细菌群落是实现厌氧氨氧化系统高效脱氮的核心,而厌氧氨氧化启动过程细菌群落多样性及其功能特征仍未被充分阐明.本研究采用升流式厌氧污泥床(UASB)反应器进行厌氧氨氧化系统启动,利用16S r RNA基因高通量测序技术并结合PICRUSt2功能预...细菌群落是实现厌氧氨氧化系统高效脱氮的核心,而厌氧氨氧化启动过程细菌群落多样性及其功能特征仍未被充分阐明.本研究采用升流式厌氧污泥床(UASB)反应器进行厌氧氨氧化系统启动,利用16S r RNA基因高通量测序技术并结合PICRUSt2功能预测分析,研究启动过程不同时间(d0、d30、d60和d90)细菌群落多样性及功能动态变化特征.结果表明,启动过程共检测到48个门、111个纲、269个目、457个科、840个属和1497个种;Candidatus_Brocadia和Candidatus_Kuenenia为检测到的厌氧氨氧化菌,且它们的相对丰度在启动过程不同时间存在显著差异(P <0.05).启动过程,细菌群落α多样性指数整体呈现显著的降低趋势(P <0.05),细菌群落结构呈现出明显的空间分异特征,且差异显著(R=0.846,P <0.01).PICRUSt2功能预测分析表明,启动过程,细菌群落具有丰富的功能多样性,一级功能层表现为有机系统和代谢方面较为活跃,二级功能层子功能基因丰度在厌氧氨氧化启动过程发生明显变化;细菌群落涉及49个参与氮素代谢的相关功能基因,且不同时间阶段参与硝化、反硝化、厌氧氨氧化、硝酸盐同化/异化还原和亚硝酸盐同化/异化还原过程的相关功能基因丰度发生明显变化.展开更多
浮游细菌是水生生态系统的重要组成部分,是水体中氮素生物地球化学循环的主要驱动力.本研究于2016年5月采集丹江口库区库心和渠首2个生态位点表层水样,采用16S r DNA Miseq高通量测序技术研究其群落组成,发现其主要由变形菌门、放线菌...浮游细菌是水生生态系统的重要组成部分,是水体中氮素生物地球化学循环的主要驱动力.本研究于2016年5月采集丹江口库区库心和渠首2个生态位点表层水样,采用16S r DNA Miseq高通量测序技术研究其群落组成,发现其主要由变形菌门、放线菌门、拟杆菌门等12门、139属细菌组成,渠首样品浮游细菌群落多样性高于库心样品. PICRUSt功能预测分析表明,浮游细菌涉及氨基酸运输和代谢、转录、能量产生和转换等24个基因功能家族,表现出功能上的丰富性.其中35个参与氮代谢的KO(表示通路)中库心高于渠首为20个,渠首高于库心的为15个.两样品中检测到涉及固氮作用(nif H)、硝化作用(hao)、反硝化作用(nar G、nir K、nor B、nos Z)、氮同化还原及异化还原作用(nas A、nar B、nap A、nir A、nir B、nrf A)参与氮循环的关键基因相对丰度.综合基因功能家族预测基因拷贝数和氮循环相关基因丰度分析,丹江口库区库浮游细菌氮代谢能力整体趋势为库心高于渠首.本研究从细菌群落组成、功能角度初步分析了丹江口库区不同生态位点氮循环的差异,为丹江口水库水环境保护提供了参考依据.展开更多
微生物是土壤元素生物地球化学循环的主要驱动力,目前库滨带植物截留和消减污染物质过程中细菌群落及其功能研究尚未清楚.本研究选取适宜丹江口库区库滨带生长的4种典型植物(草本植物香根草、芦苇、乔木植物杜梨和灌木植物假奓包叶),采...微生物是土壤元素生物地球化学循环的主要驱动力,目前库滨带植物截留和消减污染物质过程中细菌群落及其功能研究尚未清楚.本研究选取适宜丹江口库区库滨带生长的4种典型植物(草本植物香根草、芦苇、乔木植物杜梨和灌木植物假奓包叶),采用16S r DNA Miseq高通量测序技术研究根际细菌群落组成,发现其主要由变形菌门、拟杆菌门、放线菌门等31个门、343个属的细菌组成,表现出群落组成的丰富性.细菌群落分析表明香根草和芦苇细菌群落结构较为相似,但和杜梨细菌群落结构差异最大.PICRUSt功能预测分析表明,库滨带植物根际细菌主要涉及次生产物代谢的生物合成、转录、多糖生物合成和代谢、细胞生长和死亡等38个子功能,表现出功能上的丰富性.库滨带植物根际细菌代谢能力整体趋势为假奓包叶>芦苇>香根草>杜梨.本研究初步探讨了丹江口库区库滨带不同植物根际细菌群落和功能,为丹江口水库库滨带植被构建及其水环境保护提供了参考依据.展开更多
为探究鱼露快速发酵过程中细菌多样性的变化,以大黄鱼鱼卵为研究对象,通过酶解和加曲的方式快速发酵鱼露,采用16S rDNA高通量测序技术分析大黄鱼鱼卵鱼露快速发酵过程中细菌群落结构的变化,并开展基因功能预测分析。结果显示,未灭菌组(K...为探究鱼露快速发酵过程中细菌多样性的变化,以大黄鱼鱼卵为研究对象,通过酶解和加曲的方式快速发酵鱼露,采用16S rDNA高通量测序技术分析大黄鱼鱼卵鱼露快速发酵过程中细菌群落结构的变化,并开展基因功能预测分析。结果显示,未灭菌组(K组)和灭菌组(M组)鱼露的优势菌门均为厚壁菌门和变形菌门。葡萄球菌属是鱼露发酵过程中的优势菌属,相对丰度高的菌属有链球菌属、糖芽孢杆菌属、类芽孢杆菌属和希瓦氏菌属。PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states)基因功能预测显示,鱼露细菌基因功能涉及遗传信息处理、代谢等6类一级生物代谢通路,以及辅助因子与维生素的代谢、能量代谢等35个二级功能层。M组鱼露在发酵第5、10天时的细菌组成与组内其他发酵时间的样本存在明显差异,这可能是因为M组发酵前期含有相对丰度较高的芽孢杆菌属及更为丰富的二级功能预测基因。在M组鱼露发酵后期,复合曲的加入使细菌菌落发生了改变。本研究结果可为筛选功能菌、改善鱼露品质提供依据。展开更多
