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Showing papers in "Fems Microbiology Letters in 2009"


Journal ArticleDOI
TL;DR: This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria and suggests that mechanisms proposed recently in non-gut Clostridium spp.
Abstract: Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

1,529 citations


Journal ArticleDOI
TL;DR: Understanding the mechanisms of adhesion and signaling involved in fungal-bacterial interactions may lead to the development of novel therapeutic strategies for impeding microbial colonization and development of polymicrobial disease.
Abstract: Bacteria and fungi are found together in a myriad of environments and particularly in a biofilm, where adherent species interact through diverse signaling mechanisms. Yet, despite billions of years of coexistence, the area of research exploring fungal-bacterial interactions, particularly within the context of polymicrobial infections, is still in its infancy. However, reports describing a multitude of wide-ranging interactions between the fungal pathogen Candida albicans and various bacterial pathogens are on the rise. An example of a mutually beneficial interaction is coaggregation, a phenomenon that takes place in oral biofilms where the adhesion of C. albicans to oral bacteria is considered crucial for its colonization of the oral cavity. In contrast, the interaction between C. albicans and Pseudomonas aeruginosa is described as being competitive and antagonistic in nature. Another intriguing interaction is that occurring between Staphylococcus aureus and C. albicans, which although not yet fully characterized, appears to be initially synergistic. These complex interactions between such diverse and important pathogens would have significant clinical implications if they occurred in an immunocompromised host. Therefore, understanding the mechanisms of adhesion and signaling involved in fungal-bacterial interactions may lead to the development of novel therapeutic strategies for impeding microbial colonization and development of polymicrobial disease.

351 citations


Journal ArticleDOI
TL;DR: The results show that the two approaches give rise to quite different views of the diversity of the underlying samples, and standardization of which subregion from the ITS region should be sequenced is crucial to the integration of the new sequencing technologies with current mycological praxis.
Abstract: The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.

261 citations


Journal ArticleDOI
TL;DR: This article elaborates on possible future directions for microbial viability assessment using nucleic acid-modifying compounds in combination with DNA- (and potentially RNA-) amplification technologies.
Abstract: This article elaborates on possible future directions for microbial viability assessment using nucleic acid-modifying compounds in combination with DNA- (and potentially RNA-) amplification technologies Bacteria were traditionally considered viable when they could be cultured, whereas today's viability concept is based on the presence of some form of metabolic activity, responsiveness, RNA transcripts that tend to degrade rapidly after cell death, or of an intact membrane The latter criterion was the focus of recent approaches to limit detection to intact cells using ethidium monoazide or propidium monoazide Membrane integrity must, however, be considered as a very conservative criterion for microbial viability The new concept presented here aims at limiting nucleic acid-based detection to cells with an active metabolism, which might be a more appropriate viability criterion To selectively detect only cells with metabolic and respiratory activity (while excluding inactive dead cells from detection), we suggest the use of 'activity-labile compounds' In addition to their potential usefulness for viability assessment, these new compounds could also be beneficial for selectively amplifying nucleic acids of cells that have metabolic activities of interest This preferential detection of microorganisms with certain metabolic capabilities is referred to as 'molecular enrichment' in distinction to 'growth enrichment'

258 citations


Journal ArticleDOI
TL;DR: The large variety of serotypes, virulence properties, genetic relationships, epidemiology, reservoir and diagnosis of aEPEC strains from nonclassical EPEC serogroups makes it difficult to determine which strains are truly pathogenic.
Abstract: The enteropathogenic Escherichia coli (EPEC) pathotype is currently divided into two groups, typical EPEC (tEPEC) and atypical EPEC (aEPEC). The property that distinguishes these two groups is the presence of the EPEC adherence factor plasmid, which is only found in tEPEC. aEPEC strains are emerging enteropathogens that have been detected worldwide. Herein, we review the serotypes, virulence properties, genetic relationships, epidemiology, reservoir and diagnosis of aEPEC, including those strains not belonging to the classical EPEC serogroups (nonclassical EPEC serogroups). The large variety of serotypes and genetic virulence properties of aEPEC strains from nonclassical EPEC serogroups makes it difficult to determine which strains are truly pathogenic.

