繁茂膜海绵细胞内微生物多样性的研究

采用海绵组织离散、细胞分离的方法,对繁茂膜海绵细胞进行纯化、胞内微生物DNA提取,构建了繁茂膜海绵细胞内微生物的16SrDNA克隆,对其遗传多样性进行了分析,发现海绵细胞内微生物16SrDNA序列主要归类于紫硫细菌门(Proteobacteria)中的α-亚门、γ-亚门和浮霉菌门(Planctomycetes)等类群。与研磨直接提取海绵组织DNA所得海绵组织中总微生物多样性相比,海绵细胞内存在丰富的浮霉菌(23%),说明浮霉菌主要存在于海绵细胞胞内。     

Bioluminescent Bacterial Imaging In Vivo

This video describes the use of whole body bioluminesce imaging (BLI) for the study of bacterial trafficking in live mice, with an emphasis on the use of bacteria in gene and cell therapy for cancer. Bacteria present an attractive class of vector for cancer therapy, possessing a natural ability to grow preferentially within tumors following systemic administration. Bacteria engineered to express the lux gene cassette permit BLI detection of the bacteria and concurrently tumor sites. The location and levels of bacteria within tumors over time can be readily examined, visualized in two or three dimensions. The method is applicable to a wide range of bacterial species and tumor xenograft types. This article describes the protocol for analysis of bioluminescent bacteria within subcutaneous tumor bearing mice. Visualization of commensal bacteria in the Gastrointestinal tract (GIT) by BLI is also described. This powerful, and cheap, real-time imaging strategy represents an ideal method for the study of bacteria in vivo in the context of cancer research, in particular gene therapy, and infectious disease. This video outlines the procedure for studying lux-tagged E. coli in live mice, demonstrating the spatial and temporal readout achievable utilizing BLI with the IVIS system.     

Routine fluorescence in situ hybridization in soil

The use of fluorescence in situ hybridization (FISH) to identify and enumerate soil bacteria has long been hampered by the autofluorescence of soil particles masking the bacterial signals and because the need of counting hundreds of bacteria in order to achieve statistically reliable data is time consuming. Recently, it was demonstrated that Nycodenz facilitates FISH in soil by concentrating bacteria on membrane filters and avoiding autofluorescent soil particles. We present a routine protocol for FISH in soil including the use of Nycodenz. The protocol allows fast and easy enumeration of hundreds of bacteria. We propose the use of silicon grease coated slides to treat in parallel seven samples per hybridization. Further, we developed a semi-automated approach for the enumeration of bacteria by implementing macros concatenating all steps of the image analyzes in the Image J software. Using Nycodenz, software-assisted bacterial counts statistically matched eye-counts of the same images and it was possible to count 880 DAPI stained bacteria per ten images. Fifty-five percent of these bacteria were co-labelled with the FISH probe specific for the Domain Bacteria, in accordance with recent FISH studies of bacterial populations in bulk soil. With a soil slurry protocol used for comparison, soil particles impaired automatic counts of the bacteria and FISH analysis, and only 88 DAPI stained bacteria per ten images could be counted by eye. With the Nycodenz protocol, 5 mM Na(2)EDTA used as an extractant increased the number of bacteria observed by 49%. In contrast, Tween 20 (1% or 5%) had no significant effect and increased the variability between the samples. Overall, the proposed procedure allows to process a high number of samples and to achieve a time efficient FISH characterization of soil bacterial communities.     

Noninvasive optical imaging of staphylococcus aureus bacterial infection in living mice using a Bis-dipicolylamine-Zinc(II) affinity group conjugated to a near-infrared fluorophore

Optical imaging of bacterial infection in living animals is usually conducted with genetic reporters such as light-emitting enzymes or fluorescent proteins. However, there are many circumstances where genetic reporters are not applicable, and there is a need for exogenous synthetic probes that can selectively target bacteria. The focus of this study is a fluorescent imaging probe that is composed of a bacterial affinity group conjugated to a near-infrared dye. The affinity group is a synthetic zinc (II) coordination complex that targets the anionic surfaces of bacterial cells. The probe allows detection of Staphylococcus aureus infection (5 x 10 (7) cells) in a mouse leg infection model using whole animal near-infrared fluorescence imaging. Region of interest analysis showed that the signal ratio for infected leg to uninfected leg reaches 3.9 +/- 0.5 at 21 h postinjection of the probe. Ex vivo imaging of the organs produced a signal ratio of 8 for infected to uninfected leg. Immunohistochemical analysis confirmed that the probe targeted the bacterial cells in the infected tissue. Optimization of the imaging filter set lowered the background signal due to autofluorescence and substantially improved imaging contrast. The study shows that near-infrared molecular probes are amenable to noninvasive optical imaging of localized S. aureus infection.     

