Metabolic and ecological study of environmental pentose utilizing bacteria (E-PUB)

Lignocellulosic materials, such as sugar cane bagasse, a waste product of the sugarcane processing industry, agricultural residues and herbaceous crops, may serve as an abundant and comparatively cheap feedstock for largescale industrial fermentation, resulting in the production of marketable end-products. However, the complex structure of lignocellulosic materials, the presence of various hexose and pentose sugars in the hemicellulose component, and the presence of various compounds that inhibit the organisms selected for the fermentation process, all constitute barriers that add to the production costs and make full scale industrial production economically less feasible. The work presented in this thesis was conducted in order to screen microorganisms for ability to utilize pentose sugars derived from the sugar mill industrial waste. A large number of individual bacterial strains were investigated from hemi-cellulose rich material collected at the Proserpine and Maryborough sugar mills, notably soil samples from the mill sites. The research conducted to isolation of six pentose-capable Gram-positive organisms from the actinomycetes group by using pentose as a sole carbon source in the cultivation process. The isolates were identified as Corynebacterium glutamicum, Actinomyces odontolyticus, Nocardia elegans, and Propionibacterium freudenreichii all of which were isolated from the hemicellulose-enriched soil. Pentose degrading microbes are very rare in the environment, so this was a significant discovery. Previous research indicated that microbes could degrade pentose after genetic modification but the microbes discovered in this research were able to naturally utilize pentose. Six isolates, identified as four different genera, were investigated for their ability to utilize single sugars as substrates (glucose, xylose, arabinose or ribose), and also dual sugars as substrates (a hexose plus a pentose). The results demonstrated that C. glutamicum, A. odontolyticus, N. elegans, and P. freudenreichii were pentose-capable (able to grow using xylose or other pentose sugar), and also showed diauxie growth characteristics during the dual-sugar (glucose, in combination with xylose, arabinose or ribose) carbon source tests. In addition, it was shown that the isolates displayed very small differences in growth rates when grown on dual sugars as compared to single sugars, whether pentose or hexose in nature. The anabolic characteristics of C. glutamicum, A. odontolyticus, N. elegans and P. freudenreichii were subsequently investigated by qualitative analysis of their end-products, using high performance liquid chromatography (HPLC). All of the organisms produced arginine and cysteine after utilization of the pentose substrates alone. In addition, P. freudenreichii produced alanine and glycine. The end-product profile arising from culture with dual carbon sources was also tested. Interestingly, this time the product was different. All of them produced the amino acid glycine, when grown on a combination substrate-mix of glucose with xylose, and also glucose with arabinose. Only N. elegans was able to break down ribose, either singly or in combination with glucose, and the end-product of metabolism of the glucose plus ribose substrate combination was glutamic acid. The ecological analysis of microbial abundance in sugar mill waste was performed using denaturing gradient gel electrophoresis (DGGE) and also the metagenomic microarray PhyloChip method. Eleven solid samples and seven liquid samples were investigated. A very complex bacterial ecosystem was demonstrated in the seven liquid samples after testing with the PhyloChip method. It was also shown that bagasse leachate was the most different, compared to all of the other samples, by virtue of its richness in variety of taxa and the complexity of its bacterial community. The bacterial community in solid samples from Proserpine, Mackay and Maryborough sugar mills showed huge diversity. The information found from 16S rDNA sequencing results was that the bacterial genera Brevibacillus, Rhodospirillaceae, Bacillus, Vibrio and Pseudomonas were present in greatest abundance. In addition, Corynebacterium was also found in the soil samples. The metagenomic studies of the sugar mill samples demonstrate two important outcomes: firstly that the bagasse leachate, as potentially the most pentose-rich sample tested, had the most complex and diverse bacterial community; and secondly that the pentose-capable isolates that were initially discovered at the beginning of this study, were not amongst the most abundant taxonomic groups discovered in the sugar mill samples, and in fact were, as suspected, very rare. As a bioprospecting exercise, therefore, the study has discovered organisms that are naturally present, but in very small numbers, in the appropriate natural environment. This has implications for the industrial application of E-PUB, in that a seeding process using a starter culture will be necessary for industrial purposes, rather than simply assuming that natural fermentation might occur.

