A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

Defining the functional status of host-associated microbial ecosystems has proven challenging owing to the vast number of predicted genes within the microbiome and relatively poor understanding of community dynamics and community–host interaction. Metabolomic approaches, in which a large number of small molecule metabolites can be defined in a biological sample, offer a promising avenue to ‘fingerprint'' microbiota functional status. Here, we examined the effects of the human gut microbiota on the fecal and urinary metabolome of a humanized (HUM) mouse using an optimized ultra performance liquid chromatography–mass spectrometry-based method. Differences between HUM and conventional mouse urine and fecal metabolomic profiles support host-specific aspects of the microbiota''s metabolomic contribution, consistent with distinct microbial compositions. Comparison of microbiota composition and metabolome of mice humanized with different human donors revealed that the vast majority of metabolomic features observed in donor samples are produced in the corresponding HUM mice, and individual-specific features suggest ‘personalized'' aspects of functionality can be reconstituted in mice. Feeding the mice a defined, custom diet resulted in modification of the metabolite signatures, illustrating that host diet provides an avenue for altering gut microbiota functionality, which in turn can be monitored via metabolomics. Using a defined model microbiota consisting of one or two species, we show that simplified communities can drive major changes in the host metabolomic profile. Our results demonstrate that metabolomics constitutes a powerful avenue for functional characterization of the intestinal microbiota and its interaction with the host.     

去卵巢小鼠肠道菌群和血脂的变化

目的 探讨去卵巢对小鼠肠道菌群和血脂的影响。 方法 12只10周龄C57BL/6小鼠随机分为2组:假手术组(SHAM组)和去卵巢组(OVX组),每组6只,进行12周的喂养。每2周测定小鼠体质量,12周后测肝脏指数、血清三酰甘油水平和游离脂肪酸水平,小肠进行病理学检查,收集小鼠粪便并在Illumina MiSeq测序平台进行16S rRNA基因测序检测。 结果 与SHAM组相比,OVX组小鼠体质量、肝脏指数、血清三酰甘油水平和游离脂肪酸水平明显增加(t=4.745,t=15.090,t=11.140,t=4.038,均P结论 去卵巢小鼠血脂升高和肠道菌群失衡,提示肠道菌群可能是预防和治疗雌激素缺乏后脂质代谢异常的潜在靶点。     

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism

Gut microbiota dysbiosis has been implicated in a variety of systemic disorders, notably metabolic diseases including obesity and impaired liver function, but the underlying mechanisms are uncertain. To investigate this question, we transferred caecal microbiota from either obese or lean mice to antibiotic‐free, conventional wild‐type mice. We found that transferring obese‐mouse gut microbiota to mice on normal chow (NC) acutely reduces markers of hepatic gluconeogenesis with decreased hepatic PEPCK activity, compared to non‐inoculated mice, a phenotypic trait blunted in conventional NOD2 KO mice. Furthermore, transferring of obese‐mouse microbiota changes both the gut microbiota and the microbiome of recipient mice. We also found that transferring obese gut microbiota to NC‐fed mice then fed with a high‐fat diet (HFD) acutely impacts hepatic metabolism and prevents HFD‐increased hepatic gluconeogenesis compared to non‐inoculated mice. Moreover, the recipient mice exhibit reduced hepatic PEPCK and G6Pase activity, fed glycaemia and adiposity. Conversely, transfer of lean‐mouse microbiota does not affect markers of hepatic gluconeogenesis. Our findings provide a new perspective on gut microbiota dysbiosis, potentially useful to better understand the aetiology of metabolic diseases.     

Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD

To elucidate the molecular mechanisms underlying non‐alcoholic fatty liver disease (NAFLD), we recruited 86 subjects with varying degrees of hepatic steatosis (HS). We obtained experimental data on lipoprotein fluxes and used these individual measurements as personalized constraints of a hepatocyte genome‐scale metabolic model to investigate metabolic differences in liver, taking into account its interactions with other tissues. Our systems level analysis predicted an altered demand for NAD⁺ and glutathione (GSH) in subjects with high HS. Our analysis and metabolomic measurements showed that plasma levels of glycine, serine, and associated metabolites are negatively correlated with HS, suggesting that these GSH metabolism precursors might be limiting. Quantification of the hepatic expression levels of the associated enzymes further pointed to altered de novo GSH synthesis. To assess the effect of GSH and NAD⁺ repletion on the development of NAFLD, we added precursors for GSH and NAD⁺ biosynthesis to the Western diet and demonstrated that supplementation prevents HS in mice. In a proof‐of‐concept human study, we found improved liver function and decreased HS after supplementation with serine (a precursor to glycine) and hereby propose a strategy for NAFLD treatment.     