Development of radiographic and microscopic techniques for the characterization of bacterial transport in intact sediment cores from Oyster, Virginia.

The objective of this study was to ascertain the physical and mineralogical properties responsible for the retention of bacteria in subsurface sediments. The sediment core chosen for this study was a fine-grained, quartz-rich sand with minor amounts of Fe and Al hydroxides. A bacterial transport experiment was performed using an intact core collected from a recent excavation of the Butler's Bluff member of the Nassawadox formation in the borrow pit at Oyster, VA. and a 14C-labeled bacterial strain OYS2-A was selected for its relatively low adhesion. After the bacterial breakthrough was observed in the effluent, the intact core was dissected to determine the internal distribution of the injected bacteria retained in the sediment. The sediment was dried, epoxy fixed, and thin sectioned. The distribution of 14C activity in the thin sections was mapped using a phosphor screen and X-ray film. The remainder of the core was subsampled and the 14C activity of the subsamples was determined by liquid scintillation counting. The phosphor imaging technique was capable of directly imaging the distribution of radiolabeled bacteria in thin sections, because of its high sensitivity and linear response over a large activity range. The phosphor imaging signal intensity was utilized as a measure of bacterial concentration. The distribution of bacteria at the millimeter scale in the thin sections was compared to the grain size, porosity, and mineralogy as measured by scanning electron microscopy (SEM) and energy dispersive spectrum (EDS) analyses. No apparent correlation was observed between the retention or collision efficiency of bacteria in the sediment and the amount of Fe and Al hydroxides. This apparent lack of correlation can be qualitatively explained by combination of several factors including a nearly neutral surface charge of the bacterial strain, and texture of the Fe and Al hydroxides in the sediment. The combination of phosphor imaging with SEM-EDS proved to be a robust method for relating the physical and mineralogical microscopic properties of poorly indurated sediment to the distribution of adsorbed bacteria, allowing bacterial retention mechanisms to be unambiguously unraveled.     

Synthesis of N₄'-[¹⁸F]fluoroalkylated ciprofloxacin as a potential bacterial infection imaging agent for PET study

Syntheses and evaluation of fluoroalkylated ciprofloxacin analogues are described. Among these analogues, N?'-3-fluoropropylciprofloxacin (16) showed the most efficient antibacterial activity against E. coli strains (DH5α and TOP10) and a high binding affinity for DNA gyrase of bacteria. To develop bacteria-specific infection imaging agents for positron emission tomography (PET), no-carrier-added N?-3-[1?F]fluoropropylciprofloxacin ([1?F]16) was prepared in two steps from N?-3-methanesufonyloxypropylciprofloxacin, resulting in a 40% radiochemical yield (decay corrected for 100 min) via the tert-alcohol media radiofluorination protocol with high radiochemical purity (> 99%) as well as high specific activity (149 ± 75 GBq/μmol). The agent was stable (> 90%), as shown by an in vitro human serum stability assay. A bacterial uptake and blocking study of [1?F]16 using authentic compound 16 in TOP10 cells demonstrated its high specific bacterial uptake. The results suggest that this radiotracer holds promise as a useful bacterial infection radiopharmaceutical for PET imaging.     

Imaging of bubonic plague dynamics by in vivo tracking of bioluminescent Yersinia pestis

Yersinia pestis dissemination in a host is usually studied by enumerating bacteria in the tissues of animals sacrificed at different times. This laborious methodology gives only snapshots of the infection, as the infectious process is not synchronized. In this work we used in vivo bioluminescence imaging (BLI) to follow Y. pestis dissemination during bubonic plague. We first demonstrated that Y. pestis CO92 transformed with pGEN-luxCDABE stably emitted bioluminescence in vitro and in vivo, while retaining full virulence. The light produced from live animals allowed to delineate the infected organs and correlated with bacterial loads, thus validating the BLI tool. We then showed that the first step of the infectious process is a bacterial multiplication at the injection site (linea alba), followed by a colonization of the draining inguinal lymph node(s), and subsequently of the ipsilateral axillary lymph node through a direct connection between the two nodes. A mild bacteremia and an effective filtering of the blood stream by the liver and spleen probably accounted for the early bacterial blood clearance and the simultaneous development of bacterial foci within these organs. The saturation of the filtering capacity of the spleen and liver subsequently led to terminal septicemia. Our results also indicate that secondary lymphoid tissues are the main targets of Y. pestis multiplication and that colonization of other organs occurs essentially at the terminal phase of the disease. Finally, our analysis reveals that the high variability in the kinetics of infection is attributable to the time the bacteria remain confined at the injection site. However, once Y. pestis has reached the draining lymph nodes, the disease progresses extremely rapidly, leading to the invasion of the entire body within two days and to death of the animals. This highlights the extraordinary capacity of Y. pestis to annihilate the host innate immune response.     