Brief report: Intestinal dysbiosis in ankylosing spondylitis

Objective Ankylosing spondylitis (AS) is a common, highly heritable immune-mediated arthropathy that occurs in genetically susceptible individuals exposed to an unknown but likely ubiquitous environmental trigger. There is a close relationship between the gut and spondyloarthritis, as exemplified in patients with reactive arthritis, in whom a typically self-limiting arthropathy follows either a gastrointestinal or urogenital infection. Microbial involvement in AS has been suggested; however, no definitive link has been established. The aim of this study was to determine whether the gut in patients with AS carries a distinct microbial signature compared with that in the gut of healthy control subjects. Methods Microbial profiles for terminal ileum biopsy specimens obtained from patients with recent-onset tumor necrosis factor antagonist-naive AS and from healthy control subjects were generated using culture-independent 16S ribosomal RNA gene sequencing and analysis techniques. Results Our results showed that the terminal ileum microbial communities in patients with AS differ significantly (P < 0.001) from those in healthy control subjects, driven by a higher abundance of 5 families of bacteria (Lachnospiraceae [P = 0.001], Ruminococcaceae [P = 0.012], Rikenellaceae [P = 0.004], Porphyromonadaceae [P = 0.001], and Bacteroidaceae [P = 0.001]) and a decrease in the abundance of 2 families of bacteria (Veillonellaceae [P = 0.01] and Prevotellaceae [P = 0.004]). Conclusion We show evidence for a discrete microbial signature in the terminal ileum of patients with AS compared with healthy control subjects. The microbial composition was demonstrated to correlate with disease status, and greater differences were observed between disease groups than within disease groups. These results are consistent with the hypothesis that genes associated with AS act, at least in part, through effects on the gut microbiome.

Root zone microbial populations, urease activities, and purification efficiency for a constructed wetland

In order to investigate the effects of microorganisms and their urease activities in macrophytic root zones on pollutant removal, four small-scale plots (SSPs) of vertical/reverse-vertical flow wetlands were set up to determine: a) the relationship between the abundance of microorganisms in the root zones and water purification efficiency; and b) the relationship between urease activities in the root zones and pollutant removal in a constructed wetland system. Total numbers of the microbial population (bacteria, fungi, and actinomyces) along with urease activities in the macrophytic root zones were determined. In addition, the relationships between microbial populations and urease activities as well as the wastewater purification efficiencies of total phosphorus (TP), total Kjeldahl nitrogen (TKN), biochemical oxygen demand in 5 days (BOD5), and chemical oxygen demand (COD) were also analyzed. The results showed that there was a highly significant positive correlation (r = 0.9772, P < 0.01) between the number of bacteria in the root zones and BOD5 removal efficiency and a significant negative correlation (r = -0.9092, P < 0.05) between the number of fungi and the removal efficiency of TKN. Meanwhile, there was a significant positive correlation (r = 0.8830, P < 0.05) between urease activities in the root zones and the removal efficiency of TKN. Thus, during wastewater treatment in a constructed wetland system, microorganism and urease activities in the root zones were very important factors.

