Thermus thermophilus is an attractive species in the bioindustry due to its valuable natural products,abundant thermophilic enzymes,and promising fermentation capacities.However,efficient and versatile genome editing ...Thermus thermophilus is an attractive species in the bioindustry due to its valuable natural products,abundant thermophilic enzymes,and promising fermentation capacities.However,efficient and versatile genome editing tools are not available for this species.In this study,we developed an efficient genome editing tool for T.thermophilus HB27 based on its endogenous type IB,I-C,and III-A/B CRISPR-Cas systems.First,we systematically characterized the DNA interference capabilities of the different types of the native CRISPR-Cas systems in T.thermophilus HB27.We found that genomic manipulations such as gene deletion,mutation,and in situ tagging could be easily implemented by a series of genome-editing plasmids carrying an artificial self-targeting mini-CRISPR and a donor DNA responsible for the recombinant recovery.We also compared the genome editing efficiency of different CRISPR-Cas systems and the editing plasmids with donor DNAs of different lengths.Additionally,we developed a reporter gene system for T.thermophilus based on a heat-stableβ-galactosidase gene TTP0042,and constructed an engineered strain with a high production capacity of superoxide dismutases by genome modification.展开更多
The division of organisms on the Tree of Life into either a three-domain(3D)tree or a two-domain(2D)tree has been disputed for a long time.Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal ...The division of organisms on the Tree of Life into either a three-domain(3D)tree or a two-domain(2D)tree has been disputed for a long time.Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker,there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms.Here,we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life.Meanwhile,we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes.Furthermore,we propose three major directions for future research on exploring the“next one”closest Eukaryote relative,deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects,and understanding the roles of horizontal gene transfer,viruses,and mobile elements in eukaryogenesis.展开更多
Fungi are an integral part of the earth's biosphere.They are broadly distributed in all continents and ecosystems and play a diversity of roles.Here,I review our current understanding of fungal threats to humans a...Fungi are an integral part of the earth's biosphere.They are broadly distributed in all continents and ecosystems and play a diversity of roles.Here,I review our current understanding of fungal threats to humans and describe the major factors that contribute to various threats.Among the 140,000 or so known species out of the estimated six million fungal species on Earth,about 10%directly or indirectly threaten human health and welfare.Major threats include mushroom poisoning,fungal allergies,infections of crop plants,food contamination by mycotoxins,and mycoses in humans.A growing number of factors have been identified to impact various fungal threats,including human demographics,crop distributions,anthropogenic activities,pathogen dispersals,global climate change,and/or the applications of antifungal drugs and agricultural fungicides.However,while models have been developed for analyzing various processes of individual threats and threat managements,current data are primarily descriptive and incomplete,and there are significant obstacles to integration of the diverse factors into accurate quantitative assessments of fungal threats.With increasing technological advances and concerted efforts to track the spatial and temporal data on climate and environmental variables;mycotoxins in the feed and food supply chains;fungal population dynamics in crop fields,human and animal populations,and the environment;human population demographics;and the prevalence and severities of fungal allergies and diseases,our ability to accurately assess fungal threats will improve.Such improvements should help us develop holistic strategies to manage fungal threats in the future.展开更多
Identification,sorting,and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes.In this work,based on an artificial intel...Identification,sorting,and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes.In this work,based on an artificial intelligence(AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting,we developed an automatic and index-based system called EasySort AUTO,where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed,“One-Cell-One-Tube”manner.The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting.Then,a crossinterface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube,which leads to coupling with subsequent single-cell culture or sequencing.The efficiency of the system for single-cell printing is>93%.The throughput of the system for single-cell printing is~120 cells/h.Moreover,>80%of single cells of both yeast and Escherichia coli are culturable,suggesting the superior preservation of cell viability during sorting.Finally,AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples,which was validated by downstream single-cell proliferation assays.The automation,index maintenance,and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.展开更多
Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats.The role of the N-acyl homoserine lactone(AHL)-mediated signaling pathway,which is widespread in gram-ne...Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats.The role of the N-acyl homoserine lactone(AHL)-mediated signaling pathway,which is widespread in gram-negative bacteria,in the bacterial resistance process should be studied in depth.Here,we report a degrading enzyme of AHLs,MomL,that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism.The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response.The degradation of AHLs by MomL results in the inability of LasR to activate relA,which,in turn,stops the activation of downstream rpoS.Further results show that rpoS directly regulates the type VI secretion system H2-T6SS.Under MomL treatment,inactivated RpoS fails to regulate H2-T6SS;therefore,the expression of effector phospholipase A is reduced,and the adaptability of bacteria to antibiotics is weakened.MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria.Therefore,this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.展开更多
As the largest organ of the body,the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria.Furthermore,the skin bacterial microbiota plays a vital role in health and disease.Disruptio...As the largest organ of the body,the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria.Furthermore,the skin bacterial microbiota plays a vital role in health and disease.Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases.In this review,we first provide an overview of research on skin bacterial microbiota and human health,including the composition of skin bacteria in a healthy state,as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens.We then discuss the diseases that result from skin microbial dysbiosis,including atopic dermatitis,common acne,chronic wounds,psoriasis,viral transmission,cutaneous lupus,cutaneous lymphoma,and hidradenitis suppurativa.Finally,we highlight the progress that utilizes skin microorganisms for disease therapeutics,such as bacteriotherapy and skin microbiome transplantation.A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.展开更多
Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one ...Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one of the largest and most comprehensive semantic databases about coronaviruses,the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes.These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs.展开更多
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities,knowledge and technical gaps still limit the applications of microbiome engineer...Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities,knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology,especially for environmental use.Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering.Here,we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation.Moreover,a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications.A strategy to engineer microbiomes for environmental use,which avoids the build-up of toxic intermediates that pose a risk to human health,is suggested.We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.展开更多
Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron ac...Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor.To better understand DIET with methanogens,the transcriptome of Geobacter metallireducens during DIET‐based growth with G.sulfurreducens reducing fumarate was compared with G.metallireducens grown in coculture with diverse Methanosarcina.The transcriptome of G.metallireducens cocultured with G.sulfurreducens was significantly different from those with Methanosarcina.Furthermore,the transcriptome of G.metallireducens grown with Methanosarcina barkeri,which lacks outer‐surface c‐type cytochromes,differed from those of G.metallireducens cocultured with M.acetivorans or M.subterranea,which have an outer‐surface c‐type cytochrome that serves as an electrical connect for DIET.Differences in G.metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable.Cocultures with c‐type cytochrome deletion mutant strains,ΔGmet_0930,ΔGmet_0557 andΔGmet_2896,never became established with G.sulfurreducens but adapted to grow with all three Methanosarcina.Two porin–cytochrome complexes,PccF and PccG,were important for DIET;however,PccG was more important for growth with Methanosarcina.Unlike cocultures with G.sulfurreducens and M.acetivorans,electrically conductive pili were not needed for growth with M.barkeri.Shewanella oneidensis,another electroactive microbe with abundant outer‐surface c‐type cytochromes,did not grow via DIET.The results demonstrate that the presence of outer‐surface c‐type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron‐accepting partner on the physiology of the electron‐donating DIET partner.展开更多
The human gut is home to nearly 100 trillion microbes1,which constitute the human gut microecological system.The microbiota–gut–brain(MGB)axis is a two‐way communication pathway between gut microbiota and the brain...The human gut is home to nearly 100 trillion microbes1,which constitute the human gut microecological system.The microbiota–gut–brain(MGB)axis is a two‐way communication pathway between gut microbiota and the brain through the immune system,metabolism,and the enteric nervous system.An increasing amount of clinical evidence indicates that abnormal MBG axis communication caused by intestinal ecosystem imbalance can affect the development of many neurological diseases,such as Parkinson's disease,Alzheimer's disease,and autism spectrum disorder(ASD)2.展开更多
Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to me...Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin degradation.However,the mechanism of bathyarchaeial lignin degradation remains unclear.Here,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(Ca.B.ligniniphilus),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions.Ca.B.ligniniphilus possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)alamin.MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages.Heterologous expression of the mtgB gene confirmed O-demethylation activity.The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China Sea.These findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments.展开更多
Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the envir...Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a“One Health”roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the“One Health”framework provides a guide to tackle antibiotic resistance in the environment.展开更多
Impact statement We have developed a manually curated online reference database,DANMEL(http://124.239.252.254/danmel/),that addresses the lack of accurate dissection and annotation of the genetic structures of mobile ...Impact statement We have developed a manually curated online reference database,DANMEL(http://124.239.252.254/danmel/),that addresses the lack of accurate dissection and annotation of the genetic structures of mobile genetic elements(MGEs)with genes for drug resistance.DANMEL contains accurately annotated and genetically dissected reference MGEs covering 5 categories and 135 subcategories/subfamilies of MGEs.Further,DANMEL provides a detailed guide on how to precisely annotate MGEs.DANMEL also provides SEARCH/BLAST functions to facilitate finding reference MGEs.Overall,DANMEL will aid researchers to conduct in-depth genetic analysis of sequenced bacterial MGEs with drug-resistance genes and further facilitate a better understanding of bacterial MGEs associated with drug resistance at a genomic level.展开更多
Soil microorganisms critically affect the ecosystem carbon(C)balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation.However,...Soil microorganisms critically affect the ecosystem carbon(C)balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation.However,the effects of climate change drivers such as warming,precipitation change on soil microbial communities,and C dynamics remain poorly understood.Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment,here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi,and soil C efflux.Warming significantly reduced the abundance of fungi but not bacteria,increasing the relative dominance of bacteria in the soil microbial community.In particular,warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales.Also,precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria.Furthermore,the community composition of abundant,but not rare,soil fungi was significantly correlated with soil CO_(2) efflux.Our findings suggest that alterations in the fungal community composition,in response to changes in soil C and moisture,dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.展开更多
Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycli...Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.展开更多
The type I system is the most widely distributed CRISPR-Cas system identified so far.Recently,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in...The type I system is the most widely distributed CRISPR-Cas system identified so far.Recently,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic archaea.Here,we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula hispanica.When the spacer targeting the chromosomal gene was shortened from 36 to 28 bp,transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude,indicating a significant loss of interference.However,by conducting whole-genome sequencing and measuring the growth curves of the hosts,we still detected DNA cleavage and its influence on cell growth.Intriguingly,when the spacer was shortened to 24 bp,the transcription of the target gene was downregulated to 10.80%,while both interference and primed adaptation disappeared.By modifying the lengths of the spacers,the expression of the target gene could be suppressed to varying degrees.Significantly,by designing crRNAs with different spacer lengths and targeting different genes,we achieved simultaneous gene editing(cdc6E)and gene regulation(crtB)for the first time with the endogenous type I CRISPR-Cas system.展开更多
Despite the fast progress in our understanding of the complex functions of gut microbiota,it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis.To g...Despite the fast progress in our understanding of the complex functions of gut microbiota,it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis.To gain knowledge of the indigenous growth/division patterns of the diverse mouse gut bacteria with a relatively high throughput,here,we propose an integrative strategy,which combines the use of fluorescent probe labeling,confocal imaging with single‐cell sorting,and sequencing.Mouse gut bacteria sequentially labeled by two fluorescent D‐amino acid probes in vivo were first imaged by confocal microscopy to visualize their growth patterns,which can be unveiled by the distribution of the two fluorescence signals on each bacterium.Bacterial cells of interest on the imaging slide were then sorted using a laser ejection equipment,and the collected cells were then sequenced individually to identify their taxa.Our strategy allows integrated acquirement of the growth pattern knowledge of a variety of gut bacteria and their genomic information on a single‐cell basis,which should also have great potential in studying many other complex bacterial systems.展开更多
