Human microbiomics

The sequencing of the human genome has driven the study of human biology in a significant way and enabled the genome-wide study to elucidate the molecular basis of complex human diseases. Recently, the role of microbiota on human physiology and health has received much attention. The influence of gut microbiome (the collective genomes of the gut microbiota) in obesity has been demonstrated, which may pave the way for new prophylactic and therapeutic strategies such as bacteriotherapy. The significance and recent understandings in the area of “human microbiomics” are discussed here.     

生物有机肥调控对盐碱胁迫下向日葵幼苗生长及生理指标的影响

采用盆栽方法,以清洁土壤为对照,研究了盐碱胁迫下不同生物有机肥施用量(0%、2%、4%和8%)对向日葵种子发芽率和出苗率、幼苗生长及生理指标的影响.结果表明:与对照相比,盐碱胁迫(T0)7～28 d后,向日葵种子的发芽率及出苗率明显降低,种子出苗时间推迟了3 d,幼苗株高、根长、地上部分及根系鲜重、叶片中叶绿素含量、可溶性蛋白质含量均显著降低(P<0.05),而且幼苗根系对盐碱胁迫的敏感性明显大于地上部;与T0处理相比,生物有机肥施用量分别为2%(T1)、4%(T2)及8%(T3)时,向日葵种子的出苗率分别提高了56.4%(P<0.05)、64.3%(P<0.05)及85.7%(P<0.05),出苗时间提早了2～3 d,盐碱胁迫处理7 d后,T1、T2和T3处理组幼苗的生长明显增强,叶片中叶绿素含量分别提高了24.4%(P<0.05)、27.2%(P<0.05)和33.2%(P<0.05),可溶性蛋白质含量分别增加了34.4%(P<0.05)、43.6%(P<0.05)和48.8%(P<0.05);随着处理时间的延长,T1、T2和T3处理对幼苗生长及生理指标的抑制作用均表现出不同程度的降低.综上可知,盐碱胁迫条件下,施用2%～8%的生物有机肥可以明显减轻盐碱胁迫对向日葵种子出苗、幼苗生长及生理指标的抑制作用.     

<Emphasis Type="SmallCaps">l</Emphasis>-Asparaginase Production by Moderate Halophilic Bacteria Isolated from Maharloo Salt Lake

l-Asparaginase is an anti-neoplastic drug used in lymphoblastic leukemia chemotherapy. Nowadays, this enzyme derived from bacterial sources, mostly l-asparaginase II from Escherichia coli and in lesser amount l-asparaginase of Erwinia sp. has medical utilization. The long-term usage of these agents leads to allergic reactions and new asparaginase with new immunological characteristics is required. Halophilic bacteria might contain l-asparaginase with novel immunological properties that can be used in hypersensitive patients. In this experiment, we have screened moderate Halophilic bacteria for l-asparaginase production ability and showed that Halophilic bacteria produce intra- and extracellular l-asparaginase. Bacillus sp. BCCS 034 was found to produce the highest l-asparaginase (1.64 IU/ml supernatant) extracellularly.     

Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea

The continental shelf and slope in the northern South China Sea is well known for its prospect of oil/gas/gas-hydrate resources. To study microbial communities and their roles in carbon cycling, a 4.9-m sediment core was collected from the Qiongdongnan Basin on the continental slope of the South China Sea during our cruise HY4-2005-5 in 2005. Geochemical, mineralogical, and molecular phylogenetic analyses were carried out. Sulfate concentration in pore water decreased with depth. Abundant authigenic carbonates and pyrite were observed in the sediments. The bacterial community was dominated by aerobic and facultative organisms. Bacterial clone sequences belonged to the Gamma-, Alpha-, Deltaproteobacteria and Firmicutes group, and they were related to Fe(III) and/or Mn(IV) reducers, sulfate reducers, aromatic hydrocarbon degraders, thiosulfate/sulfite oxidizers, and denitrifiers. Archaeal clone sequences exhibited greater overall diversity than the bacterial clones with most sequences related to Deep-Sea Archaeal Group (DSAG), Miscellaneous Crenarchaeotic Group (MCG), and Uncultured Euryarchaeotic Clusters (UECs). Archaeal sequences related to Methanosarcinales, South African Gold Mine Euryarchaeotic Group (SAGMEG), Marine Benthic Group-D (MBG-D) were also present. Most of these groups are commonly present in deep-sea sediments, particularly in methane/organic-rich or putative methane hydrate-bearing sediments.     

