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mLife 2024年第1期3卷 143-155页

作者： Jing Zhang Qi-Yun Liang Da-Shuai Mu Fengbai Lian Ya Gong Mengqi Ye Guan-Jun Chen Yuqi Ye Zong-Jun Du state key laboratory of microbial techlogy Insttute of Micrbial TchnoogyShandong UniversityQingdaoChina Marine College Shandong UniverstyWeihaiChina Shandong University-Weihai Research Institute of Industrial Technology WeihaiChina

In the classical microbial isolation technique,the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for *** this study,we designed a simple coculture technique named the“sandwich agar plate method,”which maintains microbial interactions throughout the isolation and pure culture *** total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control *** uncultured species displayed commensal *** study found that heme was the growth-promoting factor of some marine commensal *** genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial ***,our study supported that the survival strategies of heme auxotrophy in different habitats varied *** findings highlight that cocultivation based on the“sandwich agar plate method”could be developed and used to isolate more uncultured bacteria.

关键词： cultivation growth factors heme sandwich agar plate uncultured bacteria

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

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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 *** this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic ***,by in silico analysis,we demonstrated that the *** was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity *** in vitro cultivation revealed that *** produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and ***,gavage of the *** 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 *** then performed the gavage trial using diet induced obese mice,and it revealed that the administration of *** alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory *** 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

Gut microbial interactions based on network construction and bacterial pairwise cultivation

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Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu state key laboratory of microbial Technology Shandong UniversityQingdao 266000China state key laboratory of microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus

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mLife 2024年第1期3卷 119-128页

作者： Pengpeng Zhao Xiaonan Bi Xiaoning Wang Xu Feng Yulong Shen Guanhua Yuan Qunxin She CRISPR and Archaea Biology Research Center State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina

Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression ***,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic *** this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for *** hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this *** identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference *** results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host *** mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).*** transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for *** results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the *** further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.

关键词： archaeal genetics CRISPR-Cas CRISPR escape mutations dual plasmid vectors Saccharolobus-E.coli shuttle vectors

Improved observation of colonized roots reveals the regulation of arbuscule development and senescence by drought stress in the arbuscular mycorrhizae of citrus

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Horticultural Plant Journal 2024年第2期10卷 425-436页

作者： Xilong Yin Wei Zhang Zengwei Feng Guangda Feng Honghui Zhu Qing Yao College of Horticulture South China Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China)Ministry of Agriculture and Rural AffairsGuangdong Province Key Laboratory of Microbial Signals and Disease ControlGuangzhouGuangdong 510642China key laboratory of Agricultural Microbiomics and Precision Application Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationKey Laboratory of Agricultural MicrobiomicsState Key Laboratory of Applied Microbiology Southern ChinaGuangdong Microbial Culture Collection Center(GDMCC)Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

Citrus is the typical mycorrhizal fruit tree species establishing symbiosis with arbuscular mycorrhizal (AM) fungi. However, arbuscule development and senescence in colonized citrus roots, especially in response to drought stress, remain unclear, which is mainly due to the difficulty in clearing and staining lignified roots with the conventional method. Here, we improved the observation of colonized roots of citrus plants with the sectioning method, which enabled the clear observation of AM fungal structures. Furthermore, we investigated the effects of one week of drought stress on arbuscule development and senescence with the sectioning method. Microscopy observations indicated that drought stress significantly decreased mycorrhizal colonization (F%and M%) although it did not affect plant growth performance. Fluorescence probes (WGA 488 and/or Nile red) revealed that drought stress inhibited arbuscule development by increasing the percentage of arbuscules at the early stage and decreasing the percentages of arbuscules at the midterm and mature stages. Meanwhile, drought stress accelerated arbuscule senescence, which was characterized by the increased accumulation of neutral lipids. Overall, the sectioning method developed in this study enables the in-depth investigation of arbuscule status, and drought stress can inhibit arbuscule development but accelerate arbuscule senescence in the colonized roots of citrus plants. This study paves the way to elaborately dissecting the arbuscule dynamics in the roots of fruit tree species in response to diverse abiotic stresses.