D2-4放线菌的筛选及其抗生物质研究

利用有益微生物及其代谢产物来防治植物病害，已成为一个十分活跃并具有巨大应用前景的领域。本论文采用土壤预处理等特殊方法，从长白山不同高度的土壤中筛选出1068株放线菌。通过对峙培养法和杯碟法，筛选出D1-1等10株对蔬菜病害菌具有抑制作用的菌株。离体叶片实验中发现D2-4发酵液对黄瓜、辣椒、番茄等蔬菜真菌病害具有一定的防治效果。以水和常用化学农药作为空白和药物对照，对D2-4发酵液进行了盆栽实验，结果对番茄灰霉、辣椒根腐和黄瓜枯萎病的防治效果分别为70.65％、63.27％、65.04％，初步显示出良好的防治效果。通过单因素和均匀设计实验，优化了DZ-4菌发酵培养基的组成，考察了培养时间、接种量、菌龄等对抑菌活性的影响。确定了最佳发酵培养基成分：黄豆饼粉1.10％、葡萄糖2.71％、蔗糖1.00％、NaCl0.10％、酵母膏0.10％、发酵培养基初始pH为6.61。最佳发酵时间为96h左右，培养20～24h的种子液以7％的接种量转接有利于提高抑菌活性。经发酵培养基和发酵条件的优化，发酵液抑菌活性达到了6588 u／ml，比原始发酵培养基（3678 u／ml）活性提高了79.12％。经发酵液的预处理、离子交换层析、吸附柱层析、高效液相色谱纯化等步骤，对D2-4抗生素进行了分离纯化研究。通过纸层析、纸电泳等试验最后确定该农用抗生素为弱碱性水溶性抗生素。对D2-4抗生素纯品进行了红外吸收光谱、紫外吸收光谱等理化性质的研究。

繁茂膜海绵中放线菌的鉴定及S19抗菌素主要特性的研究

近年的研究表明，海绵微生物是某些海绵天然产物的真正产生者。因此，人们将海绵微生物作为开发海绵天然产物的重要来源之一。采用琼脂块法和液体扩散法，从分离自中国黄渤海大连海域的海绵优势种—繁茂膜海绵的28株放线菌中筛选到4株具有抗菌活性的放线菌，并对它们进行生物学鉴定。采用经典和现代分类鉴定方法，对4株具有抗菌活性的繁茂膜海绵放线菌的形态特征、培养特征、生理生化特征、细胞壁化学组分和16SrRNA序列进行了研究，得出种水平的鉴定结果：Hmp-S14为西唐氏链霉菌Streptomycessetonii；Hmp-S19为灰色链霉菌Streptomyces griseus；Hmp-S24为桔橙小单抱菌Micromonospora aurantiaca；Hmp-S26为生二素链霉菌Streptomyces ambifaciens。在四株具有抗菌活性的繁茂膜海绵放线菌中，菌株Hmp-S19的抗菌活性优于其它三株，并且与已报道的20多种灰色链霉菌菌株有不同的生理生化特性，故进一步优化其发酵条件并初步研究了S19抗菌素的理化性质。通过单因子和均匀设计实验，优化菌株Hmp-S19摇瓶发酵条件。确定最佳发酵培养基：玉米粉0.6％，葡萄糖0.1％，豆饼粉0.5％，NaCl 0.3％，KH2PO40.08％，CaCO30.08％，MgSO40.02％；最佳发酵条件：接种龄30h，接种量5％，初始pH7．0，发酵时间96h，装液量100ml／50ml，培养温度28 ℃。应用二剂量法测定519一抗菌素的相对效价，为5154μ/ml，较原始发酵培养基和发酵条件（3364μ/ml）提高了53％。通过pH纸层析和捷克八溶剂系统纸层析试验，初步判定519抗菌素为两性、非水溶性I型抗菌素。Hmp-S19发酵液经预处理、萃取、硅胶柱层析、制备薄层层析等步骤，对S19抗菌素进行分离纯化得粗制品，并进行了液 相色谱一质谱检测。

