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Gut microbial interactions based on network construction and bacterial pairwise cultivation

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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Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

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mLife 2024年第1期3卷 21-41页

作者： Vadakattu V.S.R.Gupta James M.Tiedje CSIRO Agriculture&Food UrrbraeSouth AustraliaAustralia Centre for microbial Ecology Michigan State UniversityEast LansingMichiganUSA

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures *** community structure is mainly a result of the inoculum(dispersal),the selective advantages of those organisms under the habitat-based environmental attributes,and the ability of those colonizers to sustain themselves over *** soil is protective,and its microbial inhabitants have long adapted to varied soil conditions,significant portions of the soil microbial community structure are likely ***,a substantial portion of the community will not correlate to often measured soil *** suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes:(i)those that supply energy,i.e.,organic carbon and electron acceptors;(i)environmental effectors or stressors,i.e.,pH,salt,drought,and toxic chemicals;(ii)macro-organism associations,i.e.,plants and their seasonality,animals and their fecal matter,and soil fauna;and(iv)nutrients,in order,N,P,and probably of lesser importance,other micronutrients,and *** relevance of drivers also varies with spatial and time scales,for example,aggregate to field to regional,and persistent to dynamic populations to transcripts,and with the extent of phylogenetic difference,hence phenotypic differences in organismal *** present a summary matrix to provide guidance on which drivers are important for particular studies,with special emphasis on a wide range of spatial and temporal scales,and illustrate this with genomic and population(rRNA gene)data from selected studies.

关键词： abundance community structure diversity functional microbiome microorganisms

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Exploring the characteristics of microbial community and enzyme activity in the aged refuse landfill environment of Taiyuan, China

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Pedosphere 2024年第5期34卷 879-891页

作者： Fen HOU Junjie DU Yuzhou MENG Xihui WU Department of Land Resource Management School of Public Administration Shanxi University of Finance and Economics College of Life Science Shanxi Engineering Research Center of Microbial Application Technologies Shanxi Normal University

Municipal solid waste landfill is the main disposal option for domestic garbage, in which microbial activities play an important role. However, despite the widespread practice of landfilling, the metagenomic microbial profiles of landfill sites remain poorly characterized. In this study, we used a combination of physicochemical analysis, ultraviolet-visible spectrophotometry, and high-throughput Illumina shotgun sequencing to systematically investigate the changes in soil enzyme activities, microbial community structure, and functional attributes in aged refuse collected from the Xingou Municipal Solid Waste Landfill in Taiyuan, China, with ordinary topsoil from an area within 5 km of the landfill as control soil. Except for neutral phosphatase (P=0.065), the activities of urease, laccase, dehydrogenase, sucrase, neutral protease, and β-glucosidase were all significantly reduced (P microbial communities, as reflected by the higher values of community richness estimators (Chao 1 and ACE) and diversity indices (Shannon and Simpson). In total, 186 phyla, 4 354 genera, and 34 459 species were identified, with 132 phyla, 1 914 genera, and7 369 species showing significantly different abundances between the aged refuse and the control soil. Actinobacteria and Acidobacteria were identified as the dominant phyla in the control soil, whereas Proteobacteria, Euryarchaeota (archaea), and Firmicutes were found to predominate in the aged ***, Euryarchaeota and Methanoculleus were the major taxa detected in the aged refuse, but were almost completely absent in the control soil. Xenobiotic biodegradation and bacterial chemotaxis were the main functions of the microflora in the aged refuse, whereas the carbohydrate, amino acid,

关键词： functional attribute metabolism pathway municipal solid waste landfill resource utilization soil microflora

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Recent advances in the culture-independent discovery of natural products using metagenomic approaches

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Chinese Journal of Natural Medicines 2024年第2期22卷 100-111页

作者： SHEN Yiping LIU Nan WANG Zongqiang Laboratory of microbial Drug Discovery China Pharmaceutical UniversityNanjing 211198China

Natural products derived from bacterial sources have long been pivotal in the discovery of drug ***,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured *** in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent *** approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening,sequence tag-based homology screening,and bioinformatic-assisted chemical *** this process,numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic *** paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.

