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Reconstruction and Dynamics of the Human Intestinal Microbiome Observed In Situ

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Engineering 2022年第8期8卷 89-101页

作者： Xiaolin Liu Min Dai Yue Ma Na Zhao Ziyu Wang Ying Yu Yakun Xu Huijie Zhang liyuan xiang He Tian Guanghou Shui Faming Zhang Jun Wang CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Medical Center for Digestive Diseases the Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011China Clinical Trial Center Office the Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Key Lab of Holistic Integrative Enterology Nanjing Medical UniversityNanjing 210011China

The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities.However,this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract(in situ),and the infrequent availability of fecal samples prevents analysis at finer temporal scales(e.g.,hours).In our study,we utilized colonic transendoscopic enteral tubing,a technology originally developed for fecal microbiota transplantation,to sample the ileocecal microbiome twice daily;metagenomic and metatranscriptomic analyses were then conducted on these samples.A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers.The ileocecal and fecal microbiomes,as profiled in the five volunteers,were found to be similar in metagenomic profiling,yet their active genes(metatranscriptome)were found to be highly distinct.Both microbiomes were perturbed after laxative exposure;over time,they exhibited reduced dissimilarity to their pre-treatment state,thereby demonstrating resilience as an innate property of the gut microbiome,although they did not fully recover within our observation time window.Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways,particularly those related to short-chain fatty acid production,such as Propionibacterium acnes and coenzyme A biosynthesis Ⅱ.Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations.Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome,indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health.This study provides novel insights into the human gut microbiome and its inner resilience and diurnal

关键词： Diurnal rhythm Reconstruction Metagenome Metatranscriptome Metabolome Transendoscopic enteral tubing

基于日本福岛核污水排放的日本进境我国船舶压载水管理策略研究

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中国海事 2023年第9期 9-11页

作者：项丽媛张波河北海事局河北秦皇岛066004 交通运输部水运科学研究院北京100088

2023年8月24日,日本政府无视国际社会的强烈质疑和反对,单方面强行启动福岛核事故污染水排海,此举必将对海洋环境和人类健康造成不可估量的损害。通过概述核污水中放射性核素的两种扩散方式,指出船舶压载水和沉积物是放射性核素转移的... 详细信息

2023年8月24日,日本政府无视国际社会的强烈质疑和反对,单方面强行启动福岛核事故污染水排海,此举必将对海洋环境和人类健康造成不可估量的损害。通过概述核污水中放射性核素的两种扩散方式,指出船舶压载水和沉积物是放射性核素转移的一种途径,提出应对日本核污水排海的压载水管理策略,包括携带核污水进境我国船舶压载水的报告与置换要求、压载水排放的监督检查、核污水的监测与检测和相关立法建议等。

关键词：核污水排放船舶压载水策略研究

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冷等离子体技术灭活细菌芽孢的研究进展

食品工业科技 2024年第11期45卷 381-387页

作者：牛力源张殿鹤马云芳相启森郑州轻工业大学食品与生物工程学院河南郑州450001 河南省冷链食品质量与安全控制重点实验室河南郑州450001

芽孢是某些细菌营养体在环境胁迫条件下形成的休眠体,广泛存在于自然界中。芽孢结构致密,对热、紫外线辐射等环境胁迫具有较强的抗性,很难被食品工业中常规的杀菌方法所杀灭,是影响食品安全的重要因素。近年来,非热加工技术在杀灭芽孢... 详细信息

芽孢是某些细菌营养体在环境胁迫条件下形成的休眠体,广泛存在于自然界中。芽孢结构致密,对热、紫外线辐射等环境胁迫具有较强的抗性,很难被食品工业中常规的杀菌方法所杀灭,是影响食品安全的重要因素。近年来,非热加工技术在杀灭芽孢中的应用受到广泛关注。冷等离子体是一种新型非热杀菌技术,具有杀菌效率高、能耗低、无二次污染等优点,在食品工业中有广阔的应用前景。本文综述了冷等离子体杀灭食品中细菌芽孢的研究进展,总结了冷等离子体杀灭芽孢的作用机制,分析了影响冷等离子体作用效果的因素,并展望了今后的研究方向,以期为冷等离子体在食品安全控制领域的实际应用提供理论基础。

关键词：冷等离子体细菌芽孢杀灭机制影响因素

白洋淀上游流经城区前后细菌群落结构和功能与环境因子的关联研究

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生态毒理学报 2024年第2期19卷 333-348页

作者：王力源周贺秦梦史密伟郑翔河北省微生物研究所有限公司环境微生物修复工程实验室保定071051 河北大学生命科学学院保定071002 河北农业大学生命科学学院保定071001 河北省科学院地理科学研究所石家庄050011

