The gut microbiota modulates host amino acid and glutathione metabolism in mice

The gut microbiota has been proposed as an environmental factor that promotes the progression of metabolic diseases. Here, we investigated how the gut microbiota modulates the global metabolic differences in duodenum, jejunum, ileum, colon, liver, and two white adipose tissue depots obtained from conventionally raised (CONV‐R) and germ‐free (GF) mice using gene expression data and tissue‐specific genome‐scale metabolic models (GEMs). We created a generic mouse metabolic reaction (MMR) GEM, reconstructed 28 tissue‐specific GEMs based on proteomics data, and manually curated GEMs for small intestine, colon, liver, and adipose tissues. We used these functional models to determine the global metabolic differences between CONV‐R and GF mice. Based on gene expression data, we found that the gut microbiota affects the host amino acid (AA) metabolism, which leads to modifications in glutathione metabolism. To validate our predictions, we measured the level of AAs and N‐acetylated AAs in the hepatic portal vein of CONV‐R and GF mice. Finally, we simulated the metabolic differences between the small intestine of the CONV‐R and GF mice accounting for the content of the diet and relative gene expression differences. Our analyses revealed that the gut microbiota influences host amino acid and glutathione metabolism in mice.     

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。     

High-fat diet alters gut microbiota physiology in mice

The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.     

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.     

Liraglutide modulates gut microbiota and reduces NAFLD in obese mice

Metabolic disorders such as insulin resistance and diabetes are associated with obesity and nonalcoholic fatty liver disease (NAFLD). The aggressive form of a fatty liver disease may progress to cirrhosis and hepatocellular carcinoma. Furthermore, recent studies demonstrated that there is a dysbiosis in the gut microbiota associated with early stages of metabolic disease. Therefore, the identification and repurposing of drugs already used to treat insulin resistance may be an excellent option for other disorders. We evaluated the effect of liraglutide on obesity, NAFLD and gut microbiota modulation in two different animal models of obesity: the ob/ob mice and the high-fat diet (HFD)-fed mice. Liraglutide treatment induced significant weight loss in both obesity models, showed improvements in glycemic parameters and reduced inflammatory cell infiltration in the cecum and the liver. In ob/ob mice, the liraglutide treatment was able to reduce the accumulation of liver fat by 78% and reversed steatosis in the HFD mice. The gut microbiota analysis showed that liraglutide changed the overall composition as well as the relative abundance of weight-relevant phylotypes such as a reduction of Proteobacteria and an increase of Akkermansia muciniphila in the treated HFD group. We show that liraglutide can lead to weight loss and gut microbiota modulations, and is associated with an improvement of NAFLD. Furthermore, by generating a profile of the intestinal microbiota, we compiled a list of potential bacterial targets that may modulate metabolism and induce a metabolic profile that is considered normal or clinically controlled.     

