Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and stu...Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and studied.In this study,a novel lytic Pseudoalteromonas phage,denoted as vB_PalP_Y7,was isolated from sewage samples collected at the Seafood Market in Qingdao,China.vB_PalP_Y7 remained stable across a wide range of temperatures(-20–50℃)and a wide pH range(3–12).The vB_PalP_Y7 phage harbors a linear double-stranded DNA molecule of 57699 base pairs(bp)with a G+C content of 45.90%.Furthermore,it is predicted to contain 58 open reading frames(ORFs).Phylogenetic analysis and protein network relationship analysis revealed low similarity between vB_PalP_Y7 and viruses in the ICTV and IMG/VR4 database,suggesting that vB_PalP_Y7 may be a potential new genus,Miuvirus.This study contributed valuable insights to comprehend the relationship between Pseudoalteromonas phages and their host organisms.展开更多
In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV7...In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.展开更多
The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array ...The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array comparative genomic hybridization （aCGH） or single nucleotide polymorphism （SNP） chips has been applied to pediatric patients with developmental and intellectual disabilities （DD/ ID）, multiple congenital anomalies （MCA） and autistic spectrum disorders （ASD）. Evaluation of analytical and clinical validities of aCGH showed 〉 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%--20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.展开更多
Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated f...Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.展开更多
Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a centu...Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.展开更多
The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndr...The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.展开更多
Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embr...Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embryo kidney cells.A study of pathogenicity indicated that SD1511 readily infected 7–35-d-old chickens by intramuscular injection and intranasal and oral routes,causing 50%–100%mortality.The 35-d-old chickens suffered more severe infection than 7-and 21-d-old chickens with mortality highest in the intramuscular injection group.The serum from surviving chickens showed potent viral neutralizing capability.The complete genome of SD1511 was sequenced and analyzed.The strain was found to belong to the FAdV-4 cluster with more than 99%identity with the virulent FAdV-4 strains isolated in China in recent years except for some distinct variations,including deletions of open reading frame 27(ORF27),ORF48,and part of ORF19.Our findings suggest that SD1511 might be used as a prototype strain for the study of pathogenesis and vaccine development.展开更多
Cartilaginous fish(sharks,skates,rays,and chimaeras)are an important group of vertebrates facing the risk of regional extinction due to factors such as overfishing(Pacoureau et al.2021;Finucci et al.2024;Worm et al.20...Cartilaginous fish(sharks,skates,rays,and chimaeras)are an important group of vertebrates facing the risk of regional extinction due to factors such as overfishing(Pacoureau et al.2021;Finucci et al.2024;Worm et al.2024).However,knowledge of their reproduction and conservation remains limited.Understanding the genetic diversity,population structure,and reproductive behaviors of cartilaginous fish can offer valuable insights into their reproductive strategies and ecological adaptability,which are crucial for the conservation of these vulnerable species.Here,we present a chromosome-level draft genome as well as whole genome resequencing data of seven other individuals for the Kong skate(Okamejei kenojei),a species that has been reported to have a population decrease based on fisheries resource surveys(Deng&Jin 2001;Rigby et al.2021).Our analysis revealed lineage-specific genomic changes in O.kenojei,including the expansion of 69 gene families.We also assessed their genetic diversity,which showed a decline in population size over the past million years.Furthermore,we examined the egg-laying behavior of 24 adult female specimens and the incubation period of 35 embryos,indicating a low reproductive capacity.In conclusion,our findings suggest that the genetic diversity of the current wild population of O.kenojei is relatively healthy,but their reproductive output is low.Without proper management and protection,this could lead to irreversible impacts on the population,highlighting the importance of conservation efforts for this species.展开更多
