基于比较基因组学解析耐酸乳杆菌G10的多碳源利用特征

【背景】耐酸乳杆菌（Lactobacillus acetotolerans）是白酒发酵过程中的优势乳酸菌,对白酒发酵具有重要作用。L. acetotolerans G10是分离自芝麻香型白酒发酵酒醅的一株能够利用多种碳源的菌株。【目的】基于全基因组测序,解析菌株G10多碳源利用机制。【方法】通过三代测序平台Oxford Nanopore完成菌株G10全基因组测序,分别利用Circlator和Prodigal对测序数据进行组装和基因预测;通过细菌基因组分析工具（bacterial pan genome analysis tool,BPGA）进行泛基因组分析。【结果】G10能够利用22种糖类及糖类衍生物,其全基因组大小为1 627 828 bp,含有1 878个编码基因;基于Koyto Encyclopedia of Genes and Genomes （KEGG）数据库注释获得292个碳源代谢相关基因,基于Carbohydrate-Active Enzymes （CAZy）数据库注释获得44个CAZy家族的编码基因。与其他发酵食品来源的耐酸乳杆菌相比,G10基因组最小,但其总基因数量以及...     

副干酪乳杆菌PC-01全基因组测序及不同副干酪乳杆菌菌株比较基因组学分析

【背景】副干酪乳杆菌(Lactobacillus paracasei)作为乳酸菌中重要菌种之一,常被认为是优良益生菌开发的潜在资源。【目的】以L.paracasei PC-01和L.paracasei Zhang为例,分析不同L.paracasei的基因组差异和遗传背景,为菌株的鉴定和开发奠定基础。【方法】采用PacBioSMRT三代测序技术对L.paracasei PC-01进行全基因组测序,结合2株L.paracasei模式菌株和公开的36株全基因组数据,通过比较基因组学方法揭示39株L.paracasei菌株之间的差异。【结果】L.paracasei PC-01基因组不包含质粒,染色体大小为2 829 251 bp,GC含量为46.64%;L.paracasei Zhang包含一个质粒基因组大小为2 898 456 bp,GC含量为46.51%;不同L.paracasei菌株基因组大小、质粒数及GC含量均存在一定差异。L.paracasei群体为开放式基因组,基因组具有高度多样性。基于核心基因构建系统发育树对于L.paracasei种内区分效果最好,L.paracasei PC-01和L.paracasei Zhang处于不同的进化分支。约占L.paracasei PC-01基因组长度91%的片段与L.paracasei Zhang基因组匹配率大于90%,L.paracasei PC-01注释到10个与转录调节鼠李糖代谢功能相关的特有基因,如agu A、clp B等;L.paracasei Zhang包含msh A、ltr A等特有基因,与糖基转移等功能相关。【结论】通过比较基因组学揭示L.paracasei PC-01和L.paracasei Zhang的遗传信息,解析了不同L.paracasei菌株之间的差异,为L.paracasei的鉴定和应用奠定了遗传学基础。     

全基因组测序揭示两株泡菜源植物乳杆菌基因型差异和潜在益生特性北大核心

【目的】为了探究植物乳杆菌(Lactiplantibacillus plantarum)基因型差异和潜在益生特性,采用全基因组测序技术对其进行测序并解析基因组序列及生物特性。【方法】本研究基于HiSeq和PacBio测序平台,对团队前期从四川多代泡菜中分离获得、体外益生特性评价良好的潜在益生菌菌株L.plantarum Eden-Star PC06和L.plantarum Eden-Star PC108的全基因组进行测序。利用相关生物信息学软件对原始数据进行组装及其后续的功能注释、分子进化、菌株安全性、次级代谢产物合成基因簇以及益生特性相关基因进行分析。【结果】通过基因组装得到了2株植物乳杆菌的全基因组信息,L.plantarum Eden-Star PC06和Eden-Star PC108基因组大小分别为3163902 bp和3205054 bp;GC含量分别为44.68%和44.67%;分别包含3161个和3197个DNA编码序列;功能基因数据库比对结果显示2株菌在碳水化合物利用、氨基酸利用和糖基转移酶等基因上得到大量注释;通过比对数据库,在2株植物乳杆菌全基因组上发现了4个与肠液耐受相关的胆盐水解酶基因、完整的植物乳杆菌细菌素合成相关基因簇和抵御多种胁迫的益生相关基因。【结论】本研究通过全基因组测序在基因水平上探究了L.plantarum Eden-Star PC06和Eden-Star PC108基因型差异和益生特性基因,证明L.plantarum Eden-Star PC06和Eden-Star PC108是2株有应用前景的益生菌菌株,以期为筛选优良益生菌菌株和评价其益生特性提供遗传学基础。     

