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PubMed1999

The role of dendritic cells in the induction and regulation of immunity to microbial infection.

Dendritic cells (DCs) play a critical role in the initiation and regulation of immune responses. Recent advances have begun to uncover the nature and diversity of DC-pathogen interactions and the modulation of DC function by microbial stimuli. Antigen pulsed DCs have also been shown in several infection models to induce high levels of protective immunity and to display immunotherapeutic potential. The study of the function of DCs in the response to infection is thus an exciting and rapidly expanding field with important implications for both fundamental and clinical immunology.

Animals↗

PubMed2026

Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?

PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes. RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.

Humans↗

PubMed2026

Programmable in vivo mRNA circularization for enhanced gene expression in bacteria.

The minute-scale lifetime of mRNA strongly influences bacterial gene expression, whereas a robust and programmable approach to directly control the mRNA stability and topology remains elusive. Here, we develop CRESEnT (Circular RNA Expression for Stable and Enhanced Translation), a programmable in vivo mRNA circularization system based on a permuted intron-exon architecture to engineer mRNA topology. CRESEnT enables facile circularization of mRNA, which led to a substantial increase in protein expression across diverse promoters, RBS variants, genetic cargos, and bacterial hosts. Furthermore, application of CRESEnT to biosynthetic pathways increased the production of several value-added metabolites, demonstrating that mRNA circularization can be harnessed to improve the metabolic performance of microbial cell factories. Together, these results establish RNA topology engineering via circularization as a transformative axis for controlling bacterial gene expression and enhancing the functionality of microbial cells.

RNA, Messenger↗

PubMed2001

Toxicity of pesticides to aquatic microorganisms: a review.

Microorganisms contribute significantly to primary production, nutrient cycling, and decomposition in estuarine eco-systems; therefore, detrimental effects of pesticides on microbial species may have subsequent impacts on higher trophic levels. Pesticides may affect estuarine microorganisms via spills, runoff, and drift. Both the structure and the function of microbial communities may be impaired by pesticide toxicity. Pesticides may also be metabolized or bioaccumulated by microorganisms. Mechanisms of toxicity vary, depending on the type of pesticide and the microbial species exposed. Herbicides are generally most toxic to phototrophic microorganisms, exhibiting toxicity by disrupting photosynthesis. Atrazine is the most widely used and most extensively studied herbicide. Toxic effects of organophosphate and organochlorine insecticides on microbial species have also been demonstrated, although their mechanisms of toxicity in such nontarget species remain unclear. There is a great deal of variability in the toxicity of even a single pesticide among microbial species. When attempting to predict the toxicity of pesticides in estuarine ecosystems, effects of pesticide mixtures and interactions with nutrients should be considered. The toxicity of pesticides to aquatic microorganisms, especially bacteria and protozoa, is an area of research requiring further study.

Animals↗

PubMed2001

Lens crystallins and their microbial homologs: structure, stability, and function.

abg-Crystallins are the major protein components in the vertebrate eye lens--a as a molecular chaperone and b and g as structural proteins. Surprisingly, the latter two share some structural characteristics with a number of microbial stress proteins. The common denominator is not only the Greek key topology of their polypeptide chains but also their high intrinsic stability, which, in certain microbial crystallin homologs, is further enhanced by high-affinity Ca2+-binding. Recent studies of natural and mutant vertebrate bg-crystallins as well as spherulin 3a from Physarum polycephalum and Protein S from Myxococcus xanthus allowed the correlation of structure and stability of crystallins to be elucidated in some detail. From the thermodynamic point of view, stability increments come from (1) local interactions involved in the close packing of the cooperative units, (2) the all-b secondary structure of the Greek-key motif, (3) intramolecular interactions between domains, (4) intermolecular domain interactions, including 3D domain swapping and (v) excluded volume effects due to "molecular crowding" at the high cellular protein concentrations. Apart from these contributions to the Gibbs free energy of stability, significant kinetic stabilization originates from the high activation energy barrier determining the rate of unfolding from the native to the unfolded state. From the functional point of view, the high stability is responsible for the long-term transparency of the eye lens, on the one hand, and the stress resistance of the microorganisms in their dormant state on the other. Local structural perturbations due to chemical modification, wrong protein interactions, or other irreversible processes may lead to protein aggregation. A leading cataract hypothesis is that only after a-crystallin, a member of the small heat-shock protein family, is titrated out does pathological opacity occur. Understanding the structural basis of protein stability in the healthy eye lens is the route to solve the enormous medical and economical problem of cataract.

