This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.biomedcentral.com/bmcmicrobiol/ The latest articles from BMC Microbiology (ISSN 1471-2180) published by BioMed Central Background: Leifsonia xyli is a xylem-inhabiting bacterial species comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp. cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in sugarcane commercial fields and Lxc colonizes the xylem of several grasses causing either mild or no symptoms of disease. Lxx completely sequenced genome provided insights into its biology and pathogenicity. Since, IS elements are largely reported as an important source of bacterial genome diversification, and nothing is known about their role in chromosome architecture of L. xyli, a comparative analysis of Lxc and Lxx elements was performed. Results: Sample sequencing of Lxc genome and comparative analysis with Lxx complete DNA sequence, revealed a variable number of IS transposable elements acting upon genomic diversity. A detailed characterization of Lxc IS elements and a comparative review with IS elements of Lxx are presented. Each genome showed an unique set of elements although related to same IS families when considering features such as similarity among transposases, inverted and direct repeats; and element size. Most of the Lxc and Lxx IS families assigned were reported maintaining transposition at low levels using translation regulatory mechanisms, which is in agreement with our in silico analysis. Some of the IS elements were found associated with rearrangements and specific regions of each genome. Differences were also found in the effect of IS elements upon insertion, although none of the elements were preferentially associated with gene disruption. A survey of transposases among genomes of Actinobacteria showed no correlation between phylogenetic relatedness and distribution of IS families. By using Southern hybridization, we suggested that diversification of Lxc isolates is also mediated by insertion sequences in probably recent events. Conclusions: Taken together our data indicate that transposable elements are involved in genome diversification of Lxc and Lxx. The IS elements were probably acquired after the divergence of the two subspecies and they are associated with genome organization and gene contents. Besides helping on studies of IS element dynamics in general, these data will contribute to our ongoing comparative analyses aimed at understanding the biological differences of the Lxc and Lxx. http://www.biomedcentral.com/1471-2180/8/127 Marcelo M Zerillo, Marie-Anne Van Sluys, Luis Eduardo A Camargo and Claudia B Monteiro-Vitorello BMC Microbiology 2008, 8:127 2008-07-25 doi:10.1186/1471-2180-8-127 BMC Microbiology 1471-2180 8 127 2008-07-25 Background: Type 1 fimbriae are the most commonly found fimbrial appendages on the outer membrane of Salmonella enterica serotype Typhimurium. Previous investigations indicate that static broth culture favours S. Typhimurium to produce type 1 fimbriae, while non-fimbriate bacteria are obtained by growth on solid agar media. The phenotypic expression of type 1 fimbriae in S. Typhimurium is the result of the interaction and cooperation of several genes in the fim gene cluster. Other gene products that may also participate in the regulation of type 1 fimbrial expression remain uncharacterized. Results: In the present study, transposon insertion mutagenesis was performed on S. Typhimurium to generate a library to screen for those mutants that would exhibit different type 1 fimbrial phenotypes than the parental strain. Eight-two mutants were obtained from 7239 clones screened using the yeast agglutination test. Forty-four mutants produced type 1 fimbriae on both solid agar and static broth media, while none of the other 38 mutants formed type 1 fimbriae in either culture condition. The flanking sequences of the transposons from 54 mutants were cloned and sequenced. These mutants can be classified according to the functions or putative functions of the open reading frames disrupted by the transposon. Our current results indicate that the genetic determinants such as those involved in the fimbrial biogenesis and regulation, global regulators, transporter proteins, prophage-derived