A novel strain of Micrococcus sp.DUT_AHX,which was isolated from the sludge of a nitrobenzene(NB)-manufacturing plant and could utilize NB as the sole carbon source,was identified on the basis of physiological and bio...A novel strain of Micrococcus sp.DUT_AHX,which was isolated from the sludge of a nitrobenzene(NB)-manufacturing plant and could utilize NB as the sole carbon source,was identified on the basis of physiological and biochemical tests and 16S ribosomal DNA(rDNA)sequence analysis.It can grow at the temperature up to 40℃or in the presence of NaCl concentration up to 12 g/L in Luria-Bertani(LB)medium.The optimal degradation conditions are as follows:temperature 37℃,pH 7.0,and shaking speed 150 r/min.The strain involves a partial reductive pathway due to the release of ammonia and can also utilize 2-aminophenol as the sole carbon source.Furthermore,the enzyme activity tests show that crude extracts of NB-grown strain DUT_AHX mainly contain 2-aminophenol 1,6-dioxygenase activity.The exploitation of salt-tolerant bacteria will be a remarkable improvement in NB bioremediation and wastewater treatment at high salinity and high temperature.展开更多
AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into...AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into eight diarrhoea-predominant (IBS-D),eight constipation-predominant(IBS-C)and four mixed symptom-subtype(IBS-M)IBS patients,and fifteen control subjects,were analysed at three time-points with a set of fourteen quantitative real-timepolymerase chain reaction assays.All assays targeted 16S rRNA gene phylotypes putatively associated with IBS,based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobac-teria,Bacteroidetes and Firmicutes.Eight of the target phylotypes had less than 95%similarity to cultured bacterial species according to their 16S rRNA gene sequence.The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis(PCA)with linear mixed-effects models applied to the principal component scores. RESULTS:Bacterial phylotypes Clostridium cocleatum 88%,Clostridium thermosuccinogenes 85%,Coprobacillus catenaformis 91%,Ruminococcus bromii-like, Ruminococcus torques 91%,and R.torques 93%were detected from all samples analysed.A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups.The PCA on the first principal component(PC1),explaining 30.36%of the observed variation in the IBS-D patient group,was significantly altered from all other sample groups(IBS-D vs control, P=0.01;IBS-D vs IBS-M,P=0.00;IBS-D vs IBS-C, P=0.05).Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria.A phy- lotype with 85%similarity to C.thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects(-4.08±0.90 vs -3.33±1.16,P=0.04)and IBS-D and IBS-M subjects (-4.08±0.90 vs-3.08±1.38,P=0.05).Furthermore,a phylotype with 94%similarity to R.torques was more prevalent in IBS-D patients'intestinal micro- biota than in that of control subjects(-2.43±1.49 vs -4.02±1.63,P=0.01).A phylotype with 93%simi- larity to R.torques was associated with control sam- ples when compared with IBS-M(-2.41±0.53 vs -2.92±0.56,P=0.00).Additionally,a R.bromii-like phylotype was associated with IBS-C patients in com- parison to control subjects(-1.61±1.83 vs-3.69± 2.42,P=0.01).All of the above mentioned phylotype specific alterations were independent of the effect of time. CONCLUSION:Significant phylotype level alterationsin the intestinal microbiotas of IBS patients were observed,further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.展开更多
A bacteria strain for the degradation of hydrolyzed polyacrylamide (HPAM) was isolated from a curing pot in HPAM distribution station of Daqing Oilfield using Hungate anaerobic technique. The isolate was investigate...A bacteria strain for the degradation of hydrolyzed polyacrylamide (HPAM) was isolated from a curing pot in HPAM distribution station of Daqing Oilfield using Hungate anaerobic technique. The isolate was investigated from morphological, physiological, biochemical and molecular characterization. It is a Gram-negative, shortbacillus, non-spore-forming anaerobic bacteria with an optimum growth at 8.0 pH at 40℃. It can reduce sulfate to I-I2S. Alignment of 16S ribosomal DNA and 16S-23S ribosomal DNA intergenic spacer sequences suggests that this isolate is closely related to the Enterobacter cloacae. The isolate is identified as a new strain belonging to Enterobacter genus, temporarily named as Enterobacter cloacae 17. Analysis results of infrared spectroscopy (IR) show that the bacteria can use HPAM as the only carbon source, change the structure of HPAM polymer surface, and realize the hydrolysis of amide to carboxyl group by hydrolysis mechanism. It can degrade the side chain and change some functional groups, which obviously decreases the viscosity. GC-MS analysis indicates that the determined low-molecular weight degradation products of HPAM are polyacrylamide fragments with duplet bond, epoxy as well as carbonyl group, but most of them are acrylamide oligomer derivatives.展开更多
