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PubMed1999

American Society for Microbiology--99th general meeting. 30 May-3 June 1999, Chicago, IL, USA.

The American Society for Microbiology (ASM) celebrated its centenary at this meeting, which aimed to appeal to an audience with diverse microbiological interests. The program comprised six colloquia, division lectures and award sessions, division sessions, poster and special interest sessions, as well as pre-meeting workshops. The colloquia topics, selected by the ASM members advisory committee, were: pathogenesis; microbes and public health; microbial diversity; beyond the recombinant RNA revolution; molecular dissection of complex biological processes; and, host defenses. The divisional groups were: diagnostic microbiology and epidemiology; pathogenesis and host response mechanisms; general microbiology; and, molecular microbiology, physiology and virology. Each group highlighted a topic of importance to scientists from all divisions within that group and the divisional lecture was given by a distinguished scientist within one of the division's sessions.

Journal Article↗

PubMed2004

Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function.

During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.

Bacteria↗

PubMed2004

High-throughput techniques for analyzing complex bacterial communities.

A more complete understanding of microbial diversity and the environmental processes they control will require much more than a biotic inventory. It will require a deeper understanding of the basic features of systems organization and inter-population interactions. Communities, not total biomass, control net process rates driving the biogeochemical cycles sustaining the biosphere. Although the general patterns of macroorganismal diversity are relatively well known, spatial and temporal patterns of microorganismal diversity are essentially unknown. Having tools capable of resolving these patterns is a prerequisite to developing an understanding of the relationship between community structure and function. This talk discusses conceptual and technical developments that now provide the framework for systematically resolving temporal and spatial patterns of microorganisms and relating those patterns to processes at local and system levels. Of particular emphasis will be ongoing studies using highly parallel analyses with DNA microarrays for intensive monitoring of microbial populations in environmental systems. Although microarray technology is reasonably well established for studies of model organisms in well-defined laboratory settings, the application of this technology to environmental systems of uncharacterized diversity imposes additional demands on implementation; in particular, the requirement for optimized discrimination between target and non-target nucleic acids in complex, and undefined, mixtures. To increase the resolving power (information content) of our DNA microarray format, we are investigating the use of thermal dissociation of hybrids immobilized on individual array elements to resolve target and non-target sequences that differ by a single nucleotide. These studies, combined with specialized algorithms for optimizing the readout of the microarray should serve for informed environmental application. Initial studies have validated the general approach for analyses of sediment systems.

Bacteria↗

PubMed2004

PCR-DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo mozzarella cheese.

AIMS: To monitor the process and the starter effectiveness recording a series of fingerprints of the microbial diversity occurring at different steps of mozzarella cheese manufacture and to investigate the involvement of the natural starter to the achievement of the final product. METHODS AND RESULTS: Samples of raw milk, natural whey culture (NWC) used as starter, curd after ripening and final product were collected during a mozzarella cheese manufacture. Total microbial DNA was directly extracted from the dairy samples as well as bulk colonies collected from the plates of appropriate culture media generally used for viable counts of mesophilic and thermophilic lactic acid bacteria (LAB) and used in polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) experiments. The analysis of the DGGE profiles showed a strong influence of the microflora of the NWC on the whole process because after the starter addition, the profile of all the dairy samples was identical to the one shown by the NWC. Simple indexes were calculated for the DGGE profiles to have an objective estimation of biodiversity and of technological importance of specific groups of organisms. LAB grown on Man Rogosa Sharp (MRS) and Rogosa agar at 30 degrees C showed high viable counts and the highest diversity in species indicating their importance in the cheese making, which had not been considered so far. Moreover, the NWC profiles were shown to be the most similar to the curd profile suggesting to be effective in manufacture. CONCLUSIONS: The PCR-DGGE analysis showed that in premium quality manufacture the NWC used as starter had a strong influence on the microflora responsible for process development. SIGNIFICANCE AND IMPACT OF THE STUDY: The molecular approach appeared to be valid as a tool to control process development, starter effectiveness and product identity as well as to rank cheese quality.

Animals↗

PubMed2003

Production of the soluble pattern recognition receptor PTX3 by myeloid, but not plasmacytoid, dendritic cells.