241 citations


Journal Article
TL;DR: In this article, the authors reviewed the serotypes, virulence properties, genetic relationships, epidemiology, reservoir and diagnosis of aEPEC, including those strains not belonging to the classical EPEC serogroups.
Abstract: The enteropathogenic Escherichia coli (EPEC) pathotype is currently divided into two groups, typical EPEC (tEPEC) and atypical EPEC (aEPEC). The property that distinguishes these two groups is the presence of the EPEC adherence factor plasmid, which is only found in tEPEC. aEPEC strains are emerging enteropathogens that have been detected worldwide. Herein, we review the serotypes, virulence properties, genetic relationships, epidemiology, reservoir and diagnosis of aEPEC, including those strains not belonging to the classical EPEC serogroups (nonclassical EPEC serogroups). The large variety of serotypes and genetic virulence properties of aEPEC strains from nonclassical EPEC serogroups makes it difficult to determine which strains are truly pathogenic.

216 citations


Journal ArticleDOI
TL;DR: The structural gene for 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) from the endophytic plant growth-promoting bacterium Burkholderia phytofirmans PsJN was isolated and used to construct a mutant strain B. phy ToFirmans YS2, in which an internal segment of the acdS gene was deleted.
Abstract: The structural gene for 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) from the endophytic plant growth-promoting bacterium Burkholderia phytofirmans PsJN was isolated and used to construct a mutant strain B. phytofirmans YS2 (B. phytofirmans PsJN/ΔacdS), in which an internal segment of the acdS gene was deleted. The mutant YS2 lost ACC deaminase activity as well as the ability to promote the elongation of the roots of canola seedlings. Concomitant with the creation of this deletion mutant, a number of physiological changes were observed in the bacterium, including an increase in indole acetic acid synthesis, a decrease in the production of siderophores and an increase in the cellular level of the stationary-phase σ factor, RpoS. Introduction of the wild-type acdS gene into the mutant YS2 to construct strain B. phytofirmans YS3 (B. phytofirmans YS2/pRK-AcdS) restored both ACC deaminase activity and plant growth-promotion activity in strain YS3. However, the complemented mutant still showed the above-mentioned physiological changes.

197 citations


Journal ArticleDOI
TL;DR: The evidence for a continuing role for QS in P. aeruginosa CF infections is discussed, including QS activity in CF sputa and CF-relevant effects of QS-regulated products, such as pyocyanin.
Abstract: Studies on cultured cells and in infection models have shown that cell density-dependent quorum-sensing (QS) controls many of the known virulence factors of Pseudomonas aeruginosa. However, it is less clear what role QS plays in chronic human lung infections associated with cystic fibrosis (CF). The involvement of QS in biofilm development, crucial to the establishment of long-term infections, suggests a role in the early stages of infection. However, the accumulation of QS mutants during chronic CF infections has been taken to indicate that any role diminishes thereafter. Here, we discuss the evidence for a continuing role for QS in P. aeruginosa CF infections, including QS activity in CF sputa and CF-relevant effects of QS-regulated products, such as pyocyanin. Bacterial population behaviour in CF is complex, and the exact roles of QS remains unclear. Therapeutic strategies directed against QS suggest that a greater understanding of bacterial populations during infection would be a valuable research goal from a clinical perspective.

188 citations


Journal ArticleDOI
TL;DR: This review summarizes the available data concerning the structure and function of Pal and its role in pathogenesis and shows that it has recently been demonstrated that Pal is essential for bacterial survival and pathogenesis.
Abstract: The protein Pal (peptidoglycan-associated lipoprotein) is anchored in the outer membrane (OM) of Gram-negative bacteria and interacts with Tol proteins. Tol–Pal proteins form two complexes: the first is composed of three inner membrane Tol proteins (TolA, TolQ and TolR); the second consists of the TolB and Pal proteins linked to the cell's OM. These complexes interact with one another forming a multiprotein membrane-spanning system. It has recently been demonstrated that Pal is essential for bacterial survival and pathogenesis, although its role in virulence has not been clearly defined. This review summarizes the available data concerning the structure and function of Pal and its role in pathogenesis.