为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(...为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(+)-N)、总磷(total phosphorus,TP)和化学需氧量(chemical oxygen demand,COD)等含量异常剧增,伴随TS和VS的降解率下降。对照组(CK组)和0.02%、0.1%和0.5%Virkon^(TM)试验组(分别记为L组、M组和H组)的最大产CH_(4)速率分别为63.20、71.63、73.10和38.17mL/g且CH_4总产量分别降低4.48%、16.58%(P<0.001)和86.33%(P<0.001)。随着暴露时间的延长,试验组的关键酶活呈先升后降趋势,其中,H组的S-α-GC、S-β-GC、S-ACP、S-NP及S-CAT等土壤酶活被显著性抑制(P<0.05)。进一步结合高通量测序发现,在整个厌氧发酵阶段,H组Ace指数、Chao指数和Shannon指数均显著性低于CK组(P<0.01)。在门水平上,第一优势菌群为厚壁菌门,其次为变形菌门,其中厚壁菌门相对丰度随Virkon^(TM)浓度的上升而降低,而变形菌门则相反;在属水平上,随着厌氧发酵时间的延长,束毛球菌属(Trichococcus)相对丰度均出现不同程度上升,由0.19%~0.39%提升至2.80%~4.20%,而H组中史密斯氏菌属(Smithella)的相对丰度受到极显著性(P<0.001)的抑制,较CK组下降91%。同时通过PICRUSt2功能预测分析发现,各试验组微生物群落COG(clusters of orthologous groups of proteins)功能组成结构差异并不明显,未知功能及氨基酸运输和代谢为主要优势功能;结合KO(KEGG orthology)结果与KEGG(kyoto encyclopedia of genes and genomes)数据库相关基因分析发现,高浓度Virkon^(TM)显著抑制微生物群落的生长代谢活性并削弱厌氧发酵系统的甲烷合成效能,另一方面,却诱导关键功能基因K00531(anfG)的表达活性发生超量级响应,较对照组(CK)激增约272倍。其表达水平的显著上调可能通过强化关键酶活性,使系统对Virkon^(TM)消毒副产物中典型氯代污染物(氯代烷烃及氯代烯烃类化合物)的降解效率获得提升,结果可为猪粪厌氧消化处理提供参考。展开更多
OBJECTIVE:To investigate the difference in gut microbiota between population with damp-heat constitution(DHC)and balanced constitution(BC).METHODS:A multi-centered cross-sectional casecontrol study was conducted,which...OBJECTIVE:To investigate the difference in gut microbiota between population with damp-heat constitution(DHC)and balanced constitution(BC).METHODS:A multi-centered cross-sectional casecontrol study was conducted,which included 249 participants with damp-heat constitution or balanced constitution.Baseline information of participants was collected,and stool samples were collected for gut microbiota analysis.Principal coordinate analysis,linear discriminant analysis effect size analysis,receiver operating characteristic,random forest model,and phylogenetic investigation of communities by reconstruction of unobserved states methods were used to reveal the relationship between gut microbiota and the damp-heat constitution.RESULTS:Compared to those in the BC group,the richness and diversity of the microbiota,specifically those of several short-chain fatty acid producing genera such as Barnesiella,Coprobacter,and Butyricimonas,were significantly decreased