田蓟苷对高脂饮食小鼠血脂代谢的改善作用及肠道菌群的影响

目的初步探讨田蓟苷改善高脂饮食小鼠血脂代谢的作用机制。方法将60只C57BL/6J小鼠随机分为对照组、高脂饮食组及田蓟苷低、中、高剂量给药组(50、100、200 mg/kg)和阿托伐他汀给药组(10 mg/kg),每组10只,连续给药12周后,检测各组小鼠血清总胆固醇(TC)、三酰甘油(TG)、高密度脂蛋白胆固醇(HDL C)和低密度脂蛋白胆固醇(LDL C)水平。采用Western Blot法检测各组小鼠肝脏组织中SREBP 2和LDLR蛋白表达。通过16S rDNA基因实时荧光定量PCR法检测各组小鼠肠道菌群变化。结果与对照组相比,高脂饮食组小鼠血清TC、TG、HDL C和LDL C水平明显升高(t=-3.966,P=0.001;t=-3.438,P=0.003;t=3.811,P=0.001;t=-6.591,P<0.001),肝脏中SREBP 2和LDLR蛋白表达明显下调(t=7.198,P<0.001;t=8.892,P<0.001)。与高脂饮食组相比,田蓟苷高剂量给药组和阿托伐他汀给药组小鼠血清TC、LDL C水平明显降低(TC:t=2.483,P=0.023;t=3.300,P=0.004。LDL C:t=2.535,P=0.021;t=3.836,P=0.001),肝组织中的SREBP 2和LDLR蛋白水平明显上调(SREBP 2:t=-2.188,P=0.042;t=-3.317,P=0.007。LDLR:t=-2.649,P=0.016;t=-2.249,P=0.037)。与对照组相比,高脂饮食组小鼠肠道中厚壁菌门水平明显升高(t=-2.287,P=0.047),而拟杆菌门、双歧杆菌属、乳杆菌属、嗜黏蛋白阿克曼菌和普拉梭菌水平明显降低(t=3.127,P=0.006;t=2.737,P=0.014;t=3.542,P=0.002;t=3.491,P=0.003;t=2.780,P=0.012)。与高脂饮食组相比,田蓟苷高剂量给药组小鼠肠道中拟杆菌门、乳杆菌属和嗜黏蛋白阿克曼菌水平明显升高(t=-2.613,P=0.020;t=-2.558,P=0.024;t=-2.109,P=0.049)。结论田蓟苷改善高脂饮食诱导的血脂代谢紊乱可能与肝脏中SREBP 2和LDLR蛋白表达及肠道菌群结构变化有关,但其机制仍需进一步研究。     

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.     

Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits

The gastrointestinal tract harbors a complex and diverse microbiota that has an important role in host metabolism. Microbial diversity is influenced by a combination of environmental and host genetic factors and is associated with several polygenic diseases. In this study we combined next-generation sequencing, genetic mapping, and a set of physiological traits of the BXD mouse population to explore genetic factors that explain differences in gut microbiota and its impact on metabolic traits. Molecular profiling of the gut microbiota revealed important quantitative differences in microbial composition among BXD strains. These differences in gut microbial composition are influenced by host-genetics, which is complex and involves many loci. Linkage analysis defined Quantitative Trait Loci (QTLs) restricted to a particular taxon, branch or that influenced the variation of taxa across phyla. Gene expression within the gastrointestinal tract and sequence analysis of the parental genomes in the QTL regions uncovered candidate genes with potential to alter gut immunological profiles and impact the balance between gut microbial communities. A QTL region on Chr 4 that overlaps several interferon genes modulates the population of Bacteroides, and potentially Bacteroidetes and Firmicutes-the predominant BXD gut phyla. Irak4, a signaling molecule in the Toll-like receptor pathways is a candidate for the QTL on Chr15 that modulates Rikenellaceae, whereas Tgfb3, a cytokine modulating the barrier function of the intestine and tolerance to commensal bacteria, overlaps a QTL on Chr 12 that influence Prevotellaceae. Relationships between gut microflora, morphological and metabolic traits were uncovered, some potentially a result of common genetic sources of variation.     

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis

Vitamin A deficiency (A−) is a worldwide public health problem. To better understand how vitamin A status influences gut microbiota and host metabolism, we systematically analyzed urine, cecum, serum and liver samples from vitamin A sufficient (A+) and deficient (A−) mice using ¹H NMR-based metabolomics, quantitative (q)PCR and 16S rRNA gene sequencing coupled with multivariate data analysis. The microbiota in the cecum of A− mice showed compositional as well as functional shifts compared to the microbiota from A+ mice. Targeted ¹H NMR analyses revealed significant changes in microbial metabolite concentrations including higher butyrate and hippurate and decreased acetate and 4-hydroxyphenylacetate in A+ relative to A− mice. Bacterial butyrate-producing genes including butyryl-CoA:acetate CoA-transferase and butyrate kinase were significantly higher in bacteria from A+ versus bacteria from A− mice. A− mice had disturbances in multiple metabolic pathways including alterations in energy (hyperglycemia, glycogenesis, TCA cycle and lipoprotein biosynthesis), amino acid and nucleic acid metabolism. A− mice had hyperglycemia, liver dysfunction, changes in bacterial metabolism and altered gut microbial communities. Moreover, integrative analyses indicated a strong correlation between gut microbiota and host energy metabolism pathways in the liver. Vitamin A regulates host and bacterial metabolism, and the result includes alterations in energy homeostasis.     