Protocol for Rapid Fluorescence In Situ Hybridization of Bacteria in Cryosections of Microarthropods

A protocol was developed to detect bacteria inhabiting microarthropods by means of small-subunit rRNA-targeted fluorescence in situ hybridization and microscopy. The protocol is based on cryosections of whole specimens. In contrast to more commonly applied paraffin-embedding techniques, the protocol is quicker and reduces the number of manipulations which might damage the microscopic material. The method allowed the study of the bacterial colonization of Folsomia candida (Collembola) and the detection of bacteria in both the gut and tissue.     

细菌感染显像剂的研究进展

细菌感染显像剂是利用一些示踪基团(如放射性核素及荧光染料)标记对细菌具有特异性识别作用的导向物,通过检测示踪信号定位细菌感染部位。到目前为止,针对细菌内的特异性位点(如细胞壁、酶、受体等)研制和开发了一系列细菌感染显像剂(包括核素标记的抗生素、噬菌体、抗菌肽、核苷及荧光染料标记的糖类等),这些显像剂能在细菌感染部位高度特异性聚集,有望应用于临床早期诊断细菌感染。本文对这些细菌感染显像剂的种类、浓集机制及研究现状进行了概述,并在此基础上,总结了理想细菌感染显像剂所应具有的特征,为进一步研究和开发新的细菌感染显像剂提供参考。     

A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system

Plants-microorganisms interactions play a fundamental role in terrestrial ecosystems and various methods have been reported for plant-associated bacteria extraction. However, these methods exhibit notable variations and lack of some procedural details that may impact the interpretations of results. We propose here a standardized and detailed protocol for the independent extraction of bulk, rhizosphere and rhizoplan soil fractions. This protocol was applied to the sampling of different polluted soil fractions collected in the vicinity of Arabidopsis halleri dense root system. It allowed us to determine the cultivable bacterial densities in each fraction and to confirm the existence of a bacterial gradient linked to roots distance, with a higher amount of bacteria in the rhizospheric area. We suggest to use this unified procedure as a common basis for soil sampling and bacterial communities analysis from other roots systems.     

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in Bacillus subtilis, and to quantify gene regulation and its fluctuations in individual Escherichia coli cells. The protocol involves seeding and growing bacteria on small agarose pads and imaging the resulting microcolonies. Images are then reviewed and analyzed using our laboratory's custom MATLAB analysis code, which segments and tracks cells in a frame-to-frame method. This process yields quantitative expression data on cell lineages, which can illustrate dynamic expression profiles and facilitate mathematical models of gene circuits. With fast-growing bacteria, such as E. coli or B. subtilis, image acquisition can be completed in 1 d, with an additional 1-2 d for progressing through the analysis procedure.     

Intravital Microscopy of Leukocyte-endothelial and Platelet-leukocyte Interactions in Mesenterial Veins in Mice

Intravital microscopy is a method that can be used to investigate different processes in different regions and vessels in living animals. In this protocol, we describe intravital microscopy of mesentery veins. This can be performed in a short period of time with reproducible results showing leukocyte-endothelial interactions in vivo. We describe an inflammatory setting after LPS challenge of the endothelium. But in this model one can apply many different types of inflammatory conditions, like bacterial, chemical or biological and investigate the administration of drugs and their direct effects on the living animal and its impact on leukocyte recruitment. This protocol has been applied successfully to a number of different treatments of mice and their effects on inflammatory response in vessels. Herein, we describe the visualization of leukocytes and platelets by fluorescently labeling these with rhodamine 6G. Additionally, any specific imaging can be performed using targeted fluorescently labeled molecules.     