母乳源乳双歧杆菌Probio-M8的遗传特征及基因组差异比较分析

【目的】母乳源乳双歧杆菌（Bifidobacterium animalis subsp. lactis） Probio-M8具有优良的益生特性,本文拟从全基因组水平解析Probio-M8的遗传特征,并与已有益生功效的乳双歧杆菌的基因组进行比较分析。【方法】本研究基于NCBI已公开的21株乳双歧杆菌和1株模式菌株DSM10140^T的基因组数据,构建了核心基因集与泛基因集,解析该群体的系统发育关系,比较分析Probio-M8的遗传特征及功能基因组。【结果】22株乳双歧杆菌的泛基因集包含1 618个基因,其中核心基因1 514个,占泛基因集的93.57%,表明乳双歧杆菌核心基因集高度保守。以1 514个核心基因构建系统发育树,发现22株乳双歧杆菌分为两个分支,AD011单独为一个分支,Probio-M8和其他菌株与模式菌株DSM10140^T聚在同一分支,且Probio-M8与V9、BB-12、Bi-07、HN019的遗传距离极为接近。进一步分析耐药基因和毒力基因,在Probio-M8与V9、BB-12、Bi-07、HN019基因组上均检测到DfrA...     

比较基因组学分析不同来源罗伊氏乳杆菌基因多样性及生境适应性

【目的】研究34株不同来源罗伊氏乳杆菌(Lactobacillus reuteri)基因多样性及生境适应性机制,了解该菌株在肠外生境及肠内生境中适应性的异同,为L. reuteri优良菌株的开发提供理论基础。【方法】基于二代测序平台对11株源于发酵食品(酸马奶、酸粥)的L. reuteri进行测序,并应用比较基因组学将其与发酵食品、酸面团、食草动物L. reuteri分离株基因组进行比较分析。【结果】分离自酸马奶、酸粥L. reuteri基因组大小平均为2.14 Mb,GC含量平均为38.77%,且同种来源分离株系统发育关系距离较近。泛-核心基因集分别包含7242个、969个基因家族,其中酸马奶分离株特异性基因最多为459个。功能注释结果显示不同来源菌株碳水化合物、氨基酸相关基因数量及种类差异较大,仅在发酵食品和食草动物株中发现抗生素耐药性基因。注释到的碳水化合物活性酶中仅出现在发酵食品与食草动物分离株的为GH3 (β-葡萄糖苷酶等)和GH43 (β-木糖苷酶等),特有的分别为AA3 (纤维二糖脱氢酶等)和GH66 (葡萄糖转移酶等)。【结论】不同来源L. reuteri具有广泛的基因多样性,与生存环境密切相关。发酵食品分离株具有部分食草动物肠道菌株特性且具有其独特的环境适应性特征,体现了与宿主有关的环境适应能力,可加深对食品发酵和肠内环境中细菌生境适应性的理解。     