一株放线菌发酵产物抗肿瘤活性的研究

本学位论文主要研究一株放线菌发酵产物的抗肿瘤活性。先对该株放线菌进行活化培养，然后进行大批量发酵，发酵液经过冷冻离心，对离心得到的沉淀和上清液用不同极性的有机溶剂进行萃取，得到六个浸膏样品。对六个样品进行初步抗肿瘤活性检测。 然后对活性浸膏进行分离纯化和活性跟踪。本论文主要进行了如下的工作： 1、对菌种进行活化培养，利用该菌株在280C，200r.min-1条件下进行发酵实验，发酵时间为72h,发酵总量为15L。发酵液经过离心得到上清液和沉淀两部分。 2、分别用石油醚、乙酸乙酯、正丁醇萃取沉淀和上清液，得到编号为1—6的六个浸膏样品，对六个浸膏样品进行初步的细胞毒性和抗HepG2肿瘤活性实验，得出结论为5号样品活性最高。在没有分离纯化的情况下GI50达到0.76µg/mL。 3、对5号样品进行TLC实验，找出能够较好分离5号样品中各组分的溶剂组合，最后得出在氯仿：甲醇=8：1时分离效果较好。然后利用氯仿：甲醇=8：1的溶剂组合作为洗脱剂对5号样品进行过硅胶柱分离纯化并进行活性跟踪分离。 4、对分离纯化后得到的样品进行活性跟踪和结构分析。分离后得到样品A，在其浓度为10µg/ml时，抗肿瘤实验细胞的生长率为73.5%。在浓度为1.0mg/ml时，抗单纯疱疹病毒率（HSVⅡ）为74.5%。结构分析得知其分子式最可能为C41H43N8O4. This dissertation studied about the anti-tumor activity of an actinomycete fermentation product. First, we cultured the actinomycete. Second, we fermented it in large quantities, and then centrifuged the fermentation fluid; the next step is that we extract sedimentation and supernatant in different polar organic solvents, in turn to obtained six samples, which were detected about anti-tumor activity. Last, we purified active sample and tracked activity of it. We carried out the following research work: 1. Activation, culture and screening of the actinomyces was carried on. We used the screening strain to carry on the fermentation when the conditions are 280C，200r.min-1,the fermentation time is 72h. Fermentation fluid volume is 15L.And we obtained sedimentation and supernatant after fermentation fluid was centrifuged. 2. We used Petroleum ether, ethyl acetate, n-butanol separately to extract sedimentation and supernatant, and obtained six samples that were numbered 1-6. From the preliminary cell toxicity and the anti-tumor（HepG2） bioactivity experiment, we found that No.5 sample has the highest activity in the samples; the GI50 was 0.76µg/ml which has not been purified. 3. We Carried on TLC experiment on the No.5 sample, found the solvent composition that can separate each component of the No.5 sample. At last, we found that when the proportions are tri-chloromethane: methyl alcohol = 8:1, the Separation result was the best, and then we used the Solvent composition which proportion are tri-chloromethane: methyl alcohol = 8:1 as eluant to Purify No.5 sample by silica gel column. 4. We tracked the activity of pure sample obtained from Purification and analyzed structure of these substances. We got a compound A after separation, and the cell growth rate was 73.5% when its concentration was 10µg/ml. The anti-virus（HSVⅡ） rate was 74.5% when its concentration was 1.0mg/ml. We analyzed the Structure of A, and informed its molecular formula that was the most likely for C41H43N8O4.

石油污染土壤生物修复过程中微生物生态研究

The analysis on microbiological ecology for four types of oil contaminates soils showed that the bacteria utilizing the oil as carbon sources increase,wheras the fugi become less .Zooloea and Bacillu are the dominant bacteria ; Mocor and Cunninghamella ,and Fursarium are the dominant fungi streptomyces take the superiority among the actinomyces.The anaiysis on esterase activity showed that the microbes above mentioned have abilies of degrading esters. The biodeg radationrates are 55.45%,56.74%,38.37% and 45.19%respectively,after 53 days,the biodegradation rate can be increased by 12.6% when the dominant microbes are added.

