The fragments of 350 bp in 28S rRNA from the closely related monogenea of trematoda, Neobenedenia girellaeand N. melleni are obtained by polymerase chain reaction (PCR) amplified using a couple of special primers andt...The fragments of 350 bp in 28S rRNA from the closely related monogenea of trematoda, Neobenedenia girellaeand N. melleni are obtained by polymerase chain reaction (PCR) amplified using a couple of special primers andthen sequenced. The results show that the comparison of 28S rRNA sequences, with only a base varying in 337bp accounting for 0.3% genetic difference, from the relative species N. girellae and N. melleni parasitized on thedifferent fishes in different farms displays that they possess a very high genetic similarity of 99.7%, higher thanthat of 99.41% for the single species N. melleni sampled in different areas, and the intraspecific divergence of N.melleni is 0.59%. Meanwhile, the interspecific differences between the two Neobenedenia and three Benedenia (i.e., B. lutjani, B. rohdei and B. seriolae) range from 2.08% to11.73%. In addition, UPGMA and MP molecularphylogenetic trees are constructed and proved to be consistent with each other. Though the morphologicalcharacteristics and the results of genetic diversity for the two Neobenedenia show a high similarity, whether theybelong to a single species or not are still undefined, and the more genes of them should be further investigated, incombination with the systematical and detailed morphological study.展开更多
BACKGROUND Sepsis is a common disease in intensive care units,with high morbidity and mortality.Intestinal microecology plays a vital part in the development and progression of this disease,possibly because sepsis and...BACKGROUND Sepsis is a common disease in intensive care units,with high morbidity and mortality.Intestinal microecology plays a vital part in the development and progression of this disease,possibly because sepsis and its treatment cause specific changes in the composition of the intestinal flora.AIM To investigate the characteristics of intestinal flora disturbance in sepsis patients treated with antibiotics.METHODS In this prospective comparative study,we enrolled ten patients with sepsis(sepsis group),hospitalized in the Department of Critical Care Medicine of the General Hospital,Ningxia Medical University,China(a class IIIa general hospital)from February 2017 to June 2017;ten patients without sepsis hospitalized in the same period(non-sepsis group)and ten healthy individuals(control group)were also enrolled.Fecal samples collected from the three groups were subjected to 16S rRNA gene sequencing and the intestinal flora diversity,structure,and composition were determined.Additionally,the dynamics of the intestinal flora diversity,structure,and composition in sepsis patients were investigated via 16S rRNA gene sequencing of samples collected 0 d,3 d,and 7 d after admittance to the intensive care unit.Correlations between the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid and the intestinal flora composition of sepsis patients were also investigated.RESULTS Compared with the healthy control group,sepsis and non-sepsis patients showed reduced intestinal floraα-diversity and a distinct flora structure,with Firmicutes as the dominant phylum,and significantly decreased proportions of Bacteroidetes,as well as Prevotella and Lachnospira,among other genera.Of note,the proportion of Enterococcus was significantly increased in the intestinal tract of sepsis patients.Interestingly,theα-diversity in the sepsis group decreased gradually,from days 1 to 7 of treatment.However,pairwise comparisons showed that both the diversity and structure of the intestinal flora were not significantly different considering the three different time points studied.Curiously,the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid in sepsis patients correlated with the prevalence of various bacterial genera.For example,the prevalence of Ruminococcus was positively correlated with serum procalcitonin,endotoxins,and diamine oxidase;similarly,the prevalence of Roseburia was positively correlated with serum procalcitonin,endotoxins,and D-lactic acid.CONCLUSION Sepsis patients in intensive care units show dysbiosis,lasting for at least 1 wk.展开更多
This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geograph...This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit(OTU) clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel(Camelus ferus), the domestic camel(C. bactrianus) and Dunhuang wild camel(C. ferus), respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.展开更多
