动物粪便放线菌多样性及生物活性研究
|
摘要
无论从过去的抗生素筛选还是从近年来微生物基因组学的研究成果，放线菌在天然产物的产生与筛选中都占有重要地位。近年，耐药性的不断增加、顽固疾病和新疾病的不断上升，急需有效新药的问世，这使得科学家们将目光转向一些新型的放线菌资源。动物肠道是一类典型而又独特的环境，过去将粪便放线菌作为资源研究的极少。本研究以多种动物粪便为对象，通过免培养和纯培养的研究手段分析粪便放线菌群落组成，从中发掘有开发潜力的菌种资源和新物种资源；研究了菌株的活性及代谢产物,以期开辟一条放线菌资源开发利用的新途径。
本研究首先选择了7种动物（三种灵长目动物、两种熊科动物及一种专性肉食和一种杂食性动物）的粪便，通过高通量454焦磷酸测序技术，进行了细菌的多样性调查。共得到42540条细菌16S rRNA基因V3区片段有效序列，在100%和97%的序列相似度水平下对序列进行归并，分别获得2979条不同的序列和876个OTUs（可操作分类单元），其类群多达13个门，分别是厚壁菌门（Firmicutes）、拟杆菌门（Bacteroidetes）、梭杆菌门（Fusobacteria）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、螺旋体门（Spirochaetes）、蓝藻门（Cyanobacteria）、纤维杆菌门（Fibrobacteres）、柔膜菌门（Tenericutes）、酸杆菌门（Acidobacteria）、脱铁杆菌门（Deferribacteres）、疣微菌门（Verrucomicrobia）和暂定的TM7门。其中，厚壁菌门和拟杆菌门广泛存在于各样品中，并且占绝对优势。在门水平未能鉴定的序列数为1034，占合并后序列总数的34.7%，可见在动物粪便中蕴藏着数量巨大的分类地位较高的未知细菌类群。此外，经分析共有116个细菌属。多样性指数分析发现，杂食性动物川金丝猴、白眉长臂猿、黑猩猩和蓝孔雀的细菌类群多样性较高，而熊科的亚洲黑熊、大熊猫和专性肉食动物东北虎的类群多样性相对较低。另外，同属于灵长目的川金丝猴、白眉长臂猿和黑猩猩的多样性较接近；熊科的亚洲黑熊和大熊猫的多样性较相近。各多样性指数曲线均表明杂食性动物蓝孔雀和专性肉食动物东北虎的类群多样性差异最大。这表明，分类地位近且食性相近的动物，其粪便菌类群也较相近，反之则差异较大。随后，单独对放线菌类群进行分析发现，放线菌门的序列占总测序量的3.2%，分属于103个OTUs。在7份样品中，东北虎的放线菌门序列数最多达15%，其中的未知放线菌类群也最多。
获得纯培养是研究微生物生物学功能及开发利用它们的最基本前提。本工作重点研究了粪便放线菌的分离方法。结果表明，将粪便样品干热处理并配合适宜的稀释度，使用半合成培养基，添加“高浓度”的抑制剂，可以获得较好的分离效果。在此基础上，从28种动物粪便样品中获得923株放线菌，从中选取344株进行分类鉴定，它们分属于35个属，其中一个新属。粪便放线菌中，产丝的放线菌以链霉菌属分布最普遍，数量达107cfu/g；红球菌是另一个分布较广的放线菌类群，有2/3的粪便样品分离到这个属；其它非产丝放线菌以微球菌科成员占优势。本研究只分离好氧放线菌，不涉及厌氧菌。
通过形态学、生理生化、细胞化学和分子分类等分析的多相分类方法，确定了YIM100590的分类地位。该菌株是微球菌科的一个新属，被命名为Enteractinococcus gen.nov.，典型种为Enteractinococcus coprophilus sp. nov.。
对344株粪便放线菌进行的活性筛选实验发现，有76株菌抑制慢性粒细胞白血病癌细胞株（K562），71株菌抑制急性白血病细胞株（HL60）；有26株菌具较强的广谱抗菌活性；有90%以上的供试菌株有碱性磷酸盐酶、酸性磷酸酶、白氨酸芳胺酶和萘酚-AS-BI-磷酸水解酶酶活，有103株菌具纤维素酶活，174株有几丁质酶活；通过PCR检测，获得PKS I（聚酮合酶I）基因阳性菌株34株，PKS II（聚酮合酶II）阳性菌株30株，NRPS（非核糖体多肽合成酶）阳性菌株58株，CYP（细胞色素P450同工酶）阳性菌株22株。
将抗肿瘤活性强的菌株YIM100525发酵后，分离了其中的次生代谢产物，共获得9个化合物。采用波谱学技术确定化合物1、2和3为新化合物。
从以上结果总结出以下结论：第一，粪便中蕴藏着数量巨大且种类繁多的细菌类群，并且有很多分类地位较高的未知类群；第二，粪便放线菌的种类非常丰富,其中以链霉菌和红球菌占优势，微球菌亚目的成员也广泛分布，这是粪便放线菌组成的显著特征，并且存在大量的未知放线菌；第三，粪便放线菌的抗肿瘤活性、抗菌活性、酶活性比例较高，尤其是具有抗肿瘤活性的菌株较多，活性也很高，推测它们在宿主代谢和免疫活动中可能起着重要作用。深入研究这些作用的机制，对于宿主的健康研究具有重要意义；第四，由粪便放线菌分离到了结构多样、活性广泛的化合物，说明粪便放线菌也是一类产生活性先导化合物的重要资源。因此，粪便放线菌与来自土壤、海洋及植物的放线菌一样，是开发药物和其他产品的重要来源之一，应当加强粪便放线菌的研究和保护利用。本研究为粪便放线菌资源的开发利用奠定了基础。
According to the antibiotics screening or research achievements of microbe genomerecently, actinomycetes remain a rich source for natural products screening. Nowadays, newdrugs, especially antibiotics, are urgently needed to counter and reverse the spread ofantibiotic resistant pathogens and to combat life-threatening diseases as well as new diseases.All of these compel the scientists to search some actinomycetes from new sources. Animals’gut is a typical and unique environment, few researches study the fecal actinobacteria assource. In this study, we researched the diversity of fecal actinobacteria usingculture-independent and culture-dependent approaches, and got new species by polyphasictaxonomic research, and further screened and evaluated their bioactivities againstpathogenetic microorganisms and tumor cell and enzymatic activities. One strain with highantitumor activity was further studied on its secondary metabolites. The current study willprovide a new way to exploit and utilize the actinomycetes sources.
We studied the diversity of bacteria16S rRNA gene in seven fecal samples collectedfrom Yunnan Safari Park by454sequencing. A total of42540bacteria V3sequences of16SrRNA genes were obtained and clustered into2979(a threshold of100%identity) uniquesequences and876(a threshold of97%identity) OTUs (operational taxonomic units), andthey distributed at Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria,Spirochaetes, Cyanobacteria, Fibrobacteres, Tenericutes, Acidobacteria, Verrucomicrobia,Deferribacteres and TM7, total13phylums. Amoung them, Firmicutes and Bacteroideteswere dominant in all fecal samples. However,34.7%of the bacterial sequences can not beidentified into any of the known phylum, indicating that these sequences represented somenew species. The total OTUs were ditributed in116genera. Diversity Index curves showedthat the diversity in omnivorous Rhinopithecus roxellanae, Hlobates hoolock, Pan troglodytesand Pavo cristatus samples was high, but was relative low in Ursus thibetanus, Ailuiopodidaemelanoleuca and Panthera tigris altaica samples. The diversity from Primates’ fecal sampleswere similar, and Ursidae’s fecal samples were similar, too. The difference of the diversitybetween omnivorous Pavo cristatus and carnivorous Panthera tigris altaica was very large.These indicated the bacteria diversity was associated with phylogenetic relationship and feeding habit. Thereinto,3.2%sequences belong to Actinobacteria, including103OTUs. For7samples, the proportion of Actinobacteria in Panthera tigris altaica was the largest,accounting for15%, the novel Actinobacteria was the most, too.
Attaining culturable strains is essential for studying and utilizing the microorganisms,thus the isolation method of fecal Actinobacteria was researched. We found that drying andheating up the fecal samples can greatly increase the rate of the actinobacteria. Moreover,many kinds of inhibitors and chemical defined media were suitable for isolation of fecalactinobacteria. Base on this,923purified strains of actinobacteria were isolated from28animal feces samples, and344strains of them were identified as35genera, one of them isnew genus candidate. Streptomyces was the primary filamentous actinobacteria group and upto107colony forming unit (CFU) per gram of dry samples. Rhodococcus was second mostabundant, and this group appeared in2/3samples; The members of suborder Micrococcineaewere main non-filamentous actinobacteria. This study aimed at aerobic actinobacteria, notrefer to anaerobic actinobacteria.
The new genus candidate was subjected to polyphasic taxonomy study including analysisof morphological characteristics, physiological and biochemical tests, chemotaxonomicproperties, phylogenetic analysis based on16S rRNA gene sequences. Strain YIM100590was identified as a member of the novel genus of the family Micrococcaceae, the nameEnteractinococcus gen. nov. was proposed. Enteractinococcus coprophilus sp. nov. is the typespecies of new genus.
Through screening of bioactivities on the fecal Actinobacteria,76strains showed activityagainst K562cell and71strains showed activity against HL60cell by using MTT assay;26strains showed antimicrobial activity using the agar plate diffusion method; More than90%tested strains were positive for alkaline phosphatase, acid phosphatase, leucine arylamidaseand naphthol-AS-BI-phosphohydrolase activity,103could hydrolyze cellulose and174showed keratin activity; The functional gene screening results showed that34strains hadpolyketide synthase I (PKS I) gene,30strains had PKS II gene,58strains had non-ribosomalpeptide synthetase (NRPS) gene and22strains had cytochrome P450hydroxylase (CYP)gene.
Nine compounds were isolated and purified from80liter fermentation broth of strainYIM100525, which had high antitumor activity. The structure of compounds1-9wereconfirmed by spectroscopic analysis, and compounds1-3had novel structures.
The results of this work firstly showed that fecal samples harbored huge quantity ofbacteria, and many groups at phylum level were novel. Secondly, fecal actinobacteria wereabundant. The strains of genera Streptomyces and Rhodococcus were dominating, the members of suborder Micrococcineae were also abundant. This is a distinct feature for groupcomposition of fecal actinobacteria. Many novel actinobacteria existed in feces, too. Thirdly,the proportion of bioactive strains was large. We infered fecal actinobacteria was veryimportant from a nutritional, physiological and immune point of view. Further studyingmechanisms of these function of actinobacteria is significant for the health of host. Fourthly,abundant compounds with different activities were obtained from the fecal actinobacteria,which showed fecal actinobacteria was an important resource for seeking active leadcompound. In conclusion, like soil, marine and endophytic actinobacteria, fecal actinobacteriais a significant source for developing drug and other manufacture. Thus, the research,protection and utilization of fecal actinobacteria should be strengthened. This study has layedthe foundations for development and utilization of fecal actinomycete resources.
