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The human-derived novel gut commensal Luoshenia tenuis regulates body weight and food intake in mice

Food Science and Human Wellness 2024年第2期13卷 830-841页

作者： Yu Jiang Mengxuan Du Lisheng Xie Minzhi Jiang Yaokun Zhang Mingxia Bi Chang liu Hongwei liu shuangjiang liu State Key Laboratory of Microbial Technology Shandong UniversityQingdao 266237China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science Hebei UniversityBaoding 071000China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Many studies have revealed that gut microbes modulate host metabolism.In this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic disorders.First,by in silico analysis,we demonstrated that the L.tenuis was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity cohorts.Further in vitro cultivation revealed that L.tenuis produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and anti-tumor.Second,gavage of the L.tenuis significantly decreased the body weight gain and food intake of high-fat diet-feeding C57BL/6J mice,which was in parallel with the changed expression level of genes related to satiety and feeding behavior.We then performed the gavage trial using diet induced obese mice,and it revealed that the administration of L.tenuis alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory response.In summary,this study revealed a previously-unknown human gut commensal microbe that benefited host metabolism,and set the stage for the development of novel next-generation probiotic applicable for treatment of obesity and related metabolic disorders.

关键词： Luoshenia tenuis Gut microbe Feeding behavior Obesity Next-generation probiotic

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Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces

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Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1149-1162页

作者： Jiazhen Zheng Yue Li Ning liu Jihui Zhang shuangjiang liu Huarong Tan State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Microbial Biotechnology Shandong UniversityQingdao 266237China

Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products.Histone deacetylase(HDAC)inhibitors play an important role in the regulation of histone modifications in fungi,but their roles in prokaryotes remain poorly understood.Here,we investigated the global effects of the HDAC inhibitor,sodium butyrate(SB),on marine-derived Streptomyces olivaceus FXJ 8.021,particularly focusing on the activation of secondary metabolite biosynthesis.The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters(BGCs)in strain FXJ 8.021,among which the silent lobophorin BGC was activated by SB.Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis(ge00097–ge00139)and CoA-ester formation(e.g.,ge02824),as well as the glycolysis/gluconeogenesis pathway(e.g.,ge01661),was significantly up-regulated in the presence of SB.Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester,thereby increasing the precursor supply for lobophorin biosynthesis.Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated.These acetylated proteins were particularly enriched in transcriptional and translational machinery components(e.g.,elongation factor GE04399),and their correlations with the proteins involved in lobophorin biosynthesis were established by protein–protein interaction network analysis,suggesting that SB might function via a complex hierarchical.

关键词： Silent gene cluster Streptomyces Sodium butyrate Protein modification Acetylome

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The enriched gut commensal Faeciroseburia intestinalis contributes to the anti-metabolic disorders effects of the Ganoderma meroterpene derivative

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Food Science and Human Wellness 2022年第1期11卷 85-96页

作者： Shanshan Qiao Kai Wang Chang liu Nan Zhou Li Bao Jun Wang shuangjiang liu Hongwei liu State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Microbial Technology Shandong UniversityTsingdao 266237ShandongChina State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Shijitan Hospital Capital Medicinal UniversityBeijing 100038China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute qf MicrobiologyChinese Academy of SciencesBeijing 100101China

Previous study demonstrated that Ganoderma meroterpene derivative(GMD)increased the abundance of butyrate-producing bacteria in gut and subsequently delivered anti-metabolic disorder effect of host.To specify the key commensal bacteria associating with the beneficial effects,we tried to isolate and compare the microbiota from the cecal samples of GMD-and vehicle-treated ob/ob mice,and further identified butyrate-producing bacterial strains.It was found that Faeciroseburia intestinalis was enriched and 11 strains affiliated to F.intestinalis were cultivated from the gut of GMD-treated mice.In vitro assay attested butyrate production by representative strain of F.intestinalis.Oral administration with F.intestinalis further demonstrated its benefits on regulating hyperglycemia and hyperlipidemia,on decreasing plasma lipopolysaccharide(LPS)and inflammation,and on improving hepatic injuries.Treatment with F.intestinalis effectively enhanced the level of gut butyrate,which subsequently ameliorated the intestinal barrier function and activated epithelial PPAR-γ signaling pathway to regulate microbiome homeostasis in gut.Our study demonstrated that the causal relationship between the butyrate-producing bacteria and the GMD's therapeutic effects and confirmed the important function of the butyrate-producing F.intestinalis in maintaining host metabolism homeostasis.