糖脂代谢性疾病模型小鼠肠道菌群特征分析

基于16S rDNA测序研究非酒精性脂肪性肝病(NAFLD)、2型糖尿病(T2D)及动脉粥样硬化(AS)小鼠的肠道菌群特征, 分析上述疾病肠道微生物的异同。

以SPF级C57BL/6J雄鼠为对象, 分别采用高脂饮食制备NAFLD模型, 高脂饮食联合小剂量链脲佐菌素腹腔注射建立T2D模型, ApoE^-/-小鼠高脂饮食诱导AS模型, 另设对照组, 每组10只。采用试剂盒测定小鼠血清中总胆固醇(TC)、三酰甘油(TG)、低密度脂蛋白胆固醇(LDL-C)的水平。收集粪便样本, 以Illumina MiSeq测序平台, 采用QIIME2软件对肠道菌群的可分类操作单元(OTUs)数量, Alpha、Beta多样性和菌群多样性指数以及差异菌门、菌属等进行综合分析与评价, 并对肠道菌群代谢功能进行预测。

与对照组小鼠比, T2D组、NAFLD组、AS组血清中TC、TG和LDL-C水平均显著升高, 菌群多样性指数显著降低(F=14.33, P < 0.01), Firmicutes/Bacteroidetes比值逐渐升高; 双歧杆菌属(Bifidobacterium)丰度在AS组、T2D组中显著增加(F=12.15, P < 0.01), 在NAFLD组中显著下降(F=12.15, P < 0.05), 乳杆菌属(Lactobacillus)丰度在NAFLD组、AS组中著降低(F=9.35, P < 0.01), 在T2D组中显著降低。关联分析表明Lactobacillus、Akkermansia等与血脂呈负相关, Faecalibaculum、Blautia等与血脂呈正相关。肠道菌群参与代谢性疾病主要涉及碳水化合物代谢、氨基酸代谢、脂质代谢以及能量代谢等通路。

本研究阐明了NAFLD、T2D、AS肠道微生物组成与变化的共性和个性特征, 为靶向调控肠道微生物治疗代谢性疾病提供科学依据。

     

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.     

Genetic modification of iron metabolism in mice affects the gut microbiota

The composition of the gut microbiota is affected by environmental factors as well as host genetics. Iron is one of the important elements essential for bacterial growth, thus we hypothesized that changes in host iron homeostasis, may affect the luminal iron content of the gut and thereby the composition of intestinal bacteria. The iron regulatory protein 2 (Irp2) and one of the genes mutated in hereditary hemochromatosis Hfe , are both proteins involved in the regulation of systemic iron homeostasis. To test our hypothesis, fecal metal content and a selected spectrum of the fecal microbiota were analyzed from Hfe-/-, Irp2-/- and their wild type control mice. Elevated levels of iron as well as other minerals in feces of Irp2-/- mice compared to wild type and Hfe-/- mice were observed. Interestingly significant variation in the general fecal-bacterial population-patterns was observed between Irp2-/- and Hfe-/- mice. Furthermore the relative abundance of five species, mainly lactic acid bacteria, was significantly different among the mouse lines. Lactobacillus (L.) murinus and L. intestinalis were highly abundant in Irp2-/- mice, Enterococcus faecium species cluster and a species most similar to Olsenella were highly abundant in Hfe-/- mice and L. johnsonii was highly abundant in the wild type mice. These results suggest that deletion of iron metabolism genes in the mouse host affects the composition of its intestinal bacteria. Further studying the relationship between gut microbiota and genetic mutations affecting systemic iron metabolism in human should lead to clinical implications.     

