Background:Inflammatory bowel disease(IBD),comprising Crohn's disease(CD)and ulcerative colitis(UC),is a heterogeneous state of chronic intestinal inflammation.Intestinal innate immunity,including innate immune ce...Background:Inflammatory bowel disease(IBD),comprising Crohn's disease(CD)and ulcerative colitis(UC),is a heterogeneous state of chronic intestinal inflammation.Intestinal innate immunity,including innate immune cells,defends against pathogens and excessive entry of gut microbiota,while preserving immune tolerance to resident intestinal microbiota,and may be characterized by its capacity to produce a rapid and nonspecific reaction.The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic.When the intestinal ecosystem is in dysbiosis,the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota.The aim of our study was to comprehensively assess the relationship between microbial populations within UC,the signaling pathways of pathogenic gut microbe therein and the inflammatory response,as well as to understand the effects of using PE&AFWE(poppy extract[Papaver nudicaule L.]and Artemisia frigida Willd.extract)on UC modulation.Methods:A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate(DSS).Based on metagenomic sequencing to characterize the gut microbiome,the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods,as well as histopathological analysis.Results:(1)We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria.There were three types of abundance changes in the model groups:increases(Chlamydiae/Proteobacteria and Deferribacteres),decreases(Firmicutes),and no significant changes(Bacteroidetes).The UC model group was significantly different from the control group,with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold.(2)The proportion of the fecal flora in the UC group decreased by 37.5%in the Firmicutes and increased by 14.29%in the proportion of Proteobacteria compared to the control group before treatment.(3)The significantly enriched and increased signaling pathways screened were the'arachidonic acid metabolic pathway'and the'phagosomal pathway',which both showed a decreasing trend after drug administration.(4)Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration,screening for directly relevant OTU networks,the UC group was found to directly affect OTU69,followed by a cascade of effects on OTU12,OTU121,OTU93,and OTU7,which may be the pathway of action that initiated the pathological changes in normal mice.(5)We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre-and post-PE&AFWE-treated groups.Thereby,we learned that PE&AFWE can directly affect OTU90,after which it inhibits UC,inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118,which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7.(6)Histopathological observation and scoring(HS)of the colon showed that there was a significant difference between the model group and the control group(p<0.001),and that there was a significant recovery in both the sulfasalazine(SASP)and the PE&AFWE groups after the administration of the drug(p<0.0001).Conclusion:We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD,with five opportunistic pathogens directly contributing to IBD.PE&AFWE reduced the abundance of proteobacteria in the gut microbiota,and histopathology showed significant improvement.展开更多
BACKGROUND Preterm birth is the leading cause of mortality in newborns,with very-low-birthweight infants usually experiencing several complications.Breast milk is considered the gold standard of nutrition,especially f...BACKGROUND Preterm birth is the leading cause of mortality in newborns,with very-low-birthweight infants usually experiencing several complications.Breast milk is considered the gold standard of nutrition,especially for preterm infants with delayed gut colonization,because it contains beneficial microorganisms,such as Lactobacilli and Bifidobacteria.AIM To analyze the gut microbiota of breastfed preterm infants with a birth weight of 1500 g or less.METHODS An observational study was performed on preterm infants with up to 36.6 wk of gestation and a birth weight of 1500 g or less,born at the University Hospital Dr.JoséEleuterio González at Monterrey,Mexico.A total of 40 preterm neonates were classified into breast milk feeding(BM)and mixed feeding(MF)groups(21 in the BM group and 19 in the MF group),from October 2017 to June 2019.Fecal samples were collected before they were introduced to any feeding type.After full enteral feeding was achieved,the composition of the gut microbiota was analyzed using 16S rRNA gene sequencing.Numerical variables were compared using Student’s t-test or using the Mann–Whitney U test for nonparametric variables.Dominance,evenness,equitability,Margalef’s index,Fisher’s alpha,Chao-1 index,and Shannon’s diversity index were also calculated.RESULTS No significant differences were observed at the genus level between the groups.Class comparison indicated higher counts of Alphaproteobacteria and Betaproteobacteria in the initial compared to the final sample of the BM group(P<0.011).In addition,higher counts of Gammaproteobacteria were detected in the final than in the initial sample(P=0.040).According to the Margalef index,Fisher’s alpha,and Chao-1 index,a decrease in species richness from the initial to the final sample,regardless of the feeding type,was observed(P<0.050).The four predominant phyla were Bacteroidetes,Actinobacteria,Firmicutes,and Proteobacteria,with Proteobacteria being the most abundant.However,no significant differences were observed between the initial and final samples at the phylum level.CONCLUSION Breastfeeding is associated with a decrease in Alphaproteobacteria and Betaproteobacteria and an increase of Gammaproteobacteria,contributing to the literature of the gut microbiota structure of very low-birth-weight,preterm.展开更多