185 citations


Journal ArticleDOI
TL;DR: The construction of a naphthalene-degrading endophytic strain designated Pseudomonas putida VM1441(pNAH7) was found to be an efficient colonizer of plants, colonizing both the rhizosphere and interior root tissues and resulted in the protection of the host plant from the phytotoxic effects of nAPHthalene.
Abstract: Polyaromatic hydrocarbons (PAHs) are major and recalcitrant pollutants of the environment and their removal presents a significant problem. Phytoremediation has shown much promise in PAH removal from contaminated soil, but may be inhibited because the plant experiences phytotoxic effects from low-molecular-weight PAHs such as naphthalene. This paper describes the construction of a naphthalene-degrading endophytic strain designated Pseudomonas putida VM1441(pNAH7). This strain was found to be an efficient colonizer of plants, colonizing both the rhizosphere and interior root tissues. The inoculation of plants with P. putida VM1441(pNAH7) resulted in the protection of the host plant from the phytotoxic effects of naphthalene. When inoculated plants were exposed to naphthalene, both seed germination and plant transpiration rates were higher than those of the uninoculated controls. The inoculation of plants with this strain also facilitated higher (40%) naphthalene degradation rates compared with uninoculated plants in artificially contaminated soil.

183 citations


Journal ArticleDOI
TL;DR: In this article, a large collection of Fusarium oxysporum f. sp. isolates was screened for the presence of seven SIX genes (SIX1-SIX7), which can be used for unambiguous identification of the forma specialis lycopersici.
Abstract: During infection of tomato, the fungus Fusarium oxysporum f. sp. lycopersici secretes several unique proteins, called 'secreted in xylem' (Six) proteins, into the xylem sap. At least some of these proteins promote virulence towards tomato and among them, all predicted avirulence proteins that can trigger disease resistance in tomato have been found. In this study, a large, worldwide collection of F. oxysporum isolates was screened for the presence of seven SIX genes (SIX1-SIX7). The results convincingly show that identification of F. oxysporum formae speciales and races based on host-specific virulence genes can be very robust. SIX1, SIX2, SIX3 and SIX5 can be used for unambiguous identification of the forma specialis lycopersici. In addition, SIX4 can be used for the identification of race 1 strains, while polymorphisms in SIX3 can be exploited to differentiate race 2 from race 3 strains. For SIX6 and SIX7, close homologs were found in a few other formae speciales, suggesting that these genes may play a more general role in pathogenicity. Host specificity may be determined by the unique SIX genes, possibly in combination with the absence of genes that trigger resistance in the host.

Journal ArticleDOI
TL;DR: In inoculation of maize plants with A. brasilense containing higher levels of trehalose confers drought tolerance and a significant increase in leaf and root biomass, opening the possibility that A. Brasilense modified with a chimeric tre Halose biosynthetic gene from yeast could increase the biomass, grain yield and stress tolerance in other relevant crops.
Abstract: Bacteria of the genus Azospirillum increase the grain yield of several grass crops. In this work the effect of inoculating maize plants with genetically engineered Azospirillum brasilense for trehalose biosynthesis was determined. Transformed bacteria with a plasmid harboring a trehalose biosynthesis gene-fusion from Saccharomyces cerevisiae were able to grow up to 0.5M NaCl and to accumulate trehalose, whereas wild-type A. brasilense did not tolerate osmotic stress or accumulate significant levels of the disaccharide. Moreover, 85% of maize plants inoculated with transformed A. brasilense survived drought stress, in contrast with only 55% of plants inoculated with the wild-type strain. A 73% increase in biomass of maize plants inoculated with transformed A. brasilense compared with inoculation with the wild-type strain was found. In addition, there was a significant increase of leaf and root length in maize plants inoculated with transformed A. brasilense. Therefore, inoculation of maize plants with A. brasilense containing higher levels of trehalose confers drought tolerance and a significant increase in leaf and root biomass. This work opens the possibility that A. brasilense modified with a chimeric trehalose biosynthetic gene from yeast could increase the biomass, grain yield and stress tolerance in other relevant crops.

Journal ArticleDOI
TL;DR: This improved method uses a new donor strain, E. coli ST18, a hemA deletion mutant mutant defective in tetrapyrrole biosynthesis, which means that counterselection of the Escherichia coli donor strain is not required.
Abstract: We present a new method for diparental mating with the outstanding advantage that counterselection of the Escherichia coli donor strain is not required. This improved method uses a new donor strain, E. coli ST18, a hemA deletion mutant defective in tetrapyrrole biosynthesis. The hemA mutation can be complemented by addition of 5-aminolevulinic acid. Therefore, counterselection is carried out only using standard media and growth conditions optimal for the recipient strain. Consequently, recipient strains are isolated in a significantly shorter period.