PTX3 is a prototypic of long pentraxin consisting of an N-terminal portion coupled to a C-terminal pentraxin domain, the latter related to short pentraxins (C-reactive protein and serum amyloid P component). PTX3 is a soluble pattern recognition receptor, which plays a non-redundant role in resistance against selected pathogens and in female fertility. The present study was designed to analyze the production of PTX3 by human dendritic cells (DC) and to define the role of different innate immunity receptors in its induction. Human monocyte-derived DC produced copious amounts of PTX3in response to microbial ligands engaging different members of the Toll-like receptor (TLR) family (TLR1 through TLR6), whereas engagement of the mannose receptor had no substantial effect. DC werebetter producers of PTX3 than monocytes and macrophages. Freshly isolated peripheral blood myeloid DC produced PTX3 in response to diverse microbial stimuli. In contrast, plasmacytoid DC exposed to influenza virus or to CpG oligodeoxynucleotides engaging TLR9, did not produce PTX3. PTX3-expressing DC were present in inflammatory lymph nodes from HIV-infected patients. These results suggest that DC of myelomonocytic origin are a major source of PTX3, a molecule which facilitates pathogen recognition and subsequent activation of innate and adaptive immunity.

C-Reactive Protein↗

PubMed1994

TNF-alpha and IL-6 expression in perfused rat liver after intraportal candidemia vs. E. coli or S. aureus bacteremia.

We tested the hypothesis that regulation of tumor necrosis factor-alpha (TNF-alpha) and IL-6 by the liver differs after intraportal challenge with Candida albicans spp. vs. gram-negative or gram-positive bacteria, independent of microbial clearance kinetics or hepatic O2 consumption (VO2). Buffer-perfused rat livers were infected with equivalent inocula (10(9) colony-forming units) of viable Escherichia coli serotype 055:B5 (EC), exotoxin C-producing Staphylococcus aureus (SA), or two strains of yeast phase C. albicans (CA-1 and CA-2). Microbial clearance and circulating cytokine levels were assessed over 180 min while monitoring VO2 and functional parameters, after which organ-based microbial killing, cell-associated TNF-alpha, and cytokine mRNA levels were determined. Compared with saline controls (normal saline solution; NSS), circulating and cell-associated TNF-alpha and TNF-alpha transcripts minimally increased after CA. In contrast, large increases in perfusate TNF-alpha occurred after EC, peaking at 180 min [135 +/- 32 U/ml (mean + SE)], concomitant with rises in cell-associated cytokine and TNF-alpha transcripts (P < 0.01 vs. NSS). Circulating TNF-alpha also rose after SA but neither cell-associated nor mRNA levels exceeded NSS values. There were no pathogen-specific differences in microbial clearance or VO2. IL-6 gene expression paralleled that for TNF-alpha, but IL-6 bioactivity in perfusates was inhibited by TNF-alpha-dependent and -independent mechanisms. We conclude that hepatic TNF-alpha and IL-6 expression are differentially regulated after taxonomically diverse microbial challenges, with E. coli eliciting the strongest and Candida spp. the weakest stimulatory responses.

Animals↗

PubMed2000

Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste.

Microbial community dynamics in a flowerpot-using solid biowaste composting (FUSBIC) process were monitored seasonally by quinone profiling and conventional microbiological methods. The FUSBIC system, which consisted of three flowerpots (14 L or 20 L capacity) with 5-6 kg each of a soil-compost mixture (SCM) as the primary reactors, was loaded daily with household biowaste from November 1998 to October 1999. The monthly average waste reduction rate was 88.2% for the 14-L system and 92.5% for the 20-L system on a wet weight basis. The direct total microbial count detected in the 14-L primary reactors ranged from 4.5 to 9.6x10(11) cells.g(-1) of dry wt of SCM, and the viable count of aerobic heterotrophic bacteria recovered on agar plates at 28 degrees C varied from 1.9 to 5.7x10(11) CFU.g(-1) of dry wt. The quinone content of SCM samples from the 14-L and 20-L systems ranged from 160 to 353 nmol.g(-1) of dry SCM. Ubiquinones, unsaturated menaquinones, and partially saturated menaquinones constituted 15.0-36.4, 14.8-22.0, and 41.8-61.6 mol% of the total content, respectively. The major quinone types detected were usually MK-8(H(2)), MK-9(H(2)), and Q-10. Variations in quinone profiles were evaluated numerically by using two parameters, the dissimilarity index (D) and microbial divergence index (MD(q)). The upper limit of seasonal changes in the microbial community structure was about 30% as expressed by D values. The MD(q) values calculated ranged from 18 to 22. A significant positive correlation was found between seasonal temperature and bacterial populations containing partially saturated menaquinones. These results indicated that the FUSBIC system contained highly diverse microbial populations that fluctuated to some extent depending on seasonal temperature. Members of the Actinobacteria were suggested to be the major constituents of the total population present.

Journal Article↗

PubMed2006

Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea.

Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113-127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3 x 10(9) cells ml(-1) and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5 x 10(7)-1.8 x 10(8) cells ml(-1) accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).

Bacteria↗

PubMedDate not supplied

Metagenomics: an inexhaustible access to nature's diversity.