I clearly remember the day in February 1998 when I met Professor Carl Woese for the first time at his laboratory in the Department of Microbiology,the University of Illinois at Urbana–Champaign.Prof.Woese kindly gave...I clearly remember the day in February 1998 when I met Professor Carl Woese for the first time at his laboratory in the Department of Microbiology,the University of Illinois at Urbana–Champaign.Prof.Woese kindly gave me the reprint of his seminal review paper with his signature(Microbiological Reviews in 1987)1.A veritable treasure,I keep this paper in my office,having started research on the molecular biology of Archaea in 1992 and having always aspired to meet him someday.In this essay,I highlight the remarkable achievements of Carl Woese and share my memories of him,while looking back at my own research on Archaea and related aspects in Japan.展开更多
To remain competitive,proteobacteria use various contact-dependent weapon systems to defend against microbial com-petitors.The bacterial-killing type IV secretion system(T4SS)is one such powerful weapon.It commonly co...To remain competitive,proteobacteria use various contact-dependent weapon systems to defend against microbial com-petitors.The bacterial-killing type IV secretion system(T4SS)is one such powerful weapon.It commonly controls the killing/competition between species by secreting the lethal T4SS effector(T4E)proteins carrying conserved XVIPCD domains into competing cells.In this study,we sought knowledge to understand whether the bacterial-killing T4SS-producing bacteria encode T4E-like proteins and further explore their biological functions.To achieve this,we designed a T4E-guided approach to discover T4E-like proteins that are designated as atypical T4Es.Initially,this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS-producing bacteria.These homologous genes were then screened in Escherichia coli to identify antibacterial candidates(atypical T4Es)and their neighboring detoxification proteins,followed by testing their gene cotranscription and validating their physical interactions.Using this approach,we did discover two atypical T4E proteins from the plant-beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri.We also provided substantial evidence to show that the atypical T4E protein Le1637-mediated bacterial defense in interspecies interactions between L.enzymogenes and its competitors.Therefore,the newly designed T4E-guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.展开更多
Glucose and xylose are two major components of lignocellulose.Simultaneous consumption of glucose and xylose is critical for engineered microorganisms to produce fuels and chemicals from lignocellulosic biomass.Althou...Glucose and xylose are two major components of lignocellulose.Simultaneous consumption of glucose and xylose is critical for engineered microorganisms to produce fuels and chemicals from lignocellulosic biomass.Although many production limitations have been resolved,glucose‐induced inhibition of xylose transport remains a challenge.In this study,a cell growthbased screening strategy was designed to identify xylose transporters uninhibited by glucose.The glucose pathway was genetically blocked in Escherichia coli so that glucose functions only as an inhibitor and cells need xylose as the carbon source for survival.Through adaptive evolution,omics analysis and reverse metabolic engineering,a new phosphoenolpyruvate:carbohydrate phosphotransferase system(PTS)galactitol transporter(GalABC,encoded by EcolC_1640,EcolC_1641,and EcolC_1642 genes)that is not inhibited by glucose was identified.Inactivation of adenylate cyclase led to increased expression of the EcolC_1642 gene,and a point mutation in gene EcolC_1642(N13S)further enhanced xylose transport.During the second round of gene mining,AraE and a new ABC transporter(AraFGH)of xylose were identified.A point mutation in the transcription regulator araC(L156I)caused increased expression of araE and araFGH genes without arabinose induction,and a point mutation in araE(D223Y)further enhanced xylose transport.These newly identified xylose transporters can support the simultaneous consumption of glucose and xylose and have potential use in producing chemicals from lignocellulose.展开更多
基金the National Natural Science Foundation of China(32170096)the Fundamental Research Funds for the Central Universities(2662022S KPY001)Cooperation Fund of Huazhong Agricultural University-Agricultural Genomics Institute at Shenzhen(CAAS)(SZYJY2021002).
文摘Thermus thermophilus is an attractive species in the bioindustry due to its valuable natural products,abundant thermophilic enzymes,and promising fermentation capacities.However,efficient and versatile genome editing tools are not available for this species.In this study,we developed an efficient genome editing tool for T.thermophilus HB27 based on its endogenous type IB,I-C,and III-A/B CRISPR-Cas systems.First,we systematically characterized the DNA interference capabilities of the different types of the native CRISPR-Cas systems in T.thermophilus HB27.We found that genomic manipulations such as gene deletion,mutation,and in situ tagging could be easily implemented by a series of genome-editing plasmids carrying an artificial self-targeting mini-CRISPR and a donor DNA responsible for the recombinant recovery.We also compared the genome editing efficiency of different CRISPR-Cas systems and the editing plasmids with donor DNAs of different lengths.Additionally,we developed a reporter gene system for T.thermophilus based on a heat-stableβ-galactosidase gene TTP0042,and constructed an engineered strain with a high production capacity of superoxide dismutases by genome modification.