Journal ArticleDOI
TL;DR: The inhibitory properties of the microbial community of the coral mucus from the Mediterranean coral Oculina patagonica were examined and support the concept of a probiotic effect on microbial communities associated with the coral holobiont.
Abstract: The inhibitory properties of the microbial community of the coral mucus from the Mediterranean coral Oculina patagonica were examined. Out of 156 different colony morphotypes that were isolated from the coral mucus, nine inhibited the growth of Vibrio shiloi, a species previously shown to be a pathogen of this coral. An isolate identified as Pseudoalteromonas sp. was the strongest inhibitor of V. shiloi. Several isolates, especially one identified as Roseobacter sp., also showed a broad spectrum of action against the coral pathogens Vibrio coralliilyticus and Thallassomonas loyana, plus nine other selected Gram-positive and Gram-negative bacteria. Inoculation of a previously established biofilm of the Roseobacter strain with V. shiloi led to a 5-log reduction in the viable count of the pathogen within 3 h, while inoculation of a Pseudoalteromonas biofilm led to complete loss of viability of V. shiloi after 3 h. These results support the concept of a probiotic effect on microbial communities associated with the coral holobiont.

Journal ArticleDOI
TL;DR: The results suggest that OMVs from A. baumannii are an important vehicle designed to deliver effector molecules to host cells, and several putative virulence-associated proteins were also identified.
Abstract: The secretion of outer membrane vesicles (OMVs) is one of the major mechanisms by which Gram-negative bacteria deliver effector molecules to host cells. Acinetobacter baumannii is an important opportunistic pathogen in hospital-acquired infections, but the secretion system for effector molecules to induce host cell damage has not been characterized. In the present study, we investigated the secretion of OMVs from a clinical A. baumannii isolate and analyzed the comprehensive proteome of A. baumannii-derived OMVs. Acinetobacter baumannii secreted OMVs into the extracellular milieu during in vitro growth. Using 1-DE and LC-MS/MS protein identification and assignment analysis, 132 different proteins associated with OMVs were identified. These proteins were derived from outer membranes (n=26), periplasmic space (n=6), inner membranes (n=8), cytoplasm (n=43), and unknown localization or multiple localization sites (n=49) according to the cell location prediction programs. Among the proteins associated with OMVs, a potent cytotoxic molecule, outer membrane protein A, was highly enriched and several putative virulence-associated proteins were also identified. These results suggest that OMVs from A. baumannii are an important vehicle designed to deliver effector molecules to host cells.

Journal ArticleDOI
TL;DR: The results indicate that physiological responses, and perhaps environmental adaptations, to N compounds are organism specific for methanotrophs.
Abstract: Ecological studies have indicated that relative abundances of Gammaproteobacteria methanotrophs (Gamma-MOB) vs. Alphaproteobacteria methanotrophs (Alpha-MOB) in nitrogen (N) impacted soils are dictated in part by their abilities to tolerate inhibitory effects of ammonium and nitrite. In particular, ammonia is a cometabolic substrate and competitive inhibitor of methane monooxygenase. The rates of ammonia and hydroxylamine oxidation and inhibition of methane-oxidizing activity by ammonium and nitrite were compared among two Gamma-MOB and two Alpha-MOB to determine whether methanotrophs of the same class shared similar physiological profiles. Each isolate exhibited unique Km(app) for ammonia and Vmax for nitrite production with or without reductant (methane or sodium formate). The rates of nitrite production from hydroxylamine followed similar trends to rates of ammonia oxidation, indicating that hydroxylamine-oxidizing enzymes were central participants in the ammonia-oxidizing pathway. Methylomonas methanica was incapable of either ammonia or hydroxylamine oxidation. A broad range of sensitivities to ammonium and nitrite inhibition were measured with little consistency between isolates of the same class. The results indicate that physiological responses, and perhaps environmental adaptations, to N compounds are organism specific for methanotrophs.