The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introdu...The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introduced for MTBE aerobic biodegradation. After 7 d, almost all MTBE was degraded by a pure culture, a member of β-Proteobacteria named as PMI, in a closed system with oxygen supply, while only 40% MTBE was degraded in one without oxygen supply. Dissolved oxygen （DO） levels of the broth in closed systems respectively with and without H2O2 were about 5-6 and 4 mg/L. Higher DO may improve the activity of monooxygemase, which is the key enzyme of metabolic pathway from MTBE to tert-butyl alcohol and finally to CO2, and may result in the increase of the degrading activity of PM1 cell. The purge and trap GC-MS result of the broth in closed systems showed that tea-butyl alcohol, isopronol and acetone were the main intermediate products.展开更多
The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 sp...The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker contains 157 bp from the 3’ end of the 16S rRNA gene and 75 bp from the 5’ end of the 16S-23S ITS. The 157 bp allows discrimination among distantly related species. Owing to its higher rate of nucleotide substitutions, the 75 bp adds discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rRNA gene, the 232 bp marker can better discriminate among closely related γ-proteobacterial species. Third, the method is simple, rapid, suited to large screening programs and easily accessible to most laboratories. Fourth, this marker can also reveal γ-proteobacterial species which may appear misassigned and for which additional characterization appear warranted.展开更多
Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with dr...Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.展开更多
Background The study evaluated the effects of bacteriophage cocktail(BP)and ZnO administered during weaning time for piglets exposed to a non-sanitary environment.The bacteriophages were designed to eliminate Escheric...Background The study evaluated the effects of bacteriophage cocktail(BP)and ZnO administered during weaning time for piglets exposed to a non-sanitary environment.The bacteriophages were designed to eliminate Escherichia coli(K88,K99 and F41),Salmonella(typhimurium and enteritidis),and Clostridium perfreingens(types A and C).Forty 21-day-old crossbreed piglets were assigned to four treatments,including the PC(sanitary environment),NC(nonsanitary environment),BP(NC plus 108 pfu/kg BP),and ZO(NC plus 2,500 mg/kg ZnO).Piglets in the NC,BP and ZO were kept in a non-sanitary environment for 14 d,which was contaminated with the feces of infected pigs.Results Pigs in the BP and ZO treatments had a higher final body weight compared with the NC.The NC treatment showed the highest concentration of inflammatory cytokines including interleukin(IL)-1β,IL-6 and tumor necrosis factor-αin the plasma.The administration of BP and ZO showed lower myeloperoxidase concentrations compared with the NC.The NC treatment showed a lower concentration of superoxide dismutase in serum compared with the PC.Among the treatments in non-sanitary environment,the NC treatment showed a higher concentration of malondialdehyde compared with the ZO.The PC treatment showed a lower concentration of butyric acid in the feces compared with the BP treatment.Among non-sanitary treatments,the villus height in the duodenum was greater in the BP and ZO compared with the NC.The lower abundance of Proteobacteria phylum was observed in the BP and PC treatments compared with the NC.The highest relative abundance of Eubacterium was recorded in the BP treatment.The abundance of Megasphaera and Schwartzia was higher in the NC pigs compared with the BP piglets.The abundance of Desulfovibrio was lower in the supplemented treatments(BP and ZO)compared with non-supplemented(NC and PC).The abundance of Cellulosilyticum genera was higher in the BP and ZO treatments rather than in the NC.The piglets in the NC treatment had the highest abundance of Escherichia-Shigella,followed by the PC and ZO treatments.Conclusion In conclusion,these results suggest that the supplementation of bacteriophage cocktail could effectively control Proteobacteria phylum,Clostridium spp.and coliforms population and mitigated the adverse influences of weaning stress in piglets.展开更多
以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细...以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细菌,即变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)、厚壁菌门(Firmicutes)、梭杆菌门(Fusobacteria)、蓝细菌门(Cyanobacteria)、浮霉菌门(Planctomycetes)、脱铁杆菌门(Deferribacteres)、绿弯菌门(Chloroflexi);黄海和渤海刺参养殖池塘海水和沉积物中优势类群均为变形菌(变形菌比例>48%);用Shannon指数及Simpson优势度指数分析细菌的多样性,黄、渤海刺参养殖池塘中,冬季沉积物细菌Simpson优势度指数均最低,分别为0.014 89和0.016 50,Shannon指数均最高,分别为6.312和5.695。研究表明,黄海和渤海刺参养殖池塘中,冬季沉积物细菌多样性均最高。展开更多
基金National Natural Science Foundation of ChinaGrant/Award Number:81774449。