What is known about this topic?Global human cases of zoonotic influenza A(H5N6)have increased significantly in recent years,primarily due to widespread circulation of clade 2.3.4.4b virus since 2020.Concurrent with th...What is known about this topic?Global human cases of zoonotic influenza A(H5N6)have increased significantly in recent years,primarily due to widespread circulation of clade 2.3.4.4b virus since 2020.Concurrent with this trend,sporadic human infections with clade 2.3.4.4h H5N6 avian influenza virus continue to occur.The high mortality rate associated with H5N6 virus infections has emerged as a critical public health concern.What is added by this report?Through comprehensive field epidemiological investigations and laboratory analyses,we identified the infection sources for these cases and conclusively ruled out human-to-human transmission.Genetic analyses revealed that while the virus maintains its avian host tropism,it has acquired mutations that may enhance human receptor binding affinity,viral replication capacity,pathogenicity,and neuraminidase inhibitor resistance.What are the implications for public health practice?The ongoing viral mutations increase the potential for H5 subtype avian influenza viruses to overcome species barriers and cause human epidemics.Enhanced surveillance strategies incorporating advanced technologies,such as metagenomic sequencing,are essential for early risk detection and management.Special attention should be directed toward cancer patients and immunocompromised individuals,who demonstrate increased susceptibility to avian influenza virus infections and require targeted prevention and control measures.展开更多
African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A Q...African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A QTL analysis of 331 recombinant inbred lines(RILs)using 194 InDel markers identified five quantitative trait loci(QTL)associated with awn length.Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval.RNA-seq and RT-qPCR analyses,combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5.Genomic analysis revealed a large structural variation(SV)between W1411 and IRGC104165 within this region,characterized by an inversion and two large deletions.Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like(Dom-like)pattern,whereas non-cultivated accessions consisted of two distinct types:W1050-like and W1411-like.The W1411-like type was exclusively found in the AA genome of African wild rice.This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.展开更多
Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.aru...Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.展开更多
The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
In order to effectively use of phages as antimicrobial agents for controlling multidrug-resistant E.coli,it is important to understand phage biology.The isolation and research of novel bacteriophages are urgently need...In order to effectively use of phages as antimicrobial agents for controlling multidrug-resistant E.coli,it is important to understand phage biology.The isolation and research of novel bacteriophages are urgently needed for food safety and animal health.Phage is considered as a novel alternative antibacterial agents and a new way of prevent,control and treat pathogens.In this paper,we isolated and characterized a novel lytic phage from chicken samples,named vB_EscP_vE20(in brief vE20).We identified vE20 as belonging to the Podoviridae family through morphological and phylogenetic analysis.It had lytic activities against 24 out of 51 different serotypes of clinical E.coli strains,interestingly it also can lyse Salmonella species,such as Salmonella Enteritidis(S.Enteritidis)and Samonella Typhimu-rium(S.Typhimurium).One step growth curve showed that the latent period and lysis period was 10 min and 60 min,respectively.The burst size of vE20 was about 60 PFU/cell.The phage vE20 survived in a wide range of temperatures(30-60℃)and pH(3-11).The whole genome size of phage vE20 is 77,938 bps,which is double stranded DNA.There are 121 Open reading frame(ORFs)in total,and the GC-content is 42.17%,without virulence-associated,antibiotic and lysogeny related genes.Phage vE20 has high bactericidal activity in killing E.coli EXG20-1 in cultures containing 4×10^(9) cfu/mL in several MOIs culture.The results revealed the promising potential of phage vE20 as attractive candidates for the control of E.coli infections.展开更多
The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims i...The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims in the GenBank, and the nomvirus genome was amplified by RT-PCR. The PCR- products were cloned into T vector and sequenced, and the genomic nucleotide sequences were analyzed with the programs CLUSTAL W/X, DNASTAR and RAT （Recombination Analysis Tool）. The NVgz01 strain genome is 7558 bp in length and encodes three open reading frames （GenBank accession No. is DQ369797）. The genomic sequences of NVgz01 were compared with those of nomvirus in GenBank, which revealed that the homology with genogroup Ⅱ ranges between 76%-90%, and genogroup Ⅰ between 43%-44%. The ORF1 region shared 94% and 88% identity with Mc37 and Famiington strains, respectively; the capsid region （ORF2） shared 65% and 94% identity with Mc37 and Farmington strains, respectively. Phylogenetic trees were reconstructed by the neighbor-joining method. Comparative complete sequence analysis of the NVgz01 with reported human norovirus genomic sequences revealed that this isolate belongs to genogroup Ⅱ . The ORF1 and ORF2 regions shared different identity with Mc37 and Fannington strains, suggesting NVgz01 could be a recombinant virus.展开更多
