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PubMed2000

Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies.

The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.

Bacteria↗
PubMed1992

Consequences of microbial attachment: directing host cell functions with adhesins.

We take the view that adherence is not just a static process of holding hands but rather elicits a response in the targeted cell. From this point of view, adherence is an active process with an outcome. This outcome or fate is predictable only when several parameters of the host cell-adhesin interaction are known: is the adhesin acting alone or in series with other products, is the receptor up- or down-regulated at the time of ligation, which domain of the receptor is bound, and finally, which intracellular response circuits are connected to the receptor in the cell type targeted? Variations in these parameters are the basis for the ability of the adhesins of pathogens to orchestrate outcomes as disparate as simple address recognition versus actin nucleation, cytokine induction, activation of plasmin, derangement of leukocyte migration, or deposition of antibody on host cell membranes. The recognition of the relatedness of some eukaryotic and prokaryotic adhesive domains and the shared use of existing eukaryotic cell-cell interaction systems between host and pathogen suggest that the cellular interactions of interest in eukaryotic cell biology can be revealed by taking clues from the pathogens, which have studied and adapted to them the longest.

Animals↗
PubMedDate not supplied

Effect of different combinations of dietary additives on bacterial translocation and survival in gut-derived sepsis.

BACKGROUND: Dietary arginine, glutamine, and fish oil each have been shown to improve resistance to infection. The purpose of this study was to assess the potential benefit of different combinations and amounts of these components on bacterial translocation and related mortality during gut-derived sepsis. METHODS: Balb/c mice were fed for 10 days with an AIN-76A diet supplemented with different combinations and percentages of arginine, glutamine, glycine, fish oil, and medium-chain triglycerides. Controls were fed a complete AIN-76A diet or chow. After 10 days of feeding, all animals were transfused. On day 15, the animals were gavaged with 10(10) 111In-radiolabeled or unlabeled Escherichia coli and given a 30% burn injury. Animals gavaged with unlabeled bacteria were observed for survival (n = 317). Groups that showed the best survival as well as control groups were gavaged with labeled bacteria and killed 4 hours postburn (n = 60) for harvest of mesenteric lymph nodes, liver and spleen. RESULTS: Mice fed diets enriched with 5% fish oil + 2% arginine, 2% arginine + 2% glutamine, or 5% fish oil + 2% glutamine had higher survival than control groups. The animals fed fish oil+glutamine had significantly reduced translocation to the liver and spleen. Animals fed arginine+glutamine had an enhanced ability to kill translocated organisms in the liver compared with other groups. Fish oil+arginine improved both barrier function and microbial killing. CONCLUSIONS: Feeding with arginine+glutamine, fish oil+arginine, or fish oil+glutamine supplemented diets positively affects the outcome in a gut-derived sepsis model.

Animals↗
PubMed2001

Ontogeny of Toll-like receptors Tlr2 and Tlr4 in mice.

Toll-like receptors (TLR:) have recently been linked to the immunostimulatory function of microbial toxins in human and mice. TLR: signals activation of nuclear factor kappaB that leads to the production of a number of proinflammatory mediators. TLR:4 mediates the endotoxin-induced inflammatory response, whereas TLR:2 may be involved in the response to yeast and Gram-positive bacterial products. To better understand age-related changes in acute inflammatory response, we studied the ontogeny of TLR:2 and TLR:4 mRNA in murine fetal lung, liver, and placenta by quantitative reverse transcriptase-PCR. Different expression patterns were seen between the tissues and between the TLR: This is in accordance with the evidence that there are differences in the receptors for different microbial toxins and that the response is organ specific. We additionally show that the expression of TLR: was dependent on the stage of differentiation. In the liver, the levels of Tlr2 and Tlr4 were high regardless of the age. In the lung, Tlr2 and Tlr4 expression levels were barely detectable in immature fetus (d 14-15). Tlr2 and Tlr4 were increased several-fold during prenatal development and further increased after birth. The present results support the finding of a deficient inflammatory response of the immature lung to microbial toxins.

Animals↗
PubMed1994

The roles of magnesium in biotechnology.

This review highlights the important roles played by magnesium in the growth and metabolic functions of microbial and animal cells, and therefore assigns a key role for magnesium ions in biotechnology. The fundamental biochemical and physiological actions of magnesium as a regulatory cation are outlined. Such actions are deemed to be relevant in an applied sense, because Mg2+ availability in cell culture and fermentation media can dramatically influence growth and metabolism of cells. Manipulation of extracellular and intracellular magnesium ions can thus be envisaged as a relatively simplistic, but nevertheless versatile, means of physiological cell engineering. In addition, biological antagonism between calcium and magnesium at the molecular level may have profound consequences for the optimization of biotechnological processes that exploit cells. In fermentation, for example, it is argued that the efficiency of microbial conversion of substrate to product may be improved by altering Mg:Ca concentration ratios in industrial feedstocks in a way that makes more magnesium available to the cells. With particular respect to yeast-based biotechnologies, magnesium availability is seen as being crucially important in governing central pathways of carbohydrate catabolism, especially ethanolic fermentation. It is proposed that such influences of magnesium ions are expressed at the combined levels of key enzyme activation and cell membrane stabilization. The former ensures optimum flow of substrate to ethanol and the latter acts to protect yeasts from physical and chemical stress.