关键词： Arbuscular mycorrhizae Citrus Drought stress Arbuscule development Arbuscule senescence Fruit tree species

Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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Marine Life Science & Technology 2024年第2期6卷 331-348页

作者： Hao Ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu state key laboratory of microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China state key of laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal *** high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain ***,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in *** analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were *** isolate of Pseudomonas also contained genes encoding the complete degradation *** transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous *** addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial *** microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic *** information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

Rearranged 19-nor-7,8-seco-labdane diterpenoids and Diels-Alder cycloadducts from the Chinese liverwort Pallavicinia ambigua:Structural elucidation,photoinduced rearrangement,and cytotoxic activity

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Chinese Chemical Letters 2024年第3期35卷 415-418页

作者： Chunyang Zhang Yuelan Li Zhaojun Chu Shuangzhi Yuan Yanan Qiao Jiaozhen Zhang Lin Li Yueqing Zhang Ruifeng Tian Yajie Tang Hongxiang Lou Department of Natural Products Chemistry Key Lab of Chemical Biology(MOE)School of Pharmaceutical SciencesShandong UniversityJi'nan 250012China state key laboratory of microbial Technology Shandong UniversityQingdao 266237China

Two distinctive rearranged 19-nor-7,8-seco-labdane diterpenoids(1 and 2)with a novel tetracyclo[5.***.1.0^(2,5.)0^(4,10)]decane skeleton,a derivative of the open tetrahydrofuran ring(7),three dimeric compounds(8-10),and four revised homologs(3-6)were obtained from Chinese liverwort Pallavicinia *** structures were identified via combined analysis of their spectroscopic data,single-crystal X-ray diffraction patterns,and ECD *** light-driven conversion of compound 5 to compounds 1-4 demonstrated that photochemically induced postmodification involved in biosynthesis is an important way to diversify natural structures.A preliminary cytotoxicity assay revealed that compound 5 showed significant inhibition in the human prostate cancer(PC-3)cell line via an apoptotic pathway.

关键词： Liverwort Pallavicinia ambigua 19-nor-7 8-seco-Labdan diterpenoid Photoinduced rearrangement Cytotoxic activity

Understanding the rapid spread of antimicrobial resistance genes mediated by IS26

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mLife 2024年第1期3卷 101-109页

作者： Na Tang Dawei Wei Yuan Zeng Gang Zhang Chao Wang Jie Feng Yuqin Song state key laboratory of microbial Resources Institute of MicrobiologyChinese Academy of SciencesBejingChina College of Life Science University of Chinese Academy of SciencesBeijingChina

Insertion sequences(ISs)promote the transmission of antimicrobial resistance genes(ARGs)across bacterial ***,their contributions and dynamics during the transmission of resistance remain *** this study,we selected is26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission *** retrieved 2656 translocatable IS26-bounded units with ARGs(tiS26-bUs-ARGs)in complete bacterial genomes from the NCBI RefSeq *** total,124 ARGs spanning 12 classes of antibiotics were detected,and the average contribution rate of IS26 to these genes was 41.2%.We found that IS26-bounded units(IS26-bUs)mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class,showing strong transfer po-tential between strains,species,and even *** Is26-bUs expanded in bacterial populations over time,and their temporal expansion trend was significantly correlated with antibiotic *** wide dissemination could be due to the nonspecific target site preference of ***,we experimentally confirmed that the introduction of a single copy of is26 could lead to the formation of a composite transposon mediating the transmission of“passenger”*** observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.

关键词： antibiotic consumption antibiotic resistance genes horizontal gene transfer insertion sequence IS26

Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian Research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education key laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu key laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China state key laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China state key laboratory of microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of Ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened ***’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat *** is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened ***,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic ***,we identified candidate genes linked with adaptation across the current distribution of Reeves’s *** present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 *** also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those *** comparing with other threatened species,we found that Reeves’s Pheasants have low genetic *** of homozygosity suggest that the Shennongjia population has experienced serious *** demographic history results indicated that three populations experienced several declines during the glacial *** adaptative analysis among the populations identified 241 candidate genes under directional *** are involved in a large variety of processes,including the immune response and *** results suggest that the three populations should be considered as three different conservation *** current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & Technology 2024年第2期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch Hongan Long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China state key laboratory of microbial Technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic ***,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)*** rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T *** high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in *** line with this,*** D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among *** with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and *** lacks a stress response *** findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair