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Hormones and hormone-binding proteins resembling those of vertebrates are widespread in fungi, yeast and bacteria. Functional responses of microbial cells to mammalian hormones have also been found. The evolutionary roots of the vertebrate endocrine system may, therefore, be far more ancient than is generally believed.
OBJECTIVES: To determine whether biofilm-forming capacity of bacteria demonstrated in chronic rhinosinusitis (CRS) has an impact on persistence of the disease following endoscopic sinus surgery (ESS). METHOD: Thirty-one bacterial strains recovered from 19 patients with CRS at least 1 year post-ESS. Evolution of disease was assessed by questionnaire and endoscopy as favorable or unfavorable. The bacteria were cultured on a 96-well culture plaque and a semi-quantitative method using crystal violet to quantify biofilm production was used. RESULTS: Twenty-two of 31 samples produced a biofilm thicker or equal to the positive control. Biofilm production was noted in 6/10 Pseudomonas aeruginosa isolates, 8/10 Staphylococcus aureus, and 8/11 coagulase-negative staphylococci. Biofilm formation was associated with a poor evolution for Pseudomonas aeruginosa and Staphylococcus aureus, but not coagulase-negative staphylococcus. CONCLUSION: There is a correlation between in vitro biofilm-producing capacity by Pseudomonas aeruginosa and Staphylococcus aureus and unfavorable evolution after ESS, suggesting a role for biofilm production in chronic sinusitis. EBM RATING: B-2b.
The development of molecular techniques for the study of uncultured bacteria allowed the extensive study of the widespread association between insects and intracellular symbiotic bacteria. Most of the bacterial endosymbionts involved in such associations are gamma-proteobacteria, closely related to Escherichia coli. In recent years, five genomes from insect endosymbionts have been sequenced, allowing the performance of extensive genome comparative analysis that, as a complement of phylogenetic studies, and analysis on individual genes, can help to understand the different traits of this particular association, including how the symbiotic process is established, the explanation of the special features of these microbial genomes, the bases of this intimate association and the possible future that awaits the endosymbionts with extremely reduced genomes.
Ground bark and heartwood from Alnus rubra and Pseudotsuga menziesii were added to a muddy sediment from a small Oregon stream and incubated in situ. Carbon dioxide and methane production rates were increased by all amendments, the biggest increase being shown with A. rubra wood. Except for sediment amended with A. rubra wood, nitrogen fixation rates from all treatments (including the control) were approximately 0.1 nmol/g per h throughout the 6-month study period. Contrary to expectations, neither bark had a noticeable adverse effect on microbial activity, but the A. rubra wood promoted nitrogen fixation. These results help to explain the faster rate of decomposition of A. rubra wood in water compared with that of P. menziesii described in the literature. The uptake kinetics of glucose (V(max)) did not follow the same pattern as gas evolution.
Deletion of individual antibiotic resistance genes found within the variable region of integrons is demonstrated. Evidence for gene duplications and rearrangements resulting from the insertion of gene units at new locations is also presented. Deletion, duplication, and rearrangement occur only in the presence of the integron-encoded DNA integrase. These events are precise and involve loss or gain of one or more complete insert units or gene cassettes. This confirms the recent definition of gene cassettes as consisting of the gene coding sequences, all except the last 7 bases of the 59-base element found at the 3' end of the gene, and the core site located 5' to the gene (Hall et al., Mol. Microbiol. 5:1941-1959, 1991) and demonstrates that individual gene cassettes are functional units which can be independently mobilized. Both deletions and duplications can be generated by integrase-mediated cointegrate formation followed by integrase-mediated resolution involving a different pair of sites. However, deletion occurs 10 times more frequently than duplication, and we propose that the majority of deletion events are likely to involve integrase-dependent excision of the gene unit to generate a circular gene cassette. The implications of these findings in understanding the evolution of integrons and the spread of antibiotic resistance genes in bacterial populations is discussed.
Tubercular tenosynovitis is now rare, which can delay diagnosis of this disease. We report a case of tenosynovitis of the wrist in a heart transplant patient caused by an isoniazid- and streptomycin-resistant Mycobacterium tuberculosis strain. Despite immunosuppression therapy, which can lead to a smoldering evolution, molecular biology analysis of biopsies allowed a rapid diagnosis.
Sequences of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) domain were determined by direct sequencing of HIV-1 RNA in successive plasma samples from eight seroconverting patients infected with virus bearing the T215Y/F amino acid substitution associated with zidovudine (ZDV) resistance. At baseline, additional mutations associated with ZDV resistance were detected. Three patients had the M41L amino acid change, which persisted. Two patients had both the D67N and the K70R amino acid substitutions; reversion to the wild type was seen at both positions in one of these patients and at codon 70 in the other one. Reversion to the wild type at codon 215 was observed in only one of eight patients. Unusual amino acids, such as aspartic acid (D) and cysteine (C), appeared at position 215 in four patients during follow-up. These variants isolated by coculturing were sensitive to ZDV. Overgrowth of these variants suggests that they have better fitness than the original T215Y variant. Intraindividual nucleoside substitutions over time were 10 times more frequent in codons associated with ZDV resistance (41, 67, 70, 215, and 219) than in other codons of the RT domain. The predominance of nonsynonymous substitutions observed over time suggests that most changes reflect adaptation of the RT function. The variance in sequence evolution observed among patients, in particular at codon 215, supports a role for chance in the evolution of the RT domain.