in the DHC group.Regarding biological functions,flavonoid biosynthesis,propanoate metabolism,and nucleotide sugar metabolism were suppressed,while arachidonic acid metabolism and glutathione metabolism were enriched in the DHC group.Finally,a classifier based on the microbiota was constructed to discriminate between the DHC and BC populations.CONCLUSION:The gut microbiota of the DHC population exhibits significantly reduced diversity and is closely related to inflammation,metabolic disorders,and liver steatosis,which is consistent with clinical observations,thus serving as a potential diagnostic tool for traditional Chinese medicine constitution discrimination.展开更多
Pampus argenteus is a commercially valuable species in many countries.Its artificial cultivation has been impacted by intestinal flatulence,leading to increased mortality.However,the role of gut microbiota in this pro...Pampus argenteus is a commercially valuable species in many countries.Its artificial cultivation has been impacted by intestinal flatulence,leading to increased mortality.However,the role of gut microbiota in this process remains unclear.Therefore,this study utilized high-throughput sequencing of 16S rRNA genes to investigate the gut microbiota in both flatulent and healthy P.argenteus.A total of 227571 high-quality and classifiable reads,representing 312 Amplicon Sequence Variants(ASVs),were obtained.Proteobacteria emerged as the predominant phylum in all samples,with the flatulent group displaying the highest relative abundance(85.3%).Microbial diversity was significantly greater in samples from water than those from tissues.Composition analysis using Bray-Curtis distance via CPCoA revealed distinct gut microbiota compositions between the samples with flatulence and the healthy samples.Co-occurrence network analysis demonstrated that the bacterial community in the flatulent group exhibited disorder due to the high abundance of Vibrio.Functional predictive analysis(PICRUSt2)indicated that flatulence in P.argenteus was associated with impaired methane and lipid metabolism,potentially resulting in excessive methane synthesis utilizing hydrogen and acetic acid as substrates produced by Clostridium sensu stricto 1,Cetobacterium,and Peptoclostridium.This study holds significant implications for early diagnosis and prevention of intestinal flatulence through the regulation of gut microbiota.展开更多
