Porcine epidemic diarrhea virus(PEDV),an enteric coronavirus,is widely spread worldwide and causes huge economic losses.The effective measure to control the viral infection is to develop ideal vaccines.Here,the collag...Porcine epidemic diarrhea virus(PEDV),an enteric coronavirus,is widely spread worldwide and causes huge economic losses.The effective measure to control the viral infection is to develop ideal vaccines.Here,the collagenase equivalent domain(COE)of PEDV was displayed on the surface of nanoparticles(NPs)in order to develop a newer,safer and more effective subunit vaccine against PEDV.The monomeric COE was displayed on the mi3 protein,which self-assembles into nanoparticles composed of 60 subunits,using the SpyTag/SpyCatcher system.The size,zeta potential,microstructure of the COE-mi3 virus-like particles(VLPs)were investigated.The COE-mi3 VLPs that possessed good security,stability and better retention can be more efficiently taken up by antigen-presenting cells(APCs)and help promote dendritic cells(DCs)maturation.Moreover,COE-mi3 VLPs could prominently improve specifc antibody levels including neutralizing antibodies(NAbs),and serum IgG,mucosal IgA.Moreover,COE-mi3 VLPs elicited more activation of CD4^(+)and CD8^(+)T cells and production of IFN-γand IL-4 cytokines.In particular,COE-mi3 VLPs is an effectual antigen-delivery platform to enhance germinal center(GC)B cell responses.This structure-based self-assembly of NP gives great potential to be developed as a new subunit vaccines attractive platform,and may also provide new ideas for the development of other enteric coronavirus vaccines.展开更多
African swine fever(ASF),caused by the African swine fever virus(ASFV),has brought enormous economic loss and represents a major threat to the global pig industry(Vergne et al.2017).ASFVs are divided into 24 genotypes...African swine fever(ASF),caused by the African swine fever virus(ASFV),has brought enormous economic loss and represents a major threat to the global pig industry(Vergne et al.2017).ASFVs are divided into 24 genotypes based on their B646L gene,with only genotypes Ⅰ and Ⅱ circulating globally(Dixon et al.2019).展开更多
Objective Charcot-Marie-Tooth disease(CMT)severely affects patient activity,and may cause disability.However,no clinical treatment is available to reverse the disease course.The combination of CRISPR/Cas9 and iPSCs ma...Objective Charcot-Marie-Tooth disease(CMT)severely affects patient activity,and may cause disability.However,no clinical treatment is available to reverse the disease course.The combination of CRISPR/Cas9 and iPSCs may have therapeutic potential against nervous diseases,such as CMT.Methods In the present study,the skin fibroblasts of CMT type 2D(CMT2D)patients with the c.880G>A heterozygous nucleotide mutation in the GARS gene were reprogrammed into iPSCs using three plasmids(pCXLE-hSK,pCXLE-hUL and pCXLE-hOCT3/4-shp5-F).Then,CRISPR/Cas9 technology was used to repair the mutated gene sites at the iPSC level.Results An iPSC line derived from the GARS(G294R)family with fibular atrophy was successfully induced,and the mutated gene loci were repaired at the iPSC level using CRISPR/Cas9 technology.These findings lay the foundation for future research on drug screening and cell therapy.Conclusion iPSCs can differentiate into different cell types,and originate from autologous cells.Therefore,they are promising for the development of autologous cell therapies for degenerative diseases.The combination of CRISPR/Cas9 and iPSCs may open a new avenue for the treatment of nervous diseases,such as CMT.展开更多
African swine fever virus(ASFV)is a lethal pathogen that causes severe threats to the global swine industry and it has already had catastrophic socio-economic effects.To date,no licensed prophylactic vaccine exists.Li...African swine fever virus(ASFV)is a lethal pathogen that causes severe threats to the global swine industry and it has already had catastrophic socio-economic effects.To date,no licensed prophylactic vaccine exists.Limited knowledge exists about the major immunogens of ASFV and the epitope mapping of the key antigens.As such,there is a considerable requirement to understand the functional monoclonal antibodies(mAbs)and the epitope mapping may be of utmost importance in our understanding of immune responses and designing improved vaccines,therapeutics,and diagnostics.In this study,we generated an ASFV antibody phage-display library from ASFV convalescent swine PBMCs,further screened a specific ASFV major capsid protein(p72)single-chain antibody and fused with an IgG Fc fragment(scFv-83-Fc),which is a specific recognition antibody against ASFV Pig/HLJ/2018 strain.Using the scFv-83-Fc mAb,we selected a conserved epitope peptide(221MTGYKH226)of p72 retrieved from a phage-displayed random peptide library.Moreover,flow cytometry and cell uptake experiments demonstrated that the epitope peptide can significantly promote BMDCs maturation in vitro and could be effectively uptaken by DCs,which indicated its potential application in vaccine and diagnostic reagent development.Overall,this study provided a valuable platform for identifying targets for ASFV vaccine development,as well as to facilitate the optimization design of subunit vaccine and diagnostic reagents.展开更多