海洋放线菌来源的化合物卡拉霉素(kalamycin)的抗肿瘤作用和机制研究

海洋生态环境的特殊性决定了海洋中往往含有结构奇特、新颖的化学物质， 海洋药物具有药理特异性、高活性和多样性，已成为药物研发热点领域，海洋抗肿瘤药物也是其中之一。卡拉霉素（kalamycin）来源于海洋放线菌M097的聚酮类化合物，我们实验室用体外增殖抑制试验发现了卡拉霉素（kalamycin）的抗肿瘤作用。有报道其类似物lactoquinomycin和frenolicin B是肿瘤靶点AKT抑制剂，并由此推断吡喃萘醌骨架在AKT抑制过程中发挥主要作用，我们发现虽然卡拉霉素（kalamycin）含有吡喃萘醌骨架，但是并不抑制AKT及其下游信号系统；继而对卡拉霉素（kalamycin）的体外抗肿瘤作用及其机理进行了系统的分析。 采用磺酰罗丹明B（SRB）法检测卡拉霉素（kalamycin）对10株肿瘤细胞株的体外增殖抑制作用，结果表明，卡拉霉素（kalamycin）能明显抑制各种组织来源的肿瘤细胞生长，具有广泛的细胞增殖抑制作用，除对一株肺癌细胞A549抑制作用不明显外，对9株肿瘤细胞株的IC50平均值为2.5μM，并且对各个细胞株生长抑制曲线形态基本一致。采用流式细胞术证实，卡拉霉素（kalamycin）能剂量依赖地诱导结肠癌细胞HCT-116和肝癌细胞SMMC-7721发生G2/M期周期阻滞，可以诱导黑色素瘤A375细胞发生凋亡。 基于前人的报道，我们用Western blot方法检测卡拉霉素（kalamycin）对AKT信号系统的影响，用量从1μM增加到16μM，AKT、mTOR和磷酸化AKT、mTOR、GSK3β的总量都没有变化；因此我们判断卡拉霉素（kalamycin）不是通过AKT系统发挥作用，而是有另外的机制。细胞凋亡和周期阻滞的很多过程是和P53相关的，我们用卡拉霉素（kalamycin）对P53野生和缺失的HCT-116细胞的增殖抑制和凋亡诱导来分析该抑制作用是否和P53相关，结果显示卡拉霉素（kalamycin）对两种细胞的生长抑制和诱导凋亡作用无明显差异，其作用和P53途径是不相关的。 卡拉霉素（kalamycin）细胞增殖抑制作用的非选择性，表明该化合物是一个广谱的细胞增殖抑制剂。我们用体外酶反应实验分析了卡拉霉素（kalamycin）对拓扑酶的抑制作用，结果显示卡拉霉素（kalamycin）对Topo I没有抑制作用，在20μM时几乎完全抑制Topo II，呈现出显著的浓度依赖效应，抑制作用大约比VP16强十倍。用DNA伸展实验和Topo II 介导的负超螺旋 pBR322 切割实验，证实卡拉霉素（kalamycin）不是DNA嵌入剂和Topo II毒剂，而是一个催化抑制剂。在体外模拟Topo II的催化反应步骤，把整个过程分解，发现卡拉霉素（kalamycin）可以抑制Topo II介导的DNA的切割，但是对再连接没有作用；卡拉霉素（kalamycin）能抑制ATP水解的作用，但是在较高剂量时抑制作用要比阳性对照弱得多。因此，卡拉霉素（kalamycin）可能主要通过抑制Topo II介导的DNA的切割发挥作用。 肿瘤新血管生成是原发性肿瘤赖以发生、生长和转移的物质基础。我们用了多个新生血管生成模型对卡拉霉素（kalamycin）的抗新生血管生成作用进行了检测，发现卡拉霉素（kalamycin） 对内皮细胞管腔形有抑制作用，其作用效果呈现明显的剂量依赖性。卡拉霉素（kalamycin）在对内皮细胞HMEC-1在12小时内的IC50是4.39μM ，在没有显著增殖抑制作用的剂量下，对HMEC-1管腔形成依然具有抑制作用，提示卡拉霉素（kalamycin）的抗新生血管生成作用并非完全来源于其增殖抑制作用。通过体外酶反应、western blot和双荧光素酶报告基因系统分析卡拉霉素（kalamycin）抑制肿瘤新血管生成的信号途径，结果发现这种抑制作用不是依赖于酪氨酸激酶和HIF-lα途径的。 综上所述，卡拉霉素（kalamycin）不是一个AKT抑制剂，它通过专一性的抑制Topo II使肿瘤细胞发生周期阻滞和细胞凋亡，主要抑制Topo II介导的DNA的切割和ATP水解作用。同时卡拉霉素（kalamycin）可以抑制肿瘤血管管腔形成，抑制作用不依赖酪氨酸激酶和HIF-lα途径。