两株母乳源植物乳杆菌的全基因组测序分析

【背景】母乳是一个重要的益生菌筛选库,其中植物乳杆菌是一种用途广泛、适应性强的益生菌。然而不同菌株具有不同的功能,现有的生理生化方法对其潜在益生特性研究十分有限,有必要采用高通量的方法寻找具有种群特异性的优质益生菌。【目的】结合菌株生化特征在全基因组的测序与分析的基础上对两株植物乳杆菌的潜在功能进行预测,并重点找寻与肠液耐受性及细菌素的合成相关的基因,即在基因组的结构上对菌株的表型进行探究。【方法】分离筛选出两株母乳源植物乳杆菌MP55、MP37,并利用Illumina genome analyzer对菌株的全基因组进行测序,采用Prokka软件对细菌基因组进行注释,采用Carbohydrate-active enzymes (CAZy)、Koyto encyclopedia of genes and genomes(KEGG)和Clusters of orthologous genes(COG)数据库对基因组进行功能注释;同时采用Prodigal、RNAmmer等工具对编码序列、核糖体RNA进行预测,并用CGView软件绘制菌株的基因组环形图谱。【结果】通过基因组装得到了两株植物乳杆菌的全基因组信息,植物乳杆菌MP37、MP55基因组大小分别为3 204 421 bp和3 299 180 bp;(G+C)mol%含量分别为44.36%和44.46%;分别包含3 012个和3 101个DNA编码序列,结合菌株生化特征在基因组上找到4个与肠液耐受相关的基因及一段细菌素合成相关基因簇。基因组序列原始数据和拼接结果已提交至"gcMeta"平台。【结论】通过高通量测序分析在基因组水平上揭示了植物乳杆菌MP55、MP37在肠道存活性与抑制病原菌相关的可能机理。植物乳杆菌MP55、MP37是两株潜在的益生菌候选菌株,实验结果为进一步阐明其益生菌特性的功能机制提供了遗传学基础。     

内蒙古地区传统制作奶豆腐和乌日莫中乳酸菌多样性及分布特征

【背景】传统制作奶豆腐和酸性奶油(乌日莫)是内蒙古农牧地区最喜爱的食品,蕴含着十分丰富的乳酸菌资源,亟待开发利用。【目的】通过解析内蒙古农牧地区传统自制奶豆腐和乌日莫样品中乳酸菌多样性及分布特征,为优良菌株选育与利用提供资源和理论基础。【方法】采用稀释涂布法分离纯化乳酸菌,测定菌株16S rRNA基因序列鉴定种属关系,阐明乳酸菌系统发育、遗传分化及菌群结构。【结果】传统自制样品中共分离得到乳酸菌81株,主要归属于乳酸片球菌(Pediococcus acidilactici)、戊糖片球菌(Pediococcus pentosaceus)、短乳杆菌(Lactobacillus brevis)、瑞士乳杆菌(Lactobacillus helveticus)、副干酪乳杆菌(Lactobacillus paracasei)、食二酸乳杆菌(Lactobacillus diolivorans)、奥塔基乳杆菌(Lactobacillus otakiensis)、植物乳杆菌(Lactobacillus plantarum)、开菲尔乳杆菌(Lactobacillus kefir)、乳酸乳球菌(Lactoc...     

不同分离源植物乳杆菌的群体基因组分析

【背景】植物乳杆菌(Lactobacillus plantarum)广泛存在于植物、乳制品、肉制品、哺乳动物和昆虫的肠道等多种生态环境中。【目的】探究不同分离源L. plantarum基因组与其所在环境是否存在潜在的联系。【方法】利用比较基因组学对126株分离自植物、乳制品、肉制品、果蝇及哺乳动物肠道和口腔等部位的L. plantarum菌株基因组进行系统发育分析和功能基因组分析,解析不同分离源菌株间的亲缘关系和进化历程。【结果】果蝇分离株的基因组大小显著高于植物、哺乳动物肠道、肉制品和乳制品分离株(P0.05),植物和哺乳动物肠道、口腔等部位与肉制品分离株的基因组大小和编码基因数量无显著差异(P0.05)。基于单拷贝基因串联和核心基因系统发育树分析均发现,果蝇分离株和乳制品分离株分别集中聚集分布在某一分支中,其余分离源均匀分布在各个分支中。附属基因分析结果与系统发育树分析结果一致。功能基因注释结果发现,果蝇分离株的环境特异性基因参与低聚果糖和几丁质代谢,乳制品分离株的环境特异性基因参与mazEF毒素-抗毒素系统和CRISPR系统。【结论】植物乳杆菌分离株为适应较为独特的果蝇和乳制品生境而发生了适应性进化。本研究为植物乳杆菌适应性进化提供了新见解,同时为解析菌株的进化历程提供了理论基础。     