Journal ArticleDOI
TL;DR: Results indicate that A. baumannii evades complement attack through the acquisition of factor H to their surface, suggesting that AbOmpA was an important complement regulator-acquiring surface protein.
Abstract: Bacteremia is a common systemic disease caused by Acinetobacter baumannii, an important hospital-acquired pathogen among critically ill patients. The complement system is central to innate immune defense against invading bacteria in the blood. The present study investigated the susceptibility of clinical A. baumannii isolates to normal human sera (NHS), and determined the resistance mechanism of A. baumannii against complement-mediated lysis. The survival of A. baumannii isolates from bacteremic patients was significantly decreased in undiluted NHS, but they were resistant to 40% NHS. The alternative complement pathway was responsible for the direct killing of bacteria. The main regulator of the alternative complement pathway, factor H, bound to the surface of live A. baumannii treated with NHS. Factor H interacted with the outer membrane proteins with molecular sizes of 38 (AbOmpA), 32, and 24 kDa. The isogenic AbOmpA(-) mutant was highly susceptible to NHS in comparison with the wild-type A. baumannii strain, suggesting that AbOmpA was an important complement regulator-acquiring surface protein. These results indicate that A. baumannii evades complement attack through the acquisition of factor H to their surface.

Journal ArticleDOI
TL;DR: The molecular characterization of the genomes of yeasts involved in fermentation reveals that the majority arose from interspecific hybridization between two and sometimes three yeast species, which confers robust characteristics such as tolerance to environmental stress to these industrial yeasts and provides a means for adaptive evolution.
Abstract: The Saccharomyces sensu stricto genus contains many species that are industrially important for fermentation of wines, beers and ales. The molecular characterization of the genomes of yeasts involved in these processes reveals that the majority arose from interspecific hybridization between two and sometimes three yeast species. The hybridization events generated allopolyploid genomes, and subsequent recombination events between the parental genomes resulted in the formation of mosaic chromosomes. The polyploid and hybrid nature of the genomes confers robust characteristics such as tolerance to environmental stress to these industrial yeasts and provides a means for adaptive evolution.

Journal ArticleDOI
TL;DR: This work has identified the conditions under which immunity is induced, and identified the regulatory system responsible for differential (and protective) expression of immunity, and showed that CSP-induced death contributes to S. mutans biofilm formation through the release of chromosomal DNA into the extracellular matrix.
Abstract: Streptococcal competence-stimulating peptides (CSPs) were once thought to passively communicate population density in a process known classically as quorum sensing. However, recent evidence has shown that these peptides may also be inducible 'alarmones,' capable of conveying sophisticated messages in a population including the induction of altruistic cellular suicide under stressful conditions. We have previously characterized the alarmone response in Streptococcus mutans, a cariogenic resident of the oral flora, in which a novel bacteriocin-like peptide causes cell death in a subset of the population. Our objective in this work was to characterize the mechanism of immunity to cell death in S. mutans. Toward this goal, we have identified the conditions under which immunity is induced, and identified the regulatory system responsible for differential (and protective) expression of immunity. We also showed that CSP-induced death contributes to S. mutans biofilm formation through the release of chromosomal DNA into the extracellular matrix, providing a long sought-after mechanistic explanation for the role of CSP in S. mutans biofilm formation.

Journal ArticleDOI
TL;DR: In the checkerboard assay, the CHAP-SH3b fusion achieves the same level of antimicrobial synergy with lysostaphin as the full-length LysK, suggesting the need for a C-terminal binding domain.
Abstract: LysK is a staphylococcal bacteriophage endolysin composed of three domains: an N-terminal cysteine, histidine-dependent amidohydrolases/peptidases (CHAP) endopeptidase domain, a midprotein amidase 2 domain, and a C-terminal SH3b_5 (SH3b) cell wall-binding domain. Both catalytic domains are active on purified peptidoglycan by positive-ion electrospray ionization MS. The cut sites are identical to LytA (phi11 endolysin), with cleavage between d-alanine of the stem peptide and glycine of the cross-bridge peptide, and N-acetylmuramoyl-l-alanine amidase activity. Truncations of the LysK containing just the CHAP domain lyse Staphylococcus aureus cells in zymogram analysis, plate lysis, and turbidity reduction assays but have no detectable activity in a minimal inhibitory concentration (MIC) assay. In contrast, truncations harboring just the amidase lytic domain show faint activity in both the zymogram and turbidity reduction assays, but no detectable activity in either plate lysis or MIC assays. A fusion of the CHAP domain to the SH3b domain has near full-length LysK lytic activity, suggesting the need for a C-terminal binding domain. Both LysK and the CHAP-SH3b fusion were shown to lyse untreated S. aureus and the coagulase-negative strains. In the checkerboard assay, the CHAP-SH3b fusion achieves the same level of antimicrobial synergy with lysostaphin as the full-length LysK.