The chemical industry has an enormous need for innovation. To save resources, energy and time, currently more and more established chemical processes are being switched to biotechnological routes. This requires white biotechnology to discover and develop novel enzymes, biocatalysts and applications. Due to a limitation in the cultivability of microbes living in certain habitats, technologies have to be established which give access to the enormous resource of uncultivated microbial diversity. Metagenomics promises to provide new and diverse enzymes and biocatalysts as well as bioactive molecules and has the potential to make industrial biotechnology an economic, sustainable success.

Biodiversity↗

PubMed2007

Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic.

The springs at Gypsum Hill and Colour Peak on Axel Heiberg Island in the Canadian Arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on Earth. The springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of -325 mV, and contain high concentrations of sulfate and sulfide. We surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (DGGE) and analyzing clone libraries of 16S rRNA genes amplified with Bacteria and Archaea-specific primers. Dendrogram analysis of the DGGE banding patterns divided the springs into two clusters based on their geographic origin. Bacterial 16S rRNA clone sequences from the Gypsum Hill library (spring GH-4) were classified into seven phyla (Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria, Spirochaetes, and Verrucomicrobia); Deltaproteobacteria and Gammaproteobacteria sequences represented half of the clone library. Sequences related to Proteobacteria (82%), Firmicutes (9%), and Bacteroidetes (6%) constituted 97% of the bacterial clone library from Colour Peak (spring CP-1). Most GH-4 archaeal clone sequences (79%) were related to the Crenarchaeota while half of the CP-1 sequences were related to orders Halobacteriales and Methanosarcinales of the Euryarchaeota. Sequences related to the sulfur-oxidizing bacterium Thiomicrospira psychrophila dominated both the GH-4 (19%) and CP-1 (45%) bacterial libraries, and 56 to 76% of the bacterial sequences were from potential sulfur-metabolizing bacteria. These results suggest that the utilization and cycling of sulfur compounds may play a major role in the energy production and maintenance of microbial communities in these unique, cold environments.

Archaea↗

PubMed2005

Chlamydia and antigenic mimicry.

Chlamydial infections are among the most common human infections. Every year, in millions of humans, they cause infections of the eyes, the respiratory tract, the genital tract, joints, and the vasculature. Chlamydiae are obligate intracellular prokaryotic pathogens. Chlamydiae promote, in susceptible host cells that include mucosal epithelial cells, vascular endothelial cells, smooth muscle cells, and monocytes and macrophages, their survival while causing disease of varying clinical importance and consequence in their hosts. Chlamydia infections often precede the initiation of autoimmune diseases, and Chlamydiae are often found within autoimmune lesions. Thus, they have been suspected in the etiology and pathogenesis of autoimmune diseases. Autoimmune diseases have many causes. Genes, notably genes encoding cell-surface proteins that display peptides for immune recognition, the major histocompatibility complex (MHC), the environment, and the microbial diversity within the human body determine the susceptibility to autoimmune diseases. One mechanism by which infection is linked to the initiation of autoimmunity is termed molecular mimicry. Molecular mimicry describes the phenomenon of protein products from dissimilar genes sharing similar structures that elicit an immune response to both self and microbial proteins. Molecular mimicry might thus be a mechanism by which infections trigger autoimmune diseases. For the purpose of this chapter, we will focus on chlamydial proteins that mimic host self-proteins and thus contribute to initiation and maintenance of autoimmune diseases. Thus far, the strongest cases for molecular mimicry seem to have been made for chlamydial heat shock proteins 60, the DNA primase of Chlamydia trachomatis, and chlamydial OmcB proteins.

Amino Acid Sequence↗

PubMed2006

Bacterial diversity in three different Antarctic Cold Desert mineral soils.

A bacterial phylogenetic survey of three environmentally distinct Antarctic Dry Valley soil biotopes showed a high proportion of so-called "uncultured" phylotypes, with a relatively low diversity of identifiable phylotypes. Cyanobacterial phylotypic signals were restricted to the high-altitude sample, whereas many of the identifiable phylotypes, such as the members of the Actinobacteria, were found at all sample sites. Although the presence of Cyanobacteria and Actinobacteria is consistent with previous culture-dependent studies of microbial diversity in Antarctic Dry Valley mineral soils, many phylotypes identified by 16S rDNA analysis were of groups that have not hitherto been cultured from Antarctic soils. The general belief that such "extreme" environments harbor a relatively low species diversity was supported by the calculation of diversity indices. The detection of a substantial number of uncultured bacterial phylotypes showing low BLAST identities (< 95%) suggests that Antarctic Dry Valley mineral soils harbor a pool of novel psychrotrophic taxa.

Antarctic Regions↗

PubMed2005

Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes.