For comprehensive insights into the influences of sulfate on performance,microbial community and metabolic pathways in the acidification phase of a two-phase anaerobic system,a laboratory-scale acidogenic bioreactor w...For comprehensive insights into the influences of sulfate on performance,microbial community and metabolic pathways in the acidification phase of a two-phase anaerobic system,a laboratory-scale acidogenic bioreactor was continuously operated to treat wastewater with elevated sulfate concentrations from 2000 to 14000 mg/L.The results showed that the acidogenic bioreactor could achieve sulfate reduction efficiency of greater than 70%for influent sulfate content less than 12000 mg/L.Increased sulfate induced the accumulation of volatile fatty acids(VPAs),especially propionate and butyrate,which was the primary negative effects to system performance under the high-sulfate environment.High-throughput sequencing coupled with PICRUSt2 uncovered that the accumulation of VFAs was triggered by the decreasing of genes encoding short-chain acyl-CoA dehydrogenase(EC:1.3.8.1),regulating the transformation of propanoyl-CoA to propenoyl-CoA and butanoyl-CoA to crotonyl-CoA of propionate and butyrate oxidation pathways,which made these two process hardly proceed.Besides,genes encoding(EC:1.3.8.1)were mainly carried by order Clostridiales.Desulfovibrio was the most abundant sulfate-reducing bacteria and identified as the primary host of dissimilatory sulfate reduction ftinctional genes.Functional analysis indicated the dissimilatory sulfate reduction process predominated under a low sulfate environment,but was not favored under the circumstance of high-sulfate.With the increase of sulfate,the assimilatory sulfate reduction process finally overwhelmed dissimilatory as the dominant sulfate reduction pathway in acidogenic bioreactor.展开更多
文摘微生物是土壤元素生物地球化学循环的主要驱动力,目前库滨带植物截留和消减污染物质过程中细菌群落及其功能研究尚未清楚.本研究选取适宜丹江口库区库滨带生长的4种典型植物(草本植物香根草、芦苇、乔木植物杜梨和灌木植物假奓包叶),采用16S r DNA Miseq高通量测序技术研究根际细菌群落组成,发现其主要由变形菌门、拟杆菌门、放线菌门等31个门、343个属的细菌组成,表现出群落组成的丰富性.细菌群落分析表明香根草和芦苇细菌群落结构较为相似,但和杜梨细菌群落结构差异最大.PICRUSt功能预测分析表明,库滨带植物根际细菌主要涉及次生产物代谢的生物合成、转录、多糖生物合成和代谢、细胞生长和死亡等38个子功能,表现出功能上的丰富性.库滨带植物根际细菌代谢能力整体趋势为假奓包叶>芦苇>香根草>杜梨.本研究初步探讨了丹江口库区库滨带不同植物根际细菌群落和功能,为丹江口水库库滨带植被构建及其水环境保护提供了参考依据.