关键词： Faeciroseburia intestinalis Ganoderma meroditerpene derivative Gut microbiome Butyrate Hypoglycemia Hypolipidemia

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Augmentation of tribenuron methyl removal from polluted soil with Bacillus sp.strain BS2 and indigenous earthworms

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Journal of Environmental Sciences 2012年第8期24卷 1492-1497页

作者： Qiang Tang Zhiping Zhao Yajun liu Nanxi Wang Baojun Wang Yanan Wang Ningyi Zhou shuangjiang liu State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science University of Science and TechnologyHefei 230026China Key Laboratory of Microbial Engineering at the Institute of Biology Henan Academy of SciencesZhengzhou 450008China Key Laboratory of Agricultural and Environmental Microbiology Wuhan Institute of VirologyChinese Academy of Sciences44 Xiao-Hong-ShanWuhan 430071China

Tribenuron methyl （TBM） is a member of the sulfonylurea herbicide family and is widely used worldwide. In this study, TBM- degrading bacteria were enriched with TBM as potential carbon, nitrogen or sulfur source, and 44 bacterial isolates were obtained. These isolates were phylogenetically diverse, and were grouped into 25 operational taxonomic units and 14 currently known genera. Three representatives, Bacillus sp. strain BS2, Microbacterium sp. strain BS3, and Cellulosimicrobium sp. strain BSI 1, were selected, and their growth and TBM removal from culture broth were investigated. In addition, indigenous earthworms were collected and applied to augment TBM degradation in lab-scale soil column experiments. Results demonstrated that Bacillus sp. strain BS2 and earthworms significantly increased TBM removal during soil column experiments.

关键词： biodegradation of tribenuron methyl Bacillus Microbacterium Cellulosimicrobium earthworm

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Proteomic and molecular investigations revealed that Acidithiobacillus caldus adopts multiple strategies for adaptation to NaCl stress

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Chinese Science Bulletin 2014年第3期59卷 301-309页

作者： Xu Guo Chengying Jiang Yuanming Luo Mingjiang Zhang Ansgar Poetsch shuangjiang liu State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences Environmental Microbiology and Biotechnology Research Center Institute of MicrobiologyChinese Academy of Sciences Lehrstuhl for Biochemie der Pflanzen Ruhr Universitaet

Acidithiobacillus caldus plays an important role in commercial bioleaching.To understand how NaCl stress adaptation occurs in A.caldus,we grew A.caldus strain SM-1 in media containing high NaCl concentrations.SM-1 grew at concentrations of up to 1.0-mol L^(-1)NaCl,but growth was severely inhibited at higher concentrations.Proteomic analysis showed that SM-1 used multiple strategies to respond to NaCl stress.In addition to several heatshock proteins,enzymes involved in proline biosynthesis increased under NaCl stress.In addition,two DNA-binding proteins and a third protein of unknown function(Atc_(1291)),which was subsequently identified as a putative single-stranded DNA-binding protein,were up-regulated in the presence of NaCl stress.These DNA-binding proteins might play a role in response to osmotic stress.Atc_(1291)was cloned and expressed in Escherichia coli.Surprisingly,we found that E.coli BL21/pET28a-atc_(1291)grew to higher cell densities than E.coli BL21/pET28a,regardless of NaCI stress.Homologs to Atc_(1291)were identified in several groups of Proleohacleria.The role of Atc_(1291)in enhancing cell growth needs further investigation.

关键词：蛋白质组学盐胁迫 DNA结合蛋白 NaCl胁迫显示分子抑制浓度大肠杆菌

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Prediction model on hydrolysis kinetics of phthalate monoester:A density functional theory study

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Journal of Environmental Sciences 2024年第1期135卷 51-58页

作者： Tong Xu Jingwen Chen Deming Xia Weihao Tang Jiansheng Cui Chun liu shuangjiang Li College of Environmental Science and Engineering Hebei University of Science and TechnologyShijiazhuang 050000China Key Laboratory of Industrial Ecology and Environmental Engineering(Ministry of Education) School of Environmental Science and TechnologyDalian University of TechnologyDalian 116024China National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and ManagementInstitute of Eco-environmental and Soil SciencesGuangdong Academy of SciencesGuangzhou 510650China