To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the ...To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the target sequence were amplified by RT-PCR. Then the PCR-products were cloned to T vector and sequenced. The genomic nucleotide sequences were analyzed by the programs CLUSTAL W and DNASTAR. It was found that the full genomic length of HASTVgz01 strain was 6721 bp and the ORFs were 6558 bp. The 5＇ and 3＇UTR were 82 and 81 nucleotides. The genome included 3 open reading frames （ORFs） ： ORFla, ORFlb and ORF2. The 5＇-terminal ORFla started at nueleotide 83 and extended to nucleotide 2845. ORFlb （nt 2785 to nt 4332） overlaped ORFla by 61 nueleotides. The 3＇-terminal ORF2 began at nucleotide 4325 and terminated at nucleotide 6640. ORF2 had 2316 nucleotides. Compared with other astrovirus sequences in GenBank, the homology of the amino acid sequence of ORF2 of HASTVgz01 strain with that of serotype 4 was 93%. Homology with other serotypes ranged from 61% to 70%. The complete nucleotide sequence of astrovirus HASTVgz01 strain isolated from Guangzhou in China was 6721 bp in length, GenBank accession NO. DQ344027. Comparing the ORF2 of astrovirus HASTVgz01 with the known sequences of types 1-8 the highest homology was serotype 4 （93%）. Comparative sequence analysis of the HASTVgz01 ORF2 with the reported human astrovirus sequences revealed that the isolated astrovirus belongs to genotype （serotype） 4.展开更多
The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utilit...The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.展开更多
Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to ...Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to control this disease.Genetic analysis revealed that a single dominant resistance gene named PmTm4 originated from Chinese wheat line Tangmai 4 confers resistance to prevailing isolates of B.graminis f.sp.tritici isolate E09.Detailed comparative genomics analyses helped to develop closely linked markers to PmTm4 and a fine genetic map was constructed using large F2population,in which PmTm4 was located into a 0.66-c M genetic interval.The orthologous subgenome region of PmTm4in Aegilops tauschii was identified,and two resistance gene analogs（RGA）were characterized from the corresponding sequence scaffolds of Ae.tauschii draft assembly.The closely linked markers and identified Ae.tauschii orthologs in the mapping interval provide an entry point for chromosome landing and map-based cloning of PmTm4.展开更多
A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. ...A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. Koch respectively was made. In the course of germplasm development, genome analysis by means of chromosome banding, genomic in situ hybridization (GISH) or fluorescence in situ hybridization (FISH), molecular markers, particularly restriction fragment length polymorphism (RFLP) coupled with aneuploid analysis was employed for the purpose of improving breeding efficiency. Potential use of such germplasm in wheat breeding practice, basic studies and some related problems were also discussed.展开更多
A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant ce...A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.展开更多
Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this in...Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.展开更多
基金the National Natural Science Foundation of China(Nos.42188102,42120104006,41976117,42176111)the Fundamental Research Funds for the Central Universities(Nos.202172002,201812002)the funding from Andrew Mc Minn。
文摘Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and studied.In this study,a novel lytic Pseudoalteromonas phage,denoted as vB_PalP_Y7,was isolated from sewage samples collected at the Seafood Market in Qingdao,China.vB_PalP_Y7 remained stable across a wide range of temperatures(-20–50℃)and a wide pH range(3–12).The vB_PalP_Y7 phage harbors a linear double-stranded DNA molecule of 57699 base pairs(bp)with a G+C content of 45.90%.Furthermore,it is predicted to contain 58 open reading frames(ORFs).Phylogenetic analysis and protein network relationship analysis revealed low similarity between vB_PalP_Y7 and viruses in the ICTV and IMG/VR4 database,suggesting that vB_PalP_Y7 may be a potential new genus,Miuvirus.This study contributed valuable insights to comprehend the relationship between Pseudoalteromonas phages and their host organisms.
基金funded by Natural Science Foundation of Zhejiang(LQ14C010006)National Natural Science Foundation of China(81501363)Planned Science and Technology Project of Zhejiang(2014C33261)
文摘In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.