基金the National Natural Science Foundation of China(Nos.92251306,32225003,31970105,and 92051102)the Innovation Team Project of Universities in Guangdong Province(No.2020KCXTD023)+1 种基金the Shenzhen Science and Technology Program(JCYJ20200109105010363)This work was partially funded by the US-National Science Foundation grants OCE-2049478 and DBI-2047598 to K.A.
文摘The division of organisms on the Tree of Life into either a three-domain(3D)tree or a two-domain(2D)tree has been disputed for a long time.Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker,there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms.Here,we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life.Meanwhile,we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes.Furthermore,we propose three major directions for future research on exploring the“next one”closest Eukaryote relative,deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects,and understanding the roles of horizontal gene transfer,viruses,and mobile elements in eukaryogenesis.
文摘Fungi are an integral part of the earth's biosphere.They are broadly distributed in all continents and ecosystems and play a diversity of roles.Here,I review our current understanding of fungal threats to humans and describe the major factors that contribute to various threats.Among the 140,000 or so known species out of the estimated six million fungal species on Earth,about 10%directly or indirectly threaten human health and welfare.Major threats include mushroom poisoning,fungal allergies,infections of crop plants,food contamination by mycotoxins,and mycoses in humans.A growing number of factors have been identified to impact various fungal threats,including human demographics,crop distributions,anthropogenic activities,pathogen dispersals,global climate change,and/or the applications of antifungal drugs and agricultural fungicides.However,while models have been developed for analyzing various processes of individual threats and threat managements,current data are primarily descriptive and incomplete,and there are significant obstacles to integration of the diverse factors into accurate quantitative assessments of fungal threats.With increasing technological advances and concerted efforts to track the spatial and temporal data on climate and environmental variables;mycotoxins in the feed and food supply chains;fungal population dynamics in crop fields,human and animal populations,and the environment;human population demographics;and the prevalence and severities of fungal allergies and diseases,our ability to accurately assess fungal threats will improve.Such improvements should help us develop holistic strategies to manage fungal threats in the future.
基金the National Key R&D Program of China(Grant No.2021YFC2101100).
文摘Identification,sorting,and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes.In this work,based on an artificial intelligence(AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting,we developed an automatic and index-based system called EasySort AUTO,where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed,“One-Cell-One-Tube”manner.The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting.Then,a crossinterface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube,which leads to coupling with subsequent single-cell culture or sequencing.The efficiency of the system for single-cell printing is>93%.The throughput of the system for single-cell printing is~120 cells/h.Moreover,>80%of single cells of both yeast and Escherichia coli are culturable,suggesting the superior preservation of cell viability during sorting.Finally,AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples,which was validated by downstream single-cell proliferation assays.The automation,index maintenance,and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.
基金the National Natural Science Foundation of China(Nos.42176108 and 31870023)the Young Taishan Scholars Program of Shandong Province(No.tsqn202103029)+2 种基金the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0406-4)the Fundamental Research Funds for the Central Universities(No.201941009)the open research funds of the State Key Laboratory of Ophthalmology(No.303060202400368).
文摘Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats.The role of the N-acyl homoserine lactone(AHL)-mediated signaling pathway,which is widespread in gram-negative bacteria,in the bacterial resistance process should be studied in depth.Here,we report a degrading enzyme of AHLs,MomL,that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism.The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response.The degradation of AHLs by MomL results in the inability of LasR to activate relA,which,in turn,stops the activation of downstream rpoS.Further results show that rpoS directly regulates the type VI secretion system H2-T6SS.Under MomL treatment,inactivated RpoS fails to regulate H2-T6SS;therefore,the expression of effector phospholipase A is reduced,and the adaptability of bacteria to antibiotics is weakened.MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria.Therefore,this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.