Amino Acid Sequence↗

PubMed2000

Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil.

Temperature is an important factor controlling CH(4) production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37 degrees C or in a temperature gradient block covering the same temperature range at intervals of 1 degrees C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH(4) production rates increased with temperature, with an apparent activation energy of 61 kJ mol(-1). Steady-state partial pressures of the methanogenic precursor H(2) also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H(2) plus CO(2)-dependent methanogenesis was kept at -20 to -25 kJ mol of CH(4)(-1) over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 microM. Simultaneously, the relative contribution of H(2) as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to (14)CH(4), so that the carbon and electron flow to CH(4) was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and Methanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

Agriculture↗

PubMed1996

The sequence of the Mycoplasma arthritidis superantigen, MAM: identification of functional domains and comparison with microbial superantigens and plant lectin mitogens.

Mycoplasma arthritidis, an agent of chronic proliferative arthritis of rodents, secretes a potent soluble superantigen, MAM, that is active for both murine and human T and B lymphocytes. We now report the complete nucleotide and amino acid sequence of MAM and show it to be distinct from other proteins and not closely related phylogenetically to other superantigens. Two functional domains on MAM are identified based on the ability of peptides encompassing these regions to inhibit lymphocyte proliferation by the intact MAM molecule. One of these domains shares short sequences or epitopes with other microbial superantigens. The second domain contains the consensus legume lectin motif-beta, which is important for T cell activation by concanavalin (Con) A. MAM and Con A peptides containing this motif are functionally cross reactive, suggesting a novel secondary pathway for T cell activation by MAM.

Amino Acid Sequence↗

PubMedDate not supplied

Interactions among microorganisms of the indigenous intestinal flora and their influence on the host.

The animal host and its intestinal microbial flora function together as a complex ecologic system in which there is a significant impact of the intestinal flora on the host as well as of components of the microbial flora on one another. Aerobic and anaerobic bacteria of the intestinal flora influence numerous anatomic, physiologic, and immunologic parameters of the host. Constituents of the indigenous intestinal flora also engage in a multitude of antagonistic and cooperative interactions. The normal bacterial intestinal flora represents an extremely important defense mechanism, which effectively interferes with the establishment of many important enteric pathogens. Mechanisms by which microorganisms suppress the growth of other microorganisms include modification of bile acids, stimulation of peristalsis, induction of immunologic responses, depletion of essential substrates from the environment, competition for attachment sites, creation of restrictive physiologic environments, and elaboration of antibiotic-like substances. Components of the intestinal microbial flora also interact synergistically in the induction of disease or the utilization of substrate.

Animals↗

PubMed2025

A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.

The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.

Lakes↗

PubMed1995

Do de-N-glycosylation enzymes have an important role in plant cells?

In this review de-N-glycosylation was defined as the removal of the glycan(s) from a N-glycosylprotein, by means of enzymes acting on the di-N-acetylchitobiosyl part of the invariant pentasaccharide inner-core of N-glycosylproteins. Peptide-N4-(N-acetyl-beta-D-glucosaminyl) asparagine amidases (PNGase) and endo-N-acetyl-beta-D-glucosaminidases (ENGase) were both considered as de-N-glycosylation enzymes. A detailed description of the characterization and the function of plant PNGases and ENGases is presented, together with a brief presentation on the occurrence and the current knowledge on the function of microbial and animal enzymes. De-N-glycosylation of plant glycoproteins was proposed as a possible mechanism for the release of oligosaccharides displaying biological activities and the removal of N-glycans could also explain the regulation of protein activity. Each enzyme seems to have a specific function during germination and post-germinative development. All the arguments concur that de-N-glycosylation enzymes have an important role in plant cells and confirm that the N-glycosylation/de-N-glycosylation system should occur more commonly than presently recognized in living organisms.

Amidohydrolases↗

PubMed2002

Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns.

Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.

