Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine po...Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species naming.This paper describes the use of sequence data obtained from MLST databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering process.An implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLST data.Results point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic information.The use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm.展开更多
During an outbreak of diseases caused by co-infection with both parasites and bacteria in silver crucian carp （ Carassius auratus gibelio）, aerobic anoxy- genic phototrophic （AAP） bacteria in the aquatic environme...During an outbreak of diseases caused by co-infection with both parasites and bacteria in silver crucian carp （ Carassius auratus gibelio）, aerobic anoxy- genic phototrophic （AAP） bacteria in the aquatic environment were identified by PCR using the universal primers of bacterial 16S rDNA. The bacterial populations in the ponds infected and non-infected by the diseases were measured with acridine orange direct count （AODC） method, and the data were analyzed using SPSS software. The results showed that nine dominant cuhurable bacterial species： Shewanella putrefaciens, Acinetobacter sp. , Aeromonas sp. , Proteus vulgaris, Xan- thomonas sp. , Citrobacterfieundii, Morganella morganii, Vagococcus lutrae and Providencia sp. were identified, some of which were common pathogens. The bac- terial population in infected ponds was 7. 462 x 10^6 ind./ml in July, and 1. 007 4 x 10^7 ind./ml in August, and that in non-infected ponds was 1. 460 x 10x6ind./ml in July, and 1. 911 x10^6 ind./ml in August, with significant differences between the infected and non-infected ponds. The results suggested that the outbreak of diseases in silver crucian carp was to some extent related to the bacterial population in water environment.展开更多
BACKGROUND In this study,recent trends in the distribution and drug resistance of pathogenic bacteria isolated from patients treated at a burn ward between 2006 and 2019 were investigated.AIM To develop more effective...BACKGROUND In this study,recent trends in the distribution and drug resistance of pathogenic bacteria isolated from patients treated at a burn ward between 2006 and 2019 were investigated.AIM To develop more effective clinical strategies and techniques for the prevention and treatment of bacterial infections in burn patients.METHODS Clinical samples with positive bacteria were collected from patients at the burn ward in Beijing Jishuitan Hospital in China between January 2006 and December 2019.The samples were retrospectively analyzed,the distribution of pathogenic bacteria was determined,and the trends and changes in bacterial drug resistance during different period were assessed.Drug resistance in several main pathogenic bacteria from 2006 to 2011 and from 2012 to 2019 was comparatively summarized and analyzed.RESULTS Samples from 17119 patients were collected and analyzed from 2006 to 2019.Surprisingly,a total of 7960 strains of different pathogenic bacteria were isolated at this hospital.Among these bacteria,87.98%(7003/7960)of the strains were isolated from burn wounds,and only 1.34%(107/7960)were isolated from the blood of patients.In addition,49.70%(3956/7960)were identified as Grampositive bacteria,48.13%(3831/7960)were Gram-negative bacteria,and the remaining 2.17%(173/7960)were classified as fungi or other pathogens.Importantly,Staphylococcus aureus(21.68%),Pseudomonas aeruginosa(14.23%),and Staphylococcus epidermidis (9.61%) were the top three pathogens most frequentlyisolated from patients.CONCLUSION In patients treated at the burn ward in this hospital from 2006 to 2019,Staphylococcus aureus and Pseudomonas aeruginosa were the predominant clinicalpathogens responsible for bacterial infections. The circumstantial detection anddetailed monitoring of the intensity and growth of different pathogenic bacteria inclinical patients as well as tests of drug sensitivity during burn recovery areparticularly important to provide guidelines for the application of antibiotics andother related drugs. Careful collection and correct, standard culture of bacterialspecimens are also crucial to improve the efficiency of bacterial infectiondetection. Effective monitoring and timely clinical treatment in patients may helpreduce the possibility and rate of infection as well as alleviate the effects of drugresistance among patients in burn centers.展开更多
Honeybees and bumblebees play a crucial role as essential pollinators.The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host.Although bees harbor relatively...Honeybees and bumblebees play a crucial role as essential pollinators.The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host.Although bees harbor relatively simple microbial communities at the genus level,recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus.However,a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking.Here,we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria,as well as the factors that influence the gut population dynamics.We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy,by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity.On the basis of the refined species taxonomy,we constructed a curated genomic reference database,named the bee gut microbe genome sequence database(BGM-GDb).To evaluate the species-profiling performance of the curated BGM-GDb,we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system(MIDAS),and then compared the results with those obtained from a prebuilt MIDAS database.We found that compared with the default database,the BGM-GDb excelled in aligned read counts and bacterial richness.Overall,this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.展开更多
文摘Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species naming.This paper describes the use of sequence data obtained from MLST databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering process.An implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLST data.Results point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic information.The use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm.
