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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↗

PubMed2024

Metagenome reveals the possible mechanism that microbial strains promote methanogenesis during anaerobic digestion of food waste.

For better understanding the mechanism of microbial strains promoting methane production, four strains Hungatella xylanolytica A5, Bacillus licheniformis B1, Paraclostridium benzoelyticum C2 and Advenella faeciporci E1 were inoculated into anaerobic digestion systems. After bioaugmentation, the cumulative methane production of A5, B1, C2 and E1 groups elevated by 11.68%, 8.20%, 18.21% and 15.67% compared to CK group, respectively. The metagenomic analysis revealed that the species diversity and uniformity of the experimental groups was improved, and hydrolytic acidifying bacteria, represented by Clostridiaceae, Anaerolineaceae and Oscillospiraceae, and methanogens, such as Methanotrichaceae and Methanobacteriaceae, were enriched. Meanwhile, the abundance of key genes in carbohydrate, pyruvate and methane metabolism was increased in the inoculated groups, providing reasonable reasons for more methane production. The strengthening mechanism of microbial strains in this study offered a theoretical foundation for selecting a suitable bioaugmentation strategy to solve the problems of slow start-up and low methane production in anaerobic digestion.

Methane↗

PubMedDate not supplied

Secretory immunity and the bacterial IgA proteases.

The characteristics and functions of microbial IgA proteases are reviewed. These enzymes represent a structurally heterogeneous group of proteins that are secreted into the extracellular environment by bacteria capable of causing human disease. The IgA proteases, which vary in their requirements for metal ions, are neutral endopeptidases whose role in the infectious process is not known but whose pronounced substrate specificity for human proteins of the IgA1 subclass has repeatedly been demonstrated. As reagents, the IgA proteases are useful in cleaving IgA molecules to yield intact Fc alpha and Fab alpha fragments that will allow the study of the structure and function of the two large regions of IgA immunoglobulin proteins. The role, if any, of these enzymes in promoting infection by pathogenic members of the genera Neisseria, Hemophilus, and Streptococcus is not known, although the secretory immune system is primarily mediated by antibodies of the IgA isotype, among which are IgA1 subclass proteins, and these proteins are susceptible to cleavage by IgA protease. The determination of the role of these enzymes in the pathogenesis of human infection must await clearer understanding of antigenicity and antibody function at secretory sites and of the relative roles of the two subclasses of human IgA in immune defense.

Bacteria↗

PubMed2002

[Expression, purification and function of rice nonspecific lipid transfer protein].

Plant nonspecific lipid transfer protein(nsLTP) is a class of protein which has in vitro lipid transferring activity between biomembranes. In order to study the antimicrobial function of rice nonspecific lipid transfer protein, a gene LTP110 encoding rice nsLTP was cloned into ThioFusion expression vector pET32a (+) and expressed in host strain Bl21(DE3)trxB-. After induction by IPTG at 30 degrees C for 5 h, the fusion protein thio-LTP110 was in large amount produced. The expressed protein was purified by Ni2(+)-chelating Sepharose fast flow column, then digested by enterokinase. By passing through nickel affinity column again, the cleavage product, LTP110, was obtained. CD spectrum scanning from 185 nm to 250 nm showed that the recombinant protein LTP110 had similar secondary structure with the nsLTP purified from rice etiolated seedlings. Activity determination by fluorescent lipid P-96 showed that it had lipid binding activity. Microbial inhibition test results revealed that LTP110 deterred germination of the spores of rice pathogen P. oryzae, showing it might be involved in plant microbial resistance function. Therefore, it has the potential to be used in plant transgene engineering to improve plant resistance.

Antifungal Agents↗

PubMed2003

Anti-microbial activities of mannose-binding lectin.

Mannose-binding lectin (MBL; also known as mannan-binding lectin) is involved in first-line defence by binding to bacteria, viruses, protozoa and helminths through a pattern-recognition mode of detection and then initiating a range of host responses. Currently, we have been unable to extrapolate from what we know of the biochemistry of MBL binding to predict accurately the interaction of MBL with individual micro-organisms; even subtle surface alterations have been shown to have an extensive impact on MBL-mediated recognition of pathogens. MBL has a major protective effect through activation of the complement system via MBL-associated serine proteases (MASPs). This can cause the lysis of Gram-negative bacteria and also opsonize a wide spectrum of potential pathogens for phagocytosis. MBL may also influence phagocytosis in the absence of complement activation through an interaction with one or more collectin receptors. This may also be the basis for a direct effect of the protein on inflammatory responses. MBL can alter the function of microbial structures, such as gp120 of HIV, to prevent infection. The protein may also interact with the components of other cascade systems such as the clotting system, which will have a role in microbial pathogenesis. An understanding of these basic mechanisms will be vital if we are to use purified or recombinant MBL in therapeutic applications.

Bacterial Capsules↗

PubMed1997

Protistan communities in aquifers: a review.

Eukaryotic microorganisms (protists) are a very important component of microbial communities inhabiting groundwater aquifers. This is not unexpected when one considers that many protists feed heterotrophically, by means of either phagotrophy (bacterivory) or osmotrophy. Protistan numbers are usually low (< 10(2) per g dw of aquifer material) in pristine, uncontaminated aquifers but may increase by several orders of magnitude in aquifers subject to organic pollution. Small flagellates (typically 2-3(5) microns in size in situ) are by far the dominant protists in aquifers, although amoebae and occasionally ciliates may also be present in much lower numbers. Although a wealth of new taxonomic information is waiting to be brought to light, interest in the identity of aquifer protists is not exclusively academic. If verified, the following hypotheses may prove to be important towards our understanding of the functioning of microbial communities in aquifers: (1) Differences in swimming behavior between species of flagellates lead to feeding heterogeneity and niche differentiation, implying that bacterivorous flagellates graze on different subsets of the bacterial community, and therefore play different roles in controlling bacterial densities. (2) Bacterivorous flagellates grazing on bacteria capable of degrading organic compounds have an indirect effect on the overall rates of biodegradation.

Animals↗

PubMed1999

Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ.

We propose a novel method for studying the function of specific microbial groups in situ. Since natural microbial communities are dynamic both in composition and in activities, we argue that the microbial "black box" should not be regarded as homogeneous. Our technique breaks down this black box with group-specific fluorescent 16S rRNA probes and simultaneously determines 3H-substrate uptake by each of the subgroups present via microautoradiography (MAR). Total direct counting, fluorescent in situ hybridization, and MAR are combined on a single slide to determine (i) the percentages of different subgroups in a community, (ii) the percentage of total cells in a community that take up a radioactively labeled substance, and (iii) the distribution of uptake within each subgroup. The method was verified with pure cultures. In addition, in situ uptake by members of the alpha subdivision of the class Proteobacteria (alpha-Proteobacteria) and of the Cytophaga-Flavobacterium group obtained off the California coast and labeled with fluorescent oligonucleotide probes for these subgroups showed that not only do these organisms account for a large portion of the picoplankton community in the sample examined ( approximately 60% of the universal probe-labeled cells and approximately 50% of the total direct counts), but they also are significant in the uptake of dissolved amino acids in situ. Nearly 90% of the total cells and 80% of the cells belonging to the alpha-Proteobacteria and Cytophaga-Flavobacterium groups were detectable as active organisms in amino acid uptake tests. We suggest a name for our triple-labeling technique, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the "dissection" of microbial communities by type and function.

Animals↗