Metabolome and water status phenotyping of Arabidopsis under abiotic stress cues reveals new insight into ESK1 function

Metabolomic investigation of the freezing-tolerant Arabidopsis mutant esk1 revealed large alterations in polar metabolite content in roots and shoots. Stress metabolic markers were found to be among the most significant metabolic markers associated with the mutation, but also compounds related to growth regulation or nutrition. The metabolic phenotype of esk1 was also compared to that of wild type (WT) under various environmental constraints, namely cold, salinity and dehydration. The mutant was shown to express constitutively a subset of metabolic responses which fits with the core of stress metabolic responses in the WT. But remarkably, the most specific metabolic responses to cold acclimation were not phenocopied by esk1 mutation and remained fully inducible in the mutant at low temperature. Under salt stress, esk1 accumulated lower amounts of Na⁺ in leaves than the WT, and under dehydration stress its metabolic profile and osmotic potential were only slightly impacted. These phenotypes are consistent with the hypothesis of an altered water status in esk1 , which actually exhibited basic lower water content (WC) and transpiration rate (TR) than the WT. Taken together, the results suggest that ESK1 does not function as a specific cold acclimation gene, but could rather be involved in water homeostasis.     

氨基酸型肠内营养制剂支持后克罗恩病患者肠道微生物和非靶向代谢组学指标的分析

探讨氨基酸型肠内营养制剂支持后克罗恩病患者的肠道微生物和非靶向代谢组学指标的变化,为该类患者的治疗提供参考。

选择我院收治的20例克罗恩病活动期患者作为研究对象,所有患者均采用氨基酸型肠内营养制剂进行支持治疗。比较患者治疗前后肠道菌群结构、菌群多样性以及非靶向代谢组学检测结果的差异。

治疗后,患者肠道乳杆菌属（t=5.200,P＜0.001）、大肠埃希菌（t=11.974,P＜0.001）、克雷伯菌属（t=15.033,P＜0.001）、糖单胞菌（t=12.166,P＜0.001）、恶臭假单胞菌（t=31.063,P＜0.001）、肠球菌属（t=28.867,P＜0.001）数量均显著升高;同时患者肠道菌群OUTs（t=40.435,P＜0.001）、Observed species（t=5.475,P＜0.001）、Chao1指数（t=12.348,P＜0.001）、Simpson指数（t=2.961,P=0.005）、Shannon指数（t=3.330,P=0.002）均显著升高。相比治疗前,治疗后患者血清以及粪便中的氨基酸、多肽、脂肪酸、胆固醇及碳水化合物水平均显著改善。

氨基酸型肠内营养制剂支持后,克罗恩病患者肠道菌群丰度提高,同时患者脂质代谢的改善可能与氧化应激反应通路相关联。

     

乙烯调控灵芝酸生物合成关键基因的筛选

灵芝是我国著名的药用真菌,灵芝酸是其主要活性成分,具有多种药理活性。乙烯可以促进灵芝酸的生物合成,但其调控机理尚不明确。本实验利用非靶向代谢组研究发现Top 20差异代谢物中含有6种灵芝的活性成分(灵芝酸η、赤芝酸F、赤芝酸N、丹芝酸A、灵芝酸V1和灵芝酸δ),其中有4种灵芝酸(灵芝酸η、赤芝酸F、赤芝酸N和灵芝酸V1)为上调积累,2种灵芝酸(灵芝酸δ和丹芝酸A)为下调积累。通过非靶向代谢组与转录组的关联分析发现基因GL23307、GL25546和GL29595同时与3种灵芝酸积累显著相关,并通过启动子顺式元件预测,发现分别编码泛素蛋白和抑肽酶基因GL25546、GL23307的启动子区域含有响应乙烯信号的顺式作用元件GCC-box,因此,推测这两个基因在乙烯调控灵芝酸生物合成中发挥重要作用。     