Bacterial diversity of the mucosal biopsies from human jejunum, distal ileum, ascending colon and rectum were compared by analysis of PCR-amplified 16S rDNA clone libraries. A total of 347 clones from the mucosal biopsies were partially sequenced and assigned to six phylogenetic phyla of the domain Bacteria: Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, and Actinobacteria. The jejunum sample had least microbial diversity compared to the other samples and a trend towards highest diversity in ascending colon was observed. The clone libraries of distal ileum, ascending colon and rectum were not significantly different from each other (P>0.0043), but they differed significantly from the jejunum library (P=0.001). The population of sequences retrieved from jejunal biopsies was dominated by sequences closely related to Streptococcus (67%), while the population of sequences derived from distal ileum, ascending colon and rectum were dominated by sequences affiliated with Bacteroidetes (27-49%), and Clostridium clusters XIVa (20-34%) and IV (7-13%). The results indicate that the microbial community in jejunum is different from those in distal ileum, ascending colon and rectum, and that the major phylogenetic groups are similar from distal ileum to rectum.

Bacteria↗

PubMed2006

An examination of the diversity of a novel Campylobacter reservoir.

The diversity of eukaryotic populations, in particular protozoa, in the water supplies of intensively reared broilers has not been previously studied. This important food-rearing environment was screened for the molecular diversity of eukaryotes by the analysis of PCR-amplified 18S rRNA. DNA was extracted from filtered water samples that were collected from the poultry drinking water systems of five farms. The total genomic DNA was used to produce rRNA-PCR amplicons, which, with the application of TTGE, provided an overview of the eukaryotic population diversity. The rRNA-PCR amplicons were then used to generate 34 random clones that were subject to comparative sequence analysis. Twenty-five of the clones (73.5%) showed high similarity with yeasts and fungi (>92%) and 9 clones demonstrated similarity (>86%) with certain protozoan groups, including flagellates and alveolates. Further studies of the microbial diversity in the previously ignored niche of intensively reared poultry drinking water systems are required, along with subsequent in vitro co-culture assays of the detected protozoa and bacterial strains.

Animals↗

PubMed2006

Genomics for environmental microbiology.

The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environments is required to meet the promise of microbial biotechnology. To meet these new challenges, microbiologists are applying the tools of genomics and related high-throughput technologies to both cultured microbes and environmental samples. This work will lead to new views on ecosystems and biological function together with the biotechnology enabled by this science.

Environmental Microbiology↗

PubMed2000

Genetic diversity of carbofuran-degrading soil bacteria.

The genetic diversity of 128 carbofuran-degrading bacteria was determined by ARDRA (amplified ribosomal DNA restriction analysis) of 16S rDNA and restriction fragment length polymorphism analysis of the 16S-23S rDNA spacer region (IGS) using five endonucleases. The isolates were distributed in 26 distinct ARDRA groups and 45 IGS types revealing a high level of microbial diversity confirmed by ARDRA clustering and sequencing of 16S rDNA. The occurrence of a methylcarbamate-degrading gene (mcd) was monitored by polymerase chain reaction amplification using specific primers. The mcd gene was detected only in 58 bacteria and there was no clear relationship between the presence of this gene and the phylogenetic position of the strain.

Journal Article↗

PubMed2006

Anti-immunology: evasion of the host immune system by bacterial and viral pathogens.

Multicellular organisms possess very sophisticated defense mechanisms that are designed to effectively counter the continual microbial insult of the environment within the vertebrate host. However, successful microbial pathogens have in turn evolved complex and efficient methods to overcome innate and adaptive immune mechanisms, which can result in disease or chronic infections. Although the various virulence strategies used by viral and bacterial pathogens are numerous, there are several general mechanisms that are used to subvert and exploit immune systems that are shared between these diverse microbial pathogens. The success of each pathogen is directly dependant on its ability to mount an effective anti-immune response within the infected host, which can ultimately result in acute disease, chronic infection, or pathogen clearance. In this review, we highlight and compare some of the many molecular mechanisms that bacterial and viral pathogens use to evade host immune defenses.

Antigenic Variation↗

PubMed2006

Preconceptional antibiotic treatment to prevent preterm birth in women with a previous preterm delivery.

This article addresses the question of whether the uterine cavity is normally sterile and reviews the difficulties in conducting microbiologic studies of the endometrium, the limitations of conventional microbiologic techniques (cultivation-dependent), and the potential contribution of molecular microbiology to examine microbial diversity and burden of the endometrium. Issues pertaining to the diagnosis of chronic endometritis and the need for information about the prognostic value of this finding in subsequent pregnancies are discussed. The results of a randomized clinical trial of antibiotic administration versus placebo in women with a previous preterm birth are reviewed and commentary is provided. The emerging picture is that microbial-host interactions in the endometrial cavity are important for reproductive success. This is a US government work. There are no restrictions on its use.

Anti-Bacterial Agents↗