On May 1,2025,Gonzalez-Perez and colleagues(1)reported a multi-country outbreak caused by Salmonella enterica subspecies enterica serovar Mbandaka(S.Mbandaka)that resulted in over 200 cases across Europe.Finland repor...On May 1,2025,Gonzalez-Perez and colleagues(1)reported a multi-country outbreak caused by Salmonella enterica subspecies enterica serovar Mbandaka(S.Mbandaka)that resulted in over 200 cases across Europe.Finland reported the highest number of cases with 97 infections.Whole genome sequencing(WGS)and comparative genomic analyses revealed that the outbreak strains were genetically linked to previously identified strains in the United Kingdom and to pre-cooked,frozen chicken meat used in ready-to-eat products.Subsequently,on May 5,2025,the United States of America(USA)Centers for Disease Control and Prevention(CDC)announced a Salmonella outbreak associated with backyard poultry(2).As of May 19,2025,this outbreak had expanded to 104 confirmed infections,with at least 33 individuals contracting Salmonella following contact with backyard poultry.Tragically,one death has been reported in Illinois.Scientific evidence demonstrates that S.Mbandaka isolated from patient samples,and matched the strain found in shipping boxes used to transport poultry from hatcheries to agricultural retail stores.展开更多
Infections by Carbapenem-resistant Enterobacteriaceae(CRE)producing New Delhi metallo-β-lactamases(NDMs)that hydrolyze carbapenems,are difficult to treat.Considering the fact of barren antibiotic development pipeline...Infections by Carbapenem-resistant Enterobacteriaceae(CRE)producing New Delhi metallo-β-lactamases(NDMs)that hydrolyze carbapenems,are difficult to treat.Considering the fact of barren antibiotic development pipeline nowadays,revitalizing carbapenems efficacy using antibiotic adjuvants represents a promising but as-yet-unrealized tactic in combating NDMs-producing CRE,because of their off-target distributions,weak permeability to the outer membrane(OM)barrier,and limited NDMs-inactivation ability.Here,a pathogen-anchoring nano electrosensitizer,is proposed for serving as electrodynamic therapy(EDT)-activatable antibiotic adjuvant to revitalize meropenem(MEM,a typical carbapenems),through layerby-layer assembly of platinum nanoclusters(PtNCs),MEM,and maltodextrin(MA).The MA corona of electro-driven nanosensitizer promotes the efficient anchoring of PtNCs and MEM onto the surface of pathogen.Triggered by a square-wave alternating current(AC),MEM is released,PtNCs-based EDT is activated,accompanied by the generation of electro-driven reactive oxygen(ROS)at the bacterial infectious microenvironment.Subsequently,the antibacterial efficacy of MEM is thereby restored against NDMs-producing CRE through the ROS-mediated cascading effect,including the OM destruction,MEM intracellular accumulation,and NDMs inactivation.By the cooperation of MA-mediated pathogen anchoring and EDT-induced dual action,the pathogen-anchoring nano electrosensitizer revitalizes MEM efficacy against clinically isolated NDMs-producing CRE in vitro,and in mice infection model,importantly,also slows down the development of higher-level resistance in NDMsproducing CRE.The pathogen-anchoring nano electrosensitizer can fully play the therapeutic potency of carbapenems,providing a promising approach to tackle NDMs producer-induced infections.展开更多
We read the study conducted by Cui et al.published in China CDC Weekly with great interest,and would like to make comment on this matter(1).The report identified 31 Salmonella enterica serovar I 1,4,[5],12:i:-(S.I 1,4...We read the study conducted by Cui et al.published in China CDC Weekly with great interest,and would like to make comment on this matter(1).The report identified 31 Salmonella enterica serovar I 1,4,[5],12:i:-(S.I 1,4,[5],12:i:-)sequence type 8333(ST8333)genomes by the end of 2023 in the National Molecular Tracing Network for Foodborne Disease Surveillance database.The overall percentage of isolates of S.I 1,4,[5],12:i:-ST8333 remained low in their active monitoring between 2017 and 2023,and observed ST8333 in 2017.展开更多