As primary degradation products of phthalate esters,phthalate monoesters(MPEs)have been widely detected in various aquatic environments and drawn growing toxicological concerns.Hydrolysis kinetics that is of importance for assessing environmental persistence of chemicals remain elusive for MPEs.Herein,kinetics of base-catalyzed and neutral hydrolysis for 18 MPEs with different leaving groups was investigated by density functional theory calculation.Results indicate that MPEs with leaving groups having p Kaof<10 prefer dissociative transition states.MPEs are more persistent than their parents,and their hydrolysis half-lives were calculated to vary from 3.4 min to 79.2 years(p H=7–9).A quantitative structure-activity relationship model was developed for predicting the hydrolysis kinetics parameters.It was found that p Kaof the leaving groups and electronegativity of the MPEs are key factors determining the hydrolysis kinetics.This work may lay a theoretical foundation for better understanding the chemical process that governs MPE persistence in aquatic environments.

关键词： Phthalate monoesters Phthalate esters Hydrolysis Density functional theory Quantitative structure-activity relationship

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A bioaugmentation failure caused by phage infection and weak biofilm formation ability

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Journal of Environmental Sciences 2009年第8期21卷 1153-1161页

作者： FU Songzhe FAN Hongxia liu shuangjiang liu Ying liu Zhipei State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100039 China Institute of Oceanology Chinese Academy of Sciences Qingdao 266701 China

Two biological aerated filters （BAF） were setup for ammonia removal treatment of the circulation water in a marine aquaculture. One of the BAFs was bioaugmented with a heterotrophic nitrifying bacterium, Lutimonas sp. H10, where the ammonia removal was not improved and the massive inoculation was even followed by a nitrification breakdown from day 9 to 18. The nitrification was remained stable in control BAF operated under the same conditions. Fluorescent in situ hybridization （FISH） with rRNA-targeted probes and cultivable method revealed that Lutimonas sp. H10 almost disappeared from the bioaugomented BAF within 3 d, and this was mainly due to the infection of a specific phage as revealed by flask experiment, plaque assay and transmission electron observation. Analyses of 16S rRNA gene libraries showed that bacterial groups from two reactors evolved differently and an overgrowth of protozoa was observed in the bioaugmented BAF. Therefore, phage infection and poor biofilm forming ability of the inoculated strain are the main reasons for bioaugmentation failure. In addition, grazing by protozoa of the bacteria might be the reason for the nitrification breakdown in bioaugmented BAF during day 9-18.

关键词： marine culture water circulation ammonia removal Lutimonas sp. HIO nitrification breakdown fluorescent in situhybridization （FISH）

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A novel and complete gene cluster involved in the degradation of aniline by Delftia sp. AN3

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Journal of Environmental Sciences 2008年第6期20卷 717-724页

作者： ZHANG Tao ZHANG Jinglei liu shuangjiang liu Zhipei Laboratory of Environmental Microbiology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100039 China

A recombinant strain, Escherichia coli JM109-AN1, was obtained by constructing of a genomic library of the total DNA of Delftia sp. AN3 in E. coli JM109 and screening for catechol 2,3-dioxygenase activity. This recombinant strain could grow on aniline as sole carbon, nitrogen and energy source. Enzymatic assays revealed that the exogenous genes including aniline dioxygenase （AD） and catechol 2,3-dioxygenase （C230） genes could well express in the recombinant strain with the activities of AD and C230 up to 0.31 U/mg wet cell and 1.92 U/mg crude proteins, respectively. The AD or C23O of strain AN3 could only catalyze aniline or catechol but not any other substituted substrates. This recombinant strain contained a recombinant plasmid, pKC505-AN1, in which a 29.7-kb DNA fragment from Delftia sp. AN3 was inserted. Sequencing and open reading frame （orfs） analysis of this 29.7 kb fragment revealed that it contained at least 27 orfs, among them a gene cluster （consisting of at least 16 genes, named danQTA1A2BRDCEFG1HIJKG2） was responsible for the complete metabolism of aniline to TCA-cycle intermediates. This gene cluster could be divided into two main parts, the upper sequences consisted of 7 genes （danQTA1A2BRD） were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, and the central genes （danCEFG1HIJKG2） were expected to encode meta-cleavage pathway enzymes for catechol degradation to TCA-cycle intermediates. Unlike clusters tad from Delftia tsuruhatensis AD9 and tdn from Pseudomonas putida UCC22, in this gene cluster, all the genes were in the same transcriptional direction. There was only one set of C230 gene （danC） and ferredoxin-like protein gene （danD）. The presence of only one set of these two genes and specificity of AD and C230 might be the reason for strain AN3 could only degrade aniline. The products of danQTA1A2BRDC showed 99%-100% identity to those from Delftia acidovorans 7N, and 50%-85% identity to those of tad cluster from D. tsuruhatensis AD9 in amino acid residues. Be