基金supported in part by fellowship award from the China Scholarship Council to Yuan Wei
文摘The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array comparative genomic hybridization （aCGH） or single nucleotide polymorphism （SNP） chips has been applied to pediatric patients with developmental and intellectual disabilities （DD/ ID）, multiple congenital anomalies （MCA） and autistic spectrum disorders （ASD）. Evaluation of analytical and clinical validities of aCGH showed 〉 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%--20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.
基金supported by the National Natural Science Foundation of China(31820103010,31530056,and 31871773)National Key Research and Development Project(2018YFC1604206)+3 种基金Projects of Innovation and Development Pillar Program for Key Industries in Southern Xinjiang of Xinjiang Production and Construction Corps(2018DB002)National FirstClass Discipline Program of Food Science and Technology(JUFSTR20180102)BBSRC Newton Fund Joint Centre Award(BB/J004529/1)Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.
基金Supported by the National Natural Science Foundation of China-Shandong Joint Fund(No.U1706208)the National Natural Science Foundation of China(Nos.41776131,41776130)。
文摘Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.
基金supported by the Natural Science Foundation of Jiangsu Province(BK20200084)the National Natural Science Foundation of China(31871773 and 31820103010)+1 种基金the Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province and Key Talents Project of“Strengthening Health through Science and Education”of Wuxi Health and Family Planning Commission(ZDRC039)Top Talents Project of“Six-one Project”for High-level Health Talents in Jiangsu Province(LGY2018016)。
文摘The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.
基金the National Key Technology Research and Development Program of China(No.2015BAD12B01)the China Agriculture Research System(No.CARS-40-K13)
文摘Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embryo kidney cells.A study of pathogenicity indicated that SD1511 readily infected 7–35-d-old chickens by intramuscular injection and intranasal and oral routes,causing 50%–100%mortality.The 35-d-old chickens suffered more severe infection than 7-and 21-d-old chickens with mortality highest in the intramuscular injection group.The serum from surviving chickens showed potent viral neutralizing capability.The complete genome of SD1511 was sequenced and analyzed.The strain was found to belong to the FAdV-4 cluster with more than 99%identity with the virulent FAdV-4 strains isolated in China in recent years except for some distinct variations,including deletions of open reading frame 27(ORF27),ORF48,and part of ORF19.Our findings suggest that SD1511 might be used as a prototype strain for the study of pathogenesis and vaccine development.
基金supported by the National Key R&D Program of China(2022YFC3400300).
文摘Cartilaginous fish(sharks,skates,rays,and chimaeras)are an important group of vertebrates facing the risk of regional extinction due to factors such as overfishing(Pacoureau et al.2021;Finucci et al.2024;Worm et al.2024).However,knowledge of their reproduction and conservation remains limited.Understanding the genetic diversity,population structure,and reproductive behaviors of cartilaginous fish can offer valuable insights into their reproductive strategies and ecological adaptability,which are crucial for the conservation of these vulnerable species.Here,we present a chromosome-level draft genome as well as whole genome resequencing data of seven other individuals for the Kong skate(Okamejei kenojei),a species that has been reported to have a population decrease based on fisheries resource surveys(Deng&Jin 2001;Rigby et al.2021).Our analysis revealed lineage-specific genomic changes in O.kenojei,including the expansion of 69 gene families.We also assessed their genetic diversity,which showed a decline in population size over the past million years.Furthermore,we examined the egg-laying behavior of 24 adult female specimens and the incubation period of 35 embryos,indicating a low reproductive capacity.In conclusion,our findings suggest that the genetic diversity of the current wild population of O.kenojei is relatively healthy,but their reproductive output is low.Without proper management and protection,this could lead to irreversible impacts on the population,highlighting the importance of conservation efforts for this species.
基金Supported by the Fujian Natural Science Foundation(2021J01351)the Major Scientific Research Program for Young and Middle-aged Health Professionals of Fujian Province,China(Grant No.2021ZQNZD006).