proteins, and enzymes of different functions, to name a few, may play a role in the regulation of type 1 fimbrial expression in response to solid agar and static broth culture conditions. A complementation test revealed that transforming a recombinant plasmid possessing the coding sequence of a NAD(P)H-flavin reductase gene ubiB restored an ubiB mutant to exhibit the type 1 fimbrial phenotype as its parental strain. Conclusions: Genetic determinants other than the fim genes may involve in the regulation of type 1 fimbrial expression in S. Typhimurium. How each gene product may influence type 1 fimbrial expression is an interesting research topic which warrants further investigation. http://www.biomedcentral.com/1471-2180/8/126 Yin-Ching Chuang, Ke-Chuan Wang, Yi-Tseng Chen, Chia-Huei Yang, Shang-Chin Men, Chia-Chun Fan, Li-Huan Chang and Kuang-Sheng Yeh BMC Microbiology 2008, 8:126 2008-07-25 doi:10.1186/1471-2180-8-126 BMC Microbiology 1471-2180 8 126 2008-07-25 Background: The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. Results: Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). Conclusions: Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing. http://www.biomedcentral.com/1471-2180/8/125 Scot E Dowd, Todd R Callaway, Randall D Wolcott, Yan Sun, Trevor McKeehan, Robert G Hagevoort and Thomas S Edrington BMC Microbiology 2008, 8:125 2008-07-24 doi:10.1186/1471-2180-8-125 BMC Microbiology 1471-2180 8 125 2008-07-24 Background: Mycoplasma pneumoniae is a human pathogen that is a common cause of community-acquired pneumonia. It harbours a large number of lipoprotein genes, most of which are of unknown function. Because of their location on the cell surface, these proteins are likely to be involved in the bacterial response to environmental changes, or in the initial stages of infection. The aim of this study was to determine if genes encoding surface lipoproteins are differentially expressed after contact with a human cell line, or after exposure to oxidative or acidic stress. Results: Using qRT-PCR assays, we observed that the expression of a number of lipoprotein genes was up-regulated when M. pneumoniae was placed in contact with human cells. In contrast, lipoprotein expression was generally down-regulated or unchanged when exposed to either hydrogen peroxide or low pH (5.5). When exposed to low pH, the mRNA levels of four polycistronically transcribed genes in Lipoprotein Multigene Family 6 formed a gradient of decreasing quantity with increasing distance from a predicted promoter. Conclusions: The demonstrated transcriptional changes provide evidence for the functionality of these mostly unassigned genes and indicate that they are regulated in response to changes in environmental conditions. In addition we have shown that the members of Lipoprotein Gene Family 6 may be expressed polycistronically. http://www.biomedcentral.com/1471-2180/8/124 Katri M Hallamaa, Sen-Lin Tang, Nino Ficorilli and Glenn F Browning BMC Microbiology 2008, 8:124 2008-07-23 doi:10.1186/1471-2180-8-124 BMC Microbiology 1471-2180 8 124 2008-07-23 Background: Comparative morphological studies and environmental sequencing surveys indicate that marine benthic environments contain a diverse assortment of microorganisms that are just beginning to be explored and characterized. The most conspicuous predatory flagellates in these habitats range from about 20-150 microns in size and fall into three major groups of eukaryotes that are very distantly related to one another: dinoflagellates, euglenids and cercozoans. The Cercozoa is a diverse group of amoeboflagellates that cluster together in molecular phylogenies inferred mainly from ribosomal gene sequences. These molecular phylogenetic studies have demonstrated that several enigmatic taxa, previously treated as Eukaryota insertae sedis, fall within the Cercozoa, and suggest that the actual diversity of this group is largely unknown. Improved knowledge of cercozoan diversity is expected to help resolve major branches in the tree of eukaryotes and demonstrate important cellular innovations for understanding eukaryote evolution. Results: A rare tetraflagellate, Auranticordis quadriverberis n. gen. et sp., was isolated from marine sand