Introduction:Chromobacterium haemolyticum(C.haemolyticum)can cause invasive infections in humans.This study aims to reveal the genomic characteristics of C.haemolyticum and provide guidance for clinical diagnosis,trea...Introduction:Chromobacterium haemolyticum(C.haemolyticum)can cause invasive infections in humans.This study aims to reveal the genomic characteristics of C.haemolyticum and provide guidance for clinical diagnosis,treatment,prevention,and control.Methods:Species identification was performed through isolation culture and matrix-assisted laser desorption ionization time-of-flight mass spectrometry.Antibiotic susceptibility testing determined resistance phenotypes.High-throughput sequencing and bioinformatics methods were used to predict antibiotic resistance genes and virulence genes and to analyze the evolutionary characteristics of global C.hemolyticus genomes.Results:In this study,a C.haemolyticum strain was isolated from the bronchoalveolar lavage fluid of a patient in Guangxi Zhuang Autonomous Region,China.The isolate was sensitive to chloramphenicol,macrolides,and trimethoprim,while resistant to betalactams.Comparative genomics analysis revealed that most global strains carry carbapenemase-encoding genes.Phylogenetic analysis showed that the strain from this patient was closely related to a pond-derived C.haemolyticum isolate from Yangzhou,China.Conclusions:This study uncovered the genetic characteristics of C.haemolyticum from various sources worldwide,including antibiotic resistance and virulence factors,providing an important reference for clinical treatment.展开更多
Dear Editor,Human immunodeficiency virus(HIV)is a lentivirus that,if left untreated,can lead to acquired immunodeficiency syndrome(AIDS).The virus can be divided into two types based on genetic differences:HIV-1 and H...Dear Editor,Human immunodeficiency virus(HIV)is a lentivirus that,if left untreated,can lead to acquired immunodeficiency syndrome(AIDS).The virus can be divided into two types based on genetic differences:HIV-1 and HIV-2.HIV-1 is widely distributed worldwide and is the primary strain responsible for the global AIDS epidemic due to its high replication capacity,greater likelihood of transmission,and more severe clinical symptoms(Oeschger et al.,2021).展开更多
Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bac...Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains unavailable.In this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten countries.We found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously reported.The newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to Caudovirales.Approximately,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular viruses.Moreover,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses.Together,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.展开更多
基金supported by the Major Scientific and Technological Project of the Henan Province,China(221100110600)the Beijing Life Science Academy,China(2024500CA0010)+1 种基金the Major Program of National Natural Science Foundation of China(32192452)the Chinese Postdoctoral Science Foundation(2023M743209)。
文摘Porcine epidemic diarrhea virus(PEDV),an enteric coronavirus,is widely spread worldwide and causes huge economic losses.The effective measure to control the viral infection is to develop ideal vaccines.Here,the collagenase equivalent domain(COE)of PEDV was displayed on the surface of nanoparticles(NPs)in order to develop a newer,safer and more effective subunit vaccine against PEDV.The monomeric COE was displayed on the mi3 protein,which self-assembles into nanoparticles composed of 60 subunits,using the SpyTag/SpyCatcher system.The size,zeta potential,microstructure of the COE-mi3 virus-like particles(VLPs)were investigated.The COE-mi3 VLPs that possessed good security,stability and better retention can be more efficiently taken up by antigen-presenting cells(APCs)and help promote dendritic cells(DCs)maturation.Moreover,COE-mi3 VLPs could prominently improve specifc antibody levels including neutralizing antibodies(NAbs),and serum IgG,mucosal IgA.Moreover,COE-mi3 VLPs elicited more activation of CD4^(+)and CD8^(+)T cells and production of IFN-γand IL-4 cytokines.In particular,COE-mi3 VLPs is an effectual antigen-delivery platform to enhance germinal center(GC)B cell responses.This structure-based self-assembly of NP gives great potential to be developed as a new subunit vaccines attractive platform,and may also provide new ideas for the development of other enteric coronavirus vaccines.