肠道菌群与胆汁酸代谢的互相作用

肠道菌群是胃肠道的多种共生细菌和其他微生物的统称,是一个复杂而动态的微生物生态系统,有数十万亿个微生物.胆汁酸是胆汁的主要成分,由肝脏中的胆固醇合成并释放到肠道中以帮助消化吸收膳食脂肪.肠道菌群在胆汁酸代谢中发挥着重要作用,它借助胆盐水解酶和类固醇脱氢酶等通过脱氢、脱羟基和脱硫等作用改变胆汁酸池的组成;随后通过影响胆汁...     

Gut microbiota modulates osteoclast glutathione synthesis and mitochondrial biogenesis in mice subjected to ovariectomy

ObjectivesOsteoporosis is a common bone disease in the elderly mainly regulated by osteoblasts (OBs) and osteoclasts (OCs). The gut microbiota has been recognized as an important factor in many physiological and pathological processes in the host. Thus, we hypothesize that the gut microbiota is necessary for postmenopausal osteoporosis and that germ‐free (GF) mice are protected from osteoporosis.Material and MethodsOsteoporosis models were established by performing ovariectomy (OVX) in mice. Bone mass was measured by micro‐CT, and gut microbiota were assessed by 16s rDNA sequencing. Reactive oxygen species (ROS) were detected by dihydroethidium (DHE) staining in vivo and 2’,7''‐dichlorodihydrofluorescein diacetate (DCFH‐DA) staining in vitro.ResultsFirmicutes and Bacteroidetes in the intestine are pivotal in OC differentiation, and the Firmicutes/Bacteroidetes ratio (F/B ratio) is a specific indicator of osteoporosis. Furthermore, we found that Firmicutes and Bacteroidetes affect the de novo synthesis of glutathione (GSH) by regulating its key enzyme glutamate–cysteine ligase catalytic subunit (Gclc) and inhibiting mitochondrial biogenesis and ROS accumulation via the cAMP response element‐binding (CREB) pathway. In addition, supplementing OVX mice with the probiotic Lactobacillus salivarius LI01 from the Firmicutes phylum prevented osteoporosis.ConclusionsOur results reveal that GSH plays a vital role in OVX‐induced bone loss, and probiotics that affect GSH metabolism are potential therapeutic targets for overcoming osteoporosis.     

Collinsella aerofaciens对高脂饮食小鼠糖脂代谢及肠道菌群的影响

从人粪便中分离Collinsella aerofaciens,并给予正常和高脂饮食的C57BL/6J小鼠,观察Collinsella aerofaciens对小鼠糖脂代谢及肠道菌群结构的影响。

将40只C57BL/6J雄性小鼠随机分成正常饮食组（NCD组）、正常饮食+菌液组（NCD+B组）、高脂饮食组（HFD组）和高脂饮食+菌液组（HFD+B组）,每组10只。NCD组和HFD组给予100 μL的生理盐水,其余组给予Collinsella aerofaciens 1×10⁹ CFU/mL,连续灌胃12周。第0、4、8和12周通过试剂盒检测空腹血糖（FBG）、随机血糖（GLU）、总胆固醇（TC）和三酰甘油（TG）水平。第12周,对各组小鼠进行口服糖耐量和胰岛素耐量试验,并检测血浆高、低密度脂蛋白胆固醇（HDL-C、LDL-C）水平。收集小鼠粪便,采用高通量测序技术检测16S rRNA V3‒V4区序列,分析肠道菌群结构变化。

第8和12周4组小鼠间TC水平差异有统计学意义（F = 132.424,P＜0.001;F = 107.601,P＜0.001）,与NCD组相比,NCD+B组小鼠TC水平显著升高（P＜0.050）;与HFD组相比,HFD+B组小鼠TC水平显著升高（P＜0.050）。4组小鼠间HDL-C和LDL-C水平差异有统计学意义（F = 7.809,P＜0.001;F = 41.521,P＜0.001）,与NCD组相比,NCD+B组小鼠HDL-C水平显著降低（P＜0.050）,LDL-C水平显著升高（P＜0.050）;与HFD组相比,HFD+B组小鼠LDL-C水平显著升高（P＜0.050）。Spearman相关性分析发现小鼠肠道中Desulfovibrionaceae丰度与FBG、GLU、TC和LDL-C水平呈正相关（r = 0.512,P = 0.011;r = 0.445,P = 0.029;r = 0.728,P＜0.001;r = 0.758,P＜0.001）。