文摘During an outbreak of diseases caused by co-infection with both parasites and bacteria in silver crucian carp （ Carassius auratus gibelio）, aerobic anoxy- genic phototrophic （AAP） bacteria in the aquatic environment were identified by PCR using the universal primers of bacterial 16S rDNA. The bacterial populations in the ponds infected and non-infected by the diseases were measured with acridine orange direct count （AODC） method, and the data were analyzed using SPSS software. The results showed that nine dominant cuhurable bacterial species： Shewanella putrefaciens, Acinetobacter sp. , Aeromonas sp. , Proteus vulgaris, Xan- thomonas sp. , Citrobacterfieundii, Morganella morganii, Vagococcus lutrae and Providencia sp. were identified, some of which were common pathogens. The bac- terial population in infected ponds was 7. 462 x 10^6 ind./ml in July, and 1. 007 4 x 10^7 ind./ml in August, and that in non-infected ponds was 1. 460 x 10x6ind./ml in July, and 1. 911 x10^6 ind./ml in August, with significant differences between the infected and non-infected ponds. The results suggested that the outbreak of diseases in silver crucian carp was to some extent related to the bacterial population in water environment.
文摘BACKGROUND In this study,recent trends in the distribution and drug resistance of pathogenic bacteria isolated from patients treated at a burn ward between 2006 and 2019 were investigated.AIM To develop more effective clinical strategies and techniques for the prevention and treatment of bacterial infections in burn patients.METHODS Clinical samples with positive bacteria were collected from patients at the burn ward in Beijing Jishuitan Hospital in China between January 2006 and December 2019.The samples were retrospectively analyzed,the distribution of pathogenic bacteria was determined,and the trends and changes in bacterial drug resistance during different period were assessed.Drug resistance in several main pathogenic bacteria from 2006 to 2011 and from 2012 to 2019 was comparatively summarized and analyzed.RESULTS Samples from 17119 patients were collected and analyzed from 2006 to 2019.Surprisingly,a total of 7960 strains of different pathogenic bacteria were isolated at this hospital.Among these bacteria,87.98%(7003/7960)of the strains were isolated from burn wounds,and only 1.34%(107/7960)were isolated from the blood of patients.In addition,49.70%(3956/7960)were identified as Grampositive bacteria,48.13%(3831/7960)were Gram-negative bacteria,and the remaining 2.17%(173/7960)were classified as fungi or other pathogens.Importantly,Staphylococcus aureus(21.68%),Pseudomonas aeruginosa(14.23%),and Staphylococcus epidermidis (9.61%) were the top three pathogens most frequentlyisolated from patients.CONCLUSION In patients treated at the burn ward in this hospital from 2006 to 2019,Staphylococcus aureus and Pseudomonas aeruginosa were the predominant clinicalpathogens responsible for bacterial infections. The circumstantial detection anddetailed monitoring of the intensity and growth of different pathogenic bacteria inclinical patients as well as tests of drug sensitivity during burn recovery areparticularly important to provide guidelines for the application of antibiotics andother related drugs. Careful collection and correct, standard culture of bacterialspecimens are also crucial to improve the efficiency of bacterial infectiondetection. Effective monitoring and timely clinical treatment in patients may helpreduce the possibility and rate of infection as well as alleviate the effects of drugresistance among patients in burn centers.
基金supported by grants from the National Natural Science Foundation of China(32370550 and 32000346)to Xue Zhangthe program from the Sanya Institute of China Agricultural University(SYND-2021-30)by 2115 Talent Development Program of China Agricultural University grants to Xin Zhou。
文摘Honeybees and bumblebees play a crucial role as essential pollinators.The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host.Although bees harbor relatively simple microbial communities at the genus level,recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus.However,a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking.Here,we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria,as well as the factors that influence the gut population dynamics.We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy,by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity.On the basis of the refined species taxonomy,we constructed a curated genomic reference database,named the bee gut microbe genome sequence database(BGM-GDb).To evaluate the species-profiling performance of the curated BGM-GDb,we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system(MIDAS),and then compared the results with those obtained from a prebuilt MIDAS database.We found that compared with the default database,the BGM-GDb excelled in aligned read counts and bacterial richness.Overall,this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.