基金supported by the National Natural Science Fund for Distinguished Young Scholars of China(31925036 and 32025034)the Shandong Provincial Key R&D Program,China(2021LZGC001)+3 种基金the Biological Breeding-Major Projects,Institute of Zoology,Chinese Academy of Sciences and Institute of Animal Science,Chinese Academy of Agricultural Sciences(2023ZD04074 and 2023ZD0404604)the Special Project of Longhu Laboratory,China(LHLab_ZD20230012)the National Natural Science Foundation of China(32230100,32330099 and 32201257)the National Key Research and Development Program of China(2020YFA0509503,2022YFF0710703,2021YFA0805902 and 2022XAGG0121,2022YFF1002803).
文摘African swine fever(ASF),caused by the African swine fever virus(ASFV),has brought enormous economic loss and represents a major threat to the global pig industry(Vergne et al.2017).ASFVs are divided into 24 genotypes based on their B646L gene,with only genotypes Ⅰ and Ⅱ circulating globally(Dixon et al.2019).
基金supported by grants from the National Major Scientific and Technological Special Project for“Significant New Drugs Development”(No.2019ZX09301159)the“Thousand Talent Program”for Science and Technology Innovation Leader in Henan(No.194200510002)+1 种基金the Bingtuan Science and Technology Project(No.2019AB034)the Natural Science Foundation of Henan Province of China(No.202300410381).
文摘Objective Charcot-Marie-Tooth disease(CMT)severely affects patient activity,and may cause disability.However,no clinical treatment is available to reverse the disease course.The combination of CRISPR/Cas9 and iPSCs may have therapeutic potential against nervous diseases,such as CMT.Methods In the present study,the skin fibroblasts of CMT type 2D(CMT2D)patients with the c.880G>A heterozygous nucleotide mutation in the GARS gene were reprogrammed into iPSCs using three plasmids(pCXLE-hSK,pCXLE-hUL and pCXLE-hOCT3/4-shp5-F).Then,CRISPR/Cas9 technology was used to repair the mutated gene sites at the iPSC level.Results An iPSC line derived from the GARS(G294R)family with fibular atrophy was successfully induced,and the mutated gene loci were repaired at the iPSC level using CRISPR/Cas9 technology.These findings lay the foundation for future research on drug screening and cell therapy.Conclusion iPSCs can differentiate into different cell types,and originate from autologous cells.Therefore,they are promising for the development of autologous cell therapies for degenerative diseases.The combination of CRISPR/Cas9 and iPSCs may open a new avenue for the treatment of nervous diseases,such as CMT.
基金supported by the National Natural Science Foundation of China(31941001 and 32002292)the Major Science and Technology Project of Henan Province,China(221100110600)the Natural Science Foundation of Henan Province(202300410199).