Microbial flocculants have become a hot spot in recent years. A bacterial strain with high flocculating activity was isolated from seawater samples. The strain was defined as Bacillus licheniformis dhs-40 by 16S rDNA ...Microbial flocculants have become a hot spot in recent years. A bacterial strain with high flocculating activity was isolated from seawater samples. The strain was defined as Bacillus licheniformis dhs-40 by 16S rDNA identification and Biolog test. Ultrasonication test confirmed the flocculating activity of the strain was both in fermentation supernatant and cell. According to flocculating activity curve, the ideal fermentation time for collecting flocculating active substances was two days. The flocculating activity of the strain was sensitive to pH. The strain could only preserve flocculating activity while pH varied from 7 to 11. However, it could preserve flocculating activity while temperature varied from -20℃to 100 ℃ Saccharide, protein, lipid, nucleic acids qualitative test and RNase, Proteinase K treatment confirmed the flocculating active substances were proteins. Their flocculating activities were insensitive to Proteinase K.展开更多
Nonribosomal peptides (NRPs) represent a large family of natural products with great diversities of chemical structures and biological activities. The peptide backbones of NRPs are synthesized by nonribosomal peptid...Nonribosomal peptides (NRPs) represent a large family of natural products with great diversities of chemical structures and biological activities. The peptide backbones of NRPs are synthesized by nonribosomal peptide synthetases (NRPSs) that minimally consist of one adenylation (A) domain, one peptidyl carrier protein (PCP) and one condensation (C) domain. In this study, we carded out a PCR screening and identified 21 "positive" strains from 100 actinomycete strains with the degenerate primers designed from the conserved sequences of A domains of NRPSs. One of the 21 "positive" strains, Streptomyces sp. HMU0027, was selected for large-scale fermentation (9 L) based on HPLC analysis, and subsequent isolation and structural elucidation afforded seven NRPS-synthesized thiazostatin siderophore analogues (1-7). Compound 1 was a new compound containing an unusual linkage between a phenolate siderophore and a sugar moiety. These results laid the foundation for further biosynthetic research of these thiazostatin analogues and highlighted the power of genome mining technologies based on biosynthetic knowledge in NRP discovery.展开更多
The extraction of nucleic acid is recognized as one of the most essential steps in molecular biology for initiating other downstream applications such as sequencing, amplification, hybridization, and cloning. Many com...The extraction of nucleic acid is recognized as one of the most essential steps in molecular biology for initiating other downstream applications such as sequencing, amplification, hybridization, and cloning. Many commercial kits and methods are currently available that allow the extraction of only one type of nucleic acids-DNA or RNA. However, in parallel clinical detection of several diseases, a method for simultaneous extraction of both DNA and RNA from the same source is needed in such cases. In this study, a method for simultaneous extraction of DNA and RNA from bacteria based on magnetic nanoparticles(MNPs) was described. Lysis buffers were prepared to help the nucleic acid released and adsorbed to MNPs. Then, two washing buffers were used to remove the contamination of proteins and carbohydrates. The nucleic acids were finally eluted by Deoxyribonuclease(DNase) and Ribonucleases(RNase) free water. Different factors which might affect the purification of the nucleic acid were investigated, and the quantity and quality parameters of the nucleic acid were also recorded. The DNA and RNA extracted from bacteria were then respectively subjected to polymerase chain reaction(PCR) and reverse transcription PCR(RT-PCR) to further confirm its quality. The results indicated that our method can be successfully used to simultaneously extract DNA and RNA from bacteria.展开更多
文摘A novel strain of Micrococcus sp.DUT_AHX,which was isolated from the sludge of a nitrobenzene(NB)-manufacturing plant and could utilize NB as the sole carbon source,was identified on the basis of physiological and biochemical tests and 16S ribosomal DNA(rDNA)sequence analysis.It can grow at the temperature up to 40℃or in the presence of NaCl concentration up to 12 g/L in Luria-Bertani(LB)medium.The optimal degradation conditions are as follows:temperature 37℃,pH 7.0,and shaking speed 150 r/min.The strain involves a partial reductive pathway due to the release of ammonia and can also utilize 2-aminophenol as the sole carbon source.Furthermore,the enzyme activity tests show that crude extracts of NB-grown strain DUT_AHX mainly contain 2-aminophenol 1,6-dioxygenase activity.The exploitation of salt-tolerant bacteria will be a remarkable improvement in NB bioremediation and wastewater treatment at high salinity and high temperature.