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。     

Sex-dependent effects on the gut microbiota and host metabolome in type 1 diabetic mice

Sexual dimorphism exists in the onset and development of type 1 diabetes (T1D), but its potential pathological mechanism is poorly understood. In the present study, we examined sex-specific changes in the gut microbiome and host metabolome of T1D mice via 16S rRNA gene sequencing and nuclear magnetic resonance (NMR)-based metabolomics approach, and aimed to investigate potential mechanism of the gut microbiota-host metabolic interaction in the sexual dimorphism of T1D. Our results demonstrate that female mice had a greater shift in the gut microbiota than male mice during the development of T1D; however, host metabolome was more susceptible to T1D in male mice. The correlation network analysis indicates that T1D-induced host metabolic changes may be regulated by the gut microbiota in a sex-specific manner, mainly involving short-chain fatty acids (SCFAs) metabolism, energy metabolism, amino acid metabolism, and choline metabolism. Therefore, our study suggests that sex-dependent “gut microbiota-host metabolism axis” may be implicated in the sexual dimorphism of T1D, and the link between microbes and metabolites might contribute to the prevention and treatment of T1D.     

肠道微生物调控宿主食欲的研究进展

肠道微生物与宿主代谢相互作用,可调节机体的生理功能。宿主机体中存在"微生物-肠道-大脑轴",肠道菌群可通过多种途径影响中枢神经系统,进而对宿主摄食等行为产生影响。食物中不易被宿主消化吸收的膳食纤维等营养物质,被肠道微生物发酵可产生多种代谢产物,这些代谢产物作为信号分子可通过不同途径介导中枢神经系统,进而调控宿主食欲。本文主要综述了肠道微生物及其代谢产物对中枢神经系统与宿主食欲的影响及其可能的调控途径与机制,以加深肠道微生物在调控宿主食欲方面的新认识。     

Circadian orchestration of host and gut microbiota in infection

Circadian rhythms are present in almost every organism and regulate multiple aspects of biological and physiological processes (e.g. metabolism, immune responses, and microbial exposure). There exists a bidirectional circadian interaction between the host and its gut microbiota, and potential circadian orchestration of both host and gut microbiota in response to invading pathogens. In this review, we summarize what is known about these intestinal microbial oscillations and the relationships between host circadian clocks and various infectious agents (bacteria, fungi, parasites, and viruses), and discuss how host circadian clocks prime the immune system to fight pathogen infections as well as the direct effects of circadian clocks on viral activity (e.g. SARS-CoV-2 entry and replication). Finally, we consider strategies employed to realign normal circadian rhythmicity for host health, such as chronotherapy, dietary intervention, good sleep hygiene, and gut microbiota-targeted therapy. We propose that targeting circadian rhythmicity may provide therapeutic opportunities for the treatment of infectious diseases.     

肠道菌群与代谢研究进展

从出生伊始肠道菌群就依赖于宿主的基因组、营养和生活方式而变化的,与宿主共同进化发展.肠道菌群参与调控其宿主的多种代谢途径,包括宿主的免疫、营养,并且极大地影响宿主的物质能量代谢及与物质能量代谢相关疾病的发生与发展过程.同时又与多个器官共同作用,在宿主的代谢、信息传递,疾病的感染与防御方面起非常重要的作用.深入了解肠道菌群在其参与代谢的具体作用,对理解物质能量代谢相关疾病病因、优化治疗策略、调节肠道菌群、防治疾病和提高宿主健康水平具有重要作用.本研究对人类肠道菌群的形成、物质能量代谢、代谢相关疾病及其防治等方面的研究进展加以综述.