文摘Background:Inflammatory bowel disease(IBD),comprising Crohn's disease(CD)and ulcerative colitis(UC),is a heterogeneous state of chronic intestinal inflammation.Intestinal innate immunity,including innate immune cells,defends against pathogens and excessive entry of gut microbiota,while preserving immune tolerance to resident intestinal microbiota,and may be characterized by its capacity to produce a rapid and nonspecific reaction.The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic.When the intestinal ecosystem is in dysbiosis,the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota.The aim of our study was to comprehensively assess the relationship between microbial populations within UC,the signaling pathways of pathogenic gut microbe therein and the inflammatory response,as well as to understand the effects of using PE&AFWE(poppy extract[Papaver nudicaule L.]and Artemisia frigida Willd.extract)on UC modulation.Methods:A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate(DSS).Based on metagenomic sequencing to characterize the gut microbiome,the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods,as well as histopathological analysis.Results:(1)We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria.There were three types of abundance changes in the model groups:increases(Chlamydiae/Proteobacteria and Deferribacteres),decreases(Firmicutes),and no significant changes(Bacteroidetes).The UC model group was significantly different from the control group,with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold.(2)The proportion of the fecal flora in the UC group decreased by 37.5%in the Firmicutes and increased by 14.29%in the proportion of Proteobacteria compared to the control group before treatment.(3)The significantly enriched and increased signaling pathways screened were the'arachidonic acid metabolic pathway'and the'phagosomal pathway',which both showed a decreasing trend after drug administration.(4)Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration,screening for directly relevant OTU networks,the UC group was found to directly affect OTU69,followed by a cascade of effects on OTU12,OTU121,OTU93,and OTU7,which may be the pathway of action that initiated the pathological changes in normal mice.(5)We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre-and post-PE&AFWE-treated groups.Thereby,we learned that PE&AFWE can directly affect OTU90,after which it inhibits UC,inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118,which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7.(6)Histopathological observation and scoring(HS)of the colon showed that there was a significant difference between the model group and the control group(p<0.001),and that there was a significant recovery in both the sulfasalazine(SASP)and the PE&AFWE groups after the administration of the drug(p<0.0001).Conclusion:We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD,with five opportunistic pathogens directly contributing to IBD.PE&AFWE reduced the abundance of proteobacteria in the gut microbiota,and histopathology showed significant improvement.
文摘BACKGROUND Preterm birth is the leading cause of mortality in newborns,with very-low-birthweight infants usually experiencing several complications.Breast milk is considered the gold standard of nutrition,especially for preterm infants with delayed gut colonization,because it contains beneficial microorganisms,such as Lactobacilli and Bifidobacteria.AIM To analyze the gut microbiota of breastfed preterm infants with a birth weight of 1500 g or less.METHODS An observational study was performed on preterm infants with up to 36.6 wk of gestation and a birth weight of 1500 g or less,born at the University Hospital Dr.JoséEleuterio González at Monterrey,Mexico.A total of 40 preterm neonates were classified into breast milk feeding(BM)and mixed feeding(MF)groups(21 in the BM group and 19 in the MF group),from October 2017 to June 2019.Fecal samples were collected before they were introduced to any feeding type.After full enteral feeding was achieved,the composition of the gut microbiota was analyzed using 16S rRNA gene sequencing.Numerical variables were compared using Student’s t-test or using the Mann–Whitney U test for nonparametric variables.Dominance,evenness,equitability,Margalef’s index,Fisher’s alpha,Chao-1 index,and Shannon’s diversity index were also calculated.RESULTS No significant differences were observed at the genus level between the groups.Class comparison indicated higher counts of Alphaproteobacteria and Betaproteobacteria in the initial compared to the final sample of the BM group(P<0.011).In addition,higher counts of Gammaproteobacteria were detected in the final than in the initial sample(P=0.040).According to the Margalef index,Fisher’s alpha,and Chao-1 index,a decrease in species richness from the initial to the final sample,regardless of the feeding type,was observed(P<0.050).The four predominant phyla were Bacteroidetes,Actinobacteria,Firmicutes,and Proteobacteria,with Proteobacteria being the most abundant.However,no significant differences were observed between the initial and final samples at the phylum level.CONCLUSION Breastfeeding is associated with a decrease in Alphaproteobacteria and Betaproteobacteria and an increase of Gammaproteobacteria,contributing to the literature of the gut microbiota structure of very low-birth-weight,preterm.