妇科恶性肿瘤与微生物菌群的关系

近年来,随着人口老龄化和生活方式的不断改变,妇科恶性肿瘤的发病呈现上升趋势,严重损害女性生命健康。目前关于妇科恶性肿瘤的病因、发病机制尚未完全阐明。除遗传因素外,环境因素在肿瘤的发生、发展中也扮演着重要的角色。女性生殖道的解剖特点使其处于开放性结构,易受各种病原体的入侵。高通量测序及序列识别技术的不断发展与成熟,使得微生物菌群与妇科恶性肿瘤的关系成为研究的热点,阐明微生物菌群对妇科恶性肿瘤的影响至关重要,本文对微生物菌群与妇科恶性肿瘤关系的研究进展作一综述,为妇科恶性肿瘤的防治提供科学依据。     

Screening of endophytic bacteria isolated from leaves of Sambung Nyawa [Gynura procumbens (Lour.) Merr.] for cytokinin-like compounds

Endophytic bacteria are harmless in most plant species; and known to boost the growth and development of the host plants probably by secreting growth hormones. The isolation, identification and screening of endophytic bacteria for the plant growth regulators like cytokinin are needed to get the leads for their applications in agriculture sector. We describe the isolation and identification of the bacterial endophytes from the leaves of Sambung Nyawa [Gynura procumbens (Lour.) Merr.] and their screening for cytokinin-like compounds. We isolated three endophytic bacteria from the leaves of G. procumbens collected from the forest research institute of Malaysia (FRIM). They were further identified using amplified 16S rRNA gene sequence based method of bacterial identification. The ethyl acetate extracts of the isolates-broth were analyzed using cucumber cotyledon greening bioassay (CCGB) to determine the presence of cytokinin-like compounds. Consequently, the bacterial putative endophytes were identified as Psuedomonas resinovorans, Paenibacillus polymaxa, and Acenitobacter calcoaceticus. Broth-extracts from two (Psuedomonas resinovorans and Paenibacillus polymaxa) of the three putative bacterial endophytes show the positive results in their screening for cytokinin-like compounds using CCGB. Thus, we hypothesize that the bacterial putative endophytes of G. procumbens that produce cytokinin-like compounds might have a role in the growth and development of G. procumbens. ABBREVIATIONS: CCGB - Cucumber cotyledon greening bioassay, rDNA - Ribosomal DNA, K12, BAP - 6-Benzylaminopurine, Db1, MSA - Multiple sequence alignment. 8081.     

Bacterial,archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

We studied the microbial diversity in the sediment from the Kongsfjorden, Svalbard, Arctic, in the summer of 2005 based on the analysis of 16S rRNA and 18S rRNA gene clone libraries. The sequences of the cloned 16S rRNA and 18S rRNA gene inserts were used to determine the species identity or closest relatives by comparison with sequences of known species. Compared to the other samples acquired in Arctic and Antarctic, which are different from that of ours, the microbial diversity in our sediment is much higher. The bacterial sequences were grouped into 11 major lineages of the domain Bacteria: Proteobacteria (include α-, β-, γ-, δ-, and ε-Proteobacteria); Bacteroidetes; Fusobacteria; Firmicutes; Chloroflexi; Chlamydiae; Acidobacteria; Actinobacteria; Planctomycetes; Verrucomicrobiae and Lentisphaerae. Crenarchaeota were dominant in the archaeal clones containing inserts. In addition, six groups from eukaryotes including Cercozoa, Fungi, Telonema, Stramenopiles, Alveolata, and Metazoa were identified. Remarkably, the novel group Lentisphaerae was reported in Arctic sediment at the first time. Our study suggested that Arctic sediment as a unique habitat may contain substantial microbial diversity and novel species will be discovered.     