基金Supported by The Finnish Funding Agency for Technologyand Innovation,Tekes,grants No.945/401/00 and 40160/05the Finnish Graduate School of Applied Biosciences,the Academy of Finland,Grant No.214 157the Centre of Excellence on Microbial Food Safety Research,Academy of Finland
文摘AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into eight diarrhoea-predominant (IBS-D),eight constipation-predominant(IBS-C)and four mixed symptom-subtype(IBS-M)IBS patients,and fifteen control subjects,were analysed at three time-points with a set of fourteen quantitative real-timepolymerase chain reaction assays.All assays targeted 16S rRNA gene phylotypes putatively associated with IBS,based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobac-teria,Bacteroidetes and Firmicutes.Eight of the target phylotypes had less than 95%similarity to cultured bacterial species according to their 16S rRNA gene sequence.The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis(PCA)with linear mixed-effects models applied to the principal component scores. RESULTS:Bacterial phylotypes Clostridium cocleatum 88%,Clostridium thermosuccinogenes 85%,Coprobacillus catenaformis 91%,Ruminococcus bromii-like, Ruminococcus torques 91%,and R.torques 93%were detected from all samples analysed.A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups.The PCA on the first principal component(PC1),explaining 30.36%of the observed variation in the IBS-D patient group,was significantly altered from all other sample groups(IBS-D vs control, P=0.01;IBS-D vs IBS-M,P=0.00;IBS-D vs IBS-C, P=0.05).Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria.A phy- lotype with 85%similarity to C.thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects(-4.08±0.90 vs -3.33±1.16,P=0.04)and IBS-D and IBS-M subjects (-4.08±0.90 vs-3.08±1.38,P=0.05).Furthermore,a phylotype with 94%similarity to R.torques was more prevalent in IBS-D patients'intestinal micro- biota than in that of control subjects(-2.43±1.49 vs -4.02±1.63,P=0.01).A phylotype with 93%simi- larity to R.torques was associated with control sam- ples when compared with IBS-M(-2.41±0.53 vs -2.92±0.56,P=0.00).Additionally,a R.bromii-like phylotype was associated with IBS-C patients in com- parison to control subjects(-1.61±1.83 vs-3.69± 2.42,P=0.01).All of the above mentioned phylotype specific alterations were independent of the effect of time. CONCLUSION:Significant phylotype level alterationsin the intestinal microbiotas of IBS patients were observed,further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.
基金Sponsored by the Country from Branch Fund Significant International Cooperation Item(Grant No.50521140075)
文摘A bacteria strain for the degradation of hydrolyzed polyacrylamide (HPAM) was isolated from a curing pot in HPAM distribution station of Daqing Oilfield using Hungate anaerobic technique. The isolate was investigated from morphological, physiological, biochemical and molecular characterization. It is a Gram-negative, shortbacillus, non-spore-forming anaerobic bacteria with an optimum growth at 8.0 pH at 40℃. It can reduce sulfate to I-I2S. Alignment of 16S ribosomal DNA and 16S-23S ribosomal DNA intergenic spacer sequences suggests that this isolate is closely related to the Enterobacter cloacae. The isolate is identified as a new strain belonging to Enterobacter genus, temporarily named as Enterobacter cloacae 17. Analysis results of infrared spectroscopy (IR) show that the bacteria can use HPAM as the only carbon source, change the structure of HPAM polymer surface, and realize the hydrolysis of amide to carboxyl group by hydrolysis mechanism. It can degrade the side chain and change some functional groups, which obviously decreases the viscosity. GC-MS analysis indicates that the determined low-molecular weight degradation products of HPAM are polyacrylamide fragments with duplet bond, epoxy as well as carbonyl group, but most of them are acrylamide oligomer derivatives.