抗生素和高脂饮食对大鼠肠道乳杆菌多样性的影响

【目的】对正常、高脂、抗生素处理大鼠肠道内乳杆菌进行定性和定量分析,比较不同处理组大鼠肠道乳杆菌的多样性。【方法】应用纯培养和非培养技术(16S r RNA基因序列分析、变性梯度凝胶电泳、实时荧光定量PCR)对大鼠肠道乳杆菌进行分离鉴定和多样性分析。【结果】16S r RNA基因序列同源性分析结果显示,正常组大鼠肠道内分离出的乳杆菌包括约氏乳杆菌(Lactobacillus johnsonii)、鼠乳杆菌(Lactobacillus murinus)、嗜酸乳杆菌(Lactobacillus acidophilus)、罗伊氏乳杆菌(Lactobacillus reuteri)、植物乳杆菌(Lactobacillus plantarum)、肠道乳杆菌(Lactobacillus intestinals)、动物乳杆菌(Lactobacillus animalis)和阴道乳杆菌(Lactobacillus vaginalis);但L.animalis在高脂处理组大鼠肠道内未分离到,L.intestinals和L.vaginalis在抗生素处理组大鼠中未分离到。DGGE结果显示3个组别大鼠肠道中乳杆菌构成差异明显,同一组内样品间相似性较高;相较于正常组和高脂组,抗生素组的丰度较差;且正常组大鼠肠道内乳杆菌的多样性高于高脂组和抗生素组。q-PCR结果显示正常组大鼠肠道乳杆菌的数量明显高于高脂组和抗生素组,高脂组的数量也明显高于抗生素组,且3个组别之间存在显著差异(P0.01)。【结论】高脂饮食及抗生素的使用会减少肠道内乳杆菌多样性。     

一株高ACE抑制活性乳杆菌的筛选鉴定、培养条件优化及其基因组分析

【背景】乳杆菌是人体肠道益生菌,其发酵乳中可检测到血管紧张素转换酶(Angiotensin converting enzyme,ACE)抑制肽。海洋蕴藏着丰富的微生物种质资源,分布着大量的乳杆菌。【目的】从高通量测序结果中发现渤海沉积物中分布着乳杆菌资源。为了进一步开发具有ACE抑制活性的海洋乳杆菌资源,提高乳杆菌发酵乳的ACE抑制活性,筛选瑞士乳杆菌(Lactobacillus helveticus)并对其特性进行研究。【方法】采用高通量测序技术从渤海沉积物中检测乳杆菌,并对其进行富集分离,对筛选出的乳杆菌进行16S rRNA基因鉴定和全基因组测序分析,测定该菌发酵乳的ACE抑制活性,并采用正交实验优化发酵条件。【结果】渤海沉积物中含有乳杆菌并成功筛选出一株瑞士乳杆菌GY-3,其发酵乳具有较高的ACE抑制活性。该菌在发酵温度37°C,接种量3%,且在脱脂乳培养基中添加1.0%葡萄糖,0.6%大豆蛋白胨,1.0%酵母浸粉,0.04%MnSO_4·4H_2O时,抑制活性最高,可达79.52%。通过对该菌基因组进行测序研究,发现其产ACE抑制肽涉及蛋白酶系统、多肽转运系统和肽酶系统。【结论】为扩大海洋源产ACE抑制肽的乳杆菌种质资源、开发高产ACE抑制活性的发酵菌株奠定了基础,进一步研究了如何提高乳杆菌产ACE抑制肽的水平,并对其基因组进行了研究,为今后生物学特性和ACE抑制活性机理的研究奠定了基础,并对降血压相关产品的开发具有重要意义。     

Foreign exploration for Scirtothrips perseae Nakahara (Thysanoptera: Thripidae) and associated natural enemies on avocado (Persea americana Miller)

