Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads.However,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosyn...Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads.However,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria.Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods.This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening,sequence tag-based homology screening,and bioinformatic-assisted chemical synthesis.Through this process,numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories.This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.展开更多
Increasing attention has been paid to phosphate-accumulating organisms （PAOs） for their important role in biological phosphorus removal. In this study, microbial communities of PAOs cultivated under different carbon...Increasing attention has been paid to phosphate-accumulating organisms （PAOs） for their important role in biological phosphorus removal. In this study, microbial communities of PAOs cultivated under different carbon sources （sewage, glucose, and sodium acetate） were investigated and compared through culture-dependent and culture-independent methods, respectively. The results obtained using denaturing gradient gel electrophoresis （DGGE） of polymerase chain reaction-amplified 16S rDNA fragments revealed that the diversity of bacteria in a sewage-fed reactor （1#） was much higher than in a glucose-fed one （2#） and a sodium acetate-fed one （3#）; there were common PAOs in three reactors fed by different carbon sources. Five strains were separated from three systems by using a phosphaterich medium; they were from common bacteria isolated and three isolates could not be found in DGGE profile at all. Two isolates had good phosphorus removal ability. When the microbial diversity was studied, the molecular biological method was better than the culture-dependent one. When phosphorus removal characteristics were investigated, culture-dependent approach was more effective. Thus a combination of two methods is necessary to have a comprehensive view of PAOs.展开更多
Bacterial diversity in surface sediment from the Arctic Ocean was investigated by culture-dependent and-independent approaches. Conventional culture-dependent techniques revealed 11 strains based on their distinct mor...Bacterial diversity in surface sediment from the Arctic Ocean was investigated by culture-dependent and-independent approaches. Conventional culture-dependent techniques revealed 11 strains based on their distinct morphological characteristics on marine Zobell 2216E agar plates. Phylogenetic analysis showed that these isolates belonged to three major lineages of the Bacteria,γ-proteobacteria, Bacteroidetes and Actinobacteria, and that they included 10 genera. Most isolates were psychrotrophic, and NaCl was not necessary for their growth. Furthermore, they exhibited activity of at least one extracellular hydrolytic enzyme at 4＆#176;C and had various abilities to assimilate carbon sources. A total of 67 phylotypes were detected among 142 clones based on the 16S rRNA library of the total community DNA and grouped into nine major lineages of bacteria. Phylotypes afifliated withγ-,δ-andε-proteobacteria accounted for 36.7%, 21.8%and 16.9%of the total clones, respectively. The rest of the clones belonged to Bacteroidetes,α-proteobacteria, Actinobacteria, Fusobacteria, Nitrospirae and an unclassiifed group.展开更多
[Objectives] To study the endophytic bacteria diversity in the root of Peperomia dindygulensis Miq. [Methods] The root of P.dindygulensis Miq. was taken as materials,culture-independent method was applied to build 16 ...[Objectives] To study the endophytic bacteria diversity in the root of Peperomia dindygulensis Miq. [Methods] The root of P.dindygulensis Miq. was taken as materials,culture-independent method was applied to build 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq. [Results] In the 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq.,95 clones separately belonged to 46 OTUs,Phylogenetic analysis indicated that these cloning sequences separately belonged to phylum Proteobacteria,phylum Bacteroidetes,phylum Actinobacteria,phylum Nitrospirae,and phylum Gemmatimonadetes. In these,phylum Proteobacteria accounted for 70. 53% of total number of clones,so it was the most dominant group in this library. [Conclusions]The endophytic bacteria diversity in the root of P.dindygulensis Miq. is rich and this study is expected to provide scientific basis for protection,development and use of resources of P. dindygulensis Miq.展开更多
Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation of microbial groups along the food chain.While essential,these approaches provide a limited view of co...Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation of microbial groups along the food chain.While essential,these approaches provide a limited view of complex microbial ecosystems,often underestimating fastidious and viable but non-culturable microorganisms.In recent years,culture-independent tools,including sequencing and omics-based strategies,offer complemen-tary insights into microbial diversity and function.Given the global consumption of poultry meat and its sig-nificance for food safety,spoilage,and antimicrobial resistance dissemination,a comprehensive characterization of poultry-associated microbial communities is essential.This review critically examines culture-dependent and culture-independent approaches to study the microbiome,resistome,virulome,and mobilome across the poultry production chain,comparing the type of information generated,their advantages and limitations.Culturedependent methods enable quantification and isolation of viable strains,while culture-independent ap-proaches reveal microbial diversity and functional genes related to antimicrobial resistance,virulence,and ge-netic mobility.Integrating both strategies strengthens surveillance,improves risk assessment,and supports targeted interventions throughout the poultry sector.This review also highlights key priorities for future research,including greater attention to post-slaughter processing environments,a more systematic investigation of the mobilome and virulome,and the integration of multi-omics,culturomics,and quasi-metagenomics to better link microbial diversity with functional activity and viability.展开更多
Insects and their associated microbiota have developed a sustained and mutually beneficial relationship,characterized by the influence of the symbiotic microorganisms on the host's physiological processes and fitn...Insects and their associated microbiota have developed a sustained and mutually beneficial relationship,characterized by the influence of the symbiotic microorganisms on the host's physiological processes and fitness parameters.The Mediterranean fruit fly,Ceratitis capitata(Diptera:Tephritidae),is one of the world's most ubiquitous,invasive,and harmful agricultural pests.In Tunisia,the medfly is widely distributed across all bioclimatic zones.However,in the absence of surveillance,infestations can escalate drastically,causing damage levels as high as 100%.Our study aimed to characterize the microbiome profile of Tunisian medfly populations from Zaghouan,Tozeur,Siliana,and Bizerte to understand the microbial dynamics implicated in the invasiveness and adaptability potential if SIT is applied.We conducted amplicon sequencing using MiSeq Illumina and a culture-dependent approach.Our findings revealed notable differences in symbiotic communities across regions.For instance,Serratia was prevalent in Tozeur populations,while Klebsiella showed high abundance in Bizerte.The composition of the bacterial communities within the medfly populations was influenced by several factors including the environmental conditions,geographical location,developmental stage,and the sex of the insects.Investigating the intricate relationship between insects and their microbiota is pivotal for understanding their biology and developing effective pest management strategies.Additionally,the isolation of bacteria from adult and larval medflies collected in the Bizerte region revealed the presence of bacterial species that could be utilized as attractants or supplements in larval artificial diets in the case of application of the SIT aiming at producing competitive sterile males.展开更多
More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. M...More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel bio- catalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metage- nomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we dis- cuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.展开更多
To determine effects of adding jogi fish(salted Atlantic croaker,Micropogonias undulatus)on bacterial community of baechu-kimchi,a traditional fermented kimchi cabbage food of Korea,bacterial communities were identifi...To determine effects of adding jogi fish(salted Atlantic croaker,Micropogonias undulatus)on bacterial community of baechu-kimchi,a traditional fermented kimchi cabbage food of Korea,bacterial communities were identified using culture-dependent and culture-independent techniques.Viable bacteria on tryptic soy agar of jogi-baechu-kimch and baechu-kimchi were increased from 5.6 to 5.8 logarithms of colony-forming units(log CFU)/g to 9.9 and 9.5 log CFU/g after 10 days fermentation,respectively,while the pH decreased.In culture-independent analysis,Latilactobacillus sakei and Leuconostoc mesenteroides were dominant as fermentation progressed in both types of kimchi.On the other hand,in culture-dependent analysis,Leuconostoc mesenteroides was found to be unrivaled.The addition of jogi did not induce changes in bacterial communities,although Carnobacterium inhibens originating from the fish was found in early stages of kimchi fermentation.展开更多
基金supported by the Start-Up Grant from China Pharmaceutical University(No.3154070046).
文摘Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads.However,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria.Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods.This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening,sequence tag-based homology screening,and bioinformatic-assisted chemical synthesis.Through this process,numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories.This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.