文摘African swine fever virus(ASFV)is a lethal pathogen that causes severe threats to the global swine industry and it has already had catastrophic socio-economic effects.To date,no licensed prophylactic vaccine exists.Limited knowledge exists about the major immunogens of ASFV and the epitope mapping of the key antigens.As such,there is a considerable requirement to understand the functional monoclonal antibodies(mAbs)and the epitope mapping may be of utmost importance in our understanding of immune responses and designing improved vaccines,therapeutics,and diagnostics.In this study,we generated an ASFV antibody phage-display library from ASFV convalescent swine PBMCs,further screened a specific ASFV major capsid protein(p72)single-chain antibody and fused with an IgG Fc fragment(scFv-83-Fc),which is a specific recognition antibody against ASFV Pig/HLJ/2018 strain.Using the scFv-83-Fc mAb,we selected a conserved epitope peptide(221MTGYKH226)of p72 retrieved from a phage-displayed random peptide library.Moreover,flow cytometry and cell uptake experiments demonstrated that the epitope peptide can significantly promote BMDCs maturation in vitro and could be effectively uptaken by DCs,which indicated its potential application in vaccine and diagnostic reagent development.Overall,this study provided a valuable platform for identifying targets for ASFV vaccine development,as well as to facilitate the optimization design of subunit vaccine and diagnostic reagents.
基金Supported in part by grants from the Project for the Young Scientist of the Joint Funds of Science and Technology Research and Development Plan of Henan Province,China(235200810058)the National Key Research and Development Program of China(2023YFC2307101)the Young Top-Notch Talents Foundation of Henan Agricultural University(30501278).
文摘On May 1,2025,Gonzalez-Perez and colleagues(1)reported a multi-country outbreak caused by Salmonella enterica subspecies enterica serovar Mbandaka(S.Mbandaka)that resulted in over 200 cases across Europe.Finland reported the highest number of cases with 97 infections.Whole genome sequencing(WGS)and comparative genomic analyses revealed that the outbreak strains were genetically linked to previously identified strains in the United Kingdom and to pre-cooked,frozen chicken meat used in ready-to-eat products.Subsequently,on May 5,2025,the United States of America(USA)Centers for Disease Control and Prevention(CDC)announced a Salmonella outbreak associated with backyard poultry(2).As of May 19,2025,this outbreak had expanded to 104 confirmed infections,with at least 33 individuals contracting Salmonella following contact with backyard poultry.Tragically,one death has been reported in Illinois.Scientific evidence demonstrates that S.Mbandaka isolated from patient samples,and matched the strain found in shipping boxes used to transport poultry from hatcheries to agricultural retail stores.
基金supported by the National Natural Science Foundation of China(No.82402470)Postdoctoral Science Foundation of China(No.2023M743207)+2 种基金Science and Technology Key Research Project of Henan Province(No.252102311187)Postdoctoral Fellowship Program of CPSF(No.GZC20232438)Major Science and Technology Projects in Henan Province(No.241110310600).
文摘Infections by Carbapenem-resistant Enterobacteriaceae(CRE)producing New Delhi metallo-β-lactamases(NDMs)that hydrolyze carbapenems,are difficult to treat.Considering the fact of barren antibiotic development pipeline nowadays,revitalizing carbapenems efficacy using antibiotic adjuvants represents a promising but as-yet-unrealized tactic in combating NDMs-producing CRE,because of their off-target distributions,weak permeability to the outer membrane(OM)barrier,and limited NDMs-inactivation ability.Here,a pathogen-anchoring nano electrosensitizer,is proposed for serving as electrodynamic therapy(EDT)-activatable antibiotic adjuvant to revitalize meropenem(MEM,a typical carbapenems),through layerby-layer assembly of platinum nanoclusters(PtNCs),MEM,and maltodextrin(MA).The MA corona of electro-driven nanosensitizer promotes the efficient anchoring of PtNCs and MEM onto the surface of pathogen.Triggered by a square-wave alternating current(AC),MEM is released,PtNCs-based EDT is activated,accompanied by the generation of electro-driven reactive oxygen(ROS)at the bacterial infectious microenvironment.Subsequently,the antibacterial efficacy of MEM is thereby restored against NDMs-producing CRE through the ROS-mediated cascading effect,including the OM destruction,MEM intracellular accumulation,and NDMs inactivation.By the cooperation of MA-mediated pathogen anchoring and EDT-induced dual action,the pathogen-anchoring nano electrosensitizer revitalizes MEM efficacy against clinically isolated NDMs-producing CRE in vitro,and in mice infection model,importantly,also slows down the development of higher-level resistance in NDMsproducing CRE.The pathogen-anchoring nano electrosensitizer can fully play the therapeutic potency of carbapenems,providing a promising approach to tackle NDMs producer-induced infections.