Bacteria↗

PubMed2001

In search of natural substrates and inhibitors of MDR pumps.

The function of microbial MDRs remains a hotly debated subject. Given the very broad substrate specificities of some MDRs, like the RND pumps that can extrude all classes of amphipathic compounds (cationic, neutral, and anionic), it seems difficult to develop a rationale for pinpointing possible natural substrates of these translocases. At the same time, several clues can be used to guide our search for natural MDR substrates. One is the fact that amphipathic cations appear to be the preferred substrates of MDRs. These substances are extruded by MDRs of all 5 known families and are the almost exclusive substrates of SMR and MF family MDRs. The universal nature of amphipathic cations as MDR substrates suggests that these were the substances that fueled the evolution of MDR pumps. Two factors apparently favored this particular class of molecules for the role of original MDR substrates--need and opportunity. Unlike other substances, amphipathic cations accumulate in the cell driven by the membrane potential, which makes cations potentially the most dangerous toxins. At the same time, amphipathic cations are highly hydrated and do not permeate the membrane as readily as neutral compounds, making it feasible to design a defense based on an efflux pump. The paucity of known cationic (non-basic) antimicrobials might be a result of using MDR-expressing microbial cells for antibiotic discovery. Plant amphipathic cations, the berberine alkaloids, are good MDR substrates. The Berberis plants produce 5'-methoxyhydnocarpin-D, an MDR inhibitor that potentiates the action of berberine. It is suggested that the further evolution of MDR pumps was determined largely by the barrier function of the membrane they reside in. Thus Gram negative bacteria have an outer membrane barrier that slows the penetration of virtually all amphipathic molecules, and transenvelope MDRs of the RND and EmrAB-type extrude their substrates across this barrier. A low permeability of the cytoplasmic membrane of yeast similarly allows for the operation of broad-specificity ABC and MF MDRs. The presence of MDR sensors that regulate the expression of some MDR pumps strongly suggests that defense against external toxins is the function of these MDRs. The BmrR transcriptional activator of the MerR family induces expression of the Bmr pump in B. subtilis and is a sensor specifically designed to recognize amphipathic cations. Similarly, the OacR repressor binds chemically unrelated cations, which leads to the expression of the QacA pump in S. aureus. In E. coli, the EmrR sensor of the MarR repressor family binds unrelated neutral molecules, allowing for expression of the transenvelope EmrAB pump.

Anti-Bacterial Agents↗

PubMed2002

Microbial behavior in a heterogeneous world.

Most microorganisms are motile during at least part of their life cycle, because they need to find optimal conditions in a patchy world. The sheer volume of microorganisms in the biosphere means that their motile sensory behavior also contributes to the global transformation and cycling of matter. How microorganisms move and how they orient themselves using environmental cues are integral to understanding the complex structure and function of microbial communities, but although motility in response to external stimuli was first described more than 120 years ago, understanding of the cellular and molecular mechanisms involved has only been achieved more recently.

Anaerobiosis↗

PubMed1995

Effect of gamma-irradiation on the effector function of T lymphocytes in microbial control.

A chlamydial-specific T cell clone, capable of inhibiting the growth of infectious Chlamydia in vivo and in vitro, was employed to investigate the effect of gamma-irradiation on the ability of effector T cells to control infections. Clone 2.14-0 (CD4+), specific for the Chlamydia trachomatis biovar agent of mouse pneumonitis (MoPn), was irradiated with varying doses (0, 2.5, 5.0, 10.0, 20.0 and 40.0 Gy) and its biological functions and ability to inhibit the intraepithelial growth of MoPn were assessed. The results revealed that although gamma-irradiation drastically reduced the proliferative response of the clone to antigen, it did not affect the phenotype and the effector function of inhibiting chlamydial growth. The preservation of anti-chlamydial function after gamma-irradiation correlated with the retention of IFN-gamma and TNF-alpha secretion in response to antigenic stimulation. We conclude that the biologic functions of T cells requiring proliferation and differentiation are more likely to be adversely affected by gamma-irradiation on the short-term, but the effector functions, possibly associated with cytokines and cytolysis, may be preserved among persisting effector T cells in an irradiated individual.

Animals↗

PubMed2000

Microbiology of flooded rice paddies.

Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the 'greenhouse' effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure-function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate-nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).

Archaea↗

PubMedDate not supplied

Microbial genomics: from sequence to function.

The era of genomics (the study of genes and their function) began a scant dozen years ago with a suggestion by James Watson that the complete DNA sequence of the human genome be determined. Since that time, the human genome project has attracted a great deal of attention in the scientific world and the general media; the scope of the sequencing effort, and the extraordinary value that it will provide, has served to mask the enormous progress in sequencing other genomes. Microbial genome sequencing, of particular interest to the community studying emerging infectious diseases, prompted the series of articles presented in the following pages. These articles review technological and scientific advances that have occurred since publication of the Haemophilus influenzae genome sequence in July 1995; that was the first demonstration that an entire genome sequence could be deciphered by a "shotgun" approach, i.e., the sequencing and assembly of random fragments of the genome. This is now the method of choice for sequencing of most other genomes, including human (as performed by Celera Genomics).

Genome, Bacterial↗

PubMed2024

Effects of initial corncob particle size on the short-term composting for preparation of cultivation substrates for Pleurotus ostreatus.

The short-term composting based on corncob for preparing Pleurotus ostreatus cultivation medium originated from agricultural production practices and so lacked systematic investigation. In this study, the influences of a Dafen (15 mm, DFT) and Xiaofen (5 mm, XFT) initial particle size (IPS) of corncob on the microbial succession and compost quality were examined. Results demonstrated that XFT compost was better suited for mushroom cultivation due to its high biological efficiency of 70 % and the absence of contamination. The composting microbes differed significantly between the DFT and XFT composts. During composting, the genera of Bacillus, Acinetobacter, Lactobacillus, Streptomyces, and Paenibacillus were majorly found in the DFT compost, while Acinetobacter, Lactobacillus, Puccinia, Bacteroides, and Bacillus genera dominated the XFT compost. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that throughout the thermophilic phase, XFT compost had much greater relative abundances of sequences relevant to energy, carbohydrate, and amino acid metabolism than DFT compost. Analysis of network correlations and Mantel tests indicated that IPS reduction could increase microbial interactions. Overall, adjusting the IPS of corncob to 5 mm increased microbial interactions, improved compost quality, and thereby boosted the P. ostreatus yield. These findings will be pertinent in optimizing the composting process of cultivation medium for P. ostreatus.

Composting↗

PubMed2002

Collision frequencies of microbial aggregates with small particles by differential sedimentation.

Collision and coagulation rates between microbial aggregates and small particles were measured for individual aggregates (1.0-2.5 mm) that settled through a suspension of fluorescent yellow-green (YG) particles (2.83 microm) placed in a settling column. The microbial aggregates, with an average fractal dimension of 2.26, were generated in a lab-scale sequencing batch reactor (SBR) and also collected from a full-scale activated sludge (AS) treatment system. As calculated from comparisons between the settling velocities observed and those predicted by Stokes' law for impermeable particles, the average fluid collection efficiencies were 0.08 for the SBR aggregates and 0.14 for the AS flocs, which were much lower than those previously reported for nonbiological aggregates of latex microspheres. The collision frequency functions between microbial aggregates and small YG particles were 2 orders of magnitude lower than predicted by the rectilinear model but 1 order of magnitude greater than predicted by a curvilinear model. The overall scavenging efficiencies of suspended particles by the falling microbial aggregates compared well with those observed for the nonbiological aggregates, while the particle removal efficiencies from the flow internal to the microbial aggregates were 1 order of magnitude higher than those of the nonbiological aggregates. It is argued that the permeability of microbial aggregates could be reduced by exopolymeric material clogging the pores within the aggregates. The internal permeation through a bioaggregate thus may not be significant enough to be included in the calculation of its settling velocity; however, the intra-aggregate flow cannot be simply neglected where coagulation is concerned. Streamlines still can penetrate the interior of microbial aggregates, allowing greater collision frequencies with other particles than predicted by the curvilinear model. The narrow and convoluted internal flow passages resulting from the collection of extracellular polymeric substances may also contribute to the higher interior particle removal efficiencies of microbial aggregates than those of more permeable, nonbiological aggregates.

Geologic Sediments↗