Animals↗
PubMedDate not supplied

[Microbiological processes of the carbon and sulfur cycle in cold methane seeps in the North Atlantic].

Functioning of microbial communities in surface sediments of the Haakon Mosby underwater mud volcano (lat. 72 degrees N) and in gas seepage fields of the Vestnesa Ridge was investigated using Mir-1 and Mir-2 deep-sea submersibles during the 40th expedition of the research vessel Academician Mstislav Keldysh. Large areas of sedimentary deposits of the Haakon Mosby mud volcano (HMMV) and pockmarks of the Vestnesa Ridge (VR) are covered with bacterial mats 0.1 to 0.5 cm thick. The microbial community making up bacterial mats of the HMMV was predominated by large filamentous bacteria with filaments measuring up to 100 microns in length and 2 to 8 microns in width. The occurrence of rosettes allowed the observed filamentous bacteria to be referred to the morphologically similar genera Leucothrix or Thiothrix. Three morphological types of filamentous bacteria were identified in bacterial mats covering VR pockmarks. Filaments of type one are morphologically similar with representatives of the genera Thioploca or Desmanthos. Type two filaments had numerous inclusions of sulfur and resembled representatives of the genus Thiothrix. The third morphological type was constituted by single filaments made up of tightly connected disk-like cells and can, apparently, be assigned to the genus Beggiatoa. The rates of methane oxidation (up to 1570 microliters C/(dm3 day)) and sulfate reduction (up to 17 mg S/(dm3 day)) measured in surface sediments of HMMV and VR were close to the maximum rates of these processes observed in badly polluted regions of the northwestern shelf of the Black Sea. High rates of microbiological processes correlated with the high number of bacteria. The rate of methane production in sediments studied was notably lower and ranged from 0.1 to 3.5 microliters CH4/(dm3 day). Large areas of the HMMV caldera were populated by pogonophoras, represented by the two species, Sclerolinum sp. and Oligobrachia sp. The mass development of Sclerolinum sp. in the HMMV caldera was by the activity of aerobic methane-oxidizing bacteria localized inside the cells of these animals. Bacterial cells were also found in the trophosome tissue of Oligobrachia sp., but in cells of these bacteria, we did not observe the membrane structures typical of methanotrophs. The localization pattern of pogonophoras on the surface of reduced sediments suggests that the predominant bacteria in Oligobrachia tissues are sulfur-oxidizing endosymbionts.

Bacteria↗
PubMed1992

[The mechanisms of the manifestation of the genotoxic effects of binase].

The high concentrations of commercial sample of Bacillus intermedius 7P ribonuclease (binase) showed a weak mutagenic effect in Ames test and Ara-test. It has been established that binase induces the SOS-functions of microbial cell and prophage induction. The way of exogenic enzyme action through activation of RecA protein is proposed.

Bacillus↗
PubMed1983

[Lipopolysaccharide-protein complexes of the outer membrane of gram-negative bacteria].

The evidence for occurring lipopolysaccharide-protein complexes in the outer membrane of gram-negative bacteria has been summarized. The composition and supramolecular structure of these complexes as well as their functions in microbial envelope and substantial role in membrane organization have been discussed. The biological properties of the complexes as endotoxins and O-specific antigens have been considered.

Antigens, Bacterial↗
PubMed1995

[Treatment planning. Learning to solve complicated dental problems].

The importance of comprehensive care treatment planning in dental undergraduate and graduate curricula has long been underestimated. With a decreasing prevalence of dental diseases an increasing interest in the subject has been recognized. Comprehensive care treatment planning requires a strategic approach to resolve a patient's problems in a logical sequence and at a a priori estimation of treatment time and costs. The strategy outlined in this work comprises a phasing of the treatment along urgency criteria. Initially, immediate problems are resolved, followed by microbial problems, functional problems, after which a maintenance plan is established. A treatment planning model is introduced to enable students to hold track of the overall treatment plan and to advice students how to address specific dental problems.

Adult↗
PubMed1999

How stable is stable? Function versus community composition.