基金Project supported by the National Natural Science Foundation of China (No. 20476099) Zhejiang Provincial Natural Science Foundation (No. Y504272).
文摘The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introduced for MTBE aerobic biodegradation. After 7 d, almost all MTBE was degraded by a pure culture, a member of β-Proteobacteria named as PMI, in a closed system with oxygen supply, while only 40% MTBE was degraded in one without oxygen supply. Dissolved oxygen （DO） levels of the broth in closed systems respectively with and without H2O2 were about 5-6 and 4 mg/L. Higher DO may improve the activity of monooxygemase, which is the key enzyme of metabolic pathway from MTBE to tert-butyl alcohol and finally to CO2, and may result in the increase of the degrading activity of PM1 cell. The purge and trap GC-MS result of the broth in closed systems showed that tea-butyl alcohol, isopronol and acetone were the main intermediate products.
文摘The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker contains 157 bp from the 3’ end of the 16S rRNA gene and 75 bp from the 5’ end of the 16S-23S ITS. The 157 bp allows discrimination among distantly related species. Owing to its higher rate of nucleotide substitutions, the 75 bp adds discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rRNA gene, the 232 bp marker can better discriminate among closely related γ-proteobacterial species. Third, the method is simple, rapid, suited to large screening programs and easily accessible to most laboratories. Fourth, this marker can also reveal γ-proteobacterial species which may appear misassigned and for which additional characterization appear warranted.
文摘Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.
基金the support of“Cooperative Research Program for Agriculture Science and Technology Development(Project No.PJ01694303)”Rural Development Administration,Korea。
文摘Background The study evaluated the effects of bacteriophage cocktail(BP)and ZnO administered during weaning time for piglets exposed to a non-sanitary environment.The bacteriophages were designed to eliminate Escherichia coli(K88,K99 and F41),Salmonella(typhimurium and enteritidis),and Clostridium perfreingens(types A and C).Forty 21-day-old crossbreed piglets were assigned to four treatments,including the PC(sanitary environment),NC(nonsanitary environment),BP(NC plus 108 pfu/kg BP),and ZO(NC plus 2,500 mg/kg ZnO).Piglets in the NC,BP and ZO were kept in a non-sanitary environment for 14 d,which was contaminated with the feces of infected pigs.Results Pigs in the BP and ZO treatments had a higher final body weight compared with the NC.The NC treatment showed the highest concentration of inflammatory cytokines including interleukin(IL)-1β,IL-6 and tumor necrosis factor-αin the plasma.The administration of BP and ZO showed lower myeloperoxidase concentrations compared with the NC.The NC treatment showed a lower concentration of superoxide dismutase in serum compared with the PC.Among the treatments in non-sanitary environment,the NC treatment showed a higher concentration of malondialdehyde compared with the ZO.The PC treatment showed a lower concentration of butyric acid in the feces compared with the BP treatment.Among non-sanitary treatments,the villus height in the duodenum was greater in the BP and ZO compared with the NC.The lower abundance of Proteobacteria phylum was observed in the BP and PC treatments compared with the NC.The highest relative abundance of Eubacterium was recorded in the BP treatment.The abundance of Megasphaera and Schwartzia was higher in the NC pigs compared with the BP piglets.The abundance of Desulfovibrio was lower in the supplemented treatments(BP and ZO)compared with non-supplemented(NC and PC).The abundance of Cellulosilyticum genera was higher in the BP and ZO treatments rather than in the NC.The piglets in the NC treatment had the highest abundance of Escherichia-Shigella,followed by the PC and ZO treatments.Conclusion In conclusion,these results suggest that the supplementation of bacteriophage cocktail could effectively control Proteobacteria phylum,Clostridium spp.and coliforms population and mitigated the adverse influences of weaning stress in piglets.
文摘以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细菌,即变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)、厚壁菌门(Firmicutes)、梭杆菌门(Fusobacteria)、蓝细菌门(Cyanobacteria)、浮霉菌门(Planctomycetes)、脱铁杆菌门(Deferribacteres)、绿弯菌门(Chloroflexi);黄海和渤海刺参养殖池塘海水和沉积物中优势类群均为变形菌(变形菌比例>48%);用Shannon指数及Simpson优势度指数分析细菌的多样性,黄、渤海刺参养殖池塘中,冬季沉积物细菌Simpson优势度指数均最低,分别为0.014 89和0.016 50,Shannon指数均最高,分别为6.312和5.695。研究表明,黄海和渤海刺参养殖池塘中,冬季沉积物细菌多样性均最高。