文摘What is known about this topic?Global human cases of zoonotic influenza A(H5N6)have increased significantly in recent years,primarily due to widespread circulation of clade 2.3.4.4b virus since 2020.Concurrent with this trend,sporadic human infections with clade 2.3.4.4h H5N6 avian influenza virus continue to occur.The high mortality rate associated with H5N6 virus infections has emerged as a critical public health concern.What is added by this report?Through comprehensive field epidemiological investigations and laboratory analyses,we identified the infection sources for these cases and conclusively ruled out human-to-human transmission.Genetic analyses revealed that while the virus maintains its avian host tropism,it has acquired mutations that may enhance human receptor binding affinity,viral replication capacity,pathogenicity,and neuraminidase inhibitor resistance.What are the implications for public health practice?The ongoing viral mutations increase the potential for H5 subtype avian influenza viruses to overcome species barriers and cause human epidemics.Enhanced surveillance strategies incorporating advanced technologies,such as metagenomic sequencing,are essential for early risk detection and management.Special attention should be directed toward cancer patients and immunocompromised individuals,who demonstrate increased susceptibility to avian influenza virus infections and require targeted prevention and control measures.
基金supported by the National Natural Science Foundation of China (31925029,32401815)
文摘African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A QTL analysis of 331 recombinant inbred lines(RILs)using 194 InDel markers identified five quantitative trait loci(QTL)associated with awn length.Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval.RNA-seq and RT-qPCR analyses,combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5.Genomic analysis revealed a large structural variation(SV)between W1411 and IRGC104165 within this region,characterized by an inversion and two large deletions.Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like(Dom-like)pattern,whereas non-cultivated accessions consisted of two distinct types:W1050-like and W1411-like.The W1411-like type was exclusively found in the AA genome of African wild rice.This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.
基金funded by the National Natural Science Foundation of China(31771863)Science and Technology Major Project of the Fujian Province of China(2015NZ0002-2)+3 种基金Special Fund for Scientific and Technological Innovation of the Fujian Agriculture and Forestry University(KFA17168A)Doctoral Students of Fujian Agriculture and Forestry University Going Abroad to Cooperative Research(324-112110082)Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources(SKLCUSA-a201912)supported by ERDF Project“Plants as a tool for sustainable global development”(CZ.02.1.01/0.0/0.0/16_019/0000827)。
文摘Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.
文摘The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
基金supported by National Natural Science Foundation of China(No.31972764)Jiangsu Provincial Key Research and Development Program(No.BE2022361)+1 种基金One belt One road Innovation Cooperation Project of Jiangsu Province(BZ2021009)the Foundation of Coastal Agricultural Science Observation and Experimental Station of Ministry of Agriculture and Rural Affairs(No.YHS202109).
文摘In order to effectively use of phages as antimicrobial agents for controlling multidrug-resistant E.coli,it is important to understand phage biology.The isolation and research of novel bacteriophages are urgently needed for food safety and animal health.Phage is considered as a novel alternative antibacterial agents and a new way of prevent,control and treat pathogens.In this paper,we isolated and characterized a novel lytic phage from chicken samples,named vB_EscP_vE20(in brief vE20).We identified vE20 as belonging to the Podoviridae family through morphological and phylogenetic analysis.It had lytic activities against 24 out of 51 different serotypes of clinical E.coli strains,interestingly it also can lyse Salmonella species,such as Salmonella Enteritidis(S.Enteritidis)and Samonella Typhimu-rium(S.Typhimurium).One step growth curve showed that the latent period and lysis period was 10 min and 60 min,respectively.The burst size of vE20 was about 60 PFU/cell.The phage vE20 survived in a wide range of temperatures(30-60℃)and pH(3-11).The whole genome size of phage vE20 is 77,938 bps,which is double stranded DNA.There are 121 Open reading frame(ORFs)in total,and the GC-content is 42.17%,without virulence-associated,antibiotic and lysogeny related genes.Phage vE20 has high bactericidal activity in killing E.coli EXG20-1 in cultures containing 4×10^(9) cfu/mL in several MOIs culture.The results revealed the promising potential of phage vE20 as attractive candidates for the control of E.coli infections.