Journal ArticleDOI
TL;DR: This work performed the first large-scale screening of a P. aeruginosa PA14 mutant library to identify novel genes involved in persistence and identified nine new persistence mutants, which may serve as new candidate drug targets in the combat against P.aerug inosa infections.
Abstract: Persister cells are phenotypic variants that are extremely tolerant to high concentrations of antibiotics. They constitute a fraction of stationary phase cultures and biofilm populations of numerous bacterial species, such as the opportunistic pathogen Pseudomonas aeruginosa. Even though persisters are believed to be an important cause of incomplete elimination of infectious populations by antibiotics, their nature remains obscure. Most studies on persistence have focused on the model organism Escherichia coli and only a limited number of persistence genes have been identified to date. We performed the first large-scale screening of a P. aeruginosa PA14 mutant library to identify novel genes involved in persistence. A total of 5000 mutants were screened in a high-throughput manner and nine new persistence mutants were identified. Four mutants (with insertions in dinG, spuC, PA14_17880 and PA14_66140) exhibited a low persister phenotype and five mutants (in algR, pilH, ycgM, pheA and PA14_13680) displayed high persistence. These genes may serve as new candidate drug targets in the combat against P. aeruginosa infections.

Journal ArticleDOI
TL;DR: It is strongly suggested that lactate can stimulate sulphide formation by SRB present in the colon, with possible consequences for conditions such as colitis.
Abstract: High concentrations of sulphide are toxic for the gut epithelium and may contribute to bowel disease. Lactate is a favoured cosubstrate for the sulphate-reducing colonic bacterium Desulfovibrio piger, as shown here by the stimulation of sulphide formation by D. piger DSM749 by lactate in the presence of sulphate. Sulphide formation by D. piger was also stimulated in cocultures with the lactate-producing bacterium Bifidobacterium adolescentis L2-32. Other lactate-utilizing bacteria such as the butyrate-producing species Eubacterium hallii and Anaerostipes caccae are, however, expected to be in competition with the sulphate-reducing bacteria (SRB) for the lactate formed in the human colon. Strains of E. hallii and A. caccae produced 65% and 96% less butyrate from lactate, respectively, in a coculture with D. piger DSM749 than in a pure culture. In triculture experiments involving B. adolescentis L2-32, up to 50% inhibition of butyrate formation by E. hallii and A. caccae was observed in the presence of D. piger DSM749. On the other hand, sulphide formation by D. piger was unaffected by E. hallii or A. caccae in these cocultures and tricultures. These experiments strongly suggest that lactate can stimulate sulphide formation by SRB present in the colon, with possible consequences for conditions such as colitis.

Journal ArticleDOI
TL;DR: Although a general trend of genome reduction was observed, certain niche-specific genes appear to be recently acquired and appear on plasmids or adjacent to prophages.
Abstract: Lactic acid bacteria (LAB) are found to occupy a variety of ecological niches including fermented foods as well as mucosal surfaces of humans and other vertebrates. This review is based on the genomic content of LAB that is responsible for the functional and ecological diversity of these bacteria. These genomes reveal an ongoing process of reductive evolution as the LAB have specialized to different nutritionally rich environments. Species-to-species variation in the number of pseudogenes as well as genes directing nutrient uptake and metabolism reflects the adaptation of LAB to food matrices and the gastrointestinal tract. Although a general trend of genome reduction was observed, certain niche-specific genes appear to be recently acquired and appear on plasmids or adjacent to prophages. Recent work has improved our understanding of the genomic content responsible for various phenotypes that continue to be discovered, as well as those that have been exploited by man for thousands of years.

Journal ArticleDOI
TL;DR: It is concluded that gene cassettes might be readily shared between different integron classes found in environmental, commensal and pathogenic bacteria, and suggests that class 1 integrons in pathogens have access to a vast pool of gene cassette any of which could confer a phenotype of clinical relevance.
Abstract: Class 1 integrons carried by pathogens have acquired over 100 different gene cassettes encoding resistance to antimicrobial compounds, helping to generate a crisis in the management of infectious disease. It is presumed that these cassettes originated from environmental bacteria, but exchange of gene cassettes has surprisingly never been demonstrated outside laboratory or clinical contexts. We aimed to identify a natural environment where such exchanges might occur, and determine the phylogenetic range of participating integrons. Here we examine freshwater biofilms and show that families of cassettes conferring resistance to quaternary ammonium compounds (qac) are found on class 1 integrons identical to those from clinical contexts, on sequence variants of class 1 integrons only known from natural environments, and on other diverse classes of integrons only known from the chromosomes of soil and freshwater Proteobacteria. We conclude that gene cassettes might be readily shared between different integron classes found in environmental, commensal and pathogenic bacteria. This suggests that class 1 integrons in pathogens have access to a vast pool of gene cassettes, any of which could confer a phenotype of clinical relevance. Exploration of this resource might allow identification of resistance or virulence genes before they become part of multi-drug-resistant human pathogens.