本研究首先选择了7种动物（三种灵长目动物、两种熊科动物及一种专性肉食和一种杂食性动物）的粪便，通过高通量454焦磷酸测序技术，进行了细菌的多样性调查。共得到42540条细菌16S rRNA基因V3区片段有效序列，在100%和97%的序列相似度水平下对序列进行归并，分别获得2979条不同的序列和876个OTUs（可操作分类单元），其类群多达13个门，分别是厚壁菌门（Firmicutes）、拟杆菌门（Bacteroidetes）、梭杆菌门（Fusobacteria）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、螺旋体门（Spirochaetes）、蓝藻门（Cyanobacteria）、纤维杆菌门（Fibrobacteres）、柔膜菌门（Tenericutes）、酸杆菌门（Acidobacteria）、脱铁杆菌门（Deferribacteres）、疣微菌门（Verrucomicrobia）和暂定的TM7门。其中，厚壁菌门和拟杆菌门广泛存在于各样品中，并且占绝对优势。在门水平未能鉴定的序列数为1034，占合并后序列总数的34.7%，可见在动物粪便中蕴藏着数量巨大的分类地位较高的未知细菌类群。此外，经分析共有116个细菌属。多样性指数分析发现，杂食性动物川金丝猴、白眉长臂猿、黑猩猩和蓝孔雀的细菌类群多样性较高，而熊科的亚洲黑熊、大熊猫和专性肉食动物东北虎的类群多样性相对较低。另外，同属于灵长目的川金丝猴、白眉长臂猿和黑猩猩的多样性较接近；熊科的亚洲黑熊和大熊猫的多样性较相近。各多样性指数曲线均表明杂食性动物蓝孔雀和专性肉食动物东北虎的类群多样性差异最大。这表明，分类地位近且食性相近的动物，其粪便菌类群也较相近，反之则差异较大。随后，单独对放线菌类群进行分析发现，放线菌门的序列占总测序量的3.2%，分属于103个OTUs。在7份样品中，东北虎的放线菌门序列数最多达15%，其中的未知放线菌类群也最多。
获得纯培养是研究微生物生物学功能及开发利用它们的最基本前提。本工作重点研究了粪便放线菌的分离方法。结果表明，将粪便样品干热处理并配合适宜的稀释度，使用半合成培养基，添加“高浓度”的抑制剂，可以获得较好的分离效果。在此基础上，从28种动物粪便样品中获得923株放线菌，从中选取344株进行分类鉴定，它们分属于35个属，其中一个新属。粪便放线菌中，产丝的放线菌以链霉菌属分布最普遍，数量达107cfu/g；红球菌是另一个分布较广的放线菌类群，有2/3的粪便样品分离到这个属；其它非产丝放线菌以微球菌科成员占优势。本研究只分离好氧放线菌，不涉及厌氧菌。
通过形态学、生理生化、细胞化学和分子分类等分析的多相分类方法，确定了YIM100590的分类地位。该菌株是微球菌科的一个新属，被命名为Enteractinococcus gen.nov.，典型种为Enteractinococcus coprophilus sp. nov.。
对344株粪便放线菌进行的活性筛选实验发现，有76株菌抑制慢性粒细胞白血病癌细胞株（K562），71株菌抑制急性白血病细胞株（HL60）；有26株菌具较强的广谱抗菌活性；有90%以上的供试菌株有碱性磷酸盐酶、酸性磷酸酶、白氨酸芳胺酶和萘酚-AS-BI-磷酸水解酶酶活，有103株菌具纤维素酶活，174株有几丁质酶活；通过PCR检测，获得PKS I（聚酮合酶I）基因阳性菌株34株，PKS II（聚酮合酶II）阳性菌株30株，NRPS（非核糖体多肽合成酶）阳性菌株58株，CYP（细胞色素P450同工酶）阳性菌株22株。
将抗肿瘤活性强的菌株YIM100525发酵后，分离了其中的次生代谢产物，共获得9个化合物。采用波谱学技术确定化合物1、2和3为新化合物。
从以上结果总结出以下结论：第一，粪便中蕴藏着数量巨大且种类繁多的细菌类群，并且有很多分类地位较高的未知类群；第二，粪便放线菌的种类非常丰富,其中以链霉菌和红球菌占优势，微球菌亚目的成员也广泛分布，这是粪便放线菌组成的显著特征，并且存在大量的未知放线菌；第三，粪便放线菌的抗肿瘤活性、抗菌活性、酶活性比例较高，尤其是具有抗肿瘤活性的菌株较多，活性也很高，推测它们在宿主代谢和免疫活动中可能起着重要作用。深入研究这些作用的机制，对于宿主的健康研究具有重要意义；第四，由粪便放线菌分离到了结构多样、活性广泛的化合物，说明粪便放线菌也是一类产生活性先导化合物的重要资源。因此，粪便放线菌与来自土壤、海洋及植物的放线菌一样，是开发药物和其他产品的重要来源之一，应当加强粪便放线菌的研究和保护利用。本研究为粪便放线菌资源的开发利用奠定了基础。
According to the antibiotics screening or research achievements of microbe genomerecently, actinomycetes remain a rich source for natural products screening. Nowadays, newdrugs, especially antibiotics, are urgently needed to counter and reverse the spread ofantibiotic resistant pathogens and to combat life-threatening diseases as well as new diseases.All of these compel the scientists to search some actinomycetes from new sources. Animals’gut is a typical and unique environment, few researches study the fecal actinobacteria assource. In this study, we researched the diversity of fecal actinobacteria usingculture-independent and culture-dependent approaches, and got new species by polyphasictaxonomic research, and further screened and evaluated their bioactivities againstpathogenetic microorganisms and tumor cell and enzymatic activities. One strain with highantitumor activity was further studied on its secondary metabolites. The current study willprovide a new way to exploit and utilize the actinomycetes sources.
We studied the diversity of bacteria16S rRNA gene in seven fecal samples collectedfrom Yunnan Safari Park by454sequencing. A total of42540bacteria V3sequences of16SrRNA genes were obtained and clustered into2979(a threshold of100%identity) uniquesequences and876(a threshold of97%identity) OTUs (operational taxonomic units), andthey distributed at Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria,Spirochaetes, Cyanobacteria, Fibrobacteres, Tenericutes, Acidobacteria, Verrucomicrobia,Deferribacteres and TM7, total13phylums. Amoung them, Firmicutes and Bacteroideteswere dominant in all fecal samples. However,34.7%of the bacterial sequences can not beidentified into any of the known phylum, indicating that these sequences represented somenew species. The total OTUs were ditributed in116genera. Diversity Index curves showedthat the diversity in omnivorous Rhinopithecus roxellanae, Hlobates hoolock, Pan troglodytesand Pavo cristatus samples was high, but was relative low in Ursus thibetanus, Ailuiopodidaemelanoleuca and Panthera tigris altaica samples. The diversity from Primates’ fecal sampleswere similar, and Ursidae’s fecal samples were similar, too. The difference of the diversitybetween omnivorous Pavo cristatus and carnivorous Panthera tigris altaica was very large.These indicated the bacteria diversity was associated with phylogenetic relationship and feeding habit. Thereinto,3.2%sequences belong to Actinobacteria, including103OTUs. For7samples, the proportion of Actinobacteria in Panthera tigris altaica was the largest,accounting for15%, the novel Actinobacteria was the most, too.
Attaining culturable strains is essential for studying and utilizing the microorganisms,thus the isolation method of fecal Actinobacteria was researched. We found that drying andheating up the fecal samples can greatly increase the rate of the actinobacteria. Moreover,many kinds of inhibitors and chemical defined media were suitable for isolation of fecalactinobacteria. Base on this,923purified strains of actinobacteria were isolated from28animal feces samples, and344strains of them were identified as35genera, one of them isnew genus candidate. Streptomyces was the primary filamentous actinobacteria group and upto107colony forming unit (CFU) per gram of dry samples. Rhodococcus was second mostabundant, and this group appeared in2/3samples; The members of suborder Micrococcineaewere main non-filamentous actinobacteria. This study aimed at aerobic actinobacteria, notrefer to anaerobic actinobacteria.
The new genus candidate was subjected to polyphasic taxonomy study including analysisof morphological characteristics, physiological and biochemical tests, chemotaxonomicproperties, phylogenetic analysis based on16S rRNA gene sequences. Strain YIM100590was identified as a member of the novel genus of the family Micrococcaceae, the nameEnteractinococcus gen. nov. was proposed. Enteractinococcus coprophilus sp. nov. is the typespecies of new genus.
Through screening of bioactivities on the fecal Actinobacteria,76strains showed activityagainst K562cell and71strains showed activity against HL60cell by using MTT assay;26strains showed antimicrobial activity using the agar plate diffusion method; More than90%tested strains were positive for alkaline phosphatase, acid phosphatase, leucine arylamidaseand naphthol-AS-BI-phosphohydrolase activity,103could hydrolyze cellulose and174showed keratin activity; The functional gene screening results showed that34strains hadpolyketide synthase I (PKS I) gene,30strains had PKS II gene,58strains had non-ribosomalpeptide synthetase (NRPS) gene and22strains had cytochrome P450hydroxylase (CYP)gene.
Nine compounds were isolated and purified from80liter fermentation broth of strainYIM100525, which had high antitumor activity. The structure of compounds1-9wereconfirmed by spectroscopic analysis, and compounds1-3had novel structures.
The results of this work firstly showed that fecal samples harbored huge quantity ofbacteria, and many groups at phylum level were novel. Secondly, fecal actinobacteria wereabundant. The strains of genera Streptomyces and Rhodococcus were dominating, the members of suborder Micrococcineae were also abundant. This is a distinct feature for groupcomposition of fecal actinobacteria. Many novel actinobacteria existed in feces, too. Thirdly,the proportion of bioactive strains was large. We infered fecal actinobacteria was veryimportant from a nutritional, physiological and immune point of view. Further studyingmechanisms of these function of actinobacteria is significant for the health of host. Fourthly,abundant compounds with different activities were obtained from the fecal actinobacteria,which showed fecal actinobacteria was an important resource for seeking active leadcompound. In conclusion, like soil, marine and endophytic actinobacteria, fecal actinobacteriais a significant source for developing drug and other manufacture. Thus, the research,protection and utilization of fecal actinobacteria should be strengthened. This study has layedthe foundations for development and utilization of fecal actinomycete resources.