The anti-Listeria monocytogenes activity of Lactobacillus plantarum WHE 92, a pediocin AcH producer, was investigated in Munster cheese, a smear-surface soft cheese. The appearance of L. monocytogenes in the cheese, which naturally occurs solely in the crust and never before 1 week of ripening, could be prevented by spraying a cell suspension of L. plantarum WHE 92 (ca. 10(5) CFU/ml) on the cheese surface at the beginning of the ripening period. L. monocytogenes was sometimes detected at low levels (<5.0 x 10(1) CFU/g) after 7 to 11 days of ripening. However, this pathogen not be able to grow, nor did it survive the presence of L. plantarum WHE 92 in any of the samples examined until the end of the ripening not be able to grow, nor did it survive the presence of than 10(4) CFU/g in control samples. In other respects, L. plantarum WHE 92, which exists naturally in Munster cheese, did not adversely affect the evolution of the ripening process. This procedure has allowed manufacturers to successfully put an antilisterial treatment into practice in their ripening rooms.
Bacterial infections take up an important place in tropical pathology and have an increased death-rate. Among the causes of this strong mortality, the resistance of bacteria to antibiotics keeps a dominant part. We carried out, between January 1999 and December 2000 a study aiming to establish the distribution of the most frequently isolated germs at the Laboratory of Bacteriology of Fann Hospital, their sensibility to antibiotics and the different phenotypes of resistance. We noticed a predominance of enterobacteria (69.30%), notably Escherichia coli (56.76%) and Klebsiella pneumoniae (47.69%), but also Staphylococcus aureus (13.91%). Enterobacteria present 39.7% of resistant phenotypes to beta-lactams (E. coli: 61.75% and K. pneumoniae: 47.69%). Only the third generation cephalosporins and fluoroquinolons are constantly actives on enterobacteria, and 69% of S. aureus strains are resistant to methicillin, and so to all beta-lactams. Pseudomonas aeruginosa become difficult to overcome: 51.13% of the strains produce beta-lactamase. The quinolons are the most active antibiotics on this germ. It is very important to settle network that will be in charge to survey the evolution of these bacterial resistances.
The authors report a case of retroperitoneal fibrosis secondary to actinomycosis with consequences on the urinary tract. They insist on the difficulty of diagnostic, the antibiotic's sensibility and the evolution towards fibrosis which can lead to renal function deterioration.
MOTIVATION: Analysis of statistical properties of DNA sequences is important for evolutional biology as well as for DNA probe and PCR technologies. These technologies, in turn, can be used for organism identification, which implies applications in the diagnosis of infectious diseases, environmental studies, etc. RESULTS: We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5-20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, some correlation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.
Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus subtilis with corresponding those of operons in 11 complete genome sequences. We found that in many cases, gene orders within operons could be shuffled frequently during evolution, although several operon structures, such as ribosomal protein operons, were well conserved. This suggests that shuffling of a genome structure is virtually neutral in long-term evolution. Moreover, degrees of instability of the operon structures depended on the genomes examined. Variation in degrees of instability of the genome structures was likely to be related to differences in amounts of insertion sequences. Effects on transcription regulation are also discussed in association with operon destruction.
Biofilm structural heterogeneity affects a broad range of microbially catalysed processes. Solute transport limitation and autoinhibitor production, two factors that contribute to heterogeneous biofilm development, were investigated using BacMIST, a computer simulation model. BacMIST combines a cellular automaton algorithm for biofilm growth with Brownian diffusion for solute transport. The simulation represented the growth of microbial unit cells in a three-dimensional domain modelled after a repeating section of a constant depth film fermenter. The simulation was implemented to analyse the effects of various levels of transport limitation on a growing single-species biofilm. In a system with rapid solute diffusion, cells throughout the biofilm grew at their maximum rate, and no solute gradient was formed over the biofilm thickness. In increasingly transport-limited systems, the rapidly growing fraction of the biofilm population decreased, and was found exclusively at the biofilm-liquid interface. Trans-biofilm growth substrate gradients also deepened with increasing transport limitation. Autoinhibitory biofilm growth was simulated for various rates of microbially produced inhibitor transport. Inhibitor transport rates affected both the biofilm population dynamics and the resulting biofilm structures. The formation of networks of void spaces in slow-growing regions of the biofilm and the development of columns in the fast-growing regions suggested a possible mechanism for the microscopically observed evolution of channels in biofilms.