The microbial community dynamics of a functionally stable, well-mixed, methanogenic reactor fed with glucose were analyzed over a 605-day period. The reactor maintained constant pH and chemical oxygen demand removal during this period. Thirty-six rrn clones from each of seven sampling events were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) for the Bacteria and Archaea domains and by sequence analysis of dominant members of the community. Operational taxonomic units (OTUs), distinguished as unique ARDRA patterns, showed reproducible distribution for three sample replicates. The highest diversity was observed in the Bacteria domain. The 16S ribosomal DNA Bacteria clone library contained 75 OTUs, with the dominant OTU accounting for 13% of the total clones, but just 21 Archaea OTUs were found, and the most prominent OTU represented 50% of the clones from the respective library. Succession in methanogenic populations was observed, and two periods were distinguished: in the first, Methanobacterium formicicum was dominant, and in the second, Methanosarcina mazei and a Methanobacterium bryantii-related organism were dominant. Higher variability in Bacteria populations was detected, and the temporal OTU distribution suggested a chaotic pattern. Although dominant OTUs were constantly replaced from one sampling point to the next, phylogenetic analysis indicated that inferred physiologic changes in the community were not as dramatic as were genetic changes. Seven of eight dominant OTUs during the first period clustered with the spirochete group, although a cyclic pattern of substitution occurred among members within this order. A more flexible community structure characterized the second period, since a sequential replacement of a Eubacterium-related organism by an unrelated deep-branched organism and finally by a Propionibacterium-like species was observed. Metabolic differences among the dominant fermenters detected suggest that changes in carbon and electron flow occurred during the stable performance and indicate that an extremely dynamic community can maintain a stable ecosystem function.

Bacteria↗
PubMed1990

Phytoalexins as part of induced defence reactions in plants: their elicitation, function and metabolism.

Microbial infection of plants or elicitation of cell cultures initiates substantial metabolic changes directed at the induction of defence reactions. The antimicrobial phytoalexins deserve special attention because they represent one essential component of plant resistance. The great structural diversity of phytoalexins and possible cellular sites for their toxic activity are discussed. Pterocarpan phytoalexin biosynthesis in Cicer arietinum is an example of the induction of extended biosynthetic pathways, their modes of regulation and metabolic links with constitutive secondary product formation. Elicitation of plant tissues represents a technique to induce simultaneously the formation of phytoalexins and increased levels of constitutive or other secondary products that do not normally accumulate. The biological function of phytoalexins and the pathways of their degradation by pathogenic fungi are outlined. Detoxification of phytoalexins by fungi may have important consequences for the practical application of these defence compounds and for the genetic transformation of fungi and plants. Phytoalexins accumulate in plants or cell cultures only transiently, because they are readily degraded or polymerized by extracellular peroxidases.

Fungi↗
PubMed2026

Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.

Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. &#x3b2;-Diversity differed significantly between RS and GS across these three domains (P&#x2009;<&#x2009;0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P&#x2009;<&#x2009;0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.

Snow↗
PubMed2026

Whole-Genome Sequence Dataset of Rhodococcus qingshengii IEGM 267-Terpenoid Biotransformer Toward Genetic Functional Annotation.

Background/Objectives: Microbial biotransformation of monoterpenoids is a promising approach for obtaining bioactive compounds. Rhodococcus species are attractive biocatalysts due to their metabolic versatility and ability to transform hydrophobic substrates. In this study, we investigated the catalytic potential of Rhodococcus qingshengii IEGM 267 toward carveol isomers and explored genomic features that may underlie this activity. Methods: The strain was cultivated in mineral medium supplemented with (-)-trans-carveol. Biotransformation products were analyzed by TLC and GC-MS. The draft genome was sequenced, assembled, taxonomically assigned, and annotated using standard bioinformatics tools. Results: Rhodococcus qingshengii IEGM 267 efficiently converted (-)-trans-carveol to carvone. Genome analysis confirmed the taxonomic assignment of the strain and revealed a large repertoire of oxidoreductases, including monooxygenases, hydroxylases, and dehydrogenases. Seven genes encoding cytochrome P450-dependent oxygenases were identified as candidate enzymes potentially involved in carveol oxidation. Conclusions: R. qingshengii IEGM 267 is an efficient and stereoselective biocatalyst for (-)-trans-carveol oxidation. The results of bioinformatics analysis suggest an alternative enzymatic basis for this transformation and provide a foundation for future functional characterization.

Rhodococcus↗
PubMed2026

Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.

BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort. METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16&#xa0;S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis. RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients. CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.

Humans↗
PubMedDate not supplied

[Effect of conditions of culturing Pseudomonas rathonis T on characteristics of a biosensor for determining anionic surface-active agents].

The dependence of the sensitivity of a microbial biosensor of anionic surfactants (AS) on the growth phase of Pseudomonas rathonis T, a strain capable of degrading surfactants, was studied. Correlations were found between the optimum values of temperature and pH of microbial growth, substrate utilization, and functional performance of the microbial biosensor. These results allow the process of AS detection to be optimized.

Anions↗