samples. Uncultured cells were in low abundance and were individually prepared for electron microscopy and DNA sequencing. These flagellates possessed several novel features, such as (1) gliding motility associated with four bundled recurrent flagella, (2) heart-shaped cells about 35-75 microns in diam., and (3) bright orange coloration caused by linear arrays of muciferous bodies. Each cell also possessed about 2-30 pale orange bodies (usually 4-5 microns in diam.) that were enveloped by two membranes and sac-like vesicles. The innermost membrane invaginated to form unstacked thylakoids that extended towards a central pyrenoid containing tailed viral particles. Although to our knowledge, these bodies have never been described in any other eukaryote, the ultrastructure was most consistent with photosynthetic endosymbionts of cyanobacterial origin. This combination of morphological features did not allow us to assign A. quadriverberis to any known eukaryotic supergroup. Thus, we sequenced the small subunit rDNA sequence from two different isolates and demonstrated that this lineage evolved from within the Cercozoa. Conclusions: Our discovery and characterization of A. quadriverberis underscores how poorly we understand the diversity of cercozoans and, potentially, represents one of the few independent cases of primary endosymbiosis within the Cercozoa and beyond. http://www.biomedcentral.com/1471-2180/8/123 Chitchai Chantangsi, Heather J Esson and Brian S Leander BMC Microbiology 2008, 8:123 2008-07-22 doi:10.1186/1471-2180-8-123 BMC Microbiology 1471-2180 8 123 2008-07-22 Background: Yersinia pestis is the causative agent of plague and a potential agent of bioterrorism and biowarfare. The plague biothreat and the emergence of multidrug resistant plague underscore the need to increase our understanding of the intrinsic potential of Y. pestis for developing antimicrobial resistance and to anticipate the mechanisms of resistance that may emerge in Y. pestis. Identification of Y. pestis genes that when overexpressed are capable of reducing antibiotic susceptibility is a useful strategy to expose genes that this pathogen may rely upon to evolve antibiotic resistance via a vertical modality. In this study, we explored the use of a multicopy suppressor, Escherichia coli host based screening approach as a means to expose antibiotic resistance determinant candidates in Y. pestis. Results: We constructed a multicopy plasmid based, Y. pestis genome wide expression library of nearly 15,000 clones in E. coli and screened the library for suppressors of the antimicrobial activity of ofloxacin, a fluoroquinolone antibiotic. The screen permitted the identification of a transcriptional regulator encoding gene (robAYp) that increased the MIC99 of ofloxacin by 23 fold when overexpressed from a multicopy plasmid in Y. pestis. Additionally, we found that robAYp overexpression in Y. pestis conferred low level resistance to many other antibiotics and increased organic solvent tolerance. Overexpression of robAYp also upregulated the expression of several efflux pumps in Y. pestis. Conclusions: Our study provides proof of principle for the use of multicopy suppressor screening based on the tractable and easy to manipulate E. coli host as a means to identify antibiotic resistance determinant candidates of Y. pestis. http://www.biomedcentral.com/1471-2180/8/122 Karen L Stirrett, Julian A Ferreras, Sebastian M Rossi, Richard L Moy, Fabio V Fonseca and Luis E N Quadri BMC Microbiology 2008, 8:122 2008-07-21 doi:10.1186/1471-2180-8-122 BMC Microbiology 1471-2180 8 122 2008-07-21 Background: The sequenced genomes of the Brucella spp. have two urease operons, ure-1 and ure-2, but there is evidence that only one is responsible for encoding an active urease. The present work describes the purification and the enzymatic and phylogenetic characterization of urease from Brucella suis strain 1330. Additionally, the urease reactivity of sera from patients diagnosed with brucellosis was examined. Results: Urease encoded by the ure-1 operon of Brucella suis strain 1330 was purified to homogeneity using ion exchange and hydrophobic interaction chromatographies. The urease was purified 51-fold with a recovery of 12% of the