甲烷氧化菌20Z利用Embden-Meyerhof-Parnas途径高效同化甲烷

为了探究γ-变形菌纲 (Gammaproteobacteria) 甲烷氧化菌Methylomicrobium alcaliphilum 20Z的甲烷同化代谢过程。文中整合RNA-seq、LC-MS技术并结合13C标记策略对核酮糖单磷酸途径 (Ribulose monophosphate pathway) 及下游途径展开系统组学分析。M. alcaliphilum 20Z代谢物组定量分析表明Entner-Doudoroff (EDD) 途径的中间代谢物6-磷酸葡萄糖的浓度是(150.95±28.75) μmol/L,2-酮-3-脱氧-6-磷酸葡糖酸浓度低于质谱定量分析检测限,而Embden-Meyerhof-Parnas (EMP) 途径中果糖1,6-二磷酸、甘油醛-3-磷酸/二羟丙酮磷酸和磷酸烯醇式丙酮酸的浓度分别是 (1 142.02±302.88) μmol/L、(1 866.76±388.55) μmol/L和 (3 067.57±898.13) μmol/L。通过EDD和EMP途径的代谢物13C同位素动态富集研究,进一步揭示3位标记丙酮酸丰度是1位标记丙酮酸丰度的4~6倍。最后,基因表达比较分析发现EMP途径的关键基因 (如：fbaA、tpiA、gap和pykA) 的表达水平 (RPKM) 分别是2 479.2、2 493.9、2 274.6和1 846.0,而EDD途径中基因 (如：pgi、eda和edd) 的RPKM仅是263.8、341.2和225.4。综合上述结果阐明EMP途径才是M. alcaliphilum 20Z进行甲烷同化的关键通路。EMP途径代谢功能的全新阐述不但改变对Gammaproteobacteria甲烷氧化菌甲烷同化模式的传统认知,而且为甲烷高效生物催化转化提供重要的理论基础。     

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

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Urinary metabolomics fingerprinting around parturition identifies metabolites that differentiate lame dairy cows from healthy ones

Lameness is a very important disorder of periparturient dairy cows with implications on milk production and composition as well as with consequences on reproductive performance. The aetiology of lameness is not clear although there have been various hypotheses suggested over the years. The objective of this study was to metabotype the urine of dairy cows prior to, during and after the onset of lameness by evaluating at weeks −8, −4 pre-calving, the week of lameness diagnosis, and +4 and +8 weeks post-calving. We used a metabolomics approach to analyse urine samples collected from dairy cows around calving (6 cows with lameness v. 20 healthy control cows). A total of 153 metabolites were identified and quantified using an in-house MS library and classified into 6 groups including: 11 amino acids (AAs), 39 acylcarnitines (ACs), 3 biogenic amines (BAs), 84 glycerophospholipids, 15 sphingolipids and hexose. A total of 23, 36, 40, 23 and 49 metabolites were observed to be significantly different between the lame and healthy cows at −8 and −4 weeks pre-calving, week of lameness diagnosis as well as at +4 and +8 weeks post-calving, respectively. It should be noted that most of the identified metabolites were elevated; however, a few of them were also lower in lame cows. Overall, ACs and glycerophospholipids, specifically phosphatidylcholines (PCs), were the metabolite groups displaying the strongest differences in the urine of pre-lame and lame cows. Lysophosphatidylcholines (LysoPCs), although to a lesser extent than PCs, were altered at all time points. Alterations in urinary AA concentrations were also observed during the current study for four time points. During the pre-calving period, there was an observed elevation of arginine (−8 week), tyrosine (−8 week) and aspartate (−4 week), as well as a depression of urinary glutamate (−4 weeks). In the current study, it was additionally observed that concentrations of several sphingomyelins and one BA were altered in pre-lame and lame cows. Symmetric dimethylarginine was elevated at both −8 weeks pre-calving and the week of lameness diagnosis. Data showed that urinary fingerprinting might be a reliable methodology to be used in the future to differentiate lame cows from healthy ones.     

Functional microbiome deficits associated with ageing: Chronological age threshold

Composition of the gut microbiota changes during ageing, but questions remain about whether age is also associated with deficits in microbiome function and whether these changes occur sharply or progressively. The ability to define these deficits in populations of different ages may help determine a chronological age threshold at which deficits occur and subsequently identify innovative dietary strategies for active and healthy ageing. Here, active gut microbiota and associated metabolic functions were evaluated using shotgun proteomics in three well‐defined age groups consisting of 30 healthy volunteers, namely, ten infants, ten adults and ten elderly individuals. Samples from each volunteer at intervals of up to 6 months (n = 83 samples) were used for validation. Ageing gradually increases the diversity of gut bacteria that actively synthesize proteins, that is by 1.4‐fold from infants to elderly individuals. An analysis of functional deficits consistently identifies a relationship between tryptophan and indole metabolism and ageing (p < 2.8e^?8). Indeed, the synthesis of proteins involved in tryptophan and indole production and the faecal concentrations of these metabolites are directly correlated (r² > .987) and progressively decrease with age (r² > .948). An age threshold for a 50% decrease is observed ca. 11–31 years old, and a greater than 90% reduction is observed from the ages of 34–54 years. Based on recent investigations linking tryptophan with abundance of indole and other “healthy” longevity molecules and on the results from this small cohort study, dietary interventions aimed at manipulating tryptophan deficits since a relatively “young” age of 34 and, particularly, in the elderly are recommended.