关键词： aniline biodegradation Delftia sp. AN3 genomic library aniline degradative gene cluster

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Enhanced biological nutrient removal by the alliance of a heterotrophic nitrifying strain with a nitrogen removing ecosystem

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Journal of Environmental Sciences 2008年第2期20卷 216-223页

作者： Naeem ud din Ahmad XU Haiying CHEN Liping liu Zhipei liu shuangjiang State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100080 China Graduate School of Chinese Academy of Sciences Beijing 100049 China

Nitrogen removal from synthetic wastewater was investigated in an airlift bioreactor （ALB）, augmented with a novel heterotrophic nitrifier Pseudonocardia ammonioxydans H9^T under organic carbon to nitrogen ratios （Corg/N） ranging from 0 to 12. Effect of the inoculated strain was also determined on the settling properties and the removal of chemical oxygen demand （COD）. Two laboratory scale reactors were set up to achieve a stable nitrifying state under the same physicochemical conditions of hydraulic retention time （HRT）, temperature, pH and dissolved oxygen （DO）, and operated under the sequencing batch mode. The level of DO was kept at 0.5- 1.5 mg/L by periodic stirring and aeration. Each specific Corg/N ratio was continued for duration of 3 weeks. One of the reactors （BR2） was inoculated with P ammonioxydans H9^T periodically at the start of each Corg/N ratio. Sludge volumetric index （SVI） improved with the increasing Corg/N ratio, but no significant difference was detected between the two reactors. BR2 showed higher levels of nitrogen removal with the increasing heterotrophic conditions, and the ammonia removal reached to the level of 82%-88%, up to10% higher than that in the control reactor （BR1） at Corg/N ratios higher than 6; however, the ammonia removal level in experimental reactor was up to 8% lower than that in control reactor at Corg/N ratios lower than 2. The COD removal efficiency progressively increased with the increasing Corg/N ratios in both of the reactors. The COD removal percentage up to peak values of 88%-94% in BR2, up to 11% higher than that in BR1 at Corg/N ratio higher than 4. The peak values of ammonia and COD removal almost coincided with the highest number （18%-27% to total bacterial number） of the exogenous bacterium in the BR2, detected as colony forming units （CFU）. Furthermore, the removal of ammonia and COD in BR2 was closely related to the number of the inoculated strain with a coefficient index （R2） up to 0.82 and 0.85 for ammonia and COD, respectively. These results suggest tha

关键词： air-lift bioreactor （ALB） bioaugrnentation Corg/N ratio COD and ammonia removal sequencing batch mode heterotrophic nitrifier Pseudonocardia ammonioxydans H9^T

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Multiporphyrinic architectures:Advances in structural design for photodynamic therapy

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Aggregate 2024年第1期5卷 67-84页

作者： Yuwei Gao Yan Li Zhengwei Xu shuangjiang Yu Junqiu liu Hongcheng Sun College of Material Chemistry and Chemical EngineeringKey Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationHangzhou Normal UniversityHangzhouChina

Rationally designed multiporphyrinic architectures for boosting photodynamic therapy(PDT)have attracted significant attentions recently years due to their great potential for light-mediated generation of reactive oxygen species.However,there is still a gap between the structure design and their PDT performance for biomedical applications.This tutorial review provides a historical overview on(i)the basic concept of PDT for deeply understanding the porphyrin-mediated PDT reactions,(ii)developing strategies for constructing porphyrinic architectures,like nanorings,boxes,metal-organic frameworks(MOFs),covalent-organic frameworks(COFs),vesicles,etc.,where we classified into the following three categories:multiporphyrin arrays,porphyrinic frameworks,and others porphyrin assemblies,(iii)the various application scenarios for clinical cancer therapy and antibacterial infection.Also,the existing challenges and future perspectives on the innovation of porphyrinic architectures for clinical PDT applications are mentioned in the end section.Moreover,the porphyrinic nanomaterials with atomically precise architectures provide an ideal platform for investigating the relationship between structures and PDT outputs,design of personalized“all-in-one”theranostic agents,and the popularization and application in wider biomedical fields.

关键词： covalent-organic frameworks(COFs) metal-organic frameworks(MOFs) multiporphyrin arrays photodynamic therapy(PDT) porphyrinic architectures

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