细菌群落作为水生态环境的重要组成部分,其结构和功能研究可为水生态环境污染监测与治理提供技术支撑。通过对流经城区白洋淀上游河流细菌群落的高通量测序和环境因子的监测,分析城市环境因素对白洋淀上游水质的影响,并深入探究细菌群... 详细信息

细菌群落作为水生态环境的重要组成部分,其结构和功能研究可为水生态环境污染监测与治理提供技术支撑。通过对流经城区白洋淀上游河流细菌群落的高通量测序和环境因子的监测,分析城市环境因素对白洋淀上游水质的影响,并深入探究细菌群落功能与污染物动态变化的关系。结果表明,城市环境对白洋淀上游生态环境的影响较大,上、中、下游的水质等级差异显著。城区中汇入的各类污染物不仅影响细菌群落结构,使得污染严重流域高丰度的细菌种群减少和细菌群落多样性增加;还与细菌群落的硝酸盐和磷酸盐代谢功能密切相关。同时,河流虽汇集了城区的各类污染物,但下游的细菌群落结构和部分氮、磷代谢功能均有恢复为上游水平的趋势。此外,高丰度的黄杆菌属(Flavobacterium)受各类菌群和污染物的抑制作用较大,但验证其与NO-3-N污染物具有较强的相关性。对白洋淀上游流经城区前后细菌群落结构和功能与环境因子动态变化的关联研究,为白洋淀流域生态环境保护与污染治理提供理论依据。

关键词：白洋淀上游流经城区细菌群落结构与功能动态变化

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克罗恩病的自然史及其干预后的演变

胃肠病学 2020年第6期25卷 367-372页

作者：向丽园张发明南京医科大学第二附属医院消化医学中心 210011 南京医科大学附属逸夫医院微生态治疗科

克罗恩病(CD)是一种可累及全消化道并可合并肠外病变的慢性进展性疾病。近年来,CD的发病率和患病率在我国逐年上升。了解CD的自然史,对疾病危险分层、临床决策、判断预后十分重要。本文就CD流行病学全球演变、疾病的自然史、自然史的预... 详细信息

克罗恩病(CD)是一种可累及全消化道并可合并肠外病变的慢性进展性疾病。近年来,CD的发病率和患病率在我国逐年上升。了解CD的自然史,对疾病危险分层、临床决策、判断预后十分重要。本文就CD流行病学全球演变、疾病的自然史、自然史的预测因素以及改变自然史的干预手段作一综述。

关键词： Crohn病自然史流行病学并发症粪菌移植

Antimony transformation and mobilization from stibnite by an antimonite oxidizing bacterium Bosea sp. AS-1

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Journal of Environmental Sciences 2022年第1期34卷 273-281页

作者： Li xiang Chaoyang Liu Deng Liu liyuan Ma Xuan Qiu Hongmei Wang Xiaolu Lu School of Environmental Studies China University of Geosciences(Wuhan)Wuhan 430074China State Key Laboratory of Biogeology and Environmental Geology China University of Geosciences(Wuhan)Wuhan 430074China

Soils and waters are heavily contaminated by antimony in Xikuangshan(XKS)mine area.It is widely accepted that oxidative dissolution of sulfide minerals and aqueous dissolution are the most prevalent geochemical mechanisms for the release of Sb to the environment.Bosea sp.AS-1 is an antimonite-oxidizer isolated from the mine slag in Xikuangshan Sb mine.Whole genome sequencing revealed the presence of multiple sulfur-oxidizing genes,antimony(Sb)metabolism genes and carbon fixation genes in AS-1 s genome.We therefore hypothesized that under oxic conditions,AS-1 could mediate the oxidation of sulfide and Sb(Ⅲ)in stibnite(Sb_(2)S_(3))and lead to the release of Sb.Indeed,strain AS-1 was discovered as an autotrophic Sb(Ⅲ)-oxidizer.Antimony mobilization studies conducted with strain AS-1showed significantly enhanced mobilization of Sb,and complete oxidation of released Sb and sulfur to Sb(V)and sulfate.In addition,AS-1 induced a faster release of Sb under heterotrophic condition,and new acicular minerals might form.These findings support the hypothesis that microorganisms play an important role in the mobilization and transformation of Sb in XKS mine area and may contribute to our further understanding of the Sb biogeochemical redox cycle in natural environment.