引文
贝绍国，刘玉升，崔俊霞.2005.日本龟蜡蚧肠道细菌分离及鉴定研究.山东农业大学学报(自然科学版)，36(2):209~212
陈群，鲍大鹏.1999.人及动物胃肠道正常微生物群的研究.安徽农业技术师范学院学报，13(4):39~42
曹理想.2010.动物共生放线菌研究展望.微生物学通报，37(12):1811~1815
东秀珠，蔡妙英．2001．常见细菌系统鉴定手册．北京：科学出版社
顾觉奋，魏爱琳.2002.大孔网状吸附剂在微生物制药分离纯化上的应用.离子交换与吸附，18(3):281~288
黄云，詹先进，蓝家样，陈全求.2009.昆虫肠道微生物的研究进展.湖北农业科学，48(11):2887~2890
何正波，殷幼平，曹月青，董亚敏，张伟.2001.桑粒肩天牛幼虫肠道菌群的研究.微生物学报，41(6)：741~744
金红芝，李堃宝.2003.人肠道微生态系统的研究进展.科技进展，26(2)：88~91
姜怡，曹艳茹，蔡祥凤，徐丽华，姜成林.2009.三种动物粪便及一种虫体可培养放线菌的多样性及其生物活性.微生物学报，49(9):1152~1157
吉列姆，M.1987.无脊椎动物病理学杂志.49卷:37-38.西方蜜蜂幼虫粪便中的微生物.黎耀东，陈黎红译
贾文祥.2005.医学微生物学.北京:人民卫生出版社:159~169
刘威，姚文，朱伟云.2006.人体与肠道微生物间的互惠共生关系.世界华人消化杂志，14(11)：1081~1088
刘玉升，叶保华，吕飞，郑继法.2006.豆天蛾幼虫肠道细菌分离及初步鉴定研究.山东农业大学学报（自然科学版），37(3)：345~348
刘开朗，王加启，卜登攀，赵圣国.2009.人体肠道微生物多样性和功能研究进展.生态学报，5(29):2589~2594
李可，郑天凌，田蕴，袁建军.2007.南美白对虾肠道微生物群落的分子分析.微生物学报，47(4)：649~653
李旻.2009.人体肠道菌群结构与宿主代谢的相关性研究.[博士学位论文].上海：上海交通大学
黎海彬，李小梅.2005.大孔吸附树脂及其在天然产物研究中的应用.广东化工，32(3):22~25
龙玉，曹焯，潘文石.2002.秦岭野生大熊猫（Ailuropoda melanoleuca）对竹笋细胞壁的利用.北京大学学报（自然科学版），38(4):576~581
龙北国.2003.高级医学微生物学.北京:人民卫生出版社:1~6
李永儒，丁晓贝，左浩江，王嵬，黄玮，裴晓方.2010.肠道菌群与粪便性状关系初探.现代预防医学，37(9):1623~1625
马清义，任建设，史怀平.2009.人工饲养大熊猫消化道正常菌群分离与鉴定研究.畜牧·兽医，7：56~57
荣华，邱成书，胡国全，刘晓凤，张辉，费立松，徐恒，邓宇.2006.一株大熊猫肠道厌氧纤维素菌的分离鉴定、系统发育分析及生物学特性的研究.应用与环境生物学报，12(2):239~242
施曼玲，邱清波，计翔.2000.两种有鳞类爬行动物消化道微生物的研究.动物学杂志，35(6)：12~15
唐蜀昆.2007.新疆高盐环境可培养放线菌多样性研究.[云南大学博士学位论文].昆明：云南大学
王保军，刘缨，姜嘉彤，刘斌，刘双江.2007.蝎子肠道内微生物多样性研究，47(5)：888~893
徐平，李文均，高慧英，徐丽华，姜成林.2005.聚酮类化合物生物合成途径基因阳性菌株生物多样性研究.微生物学报，45(6):821~827
许月卿，彭应登，赵仁兴.2003.树脂吸附法处理磺胺脒生产废水的工艺.环境科学，24(6):139~143
袁志辉，蓝希钳，杨廷，肖杰，周泽扬.2006.家蚕肠道细菌群体调查与分析.微生物学报，46(2)：285~291
赵述森.2009.猪源益生芽抱杆菌的分离筛选与应用研究.[博士学位论文].武汉：华中农业大学
赵秀芝，刘玉升，张帆.2011.龟纹瓢虫四虫态肠道细菌分离及鉴定. Chinese Journal ofMicroecology,23(6):500~504
张敏，范小兵，杭晓敏，李堃宝，杨虹.2004.青年人肠道菌群分布及关键益生菌群落结构分析.微生物学报，44(5):621~626
朱瑞良，牛钟相，常伟山.1996.不同日龄兔肠道正常菌群的研究.中国兽医学报，16（2）:176~178
Anderson R C, Rasmussen M A, Jensen N S, Allison M J.2000. Denitrobacterium detoxificans gen.nov., sp. nov., a ruminal bacterium that respires on nitrocompounds. International Journal of Systematicand Evolutionary Microbiology,50:633~638
Anklin-mühlemann R, Bignell D E, Veivers P C, Leuthold R H, Slaytor M.1995. Morphological,Microbiological and Biochemical Studies of the Gut Flora in the Fungus-growing Termite Macrotermessubhvalinus. Journal of Insect Physiology,41(11):929~940
Arumugam M, Raes J, Pelletier E, Paslier D E, Yamada T, Mende D R, Fernandes G R, Tap J, Bruls T,Batto J M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M et al.2011.Enterotypes of the human gut microbiome. Nature, doi:10.1038/09944
Ayuso-Sacido A, Genilloud O.2005. New PCR Primers for the Screening of NRPS and PKS-ISystems in Actinomycetes: Detection and Distribution of These Biosynthetic Gene Sequences in MajorTaxonomic Groups. Microbial Ecology,49:10~24
Backhed F, Ley R E, Sonnenburg J L, Peterson D A, Gordon J I.2005. Hostbacterial mutualism in thehuman intestine. Science,307:1915~1920
Beman B L.1983. Actinomycete pathogen//Goodfellow M, Mordarski M, Williams S T. The biologyof the actinomyces. London: Academic press,457~480
Bentley S D, Chater K F, Cerde o-Tárraga A M, Challis G L, Thomson N R, James K D, Harris D E,Quail M A, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen C W, Collins M, Cronin A, FraserA, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang C H, Kieser T, Larke L, Murphy L, Oliver K, O'NeilS, Rabbinowitsch E, Rajandream M A, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R,Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell B G, Parkhill J, Hopwood D A.2002.Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature,417:141~147
Bik E M, Eckburg P B, Gill S R, Nelson K E, Purdom E A, Francois F, Perez-Perez G, Blaser M J,Relman D A.2006. Molecular analysis of the bacterial microbiota in the human stomach. Proceedings ofthe National Academy of Science U. S. A.,103(3):732~737
Bignell D E, Oskarsson H, Anderson J M.1979. Association of actinomycete-like bacteria withsoil-feeding termites (Termitidae, Termitinae). Applied and Environmental Microbiology,37:339~342
Cao Y R, Jiang Y, Jin R X, Han L, He W X, Li Y L, Huang X S, Xue Q H.2012. Enteractinococcuscoprophilus gen. nov., sp. nov., of the family Micrococcaceae isolated from Panthera tigris amoyensisfeces, transfer of Yaniella fodinae Dhanjal et al.2011to the genus Enteractinococcus as Enteractinococcusfodinae comb. nov. International Journal of Systematic and Evolutionary Microbiology, IJSEM Papers inPress. Published January6, as doi:10.1099/ijs.0.034249-0
Chu T L, Szabó I M, Szabó I.1987. Nocardia from gut actinomycetes of Glomeris hexasticha Brandt(Diplopoda). Biology and Fertility of Soils,3:113~116
Chun J, Lee J H, Jung Y, Kim M, Kim S, Kim B K, Lim Y W.2007. EzTaxon: a web-based tool forthe identification of prokaryotes based on16S ribosomal RNA gene sequences. International Journal ofSystematic and Evolutionary Microbiology,57:2259~2261
Costello E K, Lauber C L, Hamady M, Fierer N, Gordon J I, Knight R.2009. Bacterial communityvariation in human body habitats across space and time. Science,326:1694~1697
Czaran T L, Hoekstra R E, Page L.2002. Chemical warfare between microbes promotes biodiversity.Proceedings of the National Academy of Science U. S. A.,99:786~790
Daly K, Stewart C S, Flint H J, Shirazi-Beechey S P.2001. Bacterial diversity within the equine largeintestine as revealed by molecular analysis of cloned16S rRNA genes. FEMS Microbial Ecology,38:141~151
Demain A L, Sanchez S.2009. Microbial drug discovery:80years of progress. The Journal ofantibiotics,62:5~16
Dhanjal S, Ruckmani A, Cameotra S S, Pukall R, Klenk H P, Mayilraj S.2011. Yaniella fodinae sp.nov., a novel member of the genus Yaniella isolated from coal mine. International Journal of Systematicand Evolutionary Microbiology,61:535~539
Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson J K.2008. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. InternationalSociety for Microbial Ecology,2:716~727
DoBell C.1932. AntonVon Leewenhoek and ‘BigLittleAnimals’. NewYork: Harcourt Brace andCompany.
Durso L M, Harhay G P, Smith T P, Bono J L, DeSantis T Z, Harhay D M, Anderson G L, Keen J E,Laegreid W W, Clawson M L.2010. Animal-to-animal variation in fecal microbial diversity among beefcattle. Applied and Environmental Microbiology,76:4858~4862
Durvasula RV, Sundaram RK, Kirsch P, Hurwitz I, Crawford C V, Dotson E, Beard C B.2008.Genetic transformation of a corynebacterial symbiont from the chagas disease vector Triatoma infestans.Experimental Parasitology,119:94~98
Duangmal K, Ward A C, Goodfellow M.2005. Selective isolation of members of the Streptomycesviolaceoruber clade from soil. Federation of European Microbiological Societies Microbiology Letters,245:321~327
Dyszynski G.2006. RDPquery: A Java program from the Sapelo Program Microbial Observatory forautomatic classification of bacterial16S rRNA sequences based on Ribosomal Database Project taxonomyand Smith-Waterman alignment.
