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Phylogenetic and comparative genomic analysis of Lactobacillus fermentum Strains and the Key Genes Related to their Intestinal Anti-Inflammatory Effects

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Engineering 2022年第10期17卷 170-182页

作者： Yan Zhao Chengcheng Zhang Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Qixiao Zhai State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi 214122China School of Food Science and Technology Jiangnan UniversityWuxi 214122China National Engineering Research Centre for Functional Food Jiangnan UniversityWuxi 214122China International Joint Research Laboratory for Probiotics Jiangnan UniversityWuxi 214122China Beijing Innovation Centre of Food Nutrition and Human Health Beijing Technology and Business UniversityBeijing 100048China

Emerging evidence shows that some Lactobacillus fermentum(***)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of *** strains were separated from fecal samples of populations in different regions in China and their draft genomes were ***-genomic and phylogenetic characterizations of these strains and four model strains(*** 3872,CECT5716,IF03956,and VRI003)were *** analysis ind icated that there was no significant adaptive evolution between the genomes of *** strains and the geographical location,sex,ethnicity,and age of the *** *** strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type *** CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further *** *** FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar *** anti-inflammato ry mechanisms of *** FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)*** genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific *** strains.

关键词： Lactobacillus fermentum Ulcerative colitis Anti-inflammation Phylogenetic analysis comparative genomic analysis

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Alleviative effects of Bacillus coagulans strains on irritable bowel syndrome-unraveling strain specificity through physiological and genomic analysis

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Food Science and Human Wellness 2024年第4期13卷 1845-1855页

作者： Jiang Cao Leilei Yu Jianxin Zhao Hao Zhang Wei Chen Yuzheng Xue Qixiao Zhai State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi 214122China School of Food Science and Technology Jiangnan UniversityWuxi 214122China National Engineering Research Center for Functional Food Jiangnan UniversityWuxi 214122China Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch Wuxi 214122China Department of Gastroenterology Affiliated Hospital of Jiangnan UniversityWuxi 214122China

The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different ***,6 *** strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of *** strains are *** results of this study showed that the ingestion of *** GBI-30,6086,and *** CCFM1041 significantly alleviated IBS symptoms in *** contrast,other *** strains showed no or limited alleviating effects on IBS *** to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary *** strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional *** *** results also suggest that administration of *** could significantly regulate microbiota dysbiosis in animal ***,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.

关键词： Baciillus coagulans Irritable bowel syndrome Resistance to bile salts comparative genomic analysis Gut microbiota

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Fine mapping of powdery mildew resistance gene PmTm4 in wheat using comparative genomics

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Journal of Integrative Agriculture 2017年第3期16卷 540-550页

作者： XIE Jing-zhong WANG Li-li WANG Yong ZHANG Huai-zhi ZHOU Sheng-hui WU Qiu-hong CHEN Yong-xing WANG Zhen-zhong WANG Guo-xin ZHANG De-yun ZHANG Yan HU Tie-zhu LIU Zhi-yong State Key Laboratory for Agrobiotechnology China Agricultural University Beijing 100193 P.R.China Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 P.R. China China Rural Technology Development Center Beijing 100045 P.R. China College of Life Science and Technology Henan Institute of Science and Technology Xinxiang 453003 P.R. China

Powdery mildew,caused by Blumeria graminis ***,is one of the most severe wheat *** powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to control this *** analysis revealed that a single dominant resistance gene named PmTm4 originated from Chinese wheat line Tangmai 4 confers resistance to prevailing isolates of *** *** isolate *** comparative genomics analyses helped to develop closely linked markers to PmTm4 and a fine genetic map was constructed using large F2population,in which PmTm4 was located into a 0.66-c M genetic *** orthologous subgenome region of PmTm4in Aegilops tauschii was identified,and two resistance gene analogs（RGA）were characterized from the corresponding sequence scaffolds of *** draft *** closely linked markers and identified *** orthologs in the mapping interval provide an entry point for chromosome landing and map-based cloning of PmTm4.

关键词： powdery mildew resistance gene PmTm4 genetic mapping comparative genomic analysis

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genomic analysis of a pure culture of magnetotactic bacterium Terasakiella ***-1

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Journal of Oceanology and Limnology 2021年第6期39卷 2097-2106页

作者： Haijian DU Wenyan ZHANG Wei LIN Hongmiao PAN Tian XIAO Long-Fei WU College of Life Science Shandong UniversityQingdao 266237China CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdao 266071China Laboratory for Marine Ecology and Environmental Science Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China Key Laboratory of Earth and Planetary Physics Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China Institutions of Earth Science Chinese Academy of SciencesBeijing 100029China France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms Chinese Academy of SciencesBeijing 100029China Aix-Marseille University CNRSLCBMarseille F-13402France

Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed *** having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the *** this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was ***-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to *** of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to *** pure culture of Terasakiella ***-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.

关键词： magnetotactic bacteria magnetotaxis pure culture comparative genomic analysis

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Rediscovery and analysis of Phytophthora carbohydrate esterase(CE) genes revealing their evolutionary diversity

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Journal of Integrative Agriculture 2018年第4期17卷 878-891页

作者： QIAN Kun LI Deng-hui LIN Run-mao SHI Qian-qian MAO Zhen-chuan YANG Yu-hong FENG Dong-xin XIE Bing-yan Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences College of Life Sciences Beijing Normal University Key Laboratory of Biology and Genetic Improvement of Horticultural Crops Ministry of Agriculture

A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.

关键词： Phytophthora carbohydrate esterase gene prediction comparative genomic analysis evolution diversity

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