BACKGROUND: Selenocysteine (Sec) is a rare amino acid which occurs in proteins in major domains of life. It is encoded by TGA, which also serves as the signal for termination of translation, precluding identification of selenoprotein genes by available annotation tools. Information on full sets of selenoproteins (selenoproteomes) is essential for understanding the biology of selenium. Herein, we characterized the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome project. RESULTS: We identified 310 selenoprotein genes that clustered into 25 families, including 101 new selenoprotein genes that belonged to 15 families. Most of these proteins were predicted redox proteins containing catalytic selenocysteines. Several bacterial selenoproteins previously thought to be restricted to eukaryotes were detected by analyzing eukaryotic and bacterial SECIS elements, suggesting that eukaryotic and bacterial selenoprotein sets partially overlapped. The Sargasso Sea microbial selenoproteome was rich in selenoproteins and its composition was different from that observed in the combined set of completely sequenced genomes, suggesting that these genomes do not accurately represent the microbial selenoproteome. Most detected selenoproteins occurred sporadically compared to the widespread presence of their cysteine homologs, suggesting that many selenoproteins recently evolved from cysteine-containing homologs. CONCLUSIONS: This study yielded the largest selenoprotein dataset to date, doubled the number of prokaryotic selenoprotein families and provided insights into forces that drive selenocysteine evolution.
Porphyromonas gingivalis and Prevotella intermedia are obligate anaerobe gram-negative periodontopathogenic bacteria. Free-living amoebae, such as Acanthamoeba spp., are well known as environmental hosts of several human pathogens, such as Franciscella tularensis, Chlamydia pneumoniae, Legionella pneumophila and Mycobacteria spp. This study tested the ability of P. gingivalis and P. intermedia to become internalized, to survive and replicate in Acanthamoeba castellani. Our results show for the first time that P. gingivalis and P. intermedia isolated from periodontitis patients are capable of infecting A. castellani cells in vitro and are able to survive and multiply intracellularly. From our experimental data it can be suggested that periodontopathogenic bacteria might be conditioned in the evolution by amoebae and free-living amoebae can act as an environmental reservoir for these pathogens.
Heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. All mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. Here we describe the crystal structures of IsdG and IsdI, two heme-degrading enzymes from Staphylococcus aureus. The structures of both enzymes resemble the ferredoxin-like fold and form a beta-barrel at the dimer interface. Two large pockets found on the outside of the barrel contain the putative active sites. Sequence homologs of IsdG and IsdI were identified in multiple Gram-positive pathogens. Substitution of conserved IsdG amino acid residues either reduced or abolished heme degradation, suggesting a common catalytic mechanism. This mechanism of IsdG-mediated heme degradation may be similar to that of the structurally related monooxygenases, enzymes involved in the synthesis of antibiotics in Streptomyces. Our results imply the evolutionary adaptation of microbial enzymes to unique environments.
AIMS: Evaluation of composition and evolution of the coagulase-negative staphylococci (CNS) communities in two traditionally fermented sausages (salsiccia and soppressata lucana) produced in Basilicata, southern Italy. METHODS AND RESULTS: A culture-dependent approach based on isolation on selective media and identification with phenotypic and molecular methods was used. Phenotypic data of 471 strains were analysed by multivariate statistical methods by using 28 strains from culture collections and 48 strains identified by molecular methods (such as 16S rDNA sequencing, species-specific PCR assays, intergenic spacer region-PCR and PCR-denaturing gradient gel electrophoresis) as a reference. The CNS microflora of the sausages was found to be dominated by different biotypes of Staphylococcus xylosus (51.2%), followed by S. pulvereri/vitulus, S. equorum and S. saprophyticus (13.4, 10.2 and 10%, respectively). Other species (S. succinus, S. pasteuri, S. epidermidis, S. warneri and Macrococcus caseolyticus) were also present at lower levels. Identification of 25% of the isolates was impossible. CONCLUSIONS: The composition of CNS communities varied significantly with sausage type, plant and ripening time and clear differences were found among communities of salsiccia and soppressata at the end of ripening. SIGNIFICANCE AND IMPACT OF THE STUDY: Phenotypic characterization, supported by molecular and statistical analyses, can be considered a useful approach for typing a large number of isolates and for monitoring the evolution of staphylococcal communities during sausage fermentation but does not always provide a satisfactory identification of the isolates.
Catabolism of a (14)C-labelled volatile monoterpene compound (geraniol) to (14)CO(2) was investigated in soils taken from the rhizosphere at distances up to 200 cm from the trunks of three small Populus tremula trees growing at different sites in Slovenia. Emissions of limonene of up to 18 microg m(-2) h(-1) were detected from the soil surface at each site. Evolution of (14)C-labelled CO(2) was measured as a product of catabolism of (14)C-labelled geraniol introduced into the soil samples. Indigenous soil microorganisms degraded the geraniol rapidly. There was a significant difference in relative lag times and rates of catabolism along the gradient from the tree trunks, with relatively longer lag times and lower rates occurring in soil samples from the farthest point from the tree.