基金Supported in part by grants from the Project for the National Key Research and Development Program of China(2023YFC2307101)Young Scientist of the Joint Funds of Science and Technology Research and Development Plan of Henan Province,China(235200810058)Young TopNotch Talents Foundation of Henan Agricultural University(30501278).
文摘We read the study conducted by Cui et al.published in China CDC Weekly with great interest,and would like to make comment on this matter(1).The report identified 31 Salmonella enterica serovar I 1,4,[5],12:i:-(S.I 1,4,[5],12:i:-)sequence type 8333(ST8333)genomes by the end of 2023 in the National Molecular Tracing Network for Foodborne Disease Surveillance database.The overall percentage of isolates of S.I 1,4,[5],12:i:-ST8333 remained low in their active monitoring between 2017 and 2023,and observed ST8333 in 2017.
基金Supported by grants from the National Key Research and Development Program of China(2023YFC2307101)the Young TopNotch Talents Foundation of Henan Agricultural University(30501278)Project for Young Scientist of the Joint Funds of Science and Technology Research and Development Plan of Henan Province,China(235200810058).
文摘Introduction:Chromobacterium haemolyticum(C.haemolyticum)can cause invasive infections in humans.This study aims to reveal the genomic characteristics of C.haemolyticum and provide guidance for clinical diagnosis,treatment,prevention,and control.Methods:Species identification was performed through isolation culture and matrix-assisted laser desorption ionization time-of-flight mass spectrometry.Antibiotic susceptibility testing determined resistance phenotypes.High-throughput sequencing and bioinformatics methods were used to predict antibiotic resistance genes and virulence genes and to analyze the evolutionary characteristics of global C.hemolyticus genomes.Results:In this study,a C.haemolyticum strain was isolated from the bronchoalveolar lavage fluid of a patient in Guangxi Zhuang Autonomous Region,China.The isolate was sensitive to chloramphenicol,macrolides,and trimethoprim,while resistant to betalactams.Comparative genomics analysis revealed that most global strains carry carbapenemase-encoding genes.Phylogenetic analysis showed that the strain from this patient was closely related to a pond-derived C.haemolyticum isolate from Yangzhou,China.Conclusions:This study uncovered the genetic characteristics of C.haemolyticum from various sources worldwide,including antibiotic resistance and virulence factors,providing an important reference for clinical treatment.
基金This work was supported by the COVID-19 Emergency Project of the National Key Research and Development Program of China(2022YFC0867900)the National Natural Science Foundation of China(32072944)+2 种基金the Emergency Scientific Research on Epidemic Prevention and Control of Henan Province(211100310200)Science and Technology Project of Henan Province(21210230180)Medical Science and Technology project of Henan Province(LHGJ20210274).
文摘Dear Editor,Human immunodeficiency virus(HIV)is a lentivirus that,if left untreated,can lead to acquired immunodeficiency syndrome(AIDS).The virus can be divided into two types based on genetic differences:HIV-1 and HIV-2.HIV-1 is widely distributed worldwide and is the primary strain responsible for the global AIDS epidemic due to its high replication capacity,greater likelihood of transmission,and more severe clinical symptoms(Oeschger et al.,2021).
基金supported in part by grants from the National Key Research and Development Program of China(2023YFC2307101,2020YFA0509202)the Young TopNotch Talents Foundation of Henan Agricultural University(30501278)+5 种基金the major Scientific and Technological Project of Henan Province(221100110600)the Major Program of the National Natural Science Foundation of China(81991534)CAS Southeast Asia Biodiversity Research Institute(151C53KYSB20210023)the Self-supporting Program of Guangzhou Laboratory(SRPG22-001)the National Science and Technology Infrastructure of China(National Pathogen Resource Center-NPRC-32)supported by the Youth Innovation Promotion Association of CAS(Y2021034)。
文摘Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains unavailable.In this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten countries.We found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously reported.The newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to Caudovirales.Approximately,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular viruses.Moreover,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses.Together,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.