基金funded by grants from the National Key Research and Development Plan of China(2021YFC2300200,2020YFC1200100,and 2018YFA0507202)the National Natural Science Foundation of China(31825001,81730063,32188101,82102389,and 81961160737)+5 种基金the Tsinghua University Spring Breeze Fund(2020Z99CFG017)the Shenzhen Science and Technology Project(JSGG20191129144225464)the Shenzhen San‐Ming Project for Prevention and Research on Vector‐borne Diseases(SZSM201611064)the Young Elite Scientists Sponsorship Program(2021QNRC001)the Yunnan Cheng Gong Expert Work‐Station(202005AF150034)We acknowledge the provincial innovation team for the prevention and control of highly pathogenic pathogens,Institute of Medical Biology,Chinese Academy of Medical Science(202105AE160020).
文摘As the largest organ of the body,the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria.Furthermore,the skin bacterial microbiota plays a vital role in health and disease.Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases.In this review,we first provide an overview of research on skin bacterial microbiota and human health,including the composition of skin bacteria in a healthy state,as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens.We then discuss the diseases that result from skin microbial dysbiosis,including atopic dermatitis,common acne,chronic wounds,psoriasis,viral transmission,cutaneous lupus,cutaneous lymphoma,and hidradenitis suppurativa.Finally,we highlight the progress that utilizes skin microorganisms for disease therapeutics,such as bacteriotherapy and skin microbiome transplantation.A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.
基金supported by the National Key Research Program of China(grant no.2019YFE0191000)the 13th Five-year Informatization Plan of the Chinese Academy of Sciences(grant nos.XXH13506,XXH13505)the National Science Foundation for Young Scientists of China(grant no.31701157).
文摘Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one of the largest and most comprehensive semantic databases about coronaviruses,the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes.These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs.
基金the National Key R&D Program of China(2021YFA0910300)Shanghai Excellent Academic Leaders Program(20XD1421900)the National Natural Science Foundation of China(32100075 and 32030004)。
文摘Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities,knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology,especially for environmental use.Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering.Here,we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation.Moreover,a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications.A strategy to engineer microbiomes for environmental use,which avoids the build-up of toxic intermediates that pose a risk to human health,is suggested.We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
基金This study was supported by the Army Research Office and was accomplished under grant number W911NF‐17‐1‐0345.
文摘Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor.To better understand DIET with methanogens,the transcriptome of Geobacter metallireducens during DIET‐based growth with G.sulfurreducens reducing fumarate was compared with G.metallireducens grown in coculture with diverse Methanosarcina.The transcriptome of G.metallireducens cocultured with G.sulfurreducens was significantly different from those with Methanosarcina.Furthermore,the transcriptome of G.metallireducens grown with Methanosarcina barkeri,which lacks outer‐surface c‐type cytochromes,differed from those of G.metallireducens cocultured with M.acetivorans or M.subterranea,which have an outer‐surface c‐type cytochrome that serves as an electrical connect for DIET.Differences in G.metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable.Cocultures with c‐type cytochrome deletion mutant strains,ΔGmet_0930,ΔGmet_0557 andΔGmet_2896,never became established with G.sulfurreducens but adapted to grow with all three Methanosarcina.Two porin–cytochrome complexes,PccF and PccG,were important for DIET;however,PccG was more important for growth with Methanosarcina.Unlike cocultures with G.sulfurreducens and M.acetivorans,electrically conductive pili were not needed for growth with M.barkeri.Shewanella oneidensis,another electroactive microbe with abundant outer‐surface c‐type cytochromes,did not grow via DIET.The results demonstrate that the presence of outer‐surface c‐type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron‐accepting partner on the physiology of the electron‐donating DIET partner.
基金This study was supported by the National Natural Science Foundation of China(NSFC)grant 82172288.
文摘The human gut is home to nearly 100 trillion microbes1,which constitute the human gut microecological system.The microbiota–gut–brain(MGB)axis is a two‐way communication pathway between gut microbiota and the brain through the immune system,metabolism,and the enteric nervous system.An increasing amount of clinical evidence indicates that abnormal MBG axis communication caused by intestinal ecosystem imbalance can affect the development of many neurological diseases,such as Parkinson's disease,Alzheimer's disease,and autism spectrum disorder(ASD)2.