Eckburg P B, Bik E M, Bernstein C N, Purdom E, Dethlefsen L, Sargent M, Gill S R, Nelson K E,Relman D A.2005. Diversity of the Human Intestinal Microbial Flora. Science,308:1635~1638
Ezaki T, Hashimoto Y, Yabuuchi E.1989. Fluorometric deoxyribonucleic acid-deoxyribonucleic acidhybridization in microdilution wells as an alternative to membrane filter hybridization in whichradioisotopes are used to determine genetic relatedness among bacterial strains. International Journal ofSystematic Bacteriology,39:224~229
Fall S, Hamelin J, Ndiaye F, Assigbetse K, Aragno M, Chotte J L, Brauman A.2007. Differencesbetween Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and ItsMounds. Applied and Environmental Microbilogy,73(16):5199~5208
Felsenstein J.1993. PHYLIP (phylogeny inference package), version3.5c. Seattle: University ofWashington
Felsenstein J.1981. Evolutionary trees from DNA sequences: a maximum likelihood approach.Journal of Molecular Evolution,17:368~379
Fitch W M.1971. Toward defining the course of evolution: minimum change for a specific treetopology. Systematic zoology,20:406~416
Finegold S M, Attebery H R, Sutter V L.1974. Effect of diet on human fecal flora: comparison ofJapanese and American diets. The American Journal of Clinical Nutrition,27(12):1456~69
Frank D N, St Amand A L, Feldman R A, Boedeker E C, Harpaz N, Pace N R.2007.Molecular-phylogenetic characterization ofmicrobial community imbalances in human inflammatory boweldiseases. Proceedings of the National Academy of Science U. S. A.,104:13780~13785
Frey J C, Rothman J M, Pell A N, Nizeyi J B, Cranfield M R, Angert E R.2006. Fecal BacterialDiversity in a Wild Gorilla. Applied and Environmental Microbiology,72(5):3788~3792
FUJIMOTO H, NOZAWA M, OKUYAMA E, ISHIBASHI M.2003. Six New Constituents from anAscomycete, Chaetomium quadrangulatum, Found in a Screening Study Focused on Monoamine OxidaseInhibitory Activity. Chemical and Pharmaceutical Bulletin,51(3):247~251
Gandhimathi R, Arunkumar M, Selvin J, Thangavelu T, Sivaramakrishnan S, Kiran G S,Shanmughapriya S, Natarajaseenivasan K.2008. Antimicrobial potential of sponge associated marineactinomycetes. Journal de Mycologie Médicale,18:16~22
Gao R C, Huang Z X, Wu C F, Xu B, Wang X Y.2010. Culture-independent analysis of microflora ingayals (Bos frontalis) feces. African Journal of Biotechnology,9:2774~2788
Gill S R, Pop M, DeBoy R T, Eckburg P B, Turnbaugh P J, Samuel B S, Gordon J I, Relman D A,Fraser-Liggett C M, Nelson K E.2006. Metagenomic Analysis of the Human Distal Gut Microbiome,Science,312:1355~1359
Goodfellow M, Fiedler H P.2010. A guide to successful bioprospecting: informed by actinobacterialsystematics. Antonie van Leeuwenhoek,98:119~142
Gordon R E, Barnett D A, Handerhan J E, Pang C H N.1974. Nocardia coeliaca, NocardiaAutotrophica, and the nocardin strains. International Journal of Systematic Bacteriology,24:54~63
Gokhale R S, Sankaranarayanan R, Mohanty D.2007. Versatility of polyketide synthases ingenerating metabolic diversity. Current Opinion in Structural Biology,17(6):736~743
Greetham H L, Giffard C, Hutson R A, Collins M D, Gibson G R.2002. Bacteriology of the Labradordog gut: a cultural and genotypic approach. Journal of Applied Microbiology,93:640~646
Gusm o D S, Santos A V, Marini D C, Bacci Jr. M, Berbert-Molina M A., Lemos F J A.2010.Culture-dependent and culture-independent characterization of microorganisms associated with Aedesaegypti (Diptera: Culicidae)(L.) and dynamics of bacterial colonization in the midgut. Acta Tropica,115:275~281
Hartemink R, Domenech V B, Rombouts F M.1997. Lamvab－A new selective medium for theisolation of lactobacilli from faeces. Methods in Microbiology,29(1):77
Hayakawa M, Nonomura H.1987. Humic acid-vitamin agar, a new medium for the selective isolationof soil actinomycetes. Journal of Fermentation Technology,65:501~509
Hasegawa T, Takizawa M, Tanida S.1983. A rapid analysis for chemical grouping of aerobicactinomycetes. The Journal of General and Applied Microbiology,29:319~322
He L，Li W，Huang Y, Wang L, Liu Z, Lanoot B, Vancanneyt M, Swings J.2005. Streptomycesjietaisiensis sp. nov. isolated from soil in northern China. International Journal of Systematic andEvolutionary Microbiology,55:1939~1944
Hooper L V, Gordon J I.2001. Commensal host-bacterial relationships in the gut. Science,292:1115~1118
Hooper L V, Wong M H, Thelin A, Hansson L, Falk P G, Gordon J I.2001. Molecular analysis ofcommensal host-bacterial relationships in the intestine. Science,291:881~884
Holzapfel W H, Haberer P, Snel J, Schillinger U, Huis in’t Veld J H.1998. Overview of gut flora andProbiotics. International Joumal of Food Mierobiology,41(2):85~101
Hooper L V, Midtvedt T, Gordon J I.2002. How host-microbial interactions shape the nutrientenvironment of the mammalian intestine. Annual Review of Nutrition,22:283~307
Hopkins M J, Sharp R, Macfarlane G T.2001. Age and disease related changes in intestinal bacterialpopulations assessed by cell culture,16S rRNA abundance, and community cellular fatty acid profiles. Gut,48(2):198~205
Hwang Y B, Lee M Y, Park H J, Han K, Kim E S.2007. Isolation of putative polyene-producingactinomycetes strains via PCR-based genome screening for polyene-specific hydroxylase genes. ProcessBiochemistry,42:102~107
Jensen P R.2010. Linking species concepts to natural product discovery in the post-genomic era.Journal of Industrial Microbiology and Biotechnology,7:219~224
Jiang Y, Cao Y R, Wiese J, Lou K, Zhao L X, Imhoff J F, Jiang C L.2009. A new approach ofresearch and development on pharmaceuticls from actinomycetes. Journal of Life Science US,3(7):52~56
Kaltenpoth M, Winter S A, Kleinhsmmer A.2009. Localization and transmission route ofCoriobacterium glomerrans, the endosymbiont of pyrrhocorid bugs. FEMS Microbial Ecology,69:373~383
Kaltenpoth M, G ttler W, Herzner G, Strohm E.2005. Symbiotic bacteria protect wasp larvae fromfungal infestation. Current Biology,15:475~479
Kaltenpoth M, Schmitt T, Polidori C, Koedam D, Strohm E.2010. Symbiotic streptomycetes inantennal glands of the South American digger wasp genus Trachypus (Hymenoptera, Crabronidae).Physiological Entomology,35:196~200
Kemp P F, Aller J Y.2004. Bacterial diversity in aquatic and other environments: what16S rDNAlibraries can tell us. Fems Microbial Ecology,47(2):161~177
Kelly K L.1964. Inter-Society Color Council–National Bureau of Standards Color-Name ChartsIllustrated with Centroid Colors．Washington，DC：US Government Printing Office
Ketela M M, Virpi S, Halo L, Hautala A, Hakala J, Mantsala P, Ylihonko K.1999. An efficientapproach for screening minimal PKS genes from Streptomyces. FEMS Microbiology Letters,180:1~6
Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M.2011.Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchillalanigera) faeces. International Journal of Systematic and Evolutionary Microbiology,61:877~881
Kroppenstedt R M.1982. Separation of bacterial menaquinones by HPLC using reverse phase (RP18)and a silver loaded ion exchanger as stationary phases. Journal of Liquid Chromatography&RelatedTechnologies,5:2359~2367
Lawson P A, Greethan H L, Gibson G R, Giffard C, Falsen E, Collins M D.2005. Slackia faecicanissp. nov., isolated from canine faeces. International Journal of Systematic and Evolutionary Microbiology,55:1243~1246
Lee J, Mo J H, Katakura K, Alkalay I, Rucker A N, Liu Y T, Lee H K, Shen C, Cojocaru G, ShenoudaS, Kagnoff M, Eckmann L, Ben-Neriah Y, Raz E.2006. Maintenance of colonic homeostasis by distinctiveapical TLR9signalling in intestinal epithelial cells. Nature Cell Biology,8:1327~1336
Ley R E, Peterson D A, Gordon J I.2006. Ecological and evolutionary forces shaping microbialdiversity in the human intestine. Cell,124:837~848
Ley R E, Hamady M, Lozupone C, Turnbaugh P J, Ramey R R, Bircher J S, Schlegel M L, Tucker TA, Schrenzel M D, Knight R, Gordon J I.2008. Evolution of mammals and their gut microbes. Science,320:1647~1651
Ley R E, B ckhed F, Turnbaugh P, Lozupone C A, Knight R D, Gordon J I.2005. Obesity alters gutmicrobial ecology. Proceedings of the National Academy of Science U. S. A.,102(31):11071~11075
Leifson E.1960. Atlas of Bacterial Flagellation. London: Academic Press
Li W, Godzik A.2006. Cd-hit: a fast program for clustering and comparing large sets of protein ornucleotide sequences. Bioinformatics,22(13):1658~1659
Li W J, Chen H H, Xu P, Zhang Y Q, Schumann P, Tang S K, Xu L H, Jiang C L.2004. Yaniahalotolerans gen. nov., sp. nov., a novel member of the suborder Micrococcineae from saline soil in China.International Journal of Systematic and Evolutionary Microbiology,54:525~531
Li W J, Zhi X Y, Euzéby J P.2008. Proposal of Yaniellaceae fam. nov., Yaniella gen. nov. andSinobaca gen. nov. as replacements for the illegitimate prokaryotic names Yaniaceae Li et al.2005, YaniaLi et al.2004, emend Li et al.2005, and Sinococcus Li et al.2006, respectively. International Journal ofSystematic and Evolutionary Microbiology,58:525~527
Li W J, Schumann P, Zhang Y Q, Xu P, Chen G Z, Xu L H, Stackebrandt E, Jiang C L.2005.Proposal of Yaniaceae fam. nov. and Yania flava sp. nov. and emended description of the genus Yania.International Journal of Systematic and Evolutionary Microbiology,55:1933~1938
Liu W, Ahlert J, Gao Q, Wendt-Pienkowski E, Shen B, Thorson J S.2003. Rapid PCR amplificationof minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model.Proceedings of the National Academy of Science U. S. A.,100(21):11959~11963
Long H F.2011. http://baike.baidu.com/view/74071.htm#3[2011-11-07]
Lozupone C, Hamady M, Knight R.2006. UniFrac-an online tool for comparing microbial communitydiversity in a phylogenetic context. BMC Bioinformatics,7:371