基金Project supported by the Young Teacher Foundation of Donghua University(No.113-10-0044065)Key(keygrant)Project of Chinese Ministry of Education(No.107046)Program for New Century Excellent Talents in University(NCET)
文摘Increasing attention has been paid to phosphate-accumulating organisms （PAOs） for their important role in biological phosphorus removal. In this study, microbial communities of PAOs cultivated under different carbon sources （sewage, glucose, and sodium acetate） were investigated and compared through culture-dependent and culture-independent methods, respectively. The results obtained using denaturing gradient gel electrophoresis （DGGE） of polymerase chain reaction-amplified 16S rDNA fragments revealed that the diversity of bacteria in a sewage-fed reactor （1#） was much higher than in a glucose-fed one （2#） and a sodium acetate-fed one （3#）; there were common PAOs in three reactors fed by different carbon sources. Five strains were separated from three systems by using a phosphaterich medium; they were from common bacteria isolated and three isolates could not be found in DGGE profile at all. Two isolates had good phosphorus removal ability. When the microbial diversity was studied, the molecular biological method was better than the culture-dependent one. When phosphorus removal characteristics were investigated, culture-dependent approach was more effective. Thus a combination of two methods is necessary to have a comprehensive view of PAOs.
基金financially supported by the Public Science and Technology Funds for Ocean Projects(Grant nos.201005032-2 and 201205020-5)by the Special Funds for Basic Scientific Research by Central Non-profit Institutes(Grant no.GY02-2012G14)
文摘Bacterial diversity in surface sediment from the Arctic Ocean was investigated by culture-dependent and-independent approaches. Conventional culture-dependent techniques revealed 11 strains based on their distinct morphological characteristics on marine Zobell 2216E agar plates. Phylogenetic analysis showed that these isolates belonged to three major lineages of the Bacteria,γ-proteobacteria, Bacteroidetes and Actinobacteria, and that they included 10 genera. Most isolates were psychrotrophic, and NaCl was not necessary for their growth. Furthermore, they exhibited activity of at least one extracellular hydrolytic enzyme at 4＆#176;C and had various abilities to assimilate carbon sources. A total of 67 phylotypes were detected among 142 clones based on the 16S rRNA library of the total community DNA and grouped into nine major lineages of bacteria. Phylotypes afifliated withγ-,δ-andε-proteobacteria accounted for 36.7%, 21.8%and 16.9%of the total clones, respectively. The rest of the clones belonged to Bacteroidetes,α-proteobacteria, Actinobacteria, Fusobacteria, Nitrospirae and an unclassiifed group.
基金Supported by Scientific Research Foundation of Yunnan Provincial Department of Education(2015Y393)Scientific Research Project of Kunming University(XJZD1605)+1 种基金Construction Project of Key Superior and Characteristic Disciplines(Ecology)in Colleges and Universities of Yunnan Province(05000511311)Project of Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province(GXKJ201622)
文摘[Objectives] To study the endophytic bacteria diversity in the root of Peperomia dindygulensis Miq. [Methods] The root of P.dindygulensis Miq. was taken as materials,culture-independent method was applied to build 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq. [Results] In the 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq.,95 clones separately belonged to 46 OTUs,Phylogenetic analysis indicated that these cloning sequences separately belonged to phylum Proteobacteria,phylum Bacteroidetes,phylum Actinobacteria,phylum Nitrospirae,and phylum Gemmatimonadetes. In these,phylum Proteobacteria accounted for 70. 53% of total number of clones,so it was the most dominant group in this library. [Conclusions]The endophytic bacteria diversity in the root of P.dindygulensis Miq. is rich and this study is expected to provide scientific basis for protection,development and use of resources of P. dindygulensis Miq.
基金supported by Projects PID2021-123404NB-I00 and PID2024-156601NA-I00 funded by MICIU/AEI/10.13039/501100011033 and by“ERDF A way of making Europe”and by the Government of Aragón(Grant Grupo AESA A06_23 R)Department of Science,Technology,and University Education of the Government of Aragón(Spain)provided N.Merino with a Grant Odón de Buen to carry out this research.