enzyme activity and 0.24% of the total protein. The enzyme had an isoelectric point of 5, and showed optimal activity at pH 7.0 and 28-35 degrees C. The purified enzyme exhibited a Michaelis-Menten saturation kinetics with a Km of 5.60 +/- 0.69 mM. Hydroxyurea and thiourea are competitive inhibitors of the enzyme with Ki of 1.04+/-0.31 mM and 26.12+/-2.30 mM, respectively. Acetohydroxamic acid also inhibits the enzyme in a competitive way. The molecular weight estimated for the native enzyme was between 130-135 kDa by gel filtration chromatography and 157+/-7 kDa using 5-10% polyacrylamide gradient non-denaturing gel. Only three subunits in SDS-PAGE were identified: two small subunits of 14,000 Da and 15,500 Da, and a major subunit of 66,000 Da. The amino terminal sequence of the purified large subunit corresponded to the predicted amino acid sequence encoded by ureC1. The UreC1 subunit was recognized by sera from patients with acute and chronic brucellosis. By phylogenetic and cluster structure analyses, ureC1 was related to the ureC typically present in the Rhizobiales; in contrast, the ureC2 encoded in the ure-2 operon is more related to distant species. Conclusions: We have for the first time purified and characterized an active urease from B. suis. The enzyme was characterized at the kinetic, immunological and phylogenetic levels. Our results confirm that the active urease of B. suis is a product of ure-1 operon. http://www.biomedcentral.com/1471-2180/8/121 Araceli Contreras-Rodriguez, Jose Quiroz-Limon, Ana M Martins, Humberto Peralta, Eric Avila-Calderon, Nammalwar Sriranganathan, Stephen M Boyle and Ahide Lopez-Merino BMC Microbiology 2008, 8:121 2008-07-19 doi:10.1186/1471-2180-8-121 BMC Microbiology 1471-2180 8 121 2008-07-19 Background: The current tuberculosis vaccine is a live vaccine derived from Mycobacterium bovis and attenuated by serial in vitro passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Guérin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. Results: As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains while maintaining their protective efficacy, we aimed to inactivate recA by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was achieved successfully in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of recA revealed that a single nucleotide insertion in the 5' part of recA led to a translational frameshift with an early stop codon making BCG Russia a natural recA mutant. At the protein level BCG Russia failed to express RecA. Conclusion: According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental M. bovis. We hypothesize that recA inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to M. bovis AF2122/97 wild-type. http://www.biomedcentral.com/1471-2180/8/120 Peter M Keller, Erik C Böttger and Peter Sander BMC Microbiology 2008, 8:120 2008-07-17 doi:10.1186/1471-2180-8-120 BMC Microbiology 1471-2180 8 120 2008-07-17 Background: Recent studies showed that Helicobacter pylori existed in the New World prior to the arrival of Columbus. The purpose of the present study was to detect the presence of Helicobacter pylori in pre-Columbian mummies from Northern Mexico. Methods: Six samples were studied (four samples of gastric remains, tongue-soft palate, and brain remained as negative controls) from two of the six naturally mummified corpses studied (adult male and infant male). Samples were taken from tissues suitable for DNA amplification by Polymerase chain reaction (PCR). DNA was extracted and H. pylori detection was carried out by PCR and hybridized with the pHp probe from 16S rRNA gene. The purified PCR products were cloned and sequenced in both directions. DNA sequences were analyzed with ALIGN and BLAST software. A second amplification was performed using ureB gene by real-time PCR. Results: From four samples of gastric remnant, only two were H. pylori-positive for amplification of a 109 bp DNA fragment; the remaining two were negative, as were the tongue-soft palate and the brain biopsies as well. These PCR products were hybridized with a pHp probe. Nucleotide sequence analysis showed homology with H. pylori in 98 of 99% when compared with the gene bank nucleotide sequence. Only one sample of gastric remnant H. pylori-positive