Lozupone C, Knight R.2005. UniFrac: a new phylogenetic method for comparing microbialcommunities. Applied and Environmental Microbiology,71(12):8228~8235
Lynn B, Per F G, Tore M, Gordon J I.1996. A model of host-microbial interaction in an openmammalian ecosystem. Science,273:1380~1383
Mai V.2004. Dietary Modification of the Intestinal Microbiota. Nutrition Reviews,62(6):235~242
Matsui T, Tanaka J, Namihira T, Shinzato N.2012. Antibiotics production by an actinomyceteisolated from the termite gut. Journal of Basic Microbiology, doi:10.1002/jobm.201100500
Marta J F, Miros aw P Z, Tomasz D P, Marek W, Jaros aw P.2010. Gut bacterium of Dendrobaenaveneta (Annelida: Oligochaeta) possesses antimycobacterial activity. Journal of Invertebrate Pathology,105:63~73
Margulies M, Egholm M, Altman W E, et al.2005. Genome sequencing in microfabricatedhigh-density picolitre reactors. Nature,437(7057):376~380
Marmur J.1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. Journalof Molecular Biology,3:208~218
McKenna P, Hoffmann C, Minkah N, Aye P P, Lackner A, Liu Z, Lozupone C A, Hamady M, KnightR, Bushman F D.2008. The macaque gut microbiome in health, lentiviral infection, and chronicenterocolitis. PLoS Pathogens,4(2):20
McAlpine J B, Bachmann B O，Piraee M, et al.2005. Microbial genomecs as a guide to drugdiscovery and structure elucidation: ECO-02301, a new antifungal agent, as an exceple. Journal of NaturalProducts,68:493~496
Mesbah M, Premachandran U, Whitman W B.1989. Precise measurement of the G+C content ofdeoxyribonucleic acid by high-performance liquid chromatography. International Journal of SystematicBacteriology,39:159~167
Mets-Ketel M, Halo L, Munukka E, Hakala J, M nts l P, Ylihonko K.2002. Molecular Evolutionof Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and16SRibosomal DNA Genes from Various Streptomyces Species. Applied and Environmental Microbiology,68(9):4472~4479
Mitsuoka T.1992. Intestinal flora and aging. Nutrition Reviews,50(12):438~446
Minnikin D E, O’Donnell A G, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J H.1984.An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal ofMicrobiological Methods,2:233~241
Morotomi M, Nagai F, Watanabe Y.2012. Description of Christensenella minuta gen. nov., sp. nov.,isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal ofChristensenellaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology,62:144~149
Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C,Verdenelli M C, Clavel T, Koebnick C, Zunft H-J F, Doré J, Blaut M.2006. Differences in FecalMicrobiota in Different European Study Populations in Relation to Age, Gender, and Country: aCross-Sectional Study. Applied and Environmental Microbiology,72(2):1027~1033
Muyzer G, de Waal E C, Uitterlinden A G.1993. Profiling of complex microbial populations bydenaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for16S rRNA. Applied and Environmental Microbiology,59(3):695~700
Osterhage C, Kaminsky R, K nig G M, Wright A D.2000. Ascosalipyrrolidinone A, an AntimicrobialAlkaloid, from the Obligate Marine Fungus Ascochyta salicorniae. Journal of Organic Chemistry,65:6412~6417
Ozutsumi Y, Hayashi H, Sakamoto M, IItabashi H. Benno Y.2005. Culture-independent analysis offecal microbiota in cattle. Bioscience, Biotechnology, and Biochemistry,69:1793~2005
Pasti M B, Pometto A L, Nuti M P.1990. Lignin-solubilizing ability of actinomycetes isolated fromtermite (Termitidae) gut. Applied and Environmental Microbiology,56:2213~2218
Pedras M S C, Morales V M, Taylor J L.1994. PHOMAPYRONES: THREE METABOLITESFROM THE BLACKLEG FUNGUS. Phyrochmistry,36(5):1315~1318
Qin J, Li R, Raes J, Arumugam M, Burgdorf K S, et al.2010. A human gut microbial gene catalogueestablished by metagenomic sequencing. Nature,464:59~65
Rainey P B, Rainey K.2003. Evolution of cooperation and conflict in experimental bacterialpopulations. Nature,425:72~74
Rastall R A.2004. Bacteria in the gut: friends and foes and how to alter the balance. Journal ofNutrition,134:2022~2026
Rescot L M, Harley J P, Klein D A.2002. Microbiology.5thed. New York: The McGraw-Hillcompanies:344~356
Ritchie L E, Steiner J M, Suchodolski J S.2008. Assessment of microbial diversityalong the felineintestinal tract using16S rRNAgene analysis. Federation of European Microbiological Societies MicrobialEcology,66:590~598
Rondon M R, August P R, Bettermann A D, Brady S F, Grossman T H, Liles M R, Loiacono K A,Lynch B A, MacNeil I A, Minor C, Tiong C L, Gilman M, Osburne M S, Clardy J, Handelsman J,Goodman R M.2000. Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and FunctionalDiversity of Uncultured Microorganisms. Applied and Environmental Microbiology,66:254l~2547
Sasser M.1990. Identification of bacteria by gas chromatography of cellular fatty acids，MIDITechnical Note101. Newwark, DE: MIDI Inc
Schafer A, Konrad R, Kuhnigk T, Kampfer P, Herte H, Konig H.1996. Hemicellulose-degradingbacteria and yeasts from termite gut. Journal of Applied Bacteriology,80:471~478
Schloss P D, Handelsman J.2005. Introducing DOTUR, a computer program for defining operationaltaxonomic units and estimating species richness. Applied and Environmental Microbiology,71(3):1501~1506
Schleifer K H, Kandler O.1972. Peptidoglycan types of bacterial cell walls and their taxonomicimplications. Bacteriology Reveiws,36:407~477
Seshime Y, Juvvadi P R，Fujii I, Kitamoto K.2005. Discovery of a novel superfamily of type IIIpolyketide synthases in Aspergillus oryzae. Biochemical and Biophysical Research Communications,331:253~260
Shirling E B, Gottlieb D.1966. Methods for characterization of Streptomyces species. InternationalJournal of Systematic Bacteriology,16:313~340
Simpson J M, Martineau B, Jones W E, Ballam J M, Mackie R I.2002. Characterization of fecalbacterial population in canines: effecs of age, breed and dietary fiber. Microbial Ecology,44:186~197
Smriga S, Sandin S A, Azam F.2010. Abundance,diversity, and activityof microbial assemblagesassociatedwith coral reefish guts and feces. Federation of European Microbiological Societies MicrobiolEcol,73:31~42
Smibert R M, Krieg N R.1994. Phenotypic characterization. In Methods for General and MolecularBacteriology, pp.607–654. Edited by P. Gerhart, R. G. E. Murray, W. A. Wood&N. R. Krieg.Washington, DC: American Society for Microbiology
Snipes C E, Chang C J, Floss H G.1979. Biosynthesis of the antibiotic granaticin. Journal of theAmerican Chemical Society,101(3):701~706
Staunton J, Weissman K J.2001. Polyketide biosynthesis: a millennium review. Natural ProductReports,18(4):380~416
Suau A, Bonnet R, Sutren M, Godon J J, Gibson G, Collins M D, Doré J.1999. Direct rDNAcommunity analysis reveals a myriad of novel bacterial lineages within the human gut. Applied andEnvironmental Microbiology,65(1):4799~4807
Suchodoski J S, Ruaux C G., Steiner J M, Fetz K, Williams D A.2004. Application of molecularfingerprinting for qualitative asscssment of small-intestinal bacterial diversity in dogs. Journal of ClinicalMicrobiology,42:4702~4708
Suchodolski J S., Camacho J, Steiner J M.2008. Analysis of bacterial diversity in the canineduodenum, jejunum, ileum, and colon by comparative16S rRNAgene analysis. Federation of EuropeanMicrobiological Societies Microbial Ecology,66:567~578
Tan H, Deng Z, Cao L.2009. Isolation and characterization of actinomycetes from healthy goat feces.Letters in Applied Microbiology,49:248~253
Tamura K, Dudley J, Nei M, Kumar S.2007. MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Molecular Biology and Evolution,24:1596~1599
Tang S K, Wang Y, Chen Y, Lou K, Cao L L, Xu L H, Li W J.2009. Zhihengliuella alba sp. nov., andemended description of the genus Zhihengliuella. International Journal of Systematic and EvolutionaryMicrobiology,59:2025~2032
Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D G.1997. The Clustal X windowsinterface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic AcidsResearch,25:4876~4882
Thompson C J, Fink D, Nguyen L D.2002. Principles of microbial alchemy: insights from theStreptomyces coelicolor genome sequence. Genome Biology,3(7):1020
Turnbaugh P J, Hamady M, Yatsunenko T, Cantarel B L, Duncan A, Ley R E, Sogin M L, Jones W J,Roe B A, Affourtit J P, Egholm M, Henrissat B, Heath A C, Knight R, Gordon J I.2009. A core gutmicrobiome in obese and lean twins. Nature,457:480~484
Ward A C, Goodfellow M.2004. Phylogeny and functionality: taxonomy as a roadmap to genes. In:Bull AT (ed) Microbial diversity, bioprospecting. Washington, DC: ASM Press:288~313
Wang T T, Cai G X, Qiu Y P, Fei N, Zhang M H, Pang X Y, Jia W, Cai S J, Zhao L P.2012. Structuralsegregation of gut microbiota between colorectal cancer patients and healthy volunteers. The ISME journal,6(2):320~329
Watanabe K, Praseuth A P, Wang C C.2007. A comprehensive and engaging overview of the typeⅢfamily of polyketide synthases. Current Opinion in Chemical Biology,11(3):279~286
Weaver R F.2002. Molecular biology.2nded. New York: the Mc-Hill companies:784~797
Whilaman W B, Coleman D C, Wiebe W J.1998. Prokaryotes: the unseen majority. Proceedings ofthe National Academy of Science U. S. A.,94:6578~6583
Wielen P W J J, Keuzenkamp D A, Lipman L J A, Knapen F, Biesterveld S.2002. Spatial andTemporal Variation of the Intestinal Bacterial Community in Commercially Raised Broiler ChickensDuring Growth. Microbial Ecology,44(3):286~293
Williams A G, Withers S E.1981. Hemicellulose-degrading Enzymes Synthesized by Rumen Bacteria.Journal of Applied Bacteriology,51:375~385
Wishart D S, Knox C, Guo A C, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M.2008DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research,36:901~906