Scirtothrips perseae Nakahara was discovered attacking avocados in California, USA, in 1996. Host plant surveys in California indicated that S. perseae has a highly restricted host range with larvae being found only on avocados, while adults were collected from 11 different plant species. As part of a management program for this pest, a “classical” biological control program was initiated and foreign exploration was conducted to delineate the home range of S. perseae, to survey for associated natural enemies and inventory other species of phytophagous thrips on avocados grown in Mexico, Guatemala, Costa Rica, the Dominican Republic, Trinidad, and Brazil. Foreign exploration efforts indicate that S. perseae occurs on avocados grown at high altitudes (>1500 m) from Uruapan in Mexico south to areas around Guatemala City in Guatemala. In Costa Rica, S. perseae is replaced by an undescribed congener as the dominant phytophagous thrips on avocados grown at high altitudes (>1300 m). No species of Scirtothrips were found on avocados in the Dominican Republic, Trinidad, or Brazil. In total, 2136 phytophagous thrips were collected and identified, representing over 47 identified species from at least 19 genera. The significance of these species records is discussed. Of collected material 4% were potential thrips biological control agents. Natural enemies were dominated by six genera of predatory thrips (Aeolothrips, Aleurodothrips, Franklinothrips, Leptothrips, Scolothrips, and Karnyothrips). One genus each of parasitoid (Ceranisus) and predatory mite (Balaustium) were found. Based on the results of our sampling techniques, prospects for the importation of thrips natural enemies for use in a “classical” biological control program in California against S. perseae are not promising.     

Taxonomic status of the species of the green algal genusNeochloris

Komárek has recently reviewed the various species assigned to the green algal genusNeochloris Starr (Chlorococcales, Chlorococcaceae) and removed those with uninucleate vegetative cells to a new genus,Ettlia. Watanabe & Floyd, unaware ofKomárek's work, also reviewed the species ofNeochloris and distributed them among three genera—Neochloris, Chlorococcopsis gen. nov., andParietochloris gen. nov.—on the basis of details of the covering of the zoospore and the arrangement of the basal bodies of the flagellar apparatus. This paper reconciles these two treatments and makes additional recommendations at the ranks of genus, family, order, and class.     

Die GattungKarschia — Bindeglied zwischen bitunicaten Ascomyceten und lecanoralen Flechtenpilzen?

The genusKarschia, in the earlier sense, including saprophytes and parasites on lichens, has been thought to be a non-lichenized parallel genus of the lichen genusBuellia. Modern workers included it on the one hand inBuellia, on the other hand combined it with bitunicate ascomycetes. It is now proved thatKarschia is heterogeneous and contains but superficially similar members both of the genusBuellia of theLecanorales and of typical or masked bitunicateAscomycetes. Therefore, it can not be regarded as a link betweenLecanorales andDothideales. The type species ofKarschia belongs to theDothideales.

     

Systematic significance of mature embryo of bamboos

The mature embryo of seven species belonging to five genera of Indian bamboos is described. In all these the basic pattern of embryo organisation is same: the scutellar and coleoptilar bundles are not separated by an internode, the epiblast is absent, the lower portion of the scutellum and the coleorhiza are separated by a cleft and the margins of embryonic leaves overlap. The features unique to fleshy fruited bamboos are: presence of a massive scutellum, the juxtaposition of plumule and radicle and the occurrence of a bud in the axil of the coleoptile. The fleshy fruit bearing bamboos should be classified into one group, the tribeMelocanneae. Evidence is provided to recognise additional groups in the subfamilyBambusoideae.     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

Biological control of three floating water weeds,<Emphasis Type="Italic">Eichhornia crassipes,Pistia stratiotes</Emphasis>, and <Emphasis Type="Italic">Salviniamolesta</Emphasis> in the Republic of Congo

Since 1999, four specific weevils (Coleoptera, Curculionidae) were released in the Republic of Congo against three exotic floating water weeds: Neochetina eichhorniae Warner and N. bruchi Hustache against water hyacinth, Neohydronomus affinis Hustache against water lettuce, and Cyrtobagous salviniae Calder and Sands against water fern. Recoveries of exotic weevils were made from all 24 release sites except one, and all four species have established and spread (up to 800 km for water hyacinth weevils). Within a few years of releases, control of water fern and water lettuce was such that fishing and navigation could be resumed, while reductions of water hyacinth populations were only beginning.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.