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Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

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World Journal of Gastroenterology 2021年第14期27卷 1465-1482页

作者： Sarah A Malik Chencan Zhu Jinyu Li Joseph F LaComb Paula I Denoya Igor Kravets Joshua D Miller Jie Yang Melissa Kramer W Richard McCombie Charles E Robertson Daniel N Frank Ellen Li Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794United States Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource Stony Brook UniversityStony BrookNY 11794United States Department of Pathology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Surgery Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Family Population and Preventive MedicineStony Brook UniversityStony BrookNY 11794United States Cold Spring Harbor laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource Cold Spring HarborNY 11724United States Department of Medicine University of Colorado Anschutz Medical CampusAuroraCO 80045United States

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human ***-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)*** hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk *** To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection *** Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from *** 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on *** sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥*** PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach *** mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level *** confirmed increased Fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics *** coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor *** expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race *** Recent adoption of additional preoperative antibiotics as sta

关键词： Colorectal cancer Antibiotics African Continental Ancestry Group Diabetes mellitus 16S rRNA gene RNA-sequencing

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不同林型土壤微生物有机碳降解基因的多样性

生态学报 2007年第4期27卷 1412-1419页

作者：张于光张小全刘学端肖烨 Wu Liyou 中国林业科学研究院森林生态环境与保护研究所国家林业局森林生态环境重点实验室北京100091 湖南农业大学生物安全科技学院长沙410128 Environmental Sciences Division Oak Ridge National laboratory Tennessee USA 37831

应用寡聚核苷酸基因芯片,分析了米亚罗林区冷杉原始林(M-Y)和20世纪60年代云杉人工林(M-60)土壤微生物的功能基因多样性。该功能基因芯片含有与有机碳降解、碳固定、氮、磷、硫循环和金属抗性相关的1961个基因探针。在M-Y和M-60样地中... 详细信息

应用寡聚核苷酸基因芯片,分析了米亚罗林区冷杉原始林(M-Y)和20世纪60年代云杉人工林(M-60)土壤微生物的功能基因多样性。该功能基因芯片含有与有机碳降解、碳固定、氮、磷、硫循环和金属抗性相关的1961个基因探针。在M-Y和M-60样地中分别检测到39和62个具有较强杂交信号(SNR≥2)的功能基因,其基因多样性水平指数分别为3.59和4.04,杂交信号强度总值分别为480280和630560。M-Y和M-60样地中分别检测到32个和37个有机碳降解基因,占总基因的82%和60%,这些基因分属于22个不同的基因类群,分别参与木质素、木聚糖、几丁质等有机碳的降解过程。有机碳降解基因在两个样地中存在较大的多样性和丰度差异。这些结果说明了大多数的土壤微生物直接参与了土壤有机碳的降解,同时,林型不同显著影响了土壤微生物群落结构和有机碳降解微生物的多样性。

关键词：土壤有机碳功能基因芯片林型基因多样性

Lopadostoma fagi (Lopadostomataceae) on Fagus sylvatica from Italy

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Studies in Fungi 2016年第1期1卷 80-89页

作者： Daranagama DA Camporesi E Liu XZ Chamyuang S Stadler M Jingzu S Hyde KD State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing100101People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai57100Thailand School of Science Mae Fah Luang UniversityChiang Rai57100Thailand Helmholtz-Zentrum für Infektionsforschung GmbH Dept.Microbial DrugsInhoffenstrasse 738124BraunschweigGermany A.M.B.Gruppo Micologico Forlivese“Antonio Cicognani” Via Roma 18ForlìItaly A.M.B.Circolo Micologico“Giovanni Carini” C.P.314BresciaItaly Societàper gli Studi Naturalistici della Romagna C.P.144Bagnacavallo(RA)Italy

A new record of Lopadostoma fagi is described in Italy from Fagus sylvatica based on morphological and molecular *** has effused-pulvinate stromata immersed in the host tissue,with a narrow,black,carbonized *** ectostromatic disc is visible as a clypeus and surrounded by the reddish brown bark *** the combined phylogenetic analysis of ITS,LSU and RPB2 sequence data,the strain derived from the specimen clustered with other *** strains with high bootstrap support.A morphological description with detailed photographs for *** is provided in this study.