Journal ArticleDOI
TL;DR: Based on global meethanol budgets, methanol oxidation in soil is important, but has not been addressed adequately by biogeochemical studies, and recently discovered interactions with eukaryotes indicate that their ecological niches may not be defined by physicochemical parameters.
Abstract: Methanol is an atmospheric compound that is primarily released from plant polymers and impacts ozone formation. The global methanol emission rate from terrestrial ecosystems is of the same order of magnitude (4.9 x 10(12) mol year(-1)) as that of methane (10 x 10(12) mol year(-1)). The major proportion of the annual plant-released methanol does not enter the atmosphere, but may be reoxidized by biological methanol oxidation, which is catalyzed by methanol-oxidizing prokaryotes. Fifty-six aerobic methanol-oxidizing species have been isolated from soils. These methylotrophs belong to the Alpha-, Beta-, and Gammaproteobacteria, Verrucomicrobia, Firmicutes, and Actinobacteria. Their ecological niches are determined by oxygen and methanol concentration, temperature, pH, the capability to utilize nitrate as an electron acceptor, and the spectrum of nitrogen sources and utilizable multicarbon substrates. Recently discovered interactions with eukaryotes indicate that their ecological niches may not solely be defined by physicochemical parameters. Nonetheless, there are still gaps in knowledge; based on global methanol budgets, methanol oxidation in soil is important, but has not been addressed adequately by biogeochemical studies. Ratios of above-ground and soil-internal methanol oxidation are not known. The contribution to methanol-oxidation by aerobic and anaerobic methylotrophs in situ also needs further research.

Journal ArticleDOI
TL;DR: Results of matrix-assisted laser desorption/ionization time-of-flight MS analyses revealed that the predominant compounds made by all strains were C10-C10 mono- and dirhamnolipids, and Notably, E. hormaechei and one strain of A. calcoaceticus produced rhamnlipids in amounts similar to the pseudomonads.
Abstract: Novel strains of rhamnolipid-producing bacteria were isolated from soils at a biodiesel facility on the basis of their ability to grow on glycerol as a sole carbon source. Strains were identified as Acinetobacter calcoaceticus, Enterobacter asburiae, Enterobacter hormaechei, Pantoea stewartii, and Pseudomonas aeruginosa. The strains of the former five species were found to produce rhamnolipids in quantities the same as, or similar to, coisolated strains of P. aeruginosa. Measurements of surface tension revealed that that emulsifying properties of these strains were similar to levels displayed by rhamnolipids produced by P. aeruginosa. Results of matrix-assisted laser desorption/ionization time-of-flight MS analyses revealed that the predominant compounds made by all strains were C10–C10 mono- and dirhamnolipids. Notably, E. hormaechei and one strain of A. calcoaceticus produced rhamnolipids in amounts similar to the pseudomonads. As all strains examined were from the same taxonomic class of Proteobacteria, further examination of this group may reveal many additional species not previously known to produce rhamnolipids in addition to novel strains of species currently known to produce rhamnolipids.

Journal ArticleDOI
TL;DR: The long tail fiber genes from the genome of T2 were replaced with those of the IP008 phage by homologous recombination and the recombinant phage bacterial lytic activity was restored.
Abstract: The application of bacteriophages (phages) in therapy urgently requires the production of wide-host-range recombinant phages that possess strong lytic activity. The wide-host-range IP008 phage was classified by transmission electron microscopy analysis as an A2 morphotype member of the Myoviridae family of the order Caudovirales. IP008 showed a high homology (99.4% similarity in the amino acid alignment of the major capsid protein Gp 23) with KEP10, another wide-host-range phage. The long tail fiber genes (genes 37 and 38) from the genome of T2 were replaced with those of the IP008 phage by homologous recombination. The host range of the recombinant phages was identical to that of IP008. Furthermore, the recombinant phage bacterial lytic activity was restored. Future analyses of host-range mutants of the closely related phages T2 and IP008 could lead to a more precise localization of the genetic factors responsible for receptor specificity.