This study was conducted to identify bacterial strain HeNan-001 isolated from intestinal tract of healthy rex rabbit. The strain was identified by gram staining, and OD600 values at different culture time were measure...This study was conducted to identify bacterial strain HeNan-001 isolated from intestinal tract of healthy rex rabbit. The strain was identified by gram staining, and OD600 values at different culture time were measured to develop a bacterial growth curve. The metabolic pathways of the bacterium using sugar in fermentation was identified with biochemical tubes. Total RNA of the strain was extracted, and total eDNA was obtained by Oligo (dT) method. Primers were designed using Primer 5.0 hip-software according to the 16S rRNA sequence published in GenBank, through cloning, ligation to vector PMD18T, construction of PMD18T/16S rRNA vector and transformation into DHSα, plasmid was extracted and sequenced, and the sequencing result was compared with sequences in NCBI followed by drawing of phylogenetic tree. The strain was verified to be double-stranded gram-positive cocci, which could ferment glucose, mannose, maltose and sorbitol, producing acids production, but failed to ferment sucrose, serum inulin and β-galactosidase. The phylogenetie tree analysis showed that the isolated bacterium shared the highest homology with an India isolate, and belongs to diplostreptococcus. This study provides significance experimental data and theoretical guidance for further development and utilization of the bacterial strain.展开更多
Prokaryotic diversity and community composition in the water column of eight stations(63 samples) around the Antarctic Peninsula of the Southern Ocean were investigated. Through pyrosequencing of the V3–V4hypervariab...Prokaryotic diversity and community composition in the water column of eight stations(63 samples) around the Antarctic Peninsula of the Southern Ocean were investigated. Through pyrosequencing of the V3–V4hypervariable regions of the 16S ribosomal RNA gene, we characterized 4 720 089 valid reads representing 48 188operational taxonomic units(OTUs, 97% similarity). The community was dominated by the phyla Pseudomonadota(original name: Proteobacteria, 47%), Oxyphotobacteria(26%), and Bacteroidota(original name: Bacteroidetes, 18%), which comprised an average of 91% of the total OTUs in all samples. The prokaryotic community composition varied vertically within the water column. Water column prokaryotic communities exhibited a clear depth profile, with higher microbial richness and higher diversity observed with increasing water depth. Cluster analysis of the community composition of water column samples exhibited a similar trend with depth. Correlation with environmental factors suggested distinct variation in prokaryotic community composition with changes in depth, salinity, temperature and dissolved oxygen levels. Functional prediction showed presence of active nitrogen, sulphur and methane metabolic cycles along the vertical transect of the studied region. These results will improve our knowledge of prokaryotic diversity and community composition at different depth of water column for better understanding of the microbial ecology and nutrient cycles in Antarctic Peninsula region of the Southern Ocean.展开更多
Objective: The aim of this study was to investigate the prevalence of sarcopenia(SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cel...Objective: The aim of this study was to investigate the prevalence of sarcopenia(SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation(HSCT).Methods: A total of 108 patients with various hematological disorders were selected from Peking University People’s Hospital. SP was screened and diagnosed based on the 2019 Asian Sarcopenia Diagnosis Strategy. Physical measurements and fecal samples were collected, and 16S rRNA gene sequencing was conducted. Alpha and beta diversity analyses were performed to evaluate gut microbiota composition and diversity.Results: After HSCT, significant decreases in calf circumference and body mass index(BMI) were observed,accompanied by a decline in physical function. Gut microbiota analyses revealed significant differences in the relative abundance of Enterococcus, Bacteroides, Blautia and Dorea species before and after HSCT(P<0.05). Before HSCT, sarcopenic patients had lower Dorea levels and higher Phascolarctobacterium levels than non-sarcopenia patients(P<0.01). After HSCT, no significant differences in species abundance were observed. Alpha diversity analysis showed significant differences in species diversity among the groups, with the highest diversity in the postHSCT 90-day group and the lowest in the post-HSCT 30-day group. Beta diversity analysis revealed significant differences in species composition between pre-and post-HSCT time points but not between SP groups. Linear discriminant analysis effect size(LEfSe) identified Alistipes, Rikenellaceae, Alistipes putredinis, Prevotellaceae defectiva and Blautia coccoides as biomarkers for the pre-HSCT sarcopenia group. Functional predictions showed significant differences in anaerobic, biofilm-forming and oxidative stress-tolerant functions among the groups(P<0.05).Conclusions: This study demonstrated a significant decline in physical function after HSCT and identified potential gut microbiota biomarkers and functional alterations associated with SP in patients with hematological disorders. Further research is needed to explore the underlying mechanisms and potential therapeutic targets.展开更多
Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based o...Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based on the complexity of the natural geographic characteristics of the Changjiang River Estuary, the geographic distribution of sedimentary microorganisms and the causes of this distribution are largely unexplored. In this work, the surface sediment samples from the adjacent sea area of the Changjiang River Estuary were collected. Their prokaryotic diversity was examined by high-throughput sequencing technology, and the environmental factors of the bacterial community were investigated. The results indicated that the distribution of prokaryotic communities in the sediments of the study areas showed obvious spatial heterogeneity. The sampling sequences divided the sample regions into three distinct clusters. Each geographic region had a unique community structure, although Proteobacteria, Bacteroidota, Desulfobacterota, Acidobacteriota, and Actinobacteriota all existed in these three branches. Canonical correspondence analysis demonstrated that prokaryotic diversity and community distribution were significantly correlated with the geographic location of sediment, seawater depth, and in particular, nutrient content(e.g., total phosphorus, total organic carbon and dissolved oxygen). Moreover, it was found for the first time that the metal ions obviously affected the composition and distribution of the prokaryotic community in this area. In general, this work provides new insights into the structural characteristics and driving factors of prokaryotic communities under the background of the ever-changing Changjiang River Estuary.展开更多
Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that ca...Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.展开更多
Short Retraction Notice The paper does not meet the standards of "Advances in Bioscience and Biotechnology". This article has been retracted to straighten the academic record. In making this decision the Edi...Short Retraction Notice The paper does not meet the standards of "Advances in Bioscience and Biotechnology". This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE's Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Prof. Abass Alavi (EiC of ABB). Please see the article page for more details. The full retraction notice in PDF is preceding the original paper which is marked "RETRACTED".展开更多
Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted...Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.展开更多
基金This study was supported by both grants from the National“863"Development Project of China under contract No.2002AA603021the Science and Technology Depatment of Fujian Province.
文摘The fragments of 350 bp in 28S rRNA from the closely related monogenea of trematoda, Neobenedenia girellaeand N. melleni are obtained by polymerase chain reaction (PCR) amplified using a couple of special primers andthen sequenced. The results show that the comparison of 28S rRNA sequences, with only a base varying in 337bp accounting for 0.3% genetic difference, from the relative species N. girellae and N. melleni parasitized on thedifferent fishes in different farms displays that they possess a very high genetic similarity of 99.7%, higher thanthat of 99.41% for the single species N. melleni sampled in different areas, and the intraspecific divergence of N.melleni is 0.59%. Meanwhile, the interspecific differences between the two Neobenedenia and three Benedenia (i.e., B. lutjani, B. rohdei and B. seriolae) range from 2.08% to11.73%. In addition, UPGMA and MP molecularphylogenetic trees are constructed and proved to be consistent with each other. Though the morphologicalcharacteristics and the results of genetic diversity for the two Neobenedenia show a high similarity, whether theybelong to a single species or not are still undefined, and the more genes of them should be further investigated, incombination with the systematical and detailed morphological study.
基金the National Key Research and Development Program of China,No.2016YFD0400605.