Xin Y J, Huang J Y, Deng M C, Zhang W.2008. Culture-independent nested PCR method revealshigh diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp.Antonie van Leeuwenhoek,94:533~542
Xin Y J, Zhang W.2008. Marine sponge Hymeniacidon perlevis possesses high diversity of culturableactinobacteria. Journal of Biotechnology,136:607~619
Xu J, Bjursell M K, Himrod J, Deng S, Carmichael L K, Chiang H C, Hooper L V, Gordon J I.2003.A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science,299:2074~2076
Yassin A F, Hupfer H, Siering C, Klenk H P, Schumann P.2011. Auritidibacter ignavus gen. nov., sp.nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of themembers of the family Yaniellaceae Li et al.2008to the family Micrococcaceae and emended descriptionof the suborder Micrococcineae. International Journal of Systematic and Evolutionary Microbiology,61:223~230
Yang S X, Gao J M, Zhang A L, Jiang Y, Cao Y R, Laatsch H. Sannastatin.2011. A novel toxicmacrolactam polyketide glycoside produced by actinomycete Streptomyces sannanensis. Bioorganic&Medicinal Chemistry,21:3905~3908
Yildirim S, Yeoman C J, Sipos M, Torralba M, Wilson B A, Goldberg T L, Stumpf R M, Leigh S R,White B A, Nelson K E.2010. Characterization of the Fecal Microbiome from Non-Human Wild PrimatesReveals Species Specific Microbial Communities. PLoS ONE,5(11):1~11
Zazopoulos E, Huang K, Staffa A, Liu W, Bachmann B O, Nonaka K, Ahlert J, Thorson J S, Shen B,Farnet C M.2003. A genomics-guided approach for discovering and expressing cryptic metabolic pathways.Nature Biotechnology,21(2):187~190
Zhang H T, Lee Y K, Zhang W, Lee H K.2006. Culturable actinobacteria from the marine spongeHymeniacidon perleve: isolation and phylogenetic diversity by16S rRNA gene-RFLP analysis. Antonievan Leeuwenhoek,90:159~169
Zhang H, DiBaise J K, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell M D,Wing R, Rittmann B E, Krajmalnik-Brown R.2009. Human gut microbiota in obesity and after gastricbypass. Proceedings of the National Academy of Science U. S. A.,106:2365~2370
Zhang H H, Chen L.2010. Phylogenetic analysis of16S rRNA gene sequences reveals distal gut
bacterial diversity in wild wolves (Canis lupus). Molecular Biology Reports,37:4013~4022
Zhang C H, Zhang M H, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G,
Chen Y, Zhao L.2010. Interactions between gut microbiota, host genetics and diet relevant to development
of metabolic syndromes in mice. The ISME Journal,4(2):232~241
Zhu L F, Wua Q, Dai J Y, Zhang S N, Wei F W.2011. Evidence of cellulose metabolism by the giant
panda gut microbiome. Proceedings of the National Academy of Science Early Edition,1~6
www.pnas.org/cgi/doi/10.1073/pnas.1017956108
陈群，鲍大鹏.1999.人及动物胃肠道正常微生物群的研究.安徽农业技术师范学院学报，13(4):39~42
曹理想.2010.动物共生放线菌研究展望.微生物学通报，37(12):1811~1815
东秀珠，蔡妙英．2001．常见细菌系统鉴定手册．北京：科学出版社
顾觉奋，魏爱琳.2002.大孔网状吸附剂在微生物制药分离纯化上的应用.离子交换与吸附，18(3):281~288
黄云，詹先进，蓝家样，陈全求.2009.昆虫肠道微生物的研究进展.湖北农业科学，48(11):2887~2890
何正波，殷幼平，曹月青，董亚敏，张伟.2001.桑粒肩天牛幼虫肠道菌群的研究.微生物学报，41(6)：741~744
金红芝，李堃宝.2003.人肠道微生态系统的研究进展.科技进展，26(2)：88~91
姜怡，曹艳茹，蔡祥凤，徐丽华，姜成林.2009.三种动物粪便及一种虫体可培养放线菌的多样性及其生物活性.微生物学报，49(9):1152~1157
吉列姆，M.1987.无脊椎动物病理学杂志.49卷:37-38.西方蜜蜂幼虫粪便中的微生物.黎耀东，陈黎红译
贾文祥.2005.医学微生物学.北京:人民卫生出版社:159~169
刘威，姚文，朱伟云.2006.人体与肠道微生物间的互惠共生关系.世界华人消化杂志，14(11)：1081~1088
刘玉升，叶保华，吕飞，郑继法.2006.豆天蛾幼虫肠道细菌分离及初步鉴定研究.山东农业大学学报（自然科学版），37(3)：345~348
刘开朗，王加启，卜登攀，赵圣国.2009.人体肠道微生物多样性和功能研究进展.生态学报，5(29):2589~2594
李可，郑天凌，田蕴，袁建军.2007.南美白对虾肠道微生物群落的分子分析.微生物学报，47(4)：649~653
李旻.2009.人体肠道菌群结构与宿主代谢的相关性研究.[博士学位论文].上海：上海交通大学
黎海彬，李小梅.2005.大孔吸附树脂及其在天然产物研究中的应用.广东化工，32(3):22~25
龙玉，曹焯，潘文石.2002.秦岭野生大熊猫（Ailuropoda melanoleuca）对竹笋细胞壁的利用.北京大学学报（自然科学版），38(4):576~581
龙北国.2003.高级医学微生物学.北京:人民卫生出版社:1~6
李永儒，丁晓贝，左浩江，王嵬，黄玮，裴晓方.2010.肠道菌群与粪便性状关系初探.现代预防医学，37(9):1623~1625
马清义，任建设，史怀平.2009.人工饲养大熊猫消化道正常菌群分离与鉴定研究.畜牧·兽医，7：56~57
荣华，邱成书，胡国全，刘晓凤，张辉，费立松，徐恒，邓宇.2006.一株大熊猫肠道厌氧纤维素菌的分离鉴定、系统发育分析及生物学特性的研究.应用与环境生物学报，12(2):239~242
施曼玲，邱清波，计翔.2000.两种有鳞类爬行动物消化道微生物的研究.动物学杂志，35(6)：12~15
唐蜀昆.2007.新疆高盐环境可培养放线菌多样性研究.[云南大学博士学位论文].昆明：云南大学
王保军，刘缨，姜嘉彤，刘斌，刘双江.2007.蝎子肠道内微生物多样性研究，47(5)：888~893
徐平，李文均，高慧英，徐丽华，姜成林.2005.聚酮类化合物生物合成途径基因阳性菌株生物多样性研究.微生物学报，45(6):821~827
许月卿，彭应登，赵仁兴.2003.树脂吸附法处理磺胺脒生产废水的工艺.环境科学，24(6):139~143
袁志辉，蓝希钳，杨廷，肖杰，周泽扬.2006.家蚕肠道细菌群体调查与分析.微生物学报，46(2)：285~291
赵述森.2009.猪源益生芽抱杆菌的分离筛选与应用研究.[博士学位论文].武汉：华中农业大学
赵秀芝，刘玉升，张帆.2011.龟纹瓢虫四虫态肠道细菌分离及鉴定. Chinese Journal ofMicroecology,23(6):500~504
张敏，范小兵，杭晓敏，李堃宝，杨虹.2004.青年人肠道菌群分布及关键益生菌群落结构分析.微生物学报，44(5):621~626
朱瑞良，牛钟相，常伟山.1996.不同日龄兔肠道正常菌群的研究.中国兽医学报，16（2）:176~178
Anderson R C, Rasmussen M A, Jensen N S, Allison M J.2000. Denitrobacterium detoxificans gen.nov., sp. nov., a ruminal bacterium that respires on nitrocompounds. International Journal of Systematicand Evolutionary Microbiology,50:633~638
Anklin-mühlemann R, Bignell D E, Veivers P C, Leuthold R H, Slaytor M.1995. Morphological,Microbiological and Biochemical Studies of the Gut Flora in the Fungus-growing Termite Macrotermessubhvalinus. Journal of Insect Physiology,41(11):929~940
Arumugam M, Raes J, Pelletier E, Paslier D E, Yamada T, Mende D R, Fernandes G R, Tap J, Bruls T,Batto J M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M et al.2011.Enterotypes of the human gut microbiome. Nature, doi:10.1038/09944
Ayuso-Sacido A, Genilloud O.2005. New PCR Primers for the Screening of NRPS and PKS-ISystems in Actinomycetes: Detection and Distribution of These Biosynthetic Gene Sequences in MajorTaxonomic Groups. Microbial Ecology,49:10~24
Backhed F, Ley R E, Sonnenburg J L, Peterson D A, Gordon J I.2005. Hostbacterial mutualism in thehuman intestine. Science,307:1915~1920
Beman B L.1983. Actinomycete pathogen//Goodfellow M, Mordarski M, Williams S T. The biologyof the actinomyces. London: Academic press,457~480
Bentley S D, Chater K F, Cerde o-Tárraga A M, Challis G L, Thomson N R, James K D, Harris D E,Quail M A, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen C W, Collins M, Cronin A, FraserA, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang C H, Kieser T, Larke L, Murphy L, Oliver K, O'NeilS, Rabbinowitsch E, Rajandream M A, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R,Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell B G, Parkhill J, Hopwood D A.2002.Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature,417:141~147
Bik E M, Eckburg P B, Gill S R, Nelson K E, Purdom E A, Francois F, Perez-Perez G, Blaser M J,Relman D A.2006. Molecular analysis of the bacterial microbiota in the human stomach. Proceedings ofthe National Academy of Science U. S. A.,103(3):732~737
Bignell D E, Oskarsson H, Anderson J M.1979. Association of actinomycete-like bacteria withsoil-feeding termites (Termitidae, Termitinae). Applied and Environmental Microbiology,37:339~342
Cao Y R, Jiang Y, Jin R X, Han L, He W X, Li Y L, Huang X S, Xue Q H.2012. Enteractinococcuscoprophilus gen. nov., sp. nov., of the family Micrococcaceae isolated from Panthera tigris amoyensisfeces, transfer of Yaniella fodinae Dhanjal et al.2011to the genus Enteractinococcus as Enteractinococcusfodinae comb. nov. International Journal of Systematic and Evolutionary Microbiology, IJSEM Papers inPress. Published January6, as doi:10.1099/ijs.0.034249-0
Chu T L, Szabó I M, Szabó I.1987. Nocardia from gut actinomycetes of Glomeris hexasticha Brandt(Diplopoda). Biology and Fertility of Soils,3:113~116
Chun J, Lee J H, Jung Y, Kim M, Kim S, Kim B K, Lim Y W.2007. EzTaxon: a web-based tool forthe identification of prokaryotes based on16S ribosomal RNA gene sequences. International Journal ofSystematic and Evolutionary Microbiology,57:2259~2261
Costello E K, Lauber C L, Hamady M, Fierer N, Gordon J I, Knight R.2009. Bacterial communityvariation in human body habitats across space and time. Science,326:1694~1697
Czaran T L, Hoekstra R E, Page L.2002. Chemical warfare between microbes promotes biodiversity.Proceedings of the National Academy of Science U. S. A.,99:786~790
Daly K, Stewart C S, Flint H J, Shirazi-Beechey S P.2001. Bacterial diversity within the equine largeintestine as revealed by molecular analysis of cloned16S rRNA genes. FEMS Microbial Ecology,38:141~151
Demain A L, Sanchez S.2009. Microbial drug discovery:80years of progress. The Journal ofantibiotics,62:5~16
Dhanjal S, Ruckmani A, Cameotra S S, Pukall R, Klenk H P, Mayilraj S.2011. Yaniella fodinae sp.nov., a novel member of the genus Yaniella isolated from coal mine. International Journal of Systematicand Evolutionary Microbiology,61:535~539
Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson J K.2008. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. InternationalSociety for Microbial Ecology,2:716~727
DoBell C.1932. AntonVon Leewenhoek and ‘BigLittleAnimals’. NewYork: Harcourt Brace andCompany.
Durso L M, Harhay G P, Smith T P, Bono J L, DeSantis T Z, Harhay D M, Anderson G L, Keen J E,Laegreid W W, Clawson M L.2010. Animal-to-animal variation in fecal microbial diversity among beefcattle. Applied and Environmental Microbiology,76:4858~4862
Durvasula RV, Sundaram RK, Kirsch P, Hurwitz I, Crawford C V, Dotson E, Beard C B.2008.Genetic transformation of a corynebacterial symbiont from the chagas disease vector Triatoma infestans.Experimental Parasitology,119:94~98
Duangmal K, Ward A C, Goodfellow M.2005. Selective isolation of members of the Streptomycesviolaceoruber clade from soil. Federation of European Microbiological Societies Microbiology Letters,245:321~327
Dyszynski G.2006. RDPquery: A Java program from the Sapelo Program Microbial Observatory forautomatic classification of bacterial16S rRNA sequences based on Ribosomal Database Project taxonomyand Smith-Waterman alignment.