S21 Culture Independent Identification Of Bacterial Communities In The Respiratory Tract Of Patients With Copd, Healthy Non-smokers And Healthy Smokers

Introduction and aims: The role bacteria play in the development and progression of Chronic Obstructive Pulmonary Disease (COPD) is unclear. We used culture-independent methods to describe differences and/or similarities in microbial communities in the lower airways of patients with COPD, healthy non-smokers and smokers.

Methods: Bronchial wash samples were collected from patients with COPD (GOLD 1–3; n = 18), healthy non-smokers (HV; n = 11) and healthy smokers (HS; n = 8). Samples were processed using the Illumina MiSeq platform. The Shannon-Wiener Index (SW) of diversity, lung obstruction (FEV1/FVC ratio) and ordination by Non-Metric Multidimensional Scaling (NMDS) on Bray-Curtis dissimilarity indices were analysed to evaluate how samples were related. Principal component analysis (PCA) was performed to assess the effect specific taxa had within each cohort. Characteristics of each cohort are shown in Table 1.

Results: There was no difference in taxa richness between cohorts (range: 69–71; p = 0.954). Diversity (SW Index) was significantly lower in COPD samples compared to samples from HV and HS (p = 0.009 and p = 0.033, respectively). There was no significant difference between HV and HS (p = 0.186). The FEV1/FVC ratio was significantly lower for COPD compared to HV (p = 9*10–8) and HS (p = 2*10–6), respectively. NMDS analysis showed that communities belonging to either of the healthy groups were more similar to each other than they were to samples belonging to the COPD group. PCA analysis showed that members of Streptococcus sp. and Haemophilus sp. had the largest effect on the variance explained in COPD. In HS, Haemophilus sp., Fusobaterium sp., Actinomyces sp., Prevotella sp. and Veillonella sp. had the largest effect on the variance explained, while in HV Neisseria sp., Porphyromonas sp., Actinomyces sp., Atopobium sp., Prevotella and Veillonella sp. had the largest effect on the variance explained.

Conclusions: The study demonstrates that microbial communities in the lower airways of patients with COPD are significantly different from that seen in healthy comparison groups. Patients with COPD had lower microbial diversity than either of the healthy comparison groups, higher relative abundance of members of Streptococcus sp. and lower relative abundance of a number of key anaerobes.Characteristics

Efeito da combinação de antibióticos e sinvastatina sobre microrganismos de interesse endodôntico e na expressão de marcadores odontoblásticos

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Distribución del fragmento katN de Nocardia brasiliensis en especies de actinomicetos patógenos

Tesis (Maestría en Ciencias con Especialidad en Mocrobliología Médica) UANL.

Estudios in vivo e in vitro de la sensibilidad de actinomadura madurae frente a diversos antimicrobianos de reciente desarrollo

Tesis (Maestría en Ciencias con Especialidad en Microbiología Médica) UANL

La respuesta de anticuerpos anti-proteínas intracelulares de actinomicetos productores de micetoma en animales infectados o inmunizados

Tesis (Maestría en Ciencias con Especialidad en Inmunología) UANL

Determinación in vitro del efecto de la combinación de amikacina y trimetoprim-sulfametoxazol sobre Nocardia brasiliensis

Tesis (Maestría en Ciencias con Especialidad en Microbiología Médica) U.A.N.L.

Estudio de la inmunogenicidad de las proteasas de Nocardia brasiliensis y su efecto inductor de protección en el micetoma experimental en ratones Balb

Tesis (Doctorado en Ciencias con Especialidad en Inmunología) UANL