Cohabitation with farm animals rather than breeding effort increases the infection with feather‐associated bacteria in the barn swallow Hirundo rustica

Feather‐associated bacteria are widespread inhabitants of avian plumage. However, the determinants of the between‐individual variation in plumage bacterial loads are less well understood. Infection intensities can be determined by ecological factors, such as breeding habitat, and can be actively regulated by hosts via preening. Preening, yet, is a resource intensive activity, and thus might be traded‐off against reproductive investment in breeding birds. Here, we studied barn swallows Hirundo rustica to assess the bacterial cost of reproduction in relation to nesting site micro‐habitats. Barn swallows prefer to breed in the company of large‐sized farm animals, although the presence of mammalian livestock in barns assures a warm and humid micro‐climate that favours bacterial proliferation. Thus, we experimentally manipulated brood sizes of birds breeding in barns with, or without, farm animals and measured total cultivable bacteria (TCB) and feather‐degrading bacteria (FDB) from the plumage. We found that the abundance of feather‐associated bacteria (i.e. both TCB and FDB) in females, but not males, breeding in barns with livestock were significantly higher than in conspecifics breeding in empty barns. Plumage bacterial loads, however, were not affected by brood size manipulations in either sex. In addition, we report a negative relationship between both TCB and FDB and hatching date in females, and several sex and seasonal differences in plumage bacterial abundances. Our study is the first to show that breeding micro‐habitat (i.e. livestock co‐tenancy) has consequences for the abundance of feather‐associated bacteria.     

Tumour necrosis factor alpha antibody protects against lethal meningococcaemia

Tumour necrosis factor alpha (TNF-alpha) has been shown to be the principal mediator of Gram-negative bacterial endotoxin-induced shock. Nevertheless, evidence suggests that TNF-alpha plays a beneficial role in controlling bacterial infections when multiplication of the microorganism is required to kill the host. Using an infant rat model of Neisseria meningitidis infection, we found that blood TNF-alpha concentration reaches a peak three hours after intraperitoneal injection of 3 x 10(6) bacteria. Thereafter, the level of TNF-alpha decreased and was undetectable six to eight hours after infection. A correlation was observed between the magnitude of initial TNF-alpha response and a fatal outcome. Pretreatment of the animals with polyclonal anti-TNF antiserum significantly reduced mortality relative to animals pretreated with control serum. However, pretreatment of animals with anti-TNF antibody did not alter the bacterial invasion of the cerebrospinal fluid. Injection of heat-killed bacteria did not cause death and induced lower TNF-alpha levels than the same number of live bacteria. This excludes the possibility that the role of TNF-alpha is to mediate a shock induced by the endotoxin component of the bacterial inoculum. These results indicate that TNF-alpha has a deleterious effect in this model of bacteraemia. Identification of the critical factors that determine the action of TNF-alpha during lethal bacteraemia will lead to a better understanding of these diseases and the development of appropriate therapeutic intervention.     

A Note on the Flora and Fauna in the Rumen of Steers Fed a Feedlot Bloat-provoking Ration and the Effect of Penicillin

A study was made of the predominant culturable bacteria and ciliate protozoa present in the rumen of two steers that were regularly bloating on a pelleted ratio containing 22% alfalfa meal, 16% soybean oil meal, 61% barley, and 1% common salt. The ruminal microorganisms in the two animals differed as indicated by a high total culture count of bacteria, an almost complete absence of ciliate protozoa, a low pH, and a difference in the proportions of presumptively identified predominant bacterial groups in one animal (steer 26) as compared with the other (steer 32). The first exposure of the animals to procaine penicillin (75 or 150 mg per day on 2 successive days) resulted in an abnormal ruminal flora 31 hr after the first treatment as indicated by drastic drops in total and cellulolytic bacterial counts and a change in the proportions of predominant bacterial groups. The animals refused feed for 32 to 48 hr after the first treatment. After feed consumption resumed, further treatment with 75 mg penicillin on 4 successive days did not appear to greatly alter the flora and did not result in feed refusal in animal 32. In animal 26, amounts of penicillin progressing from 50 to 200 mg per day did not result in feed refusals and observations on rumen ingesta samples during this period indicated a decrease in total bacterial count, a great increase in numbers of ciliate protozoa, a higher pH, and a change in the proportions of predominant bacterial groups so that the ruminal picture was much more similar to that of animal 32 than to its own during the pre-penicillin period. Bloat was not relieved except during the period of feed refusal.