Eckburg P B, Bik E M, Bernstein C N, Purdom E, Dethlefsen L, Sargent M, Gill S R, Nelson K E,Relman D A.2005. Diversity of the Human Intestinal Microbial Flora. Science,308:1635~1638
Ezaki T, Hashimoto Y, Yabuuchi E.1989. Fluorometric deoxyribonucleic acid-deoxyribonucleic acidhybridization in microdilution wells as an alternative to membrane filter hybridization in whichradioisotopes are used to determine genetic relatedness among bacterial strains. International Journal ofSystematic Bacteriology,39:224~229
Fall S, Hamelin J, Ndiaye F, Assigbetse K, Aragno M, Chotte J L, Brauman A.2007. Differencesbetween Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and ItsMounds. Applied and Environmental Microbilogy,73(16):5199~5208
Felsenstein J.1993. PHYLIP (phylogeny inference package), version3.5c. Seattle: University ofWashington
Felsenstein J.1981. Evolutionary trees from DNA sequences: a maximum likelihood approach.Journal of Molecular Evolution,17:368~379
Fitch W M.1971. Toward defining the course of evolution: minimum change for a specific treetopology. Systematic zoology,20:406~416
Finegold S M, Attebery H R, Sutter V L.1974. Effect of diet on human fecal flora: comparison ofJapanese and American diets. The American Journal of Clinical Nutrition,27(12):1456~69
Frank D N, St Amand A L, Feldman R A, Boedeker E C, Harpaz N, Pace N R.2007.Molecular-phylogenetic characterization ofmicrobial community imbalances in human inflammatory boweldiseases. Proceedings of the National Academy of Science U. S. A.,104:13780~13785
Frey J C, Rothman J M, Pell A N, Nizeyi J B, Cranfield M R, Angert E R.2006. Fecal BacterialDiversity in a Wild Gorilla. Applied and Environmental Microbiology,72(5):3788~3792
FUJIMOTO H, NOZAWA M, OKUYAMA E, ISHIBASHI M.2003. Six New Constituents from anAscomycete, Chaetomium quadrangulatum, Found in a Screening Study Focused on Monoamine OxidaseInhibitory Activity. Chemical and Pharmaceutical Bulletin,51(3):247~251
Gandhimathi R, Arunkumar M, Selvin J, Thangavelu T, Sivaramakrishnan S, Kiran G S,Shanmughapriya S, Natarajaseenivasan K.2008. Antimicrobial potential of sponge associated marineactinomycetes. Journal de Mycologie Médicale,18:16~22
Gao R C, Huang Z X, Wu C F, Xu B, Wang X Y.2010. Culture-independent analysis of microflora ingayals (Bos frontalis) feces. African Journal of Biotechnology,9:2774~2788
Gill S R, Pop M, DeBoy R T, Eckburg P B, Turnbaugh P J, Samuel B S, Gordon J I, Relman D A,Fraser-Liggett C M, Nelson K E.2006. Metagenomic Analysis of the Human Distal Gut Microbiome,Science,312:1355~1359
Goodfellow M, Fiedler H P.2010. A guide to successful bioprospecting: informed by actinobacterialsystematics. Antonie van Leeuwenhoek,98:119~142
Gordon R E, Barnett D A, Handerhan J E, Pang C H N.1974. Nocardia coeliaca, NocardiaAutotrophica, and the nocardin strains. International Journal of Systematic Bacteriology,24:54~63
Gokhale R S, Sankaranarayanan R, Mohanty D.2007. Versatility of polyketide synthases ingenerating metabolic diversity. Current Opinion in Structural Biology,17(6):736~743
Greetham H L, Giffard C, Hutson R A, Collins M D, Gibson G R.2002. Bacteriology of the Labradordog gut: a cultural and genotypic approach. Journal of Applied Microbiology,93:640~646
Gusm o D S, Santos A V, Marini D C, Bacci Jr. M, Berbert-Molina M A., Lemos F J A.2010.Culture-dependent and culture-independent characterization of microorganisms associated with Aedesaegypti (Diptera: Culicidae)(L.) and dynamics of bacterial colonization in the midgut. Acta Tropica,115:275~281
Hartemink R, Domenech V B, Rombouts F M.1997. Lamvab－A new selective medium for theisolation of lactobacilli from faeces. Methods in Microbiology,29(1):77
Hayakawa M, Nonomura H.1987. Humic acid-vitamin agar, a new medium for the selective isolationof soil actinomycetes. Journal of Fermentation Technology,65:501~509
Hasegawa T, Takizawa M, Tanida S.1983. A rapid analysis for chemical grouping of aerobicactinomycetes. The Journal of General and Applied Microbiology,29:319~322
He L，Li W，Huang Y, Wang L, Liu Z, Lanoot B, Vancanneyt M, Swings J.2005. Streptomycesjietaisiensis sp. nov. isolated from soil in northern China. International Journal of Systematic andEvolutionary Microbiology,55:1939~1944
Hooper L V, Gordon J I.2001. Commensal host-bacterial relationships in the gut. Science,292:1115~1118
Hooper L V, Wong M H, Thelin A, Hansson L, Falk P G, Gordon J I.2001. Molecular analysis ofcommensal host-bacterial relationships in the intestine. Science,291:881~884
Holzapfel W H, Haberer P, Snel J, Schillinger U, Huis in’t Veld J H.1998. Overview of gut flora andProbiotics. International Joumal of Food Mierobiology,41(2):85~101
Hooper L V, Midtvedt T, Gordon J I.2002. How host-microbial interactions shape the nutrientenvironment of the mammalian intestine. Annual Review of Nutrition,22:283~307
Hopkins M J, Sharp R, Macfarlane G T.2001. Age and disease related changes in intestinal bacterialpopulations assessed by cell culture,16S rRNA abundance, and community cellular fatty acid profiles. Gut,48(2):198~205
Hwang Y B, Lee M Y, Park H J, Han K, Kim E S.2007. Isolation of putative polyene-producingactinomycetes strains via PCR-based genome screening for polyene-specific hydroxylase genes. ProcessBiochemistry,42:102~107
Jensen P R.2010. Linking species concepts to natural product discovery in the post-genomic era.Journal of Industrial Microbiology and Biotechnology,7:219~224
Jiang Y, Cao Y R, Wiese J, Lou K, Zhao L X, Imhoff J F, Jiang C L.2009. A new approach ofresearch and development on pharmaceuticls from actinomycetes. Journal of Life Science US,3(7):52~56
Kaltenpoth M, Winter S A, Kleinhsmmer A.2009. Localization and transmission route ofCoriobacterium glomerrans, the endosymbiont of pyrrhocorid bugs. FEMS Microbial Ecology,69:373~383
Kaltenpoth M, G ttler W, Herzner G, Strohm E.2005. Symbiotic bacteria protect wasp larvae fromfungal infestation. Current Biology,15:475~479
Kaltenpoth M, Schmitt T, Polidori C, Koedam D, Strohm E.2010. Symbiotic streptomycetes inantennal glands of the South American digger wasp genus Trachypus (Hymenoptera, Crabronidae).Physiological Entomology,35:196~200
Kemp P F, Aller J Y.2004. Bacterial diversity in aquatic and other environments: what16S rDNAlibraries can tell us. Fems Microbial Ecology,47(2):161~177
Kelly K L.1964. Inter-Society Color Council–National Bureau of Standards Color-Name ChartsIllustrated with Centroid Colors．Washington，DC：US Government Printing Office
Ketela M M, Virpi S, Halo L, Hautala A, Hakala J, Mantsala P, Ylihonko K.1999. An efficientapproach for screening minimal PKS genes from Streptomyces. FEMS Microbiology Letters,180:1~6
Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M.2011.Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchillalanigera) faeces. International Journal of Systematic and Evolutionary Microbiology,61:877~881
Kroppenstedt R M.1982. Separation of bacterial menaquinones by HPLC using reverse phase (RP18)and a silver loaded ion exchanger as stationary phases. Journal of Liquid Chromatography&RelatedTechnologies,5:2359~2367
Lawson P A, Greethan H L, Gibson G R, Giffard C, Falsen E, Collins M D.2005. Slackia faecicanissp. nov., isolated from canine faeces. International Journal of Systematic and Evolutionary Microbiology,55:1243~1246
Lee J, Mo J H, Katakura K, Alkalay I, Rucker A N, Liu Y T, Lee H K, Shen C, Cojocaru G, ShenoudaS, Kagnoff M, Eckmann L, Ben-Neriah Y, Raz E.2006. Maintenance of colonic homeostasis by distinctiveapical TLR9signalling in intestinal epithelial cells. Nature Cell Biology,8:1327~1336
Ley R E, Peterson D A, Gordon J I.2006. Ecological and evolutionary forces shaping microbialdiversity in the human intestine. Cell,124:837~848
Ley R E, Hamady M, Lozupone C, Turnbaugh P J, Ramey R R, Bircher J S, Schlegel M L, Tucker TA, Schrenzel M D, Knight R, Gordon J I.2008. Evolution of mammals and their gut microbes. Science,320:1647~1651
Ley R E, B ckhed F, Turnbaugh P, Lozupone C A, Knight R D, Gordon J I.2005. Obesity alters gutmicrobial ecology. Proceedings of the National Academy of Science U. S. A.,102(31):11071~11075
Leifson E.1960. Atlas of Bacterial Flagellation. London: Academic Press
Li W, Godzik A.2006. Cd-hit: a fast program for clustering and comparing large sets of protein ornucleotide sequences. Bioinformatics,22(13):1658~1659
Li W J, Chen H H, Xu P, Zhang Y Q, Schumann P, Tang S K, Xu L H, Jiang C L.2004. Yaniahalotolerans gen. nov., sp. nov., a novel member of the suborder Micrococcineae from saline soil in China.International Journal of Systematic and Evolutionary Microbiology,54:525~531
Li W J, Zhi X Y, Euzéby J P.2008. Proposal of Yaniellaceae fam. nov., Yaniella gen. nov. andSinobaca gen. nov. as replacements for the illegitimate prokaryotic names Yaniaceae Li et al.2005, YaniaLi et al.2004, emend Li et al.2005, and Sinococcus Li et al.2006, respectively. International Journal ofSystematic and Evolutionary Microbiology,58:525~527
Li W J, Schumann P, Zhang Y Q, Xu P, Chen G Z, Xu L H, Stackebrandt E, Jiang C L.2005.Proposal of Yaniaceae fam. nov. and Yania flava sp. nov. and emended description of the genus Yania.International Journal of Systematic and Evolutionary Microbiology,55:1933~1938
Liu W, Ahlert J, Gao Q, Wendt-Pienkowski E, Shen B, Thorson J S.2003. Rapid PCR amplificationof minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model.Proceedings of the National Academy of Science U. S. A.,100(21):11959~11963
Long H F.2011. http://baike.baidu.com/view/74071.htm#3[2011-11-07]
Lozupone C, Hamady M, Knight R.2006. UniFrac-an online tool for comparing microbial communitydiversity in a phylogenetic context. BMC Bioinformatics,7:371
Lozupone C, Knight R.2005. UniFrac: a new phylogenetic method for comparing microbialcommunities. Applied and Environmental Microbiology,71(12):8228~8235
Lynn B, Per F G, Tore M, Gordon J I.1996. A model of host-microbial interaction in an openmammalian ecosystem. Science,273:1380~1383
Mai V.2004. Dietary Modification of the Intestinal Microbiota. Nutrition Reviews,62(6):235~242
Matsui T, Tanaka J, Namihira T, Shinzato N.2012. Antibiotics production by an actinomyceteisolated from the termite gut. Journal of Basic Microbiology, doi:10.1002/jobm.201100500
Marta J F, Miros aw P Z, Tomasz D P, Marek W, Jaros aw P.2010. Gut bacterium of Dendrobaenaveneta (Annelida: Oligochaeta) possesses antimycobacterial activity. Journal of Invertebrate Pathology,105:63~73
Margulies M, Egholm M, Altman W E, et al.2005. Genome sequencing in microfabricatedhigh-density picolitre reactors. Nature,437(7057):376~380
Marmur J.1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. Journalof Molecular Biology,3:208~218
McKenna P, Hoffmann C, Minkah N, Aye P P, Lackner A, Liu Z, Lozupone C A, Hamady M, KnightR, Bushman F D.2008. The macaque gut microbiome in health, lentiviral infection, and chronicenterocolitis. PLoS Pathogens,4(2):20
