微生物菌群培养组学在动物医学中的应用

实验室条件下可培养的微生物约占自然界中微生物总数的1%，这限制了人们对99%未知微生物的认识和利用，而研究表明，那些“不可培养的微生物”是可以被开发和利用的，未能被纯培养的微生物才是未知微生物的主体。微生物培养组学探索利用多种培养条件和长时间的培养，结合基质辅助激光解吸电离飞行时间质谱法（MALDI-TOF-MS）和16S核糖体RNA（rRNA）测序可以大规模鉴定各种微生物，同时利用全基因组测序和宏基因组测序手段对未知微生物进行深入分析。本文综述了国内外近年来微生物菌群培养组学在反刍动物胃肠道、禽类盲肠及家畜鼻腔微生物菌群研究中的最新进展，探讨将动物体内菌群培养组学方法应用于动物疾病防治领域的可行性。作为一个新兴的研究方法，尽管该培养组学还存在一些不够成熟的方面，但它的发展前景十分广阔，微生物菌群培养组学方法和其他研究方法的互补已经逐渐成为发展兽医微生物学新的突破口。     

荔枝FKBP16-2基因启动子的克隆与瞬时表达分析

前期研究中发现了一个果肉低表达而叶片中高表达的荔枝基因FKBP16-2。本文克隆了该基因1 578 bp的启动子片段并对其功能进行了初步分析,结果表明:荔枝FKBP16-2基因启动子序列中含有大量的TATA-box和CAAT-box保守元件,以及TCA-element,ARE,HSE,GCN4_motif,O2-site等各种转录调控相关的顺式作用元件。该启动子能驱动GUS基因在荔枝的花、叶、根、果皮以及种子中表达而在果肉中不表达,表达具有组织特异性。     

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

普通荞麦染色体的原位PCR技术研究

[目的]探索一种适合荞麦的简单易行的染色体原位PCR技术。[方法]采用16S套式引物、4．5S套式引物与psbA引物，以栽培甜荞为材料，进行染色体原位PCR、原位套式PCR与多次原位PCR试验。[结果]高温干燥可以起到与包埋类似的作用；染色体的原位套式PCR效果比原位PCR明显，多次原位PCR次数为5-6效果较佳。16S引物和4．5S引物均显示了4对信号，但位置不同；而psbA引物是单拷贝的，仅显示出1对信号。根据这些信号的位置差异可以区分普通荞麦的5对染色体。[结论]所使用的荞麦染色体原位PCR技术简单易行。     

鲍曼不动杆菌雏鸡分离株CCGGD201101的分离、鉴定及致病性研究简

试验旨在鉴定吉林省某雏鸡孵育基地病死雏鸡组织中分离出的1株致病性菌CCGGD201101株并测定其致病性。对疑似致病菌进行生理生化试验、16S rDNA测序鉴定，并人工接种昆明鼠，测定其半数致死量，验证细菌毒力。经鉴定该菌为鲍曼不动杆菌（Acinetobacter baumannii）。以鲍曼不动杆菌CCGGD201101分离株为研究对象，并以鲍曼不动杆菌标准株（ATCC 19606）为对照，测得半数致死量，进一步证明鲍曼不动杆菌病死鸡分离株CCGGD201101具有较强致病性。     

秸秆纤维素分解细菌的筛选与鉴定

利用纤维素琼脂选择培养基和刚果红染色方法,从不同来源的土样中分离出2个菌株,测定了其纤维素酶活性、小麦秸秆降解能力,并对纤维素降解能力强的两个菌株进行了分子鉴定。结果表明,两株高效纤维素分解菌在纤维素刚果红培养基上均能形成透明水解圈,利用16S r RNA序列测序并分析Genbank中的同源性,结合形态和理化性质确定为Bacillus thuringiensis和Bacillus anthracis。在37℃,p H为7的条件下测定了纤维素酶活力,SC1-3和XR2-5-4分别为1.41和1.59。这两株37℃下经15 d后小麦秸秆失重率达19.92%和22.83%。     

Devastation of sesame (Sesamum indicum L.) crops in different agroclimatic zones of India by genetically diverse subgroups of phytoplasma

The sesame crop is highly susceptible to infection by phytoplasmas, a class of cell wall-less plant pathogenic bacteria (Mollicutes), which is responsible for widespread loss of sesame crops in both North and South India in recent years. Therefore, characterizing the pathogen population is required before the control measures can be devised and implemented. With molecular tools based on nested polymerase chain reaction (PCR) assays, sequencing, restriction profiling, and phylogenetic analysis, phyllody-affected sesame plants collected from nine different states of India were found to be infected by phytoplasmas belonging to two 16Sr groups, namely 16SrI and II. Two subgroups of phytoplasma −16SrI-B and 16SrII-D— were prevalent in symptomatic sesame samples collected from North India, whereas phytoplasma of only the 16SrII group was found in South India. However, the latter samples were diverse, belonging to three different subgroups (16SrII-A, II-C, and II-D). In addition, yearly phyllody-affected sesame samples from Delhi for 4 consecutive years (2007–2010) showed variation in the infecting phytoplasma: the subgroup 16SrII-D was detected in samples collected in 2007, and 16SrI-B was predominantly found in the samples collected in the subsequent years. The study also provides molecular evidence for the association between 16SrI-B phytoplasma and different symptoms in sesame crops such as fasciation, little leaf, and stunting. This is the first study to report the association of the phytoplasma subgroups 16SrII-A and II-D with sesame crops in India. This study provides a baseline for designing specific detection and molecular analysis strategies for quarantine purposes. It also highlights the need for examining the dynamics of seasonal or location-specific variation in vector populations to determine the pattern of infection outbreaks.     

Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin

Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon–Weiner and Simpson’s diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.     

感染16型蓝舌病病毒后绵羊部分细胞因子消长特点研究

本试验旨在探明绵羊感染16型蓝舌病病毒（Bluetongue virus type 16,BTV16）后细胞因子IFN-γ、IL-2、IL-4和IL-10的消长特点。用实时荧光定量PCR检测方法对感染BTV16后3只绵羊上述4种因子mRNA进行检测,同时设立阴性对照绵羊,并以0 d mRNA为基准,计算mRNA的相对表达量,同时检测病毒抗体效价、测量绵羊体温。结果显示,接种BTV16的3只绵羊均不同程度产生抗体和体温症状,4种细胞因子的mRNA在接种病毒2~4 d内均出现显著上升,其中IFN-γ峰值在2.58~27.84倍之间,IL-2峰值在5.24~17.19倍之间,IL-4峰值在2.16~3.43倍之间,IL-10峰值在15.78~48.77倍之间,个体上升幅度存在显著差异,4种细胞因子均在高水平持续6 d左右后逐渐下降。对照绵羊上述参数在正常范围内波动。本研究阐明了接种BTV16后绵羊细胞因子IFN-γ、IL-2、IL-4、IL-10在转录水平上的消长特点,为进一步深入开展BTV感染特征、宿主机体免疫机制研究提供参考。