基金supported financially by the Natural Science Foundation of China(Grants 42276139,42230401,42141003,41921006,92051116,91951209)2030 Project,Shanghai Jiao Tong University(Grant WH510244001)the National Postdoctoral Program for Innovative Talents(Grant No.BX20190204).
文摘Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin degradation.However,the mechanism of bathyarchaeial lignin degradation remains unclear.Here,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(Ca.B.ligniniphilus),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions.Ca.B.ligniniphilus possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)alamin.MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages.Heterologous expression of the mtgB gene confirmed O-demethylation activity.The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China Sea.These findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments.
基金supported by a Theme‐based Research Scheme grant from the Research Grants Council of the Hong Kong Special Administrative Region,China(Project no.T21‐705/20‐N).
文摘Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a“One Health”roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the“One Health”framework provides a guide to tackle antibiotic resistance in the environment.
文摘Impact statement We have developed a manually curated online reference database,DANMEL(http://124.239.252.254/danmel/),that addresses the lack of accurate dissection and annotation of the genetic structures of mobile genetic elements(MGEs)with genes for drug resistance.DANMEL contains accurately annotated and genetically dissected reference MGEs covering 5 categories and 135 subcategories/subfamilies of MGEs.Further,DANMEL provides a detailed guide on how to precisely annotate MGEs.DANMEL also provides SEARCH/BLAST functions to facilitate finding reference MGEs.Overall,DANMEL will aid researchers to conduct in-depth genetic analysis of sequenced bacterial MGEs with drug-resistance genes and further facilitate a better understanding of bacterial MGEs associated with drug resistance at a genomic level.
基金supported by National Natural Science Foundation of China (NSFC) (Nos.32371626 and 32001140)China Postdoctoral Science Foundation (No.2022T150325).
文摘Soil microorganisms critically affect the ecosystem carbon(C)balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation.However,the effects of climate change drivers such as warming,precipitation change on soil microbial communities,and C dynamics remain poorly understood.Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment,here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi,and soil C efflux.Warming significantly reduced the abundance of fungi but not bacteria,increasing the relative dominance of bacteria in the soil microbial community.In particular,warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales.Also,precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria.Furthermore,the community composition of abundant,but not rare,soil fungi was significantly correlated with soil CO_(2) efflux.Our findings suggest that alterations in the fungal community composition,in response to changes in soil C and moisture,dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.
基金supported by the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2020SP004)the National Natural Science Foundation of China(91951207,32100077,31770539,31870469,42177011,41676105,41771095,62170346)the China Postdoctoral Science Foundation(2021M703751).
文摘Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24020101)National Key R&D Program of China(2020YFA0906800)National Natural Science Foundation of China(91751201,32150020,32100499).
文摘The type I system is the most widely distributed CRISPR-Cas system identified so far.Recently,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic archaea.Here,we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula hispanica.When the spacer targeting the chromosomal gene was shortened from 36 to 28 bp,transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude,indicating a significant loss of interference.However,by conducting whole-genome sequencing and measuring the growth curves of the hosts,we still detected DNA cleavage and its influence on cell growth.Intriguingly,when the spacer was shortened to 24 bp,the transcription of the target gene was downregulated to 10.80%,while both interference and primed adaptation disappeared.By modifying the lengths of the spacers,the expression of the target gene could be suppressed to varying degrees.Significantly,by designing crRNAs with different spacer lengths and targeting different genes,we achieved simultaneous gene editing(cdc6E)and gene regulation(crtB)for the first time with the endogenous type I CRISPR-Cas system.
基金We are grateful to the National Natural Science Foundation of China(Grants 22122702,21735004,and 21775128)Innovative research team of high‐level local universities in Shanghai(SHSMU‐ZLCX20212601).