with 16S rRNA gene was also positive for ureB gene from H. pylori. Conclusion: This data supported infection with H. pylori in Mexican pre-Columbian mummies dating from approximately 1,350 AC. http://www.biomedcentral.com/1471-2180/8/119 Gonzalo Castillo-Rojas, Marco A Cerbón and Yolanda López-Vidal BMC Microbiology 2008, 8:119 2008-07-15 doi:10.1186/1471-2180-8-119 BMC Microbiology 1471-2180 8 119 2008-07-15 Background: Vector competence refers to the intrinsic permissiveness of an arthropod vector for infection, replication and transmission of a virus. Notwithstanding studies of Quantitative Trait Loci (QTL) that influence the ability of Aedes aegypti midgut (MG) to become infected with dengue virus (DENV), no study to date has been undertaken to identify genetic markers of vector competence. Furthermore, it is known that mosquito populations differ greatly in their susceptibility to flaviviruses. Differences in vector competence may, at least in part, be due to the presence of specific midgut epithelial receptors and their identification would be a significant step forward in understanding the interaction of the virus with the mosquito. The first interaction of DENV with the insect is through proteins in the apical membrane of the midgut epithelium resulting in binding and receptor-mediated endocytosis of the virus, and this determines cell permissiveness to infection. The susceptibility of mosquitoes to infection may therefore depend on their specific virus receptors. To study this interaction in Ae. aegypti strains that differ in their vector competence for DENV, we investigated the DS3 strain (susceptible to DENV), the IBO-11 strain (refractory to infection) and the membrane escape barrier strain, DMEB, which is infected exclusively in the midgut epithelial cells. Results: (1) We determined the MG proteins that bind DENV by an overlay protein binding assay (VOPBA) in Ae. aegypti mosquitoes of the DS3, DMEB and IBO-11 strains. The main protein identified had an apparent molecular weight of 67 kDa, although the protein identified in the IBO-11 strain showed a lower mass (64 kDa). (2) The midgut proteins recognized by DENV were also determined by VOPBA after two-dimensional gel electrophoresis. (3) To determine whether the same proteins were identified in all three strains, we obtained polyclonal antibodies against R67 and R64 and tested them against the three strains by immunoblotting; both antibodies recognized the 67 and 64 kDa proteins, corroborating the VOPBA results. (4) Specific antibodies against both proteins were used for immunofluorescent location by confocal microscopy; the antibodies recognized the basal lamina all along the MG, and cell membranes and intercellular spaces from the middle to the end of the posterior midgut (pPMG) in the neighborhood of the hindgut. (5) Quantitative analysis showed more intense fluorescence in DS3 and DMEB than in IBO-11. (6) The viral envelope antigen was not homogeneously distributed during MG infection but correlated with MG density and the distribution of R67/R64. Conclusions: In this paper we provide evidence that the 67 kDa protein (R67/R64), described previously as a DENV receptor, is related to vector competence in Ae. aegypti. Consequently, our results strongly suggest that this protein may be a marker of vector competence for DENV in Ae. aegypti mosquitoes. http://www.biomedcentral.com/1471-2180/8/118 Ricardo F Mercado-Curiel, William C Black and Maria de L Munoz BMC Microbiology 2008, 8:118 2008-07-15 doi:10.1186/1471-2180-8-118 BMC Microbiology 1471-2180 8 118 2008-07-15 Background: Dengue (DEN) is an infectious disease caused by the DEN virus (DENV), which belongs to the Flavivirus genus in the family Flaviviridae. It has a (+) sense RNA genome and is mainly transmitted to humans by the vector mosquito Aedes aegypti. Dengue fever (DF) and dengue hemorrhagic fever (DHF) are caused by one of four closely related virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4). Epidemiological and evolutionary studies have indicated that host and viral factors are involved in determining disease outcome and have proved the importance of viral genotype in causing severe epidemics. Host immune status and mosquito vectorial capacity are also important influences on the severity of infection. Therefore, an understanding of the relationship between virus variants with altered amino acids and high pathogenicity will provide more information on the molecular epidemiology of DEN. Accordingly, knowledge of the DENV serotypes and genotypes circulating in the latest DEN outbreaks around the world, including Mexico, will contribute to understanding DEN infections. Results: 1. We obtained 88 isolates of DENV, 27 from Oaxaca and 61 from Veracruz. 