文摘The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims in the GenBank, and the nomvirus genome was amplified by RT-PCR. The PCR- products were cloned into T vector and sequenced, and the genomic nucleotide sequences were analyzed with the programs CLUSTAL W/X, DNASTAR and RAT （Recombination Analysis Tool）. The NVgz01 strain genome is 7558 bp in length and encodes three open reading frames （GenBank accession No. is DQ369797）. The genomic sequences of NVgz01 were compared with those of nomvirus in GenBank, which revealed that the homology with genogroup Ⅱ ranges between 76%-90%, and genogroup Ⅰ between 43%-44%. The ORF1 region shared 94% and 88% identity with Mc37 and Famiington strains, respectively; the capsid region （ORF2） shared 65% and 94% identity with Mc37 and Farmington strains, respectively. Phylogenetic trees were reconstructed by the neighbor-joining method. Comparative complete sequence analysis of the NVgz01 with reported human norovirus genomic sequences revealed that this isolate belongs to genogroup Ⅱ . The ORF1 and ORF2 regions shared different identity with Mc37 and Fannington strains, suggesting NVgz01 could be a recombinant virus.
文摘To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the target sequence were amplified by RT-PCR. Then the PCR-products were cloned to T vector and sequenced. The genomic nucleotide sequences were analyzed by the programs CLUSTAL W and DNASTAR. It was found that the full genomic length of HASTVgz01 strain was 6721 bp and the ORFs were 6558 bp. The 5＇ and 3＇UTR were 82 and 81 nucleotides. The genome included 3 open reading frames （ORFs） ： ORFla, ORFlb and ORF2. The 5＇-terminal ORFla started at nueleotide 83 and extended to nucleotide 2845. ORFlb （nt 2785 to nt 4332） overlaped ORFla by 61 nueleotides. The 3＇-terminal ORF2 began at nucleotide 4325 and terminated at nucleotide 6640. ORF2 had 2316 nucleotides. Compared with other astrovirus sequences in GenBank, the homology of the amino acid sequence of ORF2 of HASTVgz01 strain with that of serotype 4 was 93%. Homology with other serotypes ranged from 61% to 70%. The complete nucleotide sequence of astrovirus HASTVgz01 strain isolated from Guangzhou in China was 6721 bp in length, GenBank accession NO. DQ344027. Comparing the ORF2 of astrovirus HASTVgz01 with the known sequences of types 1-8 the highest homology was serotype 4 （93%）. Comparative sequence analysis of the HASTVgz01 ORF2 with the reported human astrovirus sequences revealed that the isolated astrovirus belongs to genotype （serotype） 4.
基金by the National Key Research and Development Program of China(2023YFC3303701-02 and 2024YFC3306701)the National Natural Science Foundation of China(T2425014 and 32270667)+3 种基金the Natural Science Foundation of Fujian Province of China(2023J06013)the Major Project of the National Social Science Foundation of China granted to Chuan-Chao Wang(21&ZD285)Open Research Fund of State Key Laboratory of Genetic Engineering at Fudan University(SKLGE-2310)Open Research Fund of Forensic Genetics Key Laboratory of the Ministry of Public Security(2023FGKFKT07).
文摘The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.
基金financially supported by the National Natural Science Foundation of China (31371624, 31210103902)
文摘Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to control this disease.Genetic analysis revealed that a single dominant resistance gene named PmTm4 originated from Chinese wheat line Tangmai 4 confers resistance to prevailing isolates of B.graminis f.sp.tritici isolate E09.Detailed comparative genomics analyses helped to develop closely linked markers to PmTm4 and a fine genetic map was constructed using large F2population,in which PmTm4 was located into a 0.66-c M genetic interval.The orthologous subgenome region of PmTm4in Aegilops tauschii was identified,and two resistance gene analogs（RGA）were characterized from the corresponding sequence scaffolds of Ae.tauschii draft assembly.The closely linked markers and identified Ae.tauschii orthologs in the mapping interval provide an entry point for chromosome landing and map-based cloning of PmTm4.
文摘A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. Koch respectively was made. In the course of germplasm development, genome analysis by means of chromosome banding, genomic in situ hybridization (GISH) or fluorescence in situ hybridization (FISH), molecular markers, particularly restriction fragment length polymorphism (RFLP) coupled with aneuploid analysis was employed for the purpose of improving breeding efficiency. Potential use of such germplasm in wheat breeding practice, basic studies and some related problems were also discussed.
基金supported by the Special Fund for Agro-scientific Research in the Public Interest,China(201303018)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-IVFCAAS)the emarked fund for the China Agriculture Research System(CARS-25-B-01)
文摘A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.
文摘Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.