文摘为探究鱼露快速发酵过程中细菌多样性的变化,以大黄鱼鱼卵为研究对象,通过酶解和加曲的方式快速发酵鱼露,采用16S rDNA高通量测序技术分析大黄鱼鱼卵鱼露快速发酵过程中细菌群落结构的变化,并开展基因功能预测分析。结果显示,未灭菌组(K组)和灭菌组(M组)鱼露的优势菌门均为厚壁菌门和变形菌门。葡萄球菌属是鱼露发酵过程中的优势菌属,相对丰度高的菌属有链球菌属、糖芽孢杆菌属、类芽孢杆菌属和希瓦氏菌属。PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states)基因功能预测显示,鱼露细菌基因功能涉及遗传信息处理、代谢等6类一级生物代谢通路,以及辅助因子与维生素的代谢、能量代谢等35个二级功能层。M组鱼露在发酵第5、10天时的细菌组成与组内其他发酵时间的样本存在明显差异,这可能是因为M组发酵前期含有相对丰度较高的芽孢杆菌属及更为丰富的二级功能预测基因。在M组鱼露发酵后期,复合曲的加入使细菌菌落发生了改变。本研究结果可为筛选功能菌、改善鱼露品质提供依据。
文摘为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(+)-N)、总磷(total phosphorus,TP)和化学需氧量(chemical oxygen demand,COD)等含量异常剧增,伴随TS和VS的降解率下降。对照组(CK组)和0.02%、0.1%和0.5%Virkon^(TM)试验组(分别记为L组、M组和H组)的最大产CH_(4)速率分别为63.20、71.63、73.10和38.17mL/g且CH_4总产量分别降低4.48%、16.58%(P<0.001)和86.33%(P<0.001)。随着暴露时间的延长,试验组的关键酶活呈先升后降趋势,其中,H组的S-α-GC、S-β-GC、S-ACP、S-NP及S-CAT等土壤酶活被显著性抑制(P<0.05)。进一步结合高通量测序发现,在整个厌氧发酵阶段,H组Ace指数、Chao指数和Shannon指数均显著性低于CK组(P<0.01)。在门水平上,第一优势菌群为厚壁菌门,其次为变形菌门,其中厚壁菌门相对丰度随Virkon^(TM)浓度的上升而降低,而变形菌门则相反;在属水平上,随着厌氧发酵时间的延长,束毛球菌属(Trichococcus)相对丰度均出现不同程度上升,由0.19%~0.39%提升至2.80%~4.20%,而H组中史密斯氏菌属(Smithella)的相对丰度受到极显著性(P<0.001)的抑制,较CK组下降91%。同时通过PICRUSt2功能预测分析发现,各试验组微生物群落COG(clusters of orthologous groups of proteins)功能组成结构差异并不明显,未知功能及氨基酸运输和代谢为主要优势功能;结合KO(KEGG orthology)结果与KEGG(kyoto encyclopedia of genes and genomes)数据库相关基因分析发现,高浓度Virkon^(TM)显著抑制微生物群落的生长代谢活性并削弱厌氧发酵系统的甲烷合成效能,另一方面,却诱导关键功能基因K00531(anfG)的表达活性发生超量级响应,较对照组(CK)激增约272倍。其表达水平的显著上调可能通过强化关键酶活性,使系统对Virkon^(TM)消毒副产物中典型氯代污染物(氯代烷烃及氯代烯烃类化合物)的降解效率获得提升,结果可为猪粪厌氧消化处理提供参考。
基金National Nonprofit Institute Research Grant for the Institute of Basic Theory for Chinese Medicine,China Academy of Chinese Medical Sciences:Mechanism of Regulating Phlegm-Dampness Constitution to Prevent Metabolic Diseases based on Gut Microbiota-host DNA Methylation(No.YZ-202151)。
文摘OBJECTIVE:To investigate the difference in gut microbiota between population with damp-heat constitution(DHC)and balanced constitution(BC).METHODS:A multi-centered cross-sectional casecontrol study was conducted,which included 249 participants with damp-heat constitution or balanced constitution.Baseline information of participants was collected,and stool samples were collected for gut microbiota analysis.Principal coordinate analysis,linear discriminant analysis effect size analysis,receiver operating characteristic,random forest model,and phylogenetic investigation of communities by reconstruction of unobserved states methods were used to reveal the relationship between gut microbiota and the damp-heat constitution.RESULTS:Compared to those in the BC group,the richness and diversity of the microbiota,specifically those of several short-chain fatty acid producing genera such as Barnesiella,Coprobacter,and Butyricimonas,were significantly decreased in the DHC group.Regarding biological functions,flavonoid biosynthesis,propanoate metabolism,and nucleotide sugar metabolism were suppressed,while arachidonic acid metabolism and glutathione metabolism were enriched in the DHC group.Finally,a classifier based on the microbiota was constructed to discriminate between the DHC and BC populations.CONCLUSION:The gut microbiota of the DHC population exhibits significantly reduced diversity and is closely related to inflammation,metabolic disorders,and liver steatosis,which is consistent with clinical observations,thus serving as a potential diagnostic tool for traditional Chinese medicine constitution discrimination.