关键词： Metagenomics Culture-independent approach Natural product Functional screening Sequence tag-based homology screening Syn-BNP

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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

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Variation in Bombyx mori immune response against fungal pathogen Beauveria bassiana with variability in cell wallβ-1,3-glucan

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Insect Science 2024年第1期31卷 211-224页

作者： Yulong Wang Zhen Liu Xuebing Yin Shihong Liu Kai Wang Rongjie Wan Haoran Chen Xinyang Li Bo Huang Anhui Provincial Key Laboratory of microbial Pest Control Anhui Agricultural UniversityHefeiChina

Entomopathogenic fungi are protected by a cell wall with dynamic structure for adapting to various environmental conditions.β-1,3-Glucan recognition proteins activate the innate immune system of insects by recognizing surface molecules of ***,the associations between pathogenicity and the different components of entomopathogenic fungal cell walls remain *** Beauveria bassiana strains were selected that have significantly differing virulence against Bombyx *** molecular mechanisms underlying the immune response in *** were investigated using RNA sequencing,which revealed differences in the immune response to different *** strains at 12 h *** assays revealed thatβ-1,3-glucan content had an opposite trend to that of fungal virulence.β-1,3-Glucan injection upregulated BmβGRP4 expression and significantly reduced the virulence of the high-virulence strain but not that of the medium-virulence or low-virulence ***βGRP4 silencing in *** with RNA interference resulted in the opposite virulence pattern,indicating that the virulence of *** was affected by the cell walls’content ofβ-1,3-glucan,which could be recognized by Bmβ***,interference with the gene CnA(calcineurin catalytic A subunit)involved inβ-1,3-glucan synthesis eliminated differences in virulence between *** *** results indicate that strains of a single species of pathogenic fungi that have differing cell wall components are recognized differently by the innate immune system of ***.

关键词： ombyx mori BmβGRP4 innate immunity insect fungal pathogen virulence

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Nuclear transport receptors underpin plastidial retrograde signaling

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Molecular Plant 2024年第7期17卷 993-995页

作者： Min Jia Yangnan Gu Department of Plant and microbial Biology University of CaliforniaBerkeleyBerkeleyCAUSA

The nucleus integrates cytosolic and organellar signals to regulate gene expression during plant stress responses,and this process is highly dependent on shuttling of signaling molecules in and out of the *** nucleocytoplasmic transport of macromolecules is facilitated by nuclear transport receptors(NTRs).NTRs are broadly categorized into exportins,which mediate the export of cargo from the nucleus to the cytoplasm,and importins,which facilitate the import of cargo into the *** importin family comprises importin-α(IMPa)and importin-β(IMPp).IMPa proteins are adaptor proteins and composed of three functional domains:an N-terminal IMPβ-binding(IBB)domain,ten Armadillo(ARM)repeats responsible for recognizing and interacting with cargo,and an exportin-interacting domain crucial for recycling via nuclear export(Wing et al.,2022).During a nuclear transport event,*** cargo containing a classical nuclear localization signal(cNLS)through its ARM repeats and engages IMPβvia its IBB domain,forming the cargo-IMPa-IMPβternary ***βfacilitates translocation of this complex through the nuclear *** inside the nucleus,RanGTP competes with IMPa for binding to IMPβ,promoting disassembly of the transport complex and releaseofcargo.

关键词： complex. integrate ternary

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Two MADS-box proteins,AGL9 and AGL15,recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis

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Molecular Plant 2024年第7期17卷 1110-1128页

作者： Shen Zhang Devasantosh Mohanty Adnan Muzaffar Min Ni Department of Plant and microbial Biology University of Minnesota at Twin CitiesSaint PaulMinnesota MN 55108United States of AmericaUSA

Spatiotemporal regulation of gene expression by polycomb repressive complex 2(PRc2)is critical for animal and plant *** Arabidopsis fertilization independent seed(FIS)-PRC2 complex functions specifically during plant reproduction from gametogenesis to seed *** a double fertilization event,triploid endosperm proliferates early,followed by the growth of a diploid embryo,which replaces the endosperm in Arabidopsis and many *** genes critical for endosperm proliferation such as IKkU2 and MINI3 are activated after *** we report that two MADS-box AGAMOUS-LIKE(AGL)proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex at 4-5 days after pollination(DAP).Interestingly,AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4-5 DAP and promote the deposition of H3K27me3 marks at key endosperm proliferation *** of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and ***-wide analysis with cleavage Under Targets and tagmentation(CUT&Tag)sequencing and RNA sequencing revealed the landscape of endosperm H3K27me3 marks and gene expression profiles in Col-0 and agl9 ***&Tag qPCR also demonstrated the occupancy of the two MADS-box proteins and FIS-PRC2 on a few representative target *** studies suggest that MADS-box proteins could potentially recruit PRc2 to regulate many other developmental processes in plants or even in fungi and animals.

关键词： AGL9 AGL15 embryo endosperm IKU2 MEDEA MINI3

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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

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Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy,Metabolic Function,and Natural Products

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 121-134页

作者： Tao Yu Yingfeng Luo Xinyu Tan Dahe Zhao Xiaochun Bi Chenji Li Yanning Zheng Hua Xiang Songnian Hu State Key Laboratory of microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate *** alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic ***,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep *** CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 *** addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community *** and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold ***,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and ***,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

关键词： Global marine cold seep Metagenome Prokaryotic microbiome Metabolic function Natural product

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