文摘Microbial flocculants have become a hot spot in recent years. A bacterial strain with high flocculating activity was isolated from seawater samples. The strain was defined as Bacillus licheniformis dhs-40 by 16S rDNA identification and Biolog test. Ultrasonication test confirmed the flocculating activity of the strain was both in fermentation supernatant and cell. According to flocculating activity curve, the ideal fermentation time for collecting flocculating active substances was two days. The flocculating activity of the strain was sensitive to pH. The strain could only preserve flocculating activity while pH varied from 7 to 11. However, it could preserve flocculating activity while temperature varied from -20℃to 100 ℃ Saccharide, protein, lipid, nucleic acids qualitative test and RNase, Proteinase K treatment confirmed the flocculating active substances were proteins. Their flocculating activities were insensitive to Proteinase K.
基金The National Natural Science Foundation of China(Grant No.81573326,Grant No.81673332)
文摘Nonribosomal peptides (NRPs) represent a large family of natural products with great diversities of chemical structures and biological activities. The peptide backbones of NRPs are synthesized by nonribosomal peptide synthetases (NRPSs) that minimally consist of one adenylation (A) domain, one peptidyl carrier protein (PCP) and one condensation (C) domain. In this study, we carded out a PCR screening and identified 21 "positive" strains from 100 actinomycete strains with the degenerate primers designed from the conserved sequences of A domains of NRPSs. One of the 21 "positive" strains, Streptomyces sp. HMU0027, was selected for large-scale fermentation (9 L) based on HPLC analysis, and subsequent isolation and structural elucidation afforded seven NRPS-synthesized thiazostatin siderophore analogues (1-7). Compound 1 was a new compound containing an unusual linkage between a phenolate siderophore and a sugar moiety. These results laid the foundation for further biosynthetic research of these thiazostatin analogues and highlighted the power of genome mining technologies based on biosynthetic knowledge in NRP discovery.
基金supported by the National Basic Research Program of China(2014CB744501)the National High Technology Research and Development Program of China(2012AA022703)+8 种基金the National Key Special Science Program(2013ZX10004103-002)the National Natural Science Foundation of China(61201033,21205013,61271056,61527806)Projects of Development of Science and Medical Technology(201208038)Projects of Health Ministry of Nanjing(ZKX12038)the Clinical Science and Technology Special Projects in Jiangsu Province(BL2012067,BL2014094)the Talents Planning of Six Summit Fields of Jiangsu Province(2013-WSN-056)China Postdoctoral Science Foundation Funded Project(2014M551491,2015T80487)Jiangsu Planned Projects for Postdoctoral Research Funds(1302007A)the Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province
文摘The extraction of nucleic acid is recognized as one of the most essential steps in molecular biology for initiating other downstream applications such as sequencing, amplification, hybridization, and cloning. Many commercial kits and methods are currently available that allow the extraction of only one type of nucleic acids-DNA or RNA. However, in parallel clinical detection of several diseases, a method for simultaneous extraction of both DNA and RNA from the same source is needed in such cases. In this study, a method for simultaneous extraction of DNA and RNA from bacteria based on magnetic nanoparticles(MNPs) was described. Lysis buffers were prepared to help the nucleic acid released and adsorbed to MNPs. Then, two washing buffers were used to remove the contamination of proteins and carbohydrates. The nucleic acids were finally eluted by Deoxyribonuclease(DNase) and Ribonucleases(RNase) free water. Different factors which might affect the purification of the nucleic acid were investigated, and the quantity and quality parameters of the nucleic acid were also recorded. The DNA and RNA extracted from bacteria were then respectively subjected to polymerase chain reaction(PCR) and reverse transcription PCR(RT-PCR) to further confirm its quality. The results indicated that our method can be successfully used to simultaneously extract DNA and RNA from bacteria.