基金funded by the National Key R&D Program of China(No.2022YFD2400100)the Ningbo 2025 Major Project of Science Technology and Innovation(No.2021Z003)+5 种基金the Public Welfare Program of Ningbo City(Science and Technology Special Commissioner Project)(No.2022S204)the National Natural Science Foundation of China(Nos.31872195,42076118 and 42306114)the China Postdoctoral Science Foundation(No.2022M721729)the General Scientific Research Projects of Zhejiang Provincial Department of Education(No.Y202249062)the Ningbo Public Welfare Science and Technology Project(No.2021S061)the Ningbo Yongjiang Talent Introduction Programme(No.2021B-029-C)。
文摘Pampus argenteus is a commercially valuable species in many countries.Its artificial cultivation has been impacted by intestinal flatulence,leading to increased mortality.However,the role of gut microbiota in this process remains unclear.Therefore,this study utilized high-throughput sequencing of 16S rRNA genes to investigate the gut microbiota in both flatulent and healthy P.argenteus.A total of 227571 high-quality and classifiable reads,representing 312 Amplicon Sequence Variants(ASVs),were obtained.Proteobacteria emerged as the predominant phylum in all samples,with the flatulent group displaying the highest relative abundance(85.3%).Microbial diversity was significantly greater in samples from water than those from tissues.Composition analysis using Bray-Curtis distance via CPCoA revealed distinct gut microbiota compositions between the samples with flatulence and the healthy samples.Co-occurrence network analysis demonstrated that the bacterial community in the flatulent group exhibited disorder due to the high abundance of Vibrio.Functional predictive analysis(PICRUSt2)indicated that flatulence in P.argenteus was associated with impaired methane and lipid metabolism,potentially resulting in excessive methane synthesis utilizing hydrogen and acetic acid as substrates produced by Clostridium sensu stricto 1,Cetobacterium,and Peptoclostridium.This study holds significant implications for early diagnosis and prevention of intestinal flatulence through the regulation of gut microbiota.
基金We gratefully acknowledge generous support provided by the National Natural Science Foundation of China(No.51978328).
文摘For comprehensive insights into the influences of sulfate on performance,microbial community and metabolic pathways in the acidification phase of a two-phase anaerobic system,a laboratory-scale acidogenic bioreactor was continuously operated to treat wastewater with elevated sulfate concentrations from 2000 to 14000 mg/L.The results showed that the acidogenic bioreactor could achieve sulfate reduction efficiency of greater than 70%for influent sulfate content less than 12000 mg/L.Increased sulfate induced the accumulation of volatile fatty acids(VPAs),especially propionate and butyrate,which was the primary negative effects to system performance under the high-sulfate environment.High-throughput sequencing coupled with PICRUSt2 uncovered that the accumulation of VFAs was triggered by the decreasing of genes encoding short-chain acyl-CoA dehydrogenase(EC:1.3.8.1),regulating the transformation of propanoyl-CoA to propenoyl-CoA and butanoyl-CoA to crotonyl-CoA of propionate and butyrate oxidation pathways,which made these two process hardly proceed.Besides,genes encoding(EC:1.3.8.1)were mainly carried by order Clostridiales.Desulfovibrio was the most abundant sulfate-reducing bacteria and identified as the primary host of dissimilatory sulfate reduction ftinctional genes.Functional analysis indicated the dissimilatory sulfate reduction process predominated under a low sulfate environment,but was not favored under the circumstance of high-sulfate.With the increase of sulfate,the assimilatory sulfate reduction process finally overwhelmed dissimilatory as the dominant sulfate reduction pathway in acidogenic bioreactor.