McAlpine J B, Bachmann B O，Piraee M, et al.2005. Microbial genomecs as a guide to drugdiscovery and structure elucidation: ECO-02301, a new antifungal agent, as an exceple. Journal of NaturalProducts,68:493~496
Mesbah M, Premachandran U, Whitman W B.1989. Precise measurement of the G+C content ofdeoxyribonucleic acid by high-performance liquid chromatography. International Journal of SystematicBacteriology,39:159~167
Mets-Ketel M, Halo L, Munukka E, Hakala J, M nts l P, Ylihonko K.2002. Molecular Evolutionof Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and16SRibosomal DNA Genes from Various Streptomyces Species. Applied and Environmental Microbiology,68(9):4472~4479
Mitsuoka T.1992. Intestinal flora and aging. Nutrition Reviews,50(12):438~446
Minnikin D E, O’Donnell A G, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J H.1984.An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal ofMicrobiological Methods,2:233~241
Morotomi M, Nagai F, Watanabe Y.2012. Description of Christensenella minuta gen. nov., sp. nov.,isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal ofChristensenellaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology,62:144~149
Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C,Verdenelli M C, Clavel T, Koebnick C, Zunft H-J F, Doré J, Blaut M.2006. Differences in FecalMicrobiota in Different European Study Populations in Relation to Age, Gender, and Country: aCross-Sectional Study. Applied and Environmental Microbiology,72(2):1027~1033
Muyzer G, de Waal E C, Uitterlinden A G.1993. Profiling of complex microbial populations bydenaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for16S rRNA. Applied and Environmental Microbiology,59(3):695~700
Osterhage C, Kaminsky R, K nig G M, Wright A D.2000. Ascosalipyrrolidinone A, an AntimicrobialAlkaloid, from the Obligate Marine Fungus Ascochyta salicorniae. Journal of Organic Chemistry,65:6412~6417
Ozutsumi Y, Hayashi H, Sakamoto M, IItabashi H. Benno Y.2005. Culture-independent analysis offecal microbiota in cattle. Bioscience, Biotechnology, and Biochemistry,69:1793~2005
Pasti M B, Pometto A L, Nuti M P.1990. Lignin-solubilizing ability of actinomycetes isolated fromtermite (Termitidae) gut. Applied and Environmental Microbiology,56:2213~2218
Pedras M S C, Morales V M, Taylor J L.1994. PHOMAPYRONES: THREE METABOLITESFROM THE BLACKLEG FUNGUS. Phyrochmistry,36(5):1315~1318
Qin J, Li R, Raes J, Arumugam M, Burgdorf K S, et al.2010. A human gut microbial gene catalogueestablished by metagenomic sequencing. Nature,464:59~65
Rainey P B, Rainey K.2003. Evolution of cooperation and conflict in experimental bacterialpopulations. Nature,425:72~74
Rastall R A.2004. Bacteria in the gut: friends and foes and how to alter the balance. Journal ofNutrition,134:2022~2026
Rescot L M, Harley J P, Klein D A.2002. Microbiology.5thed. New York: The McGraw-Hillcompanies:344~356
Ritchie L E, Steiner J M, Suchodolski J S.2008. Assessment of microbial diversityalong the felineintestinal tract using16S rRNAgene analysis. Federation of European Microbiological Societies MicrobialEcology,66:590~598
Rondon M R, August P R, Bettermann A D, Brady S F, Grossman T H, Liles M R, Loiacono K A,Lynch B A, MacNeil I A, Minor C, Tiong C L, Gilman M, Osburne M S, Clardy J, Handelsman J,Goodman R M.2000. Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and FunctionalDiversity of Uncultured Microorganisms. Applied and Environmental Microbiology,66:254l~2547
Sasser M.1990. Identification of bacteria by gas chromatography of cellular fatty acids，MIDITechnical Note101. Newwark, DE: MIDI Inc
Schafer A, Konrad R, Kuhnigk T, Kampfer P, Herte H, Konig H.1996. Hemicellulose-degradingbacteria and yeasts from termite gut. Journal of Applied Bacteriology,80:471~478
Schloss P D, Handelsman J.2005. Introducing DOTUR, a computer program for defining operationaltaxonomic units and estimating species richness. Applied and Environmental Microbiology,71(3):1501~1506
Schleifer K H, Kandler O.1972. Peptidoglycan types of bacterial cell walls and their taxonomicimplications. Bacteriology Reveiws,36:407~477
Seshime Y, Juvvadi P R，Fujii I, Kitamoto K.2005. Discovery of a novel superfamily of type IIIpolyketide synthases in Aspergillus oryzae. Biochemical and Biophysical Research Communications,331:253~260
Shirling E B, Gottlieb D.1966. Methods for characterization of Streptomyces species. InternationalJournal of Systematic Bacteriology,16:313~340
Simpson J M, Martineau B, Jones W E, Ballam J M, Mackie R I.2002. Characterization of fecalbacterial population in canines: effecs of age, breed and dietary fiber. Microbial Ecology,44:186~197
Smriga S, Sandin S A, Azam F.2010. Abundance,diversity, and activityof microbial assemblagesassociatedwith coral reefish guts and feces. Federation of European Microbiological Societies MicrobiolEcol,73:31~42
Smibert R M, Krieg N R.1994. Phenotypic characterization. In Methods for General and MolecularBacteriology, pp.607–654. Edited by P. Gerhart, R. G. E. Murray, W. A. Wood&N. R. Krieg.Washington, DC: American Society for Microbiology
Snipes C E, Chang C J, Floss H G.1979. Biosynthesis of the antibiotic granaticin. Journal of theAmerican Chemical Society,101(3):701~706
Staunton J, Weissman K J.2001. Polyketide biosynthesis: a millennium review. Natural ProductReports,18(4):380~416
Suau A, Bonnet R, Sutren M, Godon J J, Gibson G, Collins M D, Doré J.1999. Direct rDNAcommunity analysis reveals a myriad of novel bacterial lineages within the human gut. Applied andEnvironmental Microbiology,65(1):4799~4807
Suchodoski J S, Ruaux C G., Steiner J M, Fetz K, Williams D A.2004. Application of molecularfingerprinting for qualitative asscssment of small-intestinal bacterial diversity in dogs. Journal of ClinicalMicrobiology,42:4702~4708
Suchodolski J S., Camacho J, Steiner J M.2008. Analysis of bacterial diversity in the canineduodenum, jejunum, ileum, and colon by comparative16S rRNAgene analysis. Federation of EuropeanMicrobiological Societies Microbial Ecology,66:567~578
Tan H, Deng Z, Cao L.2009. Isolation and characterization of actinomycetes from healthy goat feces.Letters in Applied Microbiology,49:248~253
Tamura K, Dudley J, Nei M, Kumar S.2007. MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Molecular Biology and Evolution,24:1596~1599
Tang S K, Wang Y, Chen Y, Lou K, Cao L L, Xu L H, Li W J.2009. Zhihengliuella alba sp. nov., andemended description of the genus Zhihengliuella. International Journal of Systematic and EvolutionaryMicrobiology,59:2025~2032
Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D G.1997. The Clustal X windowsinterface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic AcidsResearch,25:4876~4882
Thompson C J, Fink D, Nguyen L D.2002. Principles of microbial alchemy: insights from theStreptomyces coelicolor genome sequence. Genome Biology,3(7):1020
Turnbaugh P J, Hamady M, Yatsunenko T, Cantarel B L, Duncan A, Ley R E, Sogin M L, Jones W J,Roe B A, Affourtit J P, Egholm M, Henrissat B, Heath A C, Knight R, Gordon J I.2009. A core gutmicrobiome in obese and lean twins. Nature,457:480~484
Ward A C, Goodfellow M.2004. Phylogeny and functionality: taxonomy as a roadmap to genes. In:Bull AT (ed) Microbial diversity, bioprospecting. Washington, DC: ASM Press:288~313
Wang T T, Cai G X, Qiu Y P, Fei N, Zhang M H, Pang X Y, Jia W, Cai S J, Zhao L P.2012. Structuralsegregation of gut microbiota between colorectal cancer patients and healthy volunteers. The ISME journal,6(2):320~329
Watanabe K, Praseuth A P, Wang C C.2007. A comprehensive and engaging overview of the typeⅢfamily of polyketide synthases. Current Opinion in Chemical Biology,11(3):279~286
Weaver R F.2002. Molecular biology.2nded. New York: the Mc-Hill companies:784~797
Whilaman W B, Coleman D C, Wiebe W J.1998. Prokaryotes: the unseen majority. Proceedings ofthe National Academy of Science U. S. A.,94:6578~6583
Wielen P W J J, Keuzenkamp D A, Lipman L J A, Knapen F, Biesterveld S.2002. Spatial andTemporal Variation of the Intestinal Bacterial Community in Commercially Raised Broiler ChickensDuring Growth. Microbial Ecology,44(3):286~293
Williams A G, Withers S E.1981. Hemicellulose-degrading Enzymes Synthesized by Rumen Bacteria.Journal of Applied Bacteriology,51:375~385
Wishart D S, Knox C, Guo A C, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M.2008DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research,36:901~906
Xin Y J, Huang J Y, Deng M C, Zhang W.2008. Culture-independent nested PCR method revealshigh diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp.Antonie van Leeuwenhoek,94:533~542
Xin Y J, Zhang W.2008. Marine sponge Hymeniacidon perlevis possesses high diversity of culturableactinobacteria. Journal of Biotechnology,136:607~619
Xu J, Bjursell M K, Himrod J, Deng S, Carmichael L K, Chiang H C, Hooper L V, Gordon J I.2003.A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science,299:2074~2076
Yassin A F, Hupfer H, Siering C, Klenk H P, Schumann P.2011. Auritidibacter ignavus gen. nov., sp.nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of themembers of the family Yaniellaceae Li et al.2008to the family Micrococcaceae and emended descriptionof the suborder Micrococcineae. International Journal of Systematic and Evolutionary Microbiology,61:223~230
Yang S X, Gao J M, Zhang A L, Jiang Y, Cao Y R, Laatsch H. Sannastatin.2011. A novel toxicmacrolactam polyketide glycoside produced by actinomycete Streptomyces sannanensis. Bioorganic&Medicinal Chemistry,21:3905~3908
Yildirim S, Yeoman C J, Sipos M, Torralba M, Wilson B A, Goldberg T L, Stumpf R M, Leigh S R,White B A, Nelson K E.2010. Characterization of the Fecal Microbiome from Non-Human Wild PrimatesReveals Species Specific Microbial Communities. PLoS ONE,5(11):1~11
Zazopoulos E, Huang K, Staffa A, Liu W, Bachmann B O, Nonaka K, Ahlert J, Thorson J S, Shen B,Farnet C M.2003. A genomics-guided approach for discovering and expressing cryptic metabolic pathways.Nature Biotechnology,21(2):187~190
Zhang H T, Lee Y K, Zhang W, Lee H K.2006. Culturable actinobacteria from the marine spongeHymeniacidon perleve: isolation and phylogenetic diversity by16S rRNA gene-RFLP analysis. Antonievan Leeuwenhoek,90:159~169
Zhang H, DiBaise J K, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell M D,Wing R, Rittmann B E, Krajmalnik-Brown R.2009. Human gut microbiota in obesity and after gastricbypass. Proceedings of the National Academy of Science U. S. A.,106:2365~2370
Zhang H H, Chen L.2010. Phylogenetic analysis of16S rRNA gene sequences reveals distal gut
bacterial diversity in wild wolves (Canis lupus). Molecular Biology Reports,37:4013~4022
Zhang C H, Zhang M H, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G,
Chen Y, Zhao L.2010. Interactions between gut microbiota, host genetics and diet relevant to development
of metabolic syndromes in mice. The ISME Journal,4(2):232~241
Zhu L F, Wua Q, Dai J Y, Zhang S N, Wei F W.2011. Evidence of cellulose metabolism by the giant
panda gut microbiome. Proceedings of the National Academy of Science Early Edition,1~6
www.pnas.org/cgi/doi/10.1073/pnas.1017956108