文摘Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation of microbial groups along the food chain.While essential,these approaches provide a limited view of complex microbial ecosystems,often underestimating fastidious and viable but non-culturable microorganisms.In recent years,culture-independent tools,including sequencing and omics-based strategies,offer complemen-tary insights into microbial diversity and function.Given the global consumption of poultry meat and its sig-nificance for food safety,spoilage,and antimicrobial resistance dissemination,a comprehensive characterization of poultry-associated microbial communities is essential.This review critically examines culture-dependent and culture-independent approaches to study the microbiome,resistome,virulome,and mobilome across the poultry production chain,comparing the type of information generated,their advantages and limitations.Culturedependent methods enable quantification and isolation of viable strains,while culture-independent ap-proaches reveal microbial diversity and functional genes related to antimicrobial resistance,virulence,and ge-netic mobility.Integrating both strategies strengthens surveillance,improves risk assessment,and supports targeted interventions throughout the poultry sector.This review also highlights key priorities for future research,including greater attention to post-slaughter processing environments,a more systematic investigation of the mobilome and virulome,and the integration of multi-omics,culturomics,and quasi-metagenomics to better link microbial diversity with functional activity and viability.
基金Funding was provided by FAO/IAEA contract 22662,the Tunisian Ministry of Higher Education,and the University of Manouba,which also awarded a scholarship through the Doctoral School in Computer,Communication,Design,Environmental Sciences,and Technologies.
文摘Insects and their associated microbiota have developed a sustained and mutually beneficial relationship,characterized by the influence of the symbiotic microorganisms on the host's physiological processes and fitness parameters.The Mediterranean fruit fly,Ceratitis capitata(Diptera:Tephritidae),is one of the world's most ubiquitous,invasive,and harmful agricultural pests.In Tunisia,the medfly is widely distributed across all bioclimatic zones.However,in the absence of surveillance,infestations can escalate drastically,causing damage levels as high as 100%.Our study aimed to characterize the microbiome profile of Tunisian medfly populations from Zaghouan,Tozeur,Siliana,and Bizerte to understand the microbial dynamics implicated in the invasiveness and adaptability potential if SIT is applied.We conducted amplicon sequencing using MiSeq Illumina and a culture-dependent approach.Our findings revealed notable differences in symbiotic communities across regions.For instance,Serratia was prevalent in Tozeur populations,while Klebsiella showed high abundance in Bizerte.The composition of the bacterial communities within the medfly populations was influenced by several factors including the environmental conditions,geographical location,developmental stage,and the sex of the insects.Investigating the intricate relationship between insects and their microbiota is pivotal for understanding their biology and developing effective pest management strategies.Additionally,the isolation of bacteria from adult and larval medflies collected in the Bizerte region revealed the presence of bacterial species that could be utilized as attractants or supplements in larval artificial diets in the case of application of the SIT aiming at producing competitive sterile males.
基金supported by King Abdullah University of Science and Technology (KAUST),Saudi Arabia
文摘More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel bio- catalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metage- nomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we dis- cuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.
基金supported by the Korea Institute of Planning and Evaluation for Technology in Food,Agriculture and Forestry(IPET)through the High Value-added Food Technology Development Program funded by the Ministry of Agriculture,Food and Rural Affairs(MAFRA)(No.322014-5).
文摘To determine effects of adding jogi fish(salted Atlantic croaker,Micropogonias undulatus)on bacterial community of baechu-kimchi,a traditional fermented kimchi cabbage food of Korea,bacterial communities were identified using culture-dependent and culture-independent techniques.Viable bacteria on tryptic soy agar of jogi-baechu-kimch and baechu-kimchi were increased from 5.6 to 5.8 logarithms of colony-forming units(log CFU)/g to 9.9 and 9.5 log CFU/g after 10 days fermentation,respectively,while the pH decreased.In culture-independent analysis,Latilactobacillus sakei and Leuconostoc mesenteroides were dominant as fermentation progressed in both types of kimchi.On the other hand,in culture-dependent analysis,Leuconostoc mesenteroides was found to be unrivaled.The addition of jogi did not induce changes in bacterial communities,although Carnobacterium inhibens originating from the fish was found in early stages of kimchi fermentation.