文摘BACKGROUND Sepsis is a common disease in intensive care units,with high morbidity and mortality.Intestinal microecology plays a vital part in the development and progression of this disease,possibly because sepsis and its treatment cause specific changes in the composition of the intestinal flora.AIM To investigate the characteristics of intestinal flora disturbance in sepsis patients treated with antibiotics.METHODS In this prospective comparative study,we enrolled ten patients with sepsis(sepsis group),hospitalized in the Department of Critical Care Medicine of the General Hospital,Ningxia Medical University,China(a class IIIa general hospital)from February 2017 to June 2017;ten patients without sepsis hospitalized in the same period(non-sepsis group)and ten healthy individuals(control group)were also enrolled.Fecal samples collected from the three groups were subjected to 16S rRNA gene sequencing and the intestinal flora diversity,structure,and composition were determined.Additionally,the dynamics of the intestinal flora diversity,structure,and composition in sepsis patients were investigated via 16S rRNA gene sequencing of samples collected 0 d,3 d,and 7 d after admittance to the intensive care unit.Correlations between the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid and the intestinal flora composition of sepsis patients were also investigated.RESULTS Compared with the healthy control group,sepsis and non-sepsis patients showed reduced intestinal floraα-diversity and a distinct flora structure,with Firmicutes as the dominant phylum,and significantly decreased proportions of Bacteroidetes,as well as Prevotella and Lachnospira,among other genera.Of note,the proportion of Enterococcus was significantly increased in the intestinal tract of sepsis patients.Interestingly,theα-diversity in the sepsis group decreased gradually,from days 1 to 7 of treatment.However,pairwise comparisons showed that both the diversity and structure of the intestinal flora were not significantly different considering the three different time points studied.Curiously,the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid in sepsis patients correlated with the prevalence of various bacterial genera.For example,the prevalence of Ruminococcus was positively correlated with serum procalcitonin,endotoxins,and diamine oxidase;similarly,the prevalence of Roseburia was positively correlated with serum procalcitonin,endotoxins,and D-lactic acid.CONCLUSION Sepsis patients in intensive care units show dysbiosis,lasting for at least 1 wk.
基金supported by the Xinjiang Lop Nur Wild Camels National Reserve Comprehensive Scientific Research Projects by The Environmental Protection Agency of China (20100228)
文摘This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit(OTU) clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel(Camelus ferus), the domestic camel(C. bactrianus) and Dunhuang wild camel(C. ferus), respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.
基金Supported by Modern Agricultural Technology System Construction Project of Shandong Province(SDAIT-21-15)Shen Zhiqiang Innovation Team Program of Animal Science and Veterinary Service of Shandong Province(LFFW[2014]01041)
文摘This study was conducted to identify bacterial strain HeNan-001 isolated from intestinal tract of healthy rex rabbit. The strain was identified by gram staining, and OD600 values at different culture time were measured to develop a bacterial growth curve. The metabolic pathways of the bacterium using sugar in fermentation was identified with biochemical tubes. Total RNA of the strain was extracted, and total eDNA was obtained by Oligo (dT) method. Primers were designed using Primer 5.0 hip-software according to the 16S rRNA sequence published in GenBank, through cloning, ligation to vector PMD18T, construction of PMD18T/16S rRNA vector and transformation into DHSα, plasmid was extracted and sequenced, and the sequencing result was compared with sequences in NCBI followed by drawing of phylogenetic tree. The strain was verified to be double-stranded gram-positive cocci, which could ferment glucose, mannose, maltose and sorbitol, producing acids production, but failed to ferment sucrose, serum inulin and β-galactosidase. The phylogenetie tree analysis showed that the isolated bacterium shared the highest homology with an India isolate, and belongs to diplostreptococcus. This study provides significance experimental data and theoretical guidance for further development and utilization of the bacterial strain.
基金The Impact and Response of Antarctic Seas to Climate Change under contract No. IRFSOCC2020-2022。
文摘Prokaryotic diversity and community composition in the water column of eight stations(63 samples) around the Antarctic Peninsula of the Southern Ocean were investigated. Through pyrosequencing of the V3–V4hypervariable regions of the 16S ribosomal RNA gene, we characterized 4 720 089 valid reads representing 48 188operational taxonomic units(OTUs, 97% similarity). The community was dominated by the phyla Pseudomonadota(original name: Proteobacteria, 47%), Oxyphotobacteria(26%), and Bacteroidota(original name: Bacteroidetes, 18%), which comprised an average of 91% of the total OTUs in all samples. The prokaryotic community composition varied vertically within the water column. Water column prokaryotic communities exhibited a clear depth profile, with higher microbial richness and higher diversity observed with increasing water depth. Cluster analysis of the community composition of water column samples exhibited a similar trend with depth. Correlation with environmental factors suggested distinct variation in prokaryotic community composition with changes in depth, salinity, temperature and dissolved oxygen levels. Functional prediction showed presence of active nitrogen, sulphur and methane metabolic cycles along the vertical transect of the studied region. These results will improve our knowledge of prokaryotic diversity and community composition at different depth of water column for better understanding of the microbial ecology and nutrient cycles in Antarctic Peninsula region of the Southern Ocean.