基于16S rRNA基因测序的褥疮患者皮肤菌群特征研究

利用16S rRNA基因测序分析褥疮患者皮肤菌群的特征,为褥疮的预防与治疗提供新的思路。

选取江苏大学附属宜兴医院的18例住院褥疮患者为褥疮组,同时选取20例无褥疮病史的健康志愿者为健康对照组。采集两组人群的皮肤样本,并使用16S rRNA基因测序技术分析褥疮患者和健康人群皮肤菌群的物种差异。

Alpha多样性和beta多样性分析显示,褥疮患者皮肤菌群的物种数目、丰度和多样性均低于健康人群（均P＜0.05）。菌群指数分析显示,健康对照组的菌群健康指数高于褥疮组,而褥疮组患者的菌群失调指数高于健康对照组（均P＜0.05）;与此同时,褥疮组患者皮肤葡萄球菌科（Staphylococcaceae）丰度显著高于健康对照组（P＜0.05）。

褥疮患者皮肤菌群较健康人群显著紊乱,且葡萄球菌科的丰度显著增加,皮肤菌群差异可为褥疮的预防与治疗提供新思路。

     

不同大菱鲆(Scophthalmus maximus)个体肠道菌群结构差异研究

目的:肠道微生物能够帮助宿主完成多种生理生化功能,对宿主的健康生长也起到非常重要的作用。大菱鲆(Scophthalmus maximus)是我国北方最重要的海水养殖品种之一。然而,细菌性疾病的频发造成大规模的鱼类死亡。此外,许多大菱鲆致病菌也被证实是人类潜在的致病菌。因此鉴定成年养殖大菱鲆肠道中所包含的核心菌群,并筛选可能与大菱鲆或人类健康密切相关的细菌尤为重要。方法:构建三个大菱鲆个体肠道16S rRNA文库,利用限制性片段长度多态性分析(RFLP)及生物信息学技术研究三个大菱鲆个体肠道菌群结构及多样性。结果:共得到758个阳性克隆,16个OTU类型。分类分析显示,变形菌门在大菱鲆肠道中占优势地位。进一步将细菌按属来分类显示,弧菌属所占的比例最高,约为95.3%。韦恩图显示大菱鲆三个个体共有的OTU类型数量为3,分别占三个大菱鲆个体肠道文库中阳性克隆总数的94.9%、96.7%以及93.5%。分类结果显示它们分别属于条件致病菌哈氏弧菌、副溶血弧菌和创伤弧菌。结论:大菱鲆的核心肠道菌群为弧菌属,它的主要成员哈氏弧菌、副溶血弧菌和创伤弧菌对大菱鲆及人类的健康起到关键的作用。在水产养殖过程中,通过监控这些弧菌种类的浓度变化能够及时对养殖环境进行评价,并及时调整温度、水质等因素,这为预防大菱鲆细菌性疾病,保证人类健康提供重要的理论依据。     

16s rRNA基因克隆文库分析比较牙周炎患者和健康人口腔唾液微生物多样性

【目的】通过对同一地区、同一民族牙周炎患者和健康人的唾液微生物群落结构的分析,探寻牙周炎患者口腔微生物的多样性。【方法】采集甘肃东乡族自治县的东乡族牙周炎患者和健康人唾液各5例,分别记作DP(东乡牙周)和DH(东乡健康),提取细菌总DNA,构建16S r RNA基因克隆文库,测序后利用MOTHUR、MEGA 4.0、Clustal X 3.0等软件对测序结果进行分析。【结果】所有样本共检测出115个OTUs(DP 60,DH 75),归属于6个门,27个属。TM7是DP组特有的优势菌门。仅在DP组中检测到的优势菌属是梭菌属(Fusobacterium)、卟啉单胞菌属(Porphyromonas)、消化链球菌属(Peptostreptococcus)和TM7_genera。【结论】发现牙周炎患者与健康人口腔唾液微生物存在一定差异。其中,TM7、梭菌属和消化链球菌属在牙周病中的作用值得进一步研究。