The results indicate that the ruminal flora rapidly adapts to penicillin and that bloat of the feedlot type can occur in animals with widely differing numbers and kinds of bacteria and protozoa. Feedlot bloat does not appear to be correlated with the occurrence or numbers of any of the individual predominant groups of bacteria cultured.

     

In vitro Biofilm Formation in an 8-well Chamber Slide

The chronic nature of many diseases is attributed to the formation of bacterial biofilms which are recalcitrant to traditional antibiotic therapy. Biofilms are community-associated bacteria attached to a surface and encased in a matrix. The role of the extracellular matrix is multifaceted, including facilitating nutrient acquisition, and offers significant protection against environmental stresses (e.g. host immune responses). In an effort to acquire a better understanding as to how the bacteria within a biofilm respond to environmental stresses we have used a protocol wherein we visualize bacterial biofilms which have formed in an 8-well chamber slide. The biofilms were stained with the BacLight Live/Dead stain and examined using a confocal microscope to characterize the relative biofilm size, and structure under varying incubation conditions. Z-stack images were collected via confocal microscopy and analyzed by COMSTAT. This protocol can be used to help elucidate the mechanism and kinetics by which biofilms form, as well as identify components that are important to biofilm structure and stability.     

Intestinal flora of animal models of human diseases as an environmental factor

Genetically-engineered animals are known to be useful in clarifying the functions of many genes and as animal models for human diseases. However, it has been widely reported that pathophysiology is not expressed in these animals when they become germfree or SPF animals, i.e., the pathophysiology is not the result of genes alone and a combination of gene function and intestinal flora as an environmental factor are necessary. It is important to determine the roles of each of these two factors by pathophysiological analysis. Gnotobiotic mice were produced by establishment of specified bacterial species in germfree animals to form the intestinal flora of SPF animals and they were placed in barrier facilities. Measures have been taken against infections by bacteria such as Pseudomonas aeruginosa and Enterobacter cloacae. In addition, gnotobiotic mice with a highly normal physiology are required. Analysis of the effects of each bacterial species and combinations of bacteria on in vivo functions, i.e., the cross-talk between the host and intestinal flora, is essential in the creation of better laboratory animals. Monitoring of the intestinal flora, a key factor in the colonies produced, is a topic for future research.     

Zebrafish embryos as a model host for the real time analysis of Salmonella typhimurium infections

Bacterial virulence is best studied in animal models. However, the lack of possibilities for real time analysis and the need for laborious and invasive sample analysis limit the use of experimental animals. In the present study 28 h-old zebrafish embryos were infected with DsRed-labelled cells of Salmonella typhimurium. Using multidimensional digital imaging microscopy we were able to determine the exact location and fate of these bacterial pathogens in a living vertebrate host during three days. A low dose of wild-type S. typhimurium resulted in a lethal infection with bacteria residing and multiplying both in macrophage-like cells and at the epithelium of blood vessels. Lipopolysaccharide (LPS) mutants of S. typhimurium, known to be attenuated in the murine model, proved to be non-pathogenic in the zebrafish embryos and were partially lysed in the bloodstream or degraded in macrophage-like cells. However, injection of LPS mutants in the yolk of the embryo resulted in uncontrolled bacterial proliferation. Heat-killed, wild-type bacteria were completely lysed extracellularly within minutes after injection, which shows that the blood of these zebrafish embryos does already contain lytic activity. In conclusion, the zebrafish embryo model allows for rapid, non-invasive and real time analysis of bacterial infections in a vertebrate host.     

Failure of antibiotic treatment in microbial populations

The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance. Evidence that small, non-mutant subpopulations of bacteria are not affected by an antibiotic challenge has been accumulating and provides an attractive explanation for the failure of typical dosing protocols. Although a dosing challenge can kill the susceptible bacteria, the remaining persister cells can serve as a source of population regrowth. We give a condition for the failure of a periodic dosing protocol for a general chemostat model, which supports the simulations of an earlier, more specialized batch model. Our condition implies that the treatment protocol fails globally, in the sense that a mixed bacterial population will ultimately persist above a level that is independent of the initial composition of the population. We also give a sufficient condition for treatment success, at least for initial population compositions near the steady state of interest, corresponding to bacterial washout. Finally, we investigate how the speed at which the bacteria are wiped out depends on the duration of administration of the antibiotic. We find that this dependence is not necessarily monotone, implying that optimal dosing does not necessarily correspond to continuous administration of the antibiotic. Thus, genuine periodic protocols can be more advantageous in treating a wide variety of bacterial infections.