关键词： Ascomycetes phylogeny Sordariomycetes taxonomy Xylariales

Chemical and Organic Contamination of Phreatic Aquifer of Sidi Bouzid （Center West of Tunisia）

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Journal of Environmental Science and Engineering 2010年第5期4卷 6-13页

作者： S. Chaibi N. Khlif M. Chalbaoui W. Aydi laboratory of Water Environment and Energy Ecole Nationale des Ingenieurs de Sfax. Tunisia Geophysics and Water resources - Faculty of Sciences of Gafsa. Tunisia

Multi-omic Microbiome Profiles in the Female Reproductive Tract in Early Pregnancy

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Infectious Microbes & Diseases 2019年第2期1卷 49-60页

作者： Sophonie Jean Bernice Huang Hardik I.Parikh David J.Edwards J.Paul Brooks Naren Gajenthra Kumar Nihar U.Sheth Vishal Koparde Ekaterina Smirnova Snehalata Huzurbazar Philippe H.Girerd Dayanjan S.Wijesinghe Jerome F.StraussIII Myrna G.Serrano Jennifer M.Fettweis Kimberly K.Jefferson Gregory A.Buck Department of Microbiology and Immunology Virginia Commonwealth UniversityRichmondVA Center for Microbiome Engineering and Data Analysis Virginia Commonwealth UniversityRichmondVA Department of Statistical Sciences and Operations Research Virginia Commonwealth UniversityRichmondVA Supply Chain Management and Analytics School of BusinessVirginia Commonwealth UniversityRichmondVA Life Sciences Virginia Commonwealth UniversityRichmondVA DNAnexus Inc. Mountain ViewCA Frederick National laboratory for Cancer Research FrederickMD Department of Biostatistics Virginia Commonwealth UniversityRichmondVA Department of Statistics University of WyomingLaramieWY Obstetrics and Gynecology Virginia Commonwealth UniversityRichmondVA Pharmacotherapy and Outcomes Science Virginia Commonwealth UniversityRichmondVA Department of Computer Science Virginia Commonwealth UniversityRichmondVA.

The vaginal microbiome likely influences host signaling compounds within the reproductive tract,including pro-inflammatory signals,which may play an important role during *** lactobacilli are associated with positive pregnancy outcome,whereas bacterial vaginosis,a dysbiosis of the vaginal microbiome,is associated with an increased risk of adverse pregnancy outcomes including preterm *** the host response could be predicted based on the taxonomic composition of the vaginal microbiome,particularly early in pregnancy,then those predictions could potentially be used to personalize intervention methods to reduce preterm birth and other adverse *** this proof of principle study,we apply multivariate strategies to analyze 16S rRNA-based taxonomic surveys in conjunction with targeted immuno-proteomic and lipidomic data from vaginal samples from 58 women enrolled in the Multi-Omic Microbiome Study-Pregnancy Initiative during early *** between the vaginal microbiome and the vaginal lipidome have not been previously *** from this study reveal significant multiple pairwise associations between microbial taxa,specific eicosanoids and sphingomyelins,and *** the biologic significance of these associations is not yet known,these results support the utility of such multi-omic approaches as a means to predict the impact of the microbiome on the host.

关键词： vaginal microbiome preterm birth multi-omics metagenomics cytokine profiles lipidomics

Research progress on rapid psychological regulation of pathogenic microorganism epidemic situation

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Psychosomatic Medicine Research 2020年第3期2卷 66-74页

作者： Jie Gao Xing-Ping Che Yuan Liu Jian-Min Wang Ce Yang State Key laboratory of Trauma Burns and Combined InjuryInstitute of Surgery ResearchDaping HospitalThird Military Medical UniversityChongqing400042China.

Pathogenic microbial biological epidemics can cause negative emotions such as fear,anxiety,loneliness and depression,as well as somatization symptoms such as insomnia,headache,chest tightness and degenerative *** a secondary disaster of major epidemic situation,this kind of adverse psychological stress needs to be adjusted *** author reviews the rapid psychological regulation methods of novel coronavirus pneumonia(coronavirus disease 2019,Covid-19),aiming to provide a useful enlightenment for the prevention of psychological stress in microorganism epidemic situation.

关键词： Epidemic situation Novel coronavirus pneumonia Psychological stress Rapid regulation

GyrB Gene Acts as a Phylogenetic Discriminator for Bacterial Diversity in Acid Mine Drainage

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Journal of Environmental Science and Engineering 2011年第1期5卷 44-56页

作者： Y. Yang M.X. Wan W.M. Zeng J.L. Xia X.D. Liu W.Q. Qin G.Z. Qiu School of Minerals Processing and Bioengineering Central South University Changsha 410083 Hunan China Key laboratory of Biometallurgy of Ministry of Education Changsha 410083 Hunan China

To study the efficiency of DNA gyrase subunit B (gyrB) gene as means of diversity analysis, diversities of gyrB genes in three AMD samples collected from Dabaoshan Mine were studied by analyzing gyrB gene library. Many novel gyrB sequences and groups were detected. The results show that Acidithiobacillus ferrooxidans-like bacteria represented 88.0% of the bacterial population in a sample. However, other two samples showed much high diversities. These diversities were characterized by the reciprocal of Simpson’s index (1/D), and show ferrous ion strongly influenced the composition of the microbial communities. The study indicate that gyrB Gene as a phylogenetic discriminator is a good tool to study different strains in same species that were difficult to be distinguished by 16S genes. But now gyrB Gene cannot define clearly unknown sequences to certain lineage, due to the incompleteness of the gyrB database.