文摘Despite the fast progress in our understanding of the complex functions of gut microbiota,it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis.To gain knowledge of the indigenous growth/division patterns of the diverse mouse gut bacteria with a relatively high throughput,here,we propose an integrative strategy,which combines the use of fluorescent probe labeling,confocal imaging with single‐cell sorting,and sequencing.Mouse gut bacteria sequentially labeled by two fluorescent D‐amino acid probes in vivo were first imaged by confocal microscopy to visualize their growth patterns,which can be unveiled by the distribution of the two fluorescence signals on each bacterium.Bacterial cells of interest on the imaging slide were then sorted using a laser ejection equipment,and the collected cells were then sequenced individually to identify their taxa.Our strategy allows integrated acquirement of the growth pattern knowledge of a variety of gut bacteria and their genomic information on a single‐cell basis,which should also have great potential in studying many other complex bacterial systems.
文摘I clearly remember the day in February 1998 when I met Professor Carl Woese for the first time at his laboratory in the Department of Microbiology,the University of Illinois at Urbana–Champaign.Prof.Woese kindly gave me the reprint of his seminal review paper with his signature(Microbiological Reviews in 1987)1.A veritable treasure,I keep this paper in my office,having started research on the molecular biology of Archaea in 1992 and having always aspired to meet him someday.In this essay,I highlight the remarkable achievements of Carl Woese and share my memories of him,while looking back at my own research on Archaea and related aspects in Japan.
基金the National Natural Science Foundation of China(U22A20486,32072470 to G.Q.)the Natural Key Research and Development Program(2022YFD1400200 to G.Q.)+1 种基金Science and Technology project of Shanxi Branch of China National Tobacco Corporation(KJ‐2022‐04)the Jiangsu University advantage discipline construction project(80900246 to X.S.)。
文摘To remain competitive,proteobacteria use various contact-dependent weapon systems to defend against microbial com-petitors.The bacterial-killing type IV secretion system(T4SS)is one such powerful weapon.It commonly controls the killing/competition between species by secreting the lethal T4SS effector(T4E)proteins carrying conserved XVIPCD domains into competing cells.In this study,we sought knowledge to understand whether the bacterial-killing T4SS-producing bacteria encode T4E-like proteins and further explore their biological functions.To achieve this,we designed a T4E-guided approach to discover T4E-like proteins that are designated as atypical T4Es.Initially,this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS-producing bacteria.These homologous genes were then screened in Escherichia coli to identify antibacterial candidates(atypical T4Es)and their neighboring detoxification proteins,followed by testing their gene cotranscription and validating their physical interactions.Using this approach,we did discover two atypical T4E proteins from the plant-beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri.We also provided substantial evidence to show that the atypical T4E protein Le1637-mediated bacterial defense in interspecies interactions between L.enzymogenes and its competitors.Therefore,the newly designed T4E-guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.
基金supported by grants from National Key R&D Program of China(2019YFA0904900)National Natural Science Foundation of China(31870058).
文摘Glucose and xylose are two major components of lignocellulose.Simultaneous consumption of glucose and xylose is critical for engineered microorganisms to produce fuels and chemicals from lignocellulosic biomass.Although many production limitations have been resolved,glucose‐induced inhibition of xylose transport remains a challenge.In this study,a cell growthbased screening strategy was designed to identify xylose transporters uninhibited by glucose.The glucose pathway was genetically blocked in Escherichia coli so that glucose functions only as an inhibitor and cells need xylose as the carbon source for survival.Through adaptive evolution,omics analysis and reverse metabolic engineering,a new phosphoenolpyruvate:carbohydrate phosphotransferase system(PTS)galactitol transporter(GalABC,encoded by EcolC_1640,EcolC_1641,and EcolC_1642 genes)that is not inhibited by glucose was identified.Inactivation of adenylate cyclase led to increased expression of the EcolC_1642 gene,and a point mutation in gene EcolC_1642(N13S)further enhanced xylose transport.During the second round of gene mining,AraE and a new ABC transporter(AraFGH)of xylose were identified.A point mutation in the transcription regulator araC(L156I)caused increased expression of araE and araFGH genes without arabinose induction,and a point mutation in araE(D223Y)further enhanced xylose transport.These newly identified xylose transporters can support the simultaneous consumption of glucose and xylose and have potential use in producing chemicals from lignocellulose.