Journal ArticleDOI
TL;DR: The ability of selected probiotic Lactobacillus strains to prevent C. jejuni-mediated disease pathogenesis depends on the pathogen strain, probiotic strain and the epithelial cell type selected, which supports the concept of probiotics strain selectivity.
Abstract: Campylobacter jejuni is the most common bacterial cause of enterocolitis in humans, leading to diarrhoea and chronic extraintestinal diseases. Although probiotics are effective in preventing other enteric infections, beneficial microorganisms have not been extensively studied with C. jejuni. The aim of this study was to delineate the ability of selected probiotic Lactobacillus strains to reduce epithelial cell invasion by C. jejuni. Human colon T84 and embryonic intestine 407 epithelial cells were pretreated with Lactobacillus strains and then infected with two prototypic C. jejuni pathogens. Lactobacillus helveticus, strain R0052 reduced C. jejuni invasion into T84 cells by 35-41%, whereas Lactobacillus rhamnosus R0011 did not reduce pathogen invasion. Lactobacillus helveticus R0052 also decreased invasion of one C. jejuni isolate (strain 11168) into intestine 407 cells by 55%. Lactobacillus helveticus R0052 adhered to both epithelial cell types, which suggest that competitive exclusion could contribute to protection by probiotics. Taken together, these findings indicate that the ability of selected probiotics to prevent C. jejuni-mediated disease pathogenesis depends on the pathogen strain, probiotic strain and the epithelial cell type selected. The data support the concept of probiotic strain selectivity, which is dependent on the setting in which it is being evaluated and tested.

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TL;DR: It is concluded that MgCRZ1 is essential for growth, development, and full virulence of M. grisea.
Abstract: Calcineurin, a conserved Ca(2+)/calmodulin-regulated protein phosphatase, is an important mediator of calcium-dependent signal transduction pathways in many organisms. In Saccharomyces cerevisiae, calcineurin positively regulates transcription in response to stress by dephosphorylating the transcription factor Crz1p. Here we describe the identification, cloning, and function of the gene encoding the Magnaporthe grisea CRZ1 homolog, MgCRZ1. Specifically, we demonstrated that MgCRZ1 partially complemented a yeast Deltacrz1 mutant and exhibited Ca(2+) and calcineurin activity-dependent cellular localization. Targeted disruption of MgCRZ1 resulted in hypersensitivity to Ca(2+). Compared with the wild-type Guy11 strain, the Deltacrz1 mutants formed significantly reduced numbers of conidia and a large portion of abnormal appressoria (>50%) that exhibited little or no melanin production. Lipid metabolism was delayed, and the level of turgor pressure within the appressoria declined, thereby notably attenuating mutant pathogenicity. We conclude that MgCRZ1 is essential for growth, development, and full virulence of M. grisea.

Journal ArticleDOI
TL;DR: A group of 46 Sphingomonas-like isolates, which originated from two rice varieties grown in two soils in Brazil, were characterized based on morphological, physiological and genetic analyses.
Abstract: So far, the occurrence of nitrogen-fixing Sphingomonas bacteria has been restricted to three strains of Sphingomonas azotifigens. In this work, a group of 46 Sphingomonas-like isolates, which originated from two rice varieties grown in two soils in Brazil, were characterized based on morphological, physiological and genetic analyses. The PCR genus specifically applied indicated that all 46 isolates belonged to the Sphingomonas genus and confirmed the results based on the yellow pigment of the colonies grown on potato agar medium and the BIOLOG data. It was also observed that 22 isolates are nitrogen-fixing bacteria as determined by the acetylene reduction method and confirmed by nifH gene detection. The genetic diversity based on the 16S rRNA analysis (amplified rDNA restriction analysis) showed that the isolates formed two distinct groups at a similarity value of 60%. Furthermore, five clusters at 60% similarity were observed with the 16S-23S intergenic space (ribosomal intergenic space analysis) analysis. Sequencing of the 16S rRNA gene and nifH fragments showed that most of the 22 nitrogen-fixing isolates formed clusters apart from that of the S. azotifigens. This is the first report on the occurrence of nitrogen-fixing Sphingomonas bacteria associated with rice grown in Brazil.