关键词： rB基因细菌多样性系统发育酸性矿井水鉴别 B基因序列多样性分析基因多样性

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PNAS:科学家发现新的精子运动调节器

现代生物医学进展 2017年第27期17卷 I0001-I0002页

作者： Castaneda, Julio M. Hua, Rong Miyata, Haruhiko Oji, Asami Guo, Yueshuai Cheng, Yiwei Zhou, Tao Guo, Xuejiang Cui, Yiqiang Shen, Bin Wang, Zibin Hu, Zhibin Zhou, Zuomin Sha, Jiahao Prunskaite-Hyyrylainen, Renata Yu, Zhifeng Ramirez-Solis, Ramiro Ikawa, Masahito Matzuk, Martin M. Liu, Mingxi Baylor Coll Med Dept Pathol & Immunol Houston TX 77030 USA Osaka Univ Res Inst Microbial Dis Suita Osaka 5650871 Japan Nanjing Med Univ State Key Lab Reprod Med Nanjing 210029 Jiangsu Peoples R China Nanjing Med Univ Dept Histol & Embryol Nanjing 210029 Jiangsu Peoples R China Osaka Univ Grad Sch Pharmaceut Sci Suita Osaka 5650871 Japan Nanjing Med Univ Anim Core Facil Nanjing 210029 Jiangsu Peoples R China Baylor Coll Med Ctr Reprod Med Houston TX 77030 USA Univ Oulu Fac Biochem & Mol Med FI-90014 Oulu Finland Baylor Coll Med Ctr Drug Discovery Houston TX 77030 USA Wellcome Trust Sanger Inst Hinxton CB10 1SA England Univ Tokyo Inst Med Sci Minato Ku Tokyo 1088639 Japan Baylor Coll Med Dept Mol & Cellular Biol Houston TX 77030 USA Baylor Coll Med Dept Mol & Human Genet Houston TX 77030 USA Baylor Coll Med Dept Pharmacol Houston TX 77030 USA

南京医科大学生殖医学国家重点实验室、基础医学院组织胚胎学系刘明兮课题组与贝勒医学院***课题组、大阪大学MasahitoIkawa课题组等共同解析了一个精子运动调节基因TCTE1，结果发表于《美国科学院院刊》（PNAs）。

关键词：精子运动调节器科学家国家重点实验室组织胚胎学课题组生殖医学医科大学

Effects of Different Proportions of Spent Pleurotus ostreatus Substrate on Seed Germination and Seedling Growth of Mung Beans

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Agricultural Biotechnology 2019年第2期8卷 81-85页

作者： Ling WANG Shuang YANG Yihong HU Chenzhong JIN Zhi ZENG Collaborative Innovation Center for Field Weeds Control Hunan University of HumanitiesScience and Technology Key laboratory of Pesticide Harmless Application Hunan University of HumanitiesScience and Technology

[Objectives] This study was conducted to investigate the effects of different proportions of spent Pleurotus ostreatus substrate on the germination and seedling growth of mung beans. [Methods] The cellulose-degrading bacteria HB8 and HF1 were mixed with a commercially available microbial composting agent, respectively, for the composting of spent P. ostreatus substrate. Mung beans were cultivated with different proportions of spent mushroom substrate compost and soil. The seed germination rate, plant height, fresh weight and chlorophyll content of mung bean were used as indicators to investigate the effects of the organic fertilizer from spent P. ostreatus substrate on the growth of mung bean seedlings. [Results] The addition of cellulose-degrading bacteria can significantly improve the composting effect of the spent mushroom substrate. After 8 d of cultivation of mung beans with different ratios of the mushroom substrate organic fertilizer, 50% of the organic fertilizer can make the plant height, fresh weight and leaf chlorophyll content of mung bean seedlings reach the highest value and was suitable for mung bean breeding and cultivation. [Conclusions] This study provides scientific basis and technical indicators for the rapid and harmless treatment of spent mushroom substrate and its application in crop cultivation and nursery.

关键词： Cellulose-degrading bacteria Organic fertilizer from spent Pleurotus ostreatus substrate Mung bean Seed germination rate