人粪便中分离的Collinsella aerofaciens可以影响小鼠糖脂代谢,可能与其破坏肠道菌群平衡有关,同时为防治血糖血脂异常代谢提供靶点。

     

The role of short-chain fatty acids in the interplay between diet,gut microbiota,and host energy metabolism

Short-chain fatty acids (SCFAs), the end products of fermentation of dietary fibers by the anaerobic intestinal microbiota, have been shown to exert multiple beneficial effects on mammalian energy metabolism. The mechanisms underlying these effects are the subject of intensive research and encompass the complex interplay between diet, gut microbiota, and host energy metabolism. This review summarizes the role of SCFAs in host energy metabolism, starting from the production by the gut microbiota to the uptake by the host and ending with the effects on host metabolism. There are interesting leads on the underlying molecular mechanisms, but there are also many apparently contradictory results. A coherent understanding of the multilevel network in which SCFAs exert their effects is hampered by the lack of quantitative data on actual fluxes of SCFAs and metabolic processes regulated by SCFAs. In this review we address questions that, when answered, will bring us a great step forward in elucidating the role of SCFAs in mammalian energy metabolism.     

Reconstruction of pathways associated with amino acid metabolism in human mitochondria

We have used a bioinformatics approach for the identification and reconstruction of metabolic pathways associated with amino acid metabolism in human mitochondria. Human mitochondrial proteins determined by experimental and computational methods have been superposed on the reference pathways from the KEGG database to identify mitochondrial pathways. Enzymes at the entry and exit points for each reconstructed pathway were identified, and mitochondrial solute carrier proteins were determined where applicable. Intermediate enzymes in the mitochondrial pathways were identified based on the annotations available from public databases, evidence in current literature, or our MITOPRED program, which predicts the mitochondrial localization of proteins. Through integration of the data derived from experimental, bibliographical, and computational sources, we reconstructed the amino acid metabolic pathways in human mitochondria, which could help better understand the mitochondrial metabolism and its role in human health.     

The interplay between host cellular and gut microbial metabolism in NAFLD development and prevention

Metabolism regulation centred on insulin resistance is increasingly important in nonalcoholic fatty liver disease (NAFLD). This review focuses on the interactions between the host cellular and gut microbial metabolism during the development of NAFLD. The cellular metabolism of essential nutrients, such as glucose, lipids and amino acids, is reconstructed with inflammation, immune mechanisms and oxidative stress, and these alterations modify the intestinal, hepatic and systemic environments, and regulate the composition and activity of gut microbes. Microbial metabolites, such as short-chain fatty acids, secondary bile acids, protein fermentation products, choline and ethanol and bacterial toxicants, such as lipopolysaccharides, peptidoglycans and bacterial DNA, play vital roles in NAFLD. The microbe–metabolite relationship is crucial for the modulation of intestinal microbial composition and metabolic activity. The intestinal microbiota and their metabolites participate in epithelial cell metabolism via a series of cell receptors and signalling pathways and remodel the metabolism of various cells in the liver via the gut–liver axis. Microbial metabolic manipulation is a promising strategy for NAFLD prevention, but larger-sampled clinical trials are required for future application.     

Prion protein regulates glutathione metabolism and neural glutamate and cysteine uptake via excitatory amino acid transporter 3

Prion protein (PrP) plays crucial roles in regulating antioxidant systems to improve cell defenses against cellular stress. Here, we show that the interactions of PrP with the excitatory amino acid transporter 3 (EAAT3), γ‐glutamyl transpeptidase (γ‐GT), and multi‐drug resistance protein 1 (MRP1) in astrocytes and the interaction between PrP and EAAT3 in neurons regulate the astroglial and neuronal metabolism of the antioxidant glutathione. Ablation of PrP in astrocytes and cerebellar neurons leads to dysregulation of EAAT3‐mediated uptake of glutamate and cysteine, which are precursors for the synthesis of glutathione. In PrP‐deficient astrocytes, levels of intracellular glutathione are increased, and under oxidative stress, levels of extracellular glutathione are increased, due to (i) increased glutathione release via MRP1 and (ii) reduced activity of the glutathione‐degrading enzyme γ‐GT. In PrP‐deficient cerebellar neurons, cell death is enhanced under oxidative stress and glutamate excitotoxicity, when compared to wild‐type cerebellar neurons. These results indicate a functional interplay of PrP with EAAT3, MRP1 and γ‐GT in astrocytes and of PrP and EAAT3 in neurons, suggesting that these interactions play an important role in the metabolic cross‐talk between astrocytes and neurons and in protection of neurons by astrocytes from oxidative and glutamate‐induced cytotoxicity.