关键词： Antimonite oxidation Bosea sp.AS-1 Stibnite Antimony mobilization Xikuangshan mine area

Production Dynamic Prediction Method of Waterflooding Reservoir Based on Deep Convolution Generative Adversarial Network(DC-GAN)

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Energy Engineering 2022年第5期119卷 1905-1922页

作者： liyuan Xin xiang Rao Xiaoyin Peng Yunfeng Xu Jiating Chen Cooperative Innovation Center of Unconventional Oil and Gas(Ministry of Education&Hubei Province) Yangtze UniversityWuhan430100China Key Laboratory of Drilling and Production Engineering for Oil and Gas Wuhan430100China School of Petroleum Engineering Yangtze UniversityWuhan430100China

The rapid production dynamic prediction of water-flooding reservoirs based on well location deployment has been the basis of production optimization of water-flooding reservoirs.Considering that the construction of geological models with traditional numerical simulation software is complicated,the computational efficiency of the simulation calculation is often low,and the numerical simulation tools need to be repeated iteratively in the process of model optimization,machine learning methods have been used for fast reservoir simulation.However,traditional artificial neural network(ANN)has large degrees of freedom,slow convergence speed,and complex network model.This paper aims to predict the production performance of water flooding reservoirs based on a deep convolutional generative adversarial network(DC-GAN)model,and establish a dynamic mapping relationship between well location deployment and output oil saturation.The network structure is based on an improved U-Net framework.Through a deep convolutional network and deconvolution network,the features of input well deployment images are extracted,and the stability of the adversarial model is strengthened.The training speed and accuracy of the proxy model are improved,and the oil saturation of water flooding reservoirs is dynamically predicted.The results show that the trained DC-GAN has significant advantages in predicting oil saturation by the well-location employment map.The cosine similarity between the oil saturation map given by the trained DC-GAN and the oil saturation map generated by the numerical simulator is compared.In above,DC-GAN is an effective method to conduct a proxy model to quickly predict the production performance of water flooding reservoirs.

关键词： Waterflooding reservoir well location deployment dynamic prediction DC-GAN

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粪菌移植在艰难梭菌感染治疗中的应用

临床荟萃 2018年第5期33卷 385-389页

作者：向丽园张发明南京医科大学第二附属医院消化医学中心江苏南京210011 南京医科大学附属逸夫医院微生态治疗科江苏南京211166

粪菌移植(Fecal microbiota transplantation,FMT)已被美国医学指南、欧洲专家共识推荐用于成人复发性艰难梭菌感染(Clostridium difficileinfection,CDI)。本文主要就FMT治疗CDI的适应证、临床流程、安全性、伦理与监管等的研究进展及... 详细信息

粪菌移植(Fecal microbiota transplantation,FMT)已被美国医学指南、欧洲专家共识推荐用于成人复发性艰难梭菌感染(Clostridium difficileinfection,CDI)。本文主要就FMT治疗CDI的适应证、临床流程、安全性、伦理与监管等的研究进展及中国医生的治疗选择进行综述。

关键词：梭菌感染移植粪菌

利用制革肉渣废弃物发酵生产饲用蛋白酶的研究

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饲料工业 2024年第13期45卷 83-90页

作者：刘春卯赵露魏治静吴芳彤曹倩荣郑翔秦梦王力源河北省微生物研究所有限公司河北保定071051 河北省科学院生物研究所河北石家庄050052

制革肉渣固体废弃物是一类富含蛋白质的废弃物,长期堆放易腐败变质,污染环境,因此如何开发其价值是目前制革企业比较关注的问题。本研究采用生物酶法将制革肉渣固体废弃物制备成肉渣水解液,通过试验确定肉渣水解液干粉的制备工艺,设定... 详细信息

制革肉渣固体废弃物是一类富含蛋白质的废弃物,长期堆放易腐败变质,污染环境,因此如何开发其价值是目前制革企业比较关注的问题。本研究采用生物酶法将制革肉渣固体废弃物制备成肉渣水解液,通过试验确定肉渣水解液干粉的制备工艺,设定进风口温度为140℃、流速为17 r/min,肉渣水解液干粉可获得最大收率。此干粉可作为氮源用于饲用蛋白酶的发酵生产。在单因素试验的基础上,利用响应面分析法,筛选出肉渣水解液干粉的最佳添加比例,同时优化培养基。结果表明,肉渣水解液干粉作为氮源时,基因工程菌株WB800N/pHT43-npr产酶的最佳培养基为糊精30 g/L,肉渣水解液干粉20 g/L,MnSO_(4) 26 mg/L,CaCl_(2) 0.05 g/L,蛋白酶发酵活性可达1 203.5 U/mL,与基础发酵培养基相比,酶活性提高了约10%。这为制革肉渣固体废弃物的资源化利用开辟了新的途径。

关键词：制革肉渣固体废弃物基因工程菌株喷雾干燥发酵条件优化资源化利用