基金supported by Grant National Key R&D Program of China (No.2020YFC2005600 and No.2020YFC2005605)。
文摘Objective: The aim of this study was to investigate the prevalence of sarcopenia(SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation(HSCT).Methods: A total of 108 patients with various hematological disorders were selected from Peking University People’s Hospital. SP was screened and diagnosed based on the 2019 Asian Sarcopenia Diagnosis Strategy. Physical measurements and fecal samples were collected, and 16S rRNA gene sequencing was conducted. Alpha and beta diversity analyses were performed to evaluate gut microbiota composition and diversity.Results: After HSCT, significant decreases in calf circumference and body mass index(BMI) were observed,accompanied by a decline in physical function. Gut microbiota analyses revealed significant differences in the relative abundance of Enterococcus, Bacteroides, Blautia and Dorea species before and after HSCT(P<0.05). Before HSCT, sarcopenic patients had lower Dorea levels and higher Phascolarctobacterium levels than non-sarcopenia patients(P<0.01). After HSCT, no significant differences in species abundance were observed. Alpha diversity analysis showed significant differences in species diversity among the groups, with the highest diversity in the postHSCT 90-day group and the lowest in the post-HSCT 30-day group. Beta diversity analysis revealed significant differences in species composition between pre-and post-HSCT time points but not between SP groups. Linear discriminant analysis effect size(LEfSe) identified Alistipes, Rikenellaceae, Alistipes putredinis, Prevotellaceae defectiva and Blautia coccoides as biomarkers for the pre-HSCT sarcopenia group. Functional predictions showed significant differences in anaerobic, biofilm-forming and oxidative stress-tolerant functions among the groups(P<0.05).Conclusions: This study demonstrated a significant decline in physical function after HSCT and identified potential gut microbiota biomarkers and functional alterations associated with SP in patients with hematological disorders. Further research is needed to explore the underlying mechanisms and potential therapeutic targets.
基金The National Natural Science Foundation of China under contract Nos 32000074 and 42176130the Science and Technology Planning Project of Guangxi under contract No. AA21196002+4 种基金the Natural Science Foundation of Shandong Province under contract No. ZR2021MD044the Tai Mountain Industry Leading Talent of Shandong under contract No. 2019TSCYCX-06the Key Research and Development Program of Shandong Province under contract No. 2021TZXD008the Biosafety Research Program under contract No.20SWAQX04the Shandong Program of Pilot National Laboratory for Marine Science and Technology (Qingdao)under contract No. 2022QNLM030003-1。
文摘Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based on the complexity of the natural geographic characteristics of the Changjiang River Estuary, the geographic distribution of sedimentary microorganisms and the causes of this distribution are largely unexplored. In this work, the surface sediment samples from the adjacent sea area of the Changjiang River Estuary were collected. Their prokaryotic diversity was examined by high-throughput sequencing technology, and the environmental factors of the bacterial community were investigated. The results indicated that the distribution of prokaryotic communities in the sediments of the study areas showed obvious spatial heterogeneity. The sampling sequences divided the sample regions into three distinct clusters. Each geographic region had a unique community structure, although Proteobacteria, Bacteroidota, Desulfobacterota, Acidobacteriota, and Actinobacteriota all existed in these three branches. Canonical correspondence analysis demonstrated that prokaryotic diversity and community distribution were significantly correlated with the geographic location of sediment, seawater depth, and in particular, nutrient content(e.g., total phosphorus, total organic carbon and dissolved oxygen). Moreover, it was found for the first time that the metal ions obviously affected the composition and distribution of the prokaryotic community in this area. In general, this work provides new insights into the structural characteristics and driving factors of prokaryotic communities under the background of the ever-changing Changjiang River Estuary.
基金thank the State of Sao Paulo Research Foundation(FAPESP-Process 2011/07951-5)for the financial support.
文摘Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.
文摘Short Retraction Notice The paper does not meet the standards of "Advances in Bioscience and Biotechnology". This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE's Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Prof. Abass Alavi (EiC of ABB). Please see the article page for more details. The full retraction notice in PDF is preceding the original paper which is marked "RETRACTED".
文摘Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.