     

Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture

A dynamic flux balance model based on a genome-scale metabolic network reconstruction is developed for in silico analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Metabolic engineering strategies previously identified for their enhanced steady-state biomass and/or ethanol yields are evaluated for fed-batch performance in glucose and glucose/xylose media. Dynamic analysis is shown to provide a single quantitative measure of fed-batch ethanol productivity that explicitly handles the possible tradeoff between the biomass and ethanol yields. Productivity optimization conducted to rank achievable fed-batch performance demonstrates that the genetic manipulation strategy and the fed-batch operating policy should be considered simultaneously. A library of candidate gene insertions is assembled and directly screened for their achievable ethanol productivity in fed-batch culture. A number of novel gene insertions with ethanol productivities identical to the best metabolic engineering strategies reported in previous studies are identified, thereby providing additional targets for experimental evaluation. The top performing gene insertions were substrate dependent, with the highest ranked insertions for glucose media yielding suboptimal performance in glucose/xylose media. The analysis results suggest that enhancements in biomass yield are most beneficial for the enhancement of fed-batch ethanol productivity by recombinant xylose utilizing yeast strains. We conclude that steady-state flux balance analysis is not sufficient to predict fed-batch performance and that the media, genetic manipulations, and fed-batch operating policy should be considered simultaneously to achieve optimal metabolite productivity.     

益生菌干预对高脂高糖饮食诱导肥胖小鼠肠道菌群及脂代谢影响的研究

目的 探讨益生菌干预对高脂高糖饮食诱导肥胖小鼠肠道菌群及脂代谢的影响。方法 C57BL/6J雌性小鼠30只随机分为正常对照组、肥胖组和益生菌干预组,每组10只,分别给予标准饲料、高脂高糖饲料以及高脂高糖饲料同时给予益生菌干预,连续喂养6周,测量并分析三组小鼠的体重。留取小鼠粪便样本,应用PCR-DGGE法分析菌群,应用酶反应比色法分析三组小鼠血脂情况。结果 与正常对照组小鼠相比,肥胖小鼠体重明显增加,益生菌干预组小鼠体重略有增加;肥胖组小鼠肠道菌群紊乱,与正常对照组分别聚为两大类,益生菌干预组小鼠肠道菌群与正常对照组聚为一大类。肥胖小鼠血清总胆固醇、低密度脂蛋白含量升高,益生菌干预组小鼠较肥胖组血清总胆固醇、低密度脂蛋白含量降低,但与正常对照组仍有差异。结论 高脂高糖饮食诱导肥胖小鼠存在肠道菌群结构失调及脂代谢异常,益生菌干预可以改善肥胖小鼠菌群失调以及脂代谢紊乱。     

A high-fat diet and high-fat and high-cholesterol diet may affect glucose and lipid metabolism differentially through gut microbiota in mice

This study was conducted to investigate the effects of a high-fat diet (HFD) and high-fat and high-cholesterol diet (HFHCD) on glucose and lipid metabolism and on the intestinal microbiota of the host animal. A total of 30 four-week-old female C57BL/6 mice were randomly divided into three groups (n=10) and fed with a normal diet (ND), HFD, or HFHCD for 12 weeks, respectively. The HFD significantly increased body weight and visceral adipose accumulation and partly lowered oral glucose tolerance compared with the ND and HFHCD. The HFHCD increased liver weight, liver fat infiltration, liver triglycerides, and liver total cholesterol compared with the ND and HFD. Moreover, it increased serum high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and total cholesterol compared with the ND and HFD and upregulated alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase significantly. The HFHCD also significantly decreased the α-diversity of the fecal bacteria of the mice, to a greater extent than the HFD. The composition of fecal bacteria among the three groups was apparently different. Compared with the HFHCD-fed mice, the HFD-fed mice had more Oscillospira, Odoribacter, Bacteroides, and [Prevotella], but less [Ruminococcus] and Akkermansia. Cecal short-chain fatty acids were significantly decreased after the mice were fed the HFD or HFHCD for 12 weeks. Our findings indicate that an HFD and HFHCD can alter the glucose and lipid metabolism of the host animal differentially; modifications of intestinal microbiota and their metabolites may be an important underlying mechanism.