targeting these metabolites for CRC management were critically reviewed, including diet modulation, probiotics/prebiotics, fecal microbiota transplantation, as well as more precise measures such as engineered bacteria, phage therapy and chemopreventive drugs. A better understanding of the interplay between detrimental microbial metabolites and CRC would hold great promise against CRC.

TMAO promotes apoptosis and oxidative stress of pancreatic acinar cells by mediating IRE1α-XBP-1 pathway

BACKGROUND

Acute pancreatitis caused by hyperlipidemia is a severe life-threatening condition. Therefore, it is urgent to develop new therapeutic methods to treat this disease.

METHODS

Cell viability was determined by the Cell Counting Kit-8 (CCK-8) assay. Western blotting (WB) was used to detect the expression levels of apoptotic and endoribonuclease inositol-requiring enzyme 1α (IRE1α)/X-box binding protein 1 (XBP-1) pathway-associated proteins. The induction of cell apoptosis was determined using flow cytometry. The expression levels of the oxidative stress indicators were measured by an enzyme-linked immunosorbent assay.

RESULTS

WB analysis and the CCK-8 assay demonstrated that trimethylamine-N-oxide (TMAO) decreased cell viability and facilitated apoptosis of MPC-83 cells in a dose-dependent manner. Furthermore, the induction of oxidative stress was assessed by evaluating the levels of specific markers, including hydrogen peroxide, reactive oxygen species, nitric oxide, and superoxide dismutase. The levels of the aforementioned markers were increased in the TMAO-treated group. Subsequently, the IRE1α/XBP-1 pathway-associated proteins were analyzed by WB analysis and the data demonstrated that the regulatory effects of TMAO on MPC-83 cells were meditated by the IRE1α/XBP-1 signaling pathway. Subsequently, rescue experiments were performed to further assess the effects of TMAO.

CONCLUSION

The present study provides evidence on the application of TMAO as a potential diagnostic and therapeutic strategy for the therapeutic intervention of hyperlipidemic acute pancreatitis.

Gut microbiome and metabolic response in non-alcoholic fatty liver disease

Fatty liver disease (FLD) is one of the largest burdens to human health worldwide and is associated with gut microbiome and metabolite stability. Engineered liver tissues have shown promise in restoring liver functions in non-alcoholic FLD (NAFLD), hepatitis and cirrhosis. Fatty liver, largely noted in obesity and hepatic cancer, is highly fatal and has led to a global increase in death rates. It is associated with complex metabolic reprogramming too. A standard approach to therapy in the newly diagnosed setting includes surgery or identification of biomarkers/ metabolites for therapeutic purposes, which ultimately focus on improvement of liver health in patients. As such there are no standard procedures for patient care, but depending on the severity, systemic therapy with either genomic, proteomic or metabolomic profiling form potential options. Better comparisons and study of underlying mechanisms in gut microbiome-based metabolic functions in obesity are urgently required. Today, an emerging field, focusing on metabolomic approaches and metabolic phenotyping, involved in high-throughput identification of metabolome in obesity and gut disorders, is involved in biomarker and metabolite identification. There are supporting technologies and approaches in NAFLD that throw light on the metabolites and gut microbiome, and also on the understanding of the risk factors of obesity along with liver cancer metabolic reaction networks. We discuss the current state of NAFLD metabolites, gut micro-environmental changes, and the further challenges in digital metabolomics profiling. Innovative clinical trial designs, with biomarker-enrichment strategies that are required to improve the outcome of NAFLD in patients are also discussed.

Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants

Cesarean delivery and formula feeding have both been implicated as important factors associated with perturbations to the infant gut microbiome. To investigate the functional metabolic response of the infant gut microbial milieu to these factors, we profiled the stool metabolomes of 121 infants from a US pregnancy cohort study at approximately 6 weeks of life and evaluated associations with delivery mode and feeding method. Multivariate analysis of six-week stool metabolomic profiles indicated discrimination by both delivery mode and diet. For diet, exclusively breast-fed infants exhibited metabolomic profiles that were distinct from both exclusively formula-fed and combination-fed infants, which were relatively more similar to each other in metabolomic profile. We also identified individual metabolites that were important for differentiating delivery mode groups and feeding groups and metabolic pathways related to delivery mode and feeding type. We conclude based on previous work and this current study that the microbial communities colonizing the gastrointestinal tracts of infants are not only taxonomically, but also functionally distinct when compared according to delivery mode and feeding groups. Further, different sets of metabolites and metabolic pathways define delivery mode and diet metabotypes.

Untargeted analysis of the serum metabolome in cats with exocrine pancreatic insufficiency

Exocrine pancreatic insufficiency (EPI) causes chronic digestive dysfunction in cats, but its pathogenesis and pathophysiology are poorly understood. Untargeted metabolomics is a promising analytic methodology that can reveal novel metabolic features and biomarkers of clinical disease syndromes. The purpose of this preliminary study was to use untargeted analysis of the serum metabolome to discover novel aspects of the pathobiology of EPI in cats. Serum samples were collected from 5 cats with EPI and 8 healthy controls. The diagnosis of EPI was confirmed by measurement of subnormal serum feline trypsin-like immunoreactivity (fTLI). Untargeted quantification of serum metabolite utilized ultra-high-performance liquid chromatography-tandem mass spectroscopy. Cats with EPI had significantly increased serum quantities of long-chain fatty acids, polyunsaturated fatty acids, mevalonate pathway intermediates, and endocannabinoids compared with healthy controls. Diacylglycerols, phosphatidylethanolamines, amino acid derivatives, and microbial metabolites were significantly decreased in cats with EPI compared to healthy controls. Diacyclglycerols and amino acid metabolites were positively correlated, and sphingolipids and long-chain fatty acids were negatively correlated with serum fTLI, respectively. These results suggest that EPI in cats is associated with increased lipolysis of peripheral adipose stores, dysfunction of the mevalonate pathway, and altered amino acid metabolism. Differences in microbial metabolites indicate that feline EPI is also associated with enteric microbial dysbiosis. Targeted studies of the metabolome of cats with EPI are warranted to further elucidate the mechanisms of these metabolic derangements and their influence on the pathogenesis and pathophysiology of EPI in cats.