2. Of these 88 isolates, 16 were serotype 1; 62 serotype 2; 7 serotype 3; and 2 serotype 4. One isolate had 2 serotypes (DENV-2 and -1). 3. Partial nucleotide sequences of the genes encoding C- prM (14 sequences), the NS3 helicase domain (7 sequences), the NS5 S-adenosyl methionine transferase domain (7 sequences) and the RNA-dependent RNA polymerase (RdRp) domain (18 sequences) were obtained. Phylogenetic analysis showed that DENV-2 isolates belonged to the Asian/American genotype. In addition, the Asian/American genotype was divided into two clusters, one containing the isolates from 2001 and the other the isolates from 2005-2006 with high bootstrap support of 94%. Conclusions: DENV-2 was the predominant serotype in the DF and DHF outbreak from 2005 to 2006 in Oaxaca State as well as in the 2006 outbreak in Veracruz State, with the Asian/American genotype prevalent in both states. Interestingly, DENV-1 and DENV-2 were the only serotypes related to DHF cases. In contrast, DENV-3 and DENV-4 were poorly represented according to epidemiological data reported in Mexico. We found that isoleucine was replaced by valine at residue 106 of protein C in the isolates from these 2005-2006 outbreaks and in those from the 1997, 1998 and 2001 outbreaks in the Caribbean islands. We suggested that this amino acid change may be used as a signature for isolates arising in the Caribbean islands and pertaining to the Asian/American genotype. Other amino acid changes are specific for the Asian/American, Asian and American strains. http://www.biomedcentral.com/1471-2180/8/117 Catalina E Gardella-Garcia, Gerardo Perez-Ramirez, Joel Navarrete-Espinosa, Alejandro Cisneros, Fabiola Jimenez-Rojas, Luis R Ramirez-Palacios, Rocio Rosado-Leon, Minerva Camacho-Nuez and Maria de L Munoz BMC Microbiology 2008, 8:117 2008-07-15 doi:10.1186/1471-2180-8-117 BMC Microbiology 1471-2180 8 117 2008-07-15 Background: Kexin-like proteinases are a subfamily of the subtilisin-like serine proteinases with multiple regulatory functions in eukaryotes. In the yeast Saccharomyces cerevisiae the Kex2 protein is biochemically well investigated, however, with the exception of a few well known proteins such as the alpha-pheromone precursors, killer toxin precursors and aspartic proteinase propeptides, very few substrates are known. Fungal kex2 deletion mutants display pleiotropic phenotypes that are thought to result from the failure to proteolytically activate such substrates. Results: In this study we have aimed at providing an improved assembly of Kex2 target proteins to explain the phenotypes observed in fungal kex2 deletion mutants by in vitro digestion of recombinant substrates from Candida albicans and C. glabrata. We identified CaEce1, CA0365, one member of the Pry protein family and CaOps4-homolog proteins as novel Kex2 substrates. Statistical analysis of the cleavage sites revealed extended subsite recognition of negatively charged residues in the P1', P2' and P4' positions, which is also reflected in construction of the respective binding pockets in the ScKex2 enzyme. Additionally, we provide evidence for the existence of structural constrains in potential substrates prohibiting proteolysis. Conclusion: Furthermore, by using purified Kex2 proteinases from S. cerevisiae, P. pastoris, C. albicans and C. glabrata, we show that while the substrate specificity is generally conserved between organisms, the proteinases are still distinct from each other and are likely to have additional unique substrate recognition. http://www.biomedcentral.com/1471-2180/8/116 Oliver Bader, Yannick Krauke and Bernhard Hube BMC Microbiology 2008, 8:116 2008-07-14 doi:10.1186/1471-2180-8-116 BMC Microbiology 1471-2180 8 116 2008-07-14