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PubMedDate not supplied

[Concept of a probiotic preparation, containing original microbial metabolites].

The biological functions of Escherichia coli M-17 exometabolites, contained in the synthetic composition of the autostimulating preparation "Actoflor-C", were evaluated. As shown by in vitro experiments, the composition had higher stimulating activity with respectto some microorganisms of the normal microflora, in comparison with the prototype preparation "Actoflor". High doses of the preparation "Actoflor-C" were supposedly capable of having not only positive influence on the development of microbiocenosis, but also of producing therapeutic action and primarily on intestinal epithelial cells by compensating the insufficient supply of bacterial metabolites in dysbiotic states. The presented data made it possible to believe that the functional activity of microbiocenosis was greatly determined by the system of metabolic regulation. The presented results formed the basis for the use of bacterial metabolites in the therapeutic of microbiocenosis in man.

Bacteria↗
PubMed2003

Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples.

In situ assays, based on monoclonal antibodies (mAbs), were developed to study the microbial expression of the bacterial dissimilatory copper-containing nitrite reductase gene (DnirK), one of the key enzymes involved in denitrification, in different ecosystems. With a combination of an anti-DnirK mAb and phylogenetic oligonucleotide probes, it is possible to bring structural and functional aspects of microbial communities together. To perform a double labelling, yielding a high signal strength for both the oligonucleotide and the antibody, cells have to be labelled with the oligonucleotide first followed by immunostaining. When the labelling sequence was changed, the accessibility for the oligonucleotide was reduced if high amounts of DnirK were expressed. Using flow cytometry, it was possible to sort bacterial cells, which were stained by the antibody, from nonlabelled cells. This technique provides means for a detailed analysis of populations, which express DnirK genes in the environment, including structural aspects of a community and detailed promoter studies. Using the immunostaining approach, it was possible to identify bacteria, which have the DnirK system expressed, in samples from a wastewater sewage treatment plant as well as in samples from the rhizosphere of wheat roots. Furthermore, expression studies using an Ochrobactrum anthropi strain were carried out to investigate the correlation between N(2)O production rates and DnirK expression in batch cultures, which had been shifted from aerobic to anaerobic conditions. As expected, expression of DnirK was the highest during periods with the greatest synthesis rates for N(2)O. However, the amount of expressed enzyme was not reduced in the cells, although the N(2)O production rates dropped in the cultures 12 h after the shift from aerobic to anaerobic conditions.

Antibodies, Monoclonal↗
PubMed2004

Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function.

During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.

Bacteria↗
PubMed2002

Mouse plasmacytoid cells: long-lived cells, heterogeneous in surface phenotype and function, that differentiate into CD8(+) dendritic cells only after microbial stimulus.

The CD45RA(hi)CD11c(int) plasmacytoid predendritic cells (p-preDCs) of mouse lymphoid organs, when stimulated in culture with CpG or influenza virus, produce large amounts of type I interferons and transform without division into CD8(+)CD205(-) DCs. P-preDCs express CIRE, the murine equivalent of DC-specific intercellular adhesion molecule 3 grabbing nonintegrin (DC-SIGN). P-preDCs are divisible by CD4 expression into two subgroups differing in turnover rate and in response to Staphylococcus aureus. The kinetics of bromodeoxyuridine labeling and the results of transfer to normal recipient mice indicate that CD4(-) p-preDCs are the immediate precursors of CD4(+) p-preDCs. Similar experiments indicate that p-preDCs are normally long lived and are not the precursors of the short-lived steady-state conventional DCs. However, in line with the culture studies on transfer to influenza virus-stimulated mice the p-preDCs transform into CD8(+)CD205(-) DCs, distinct from conventional CD8(+)CD205(+) DCs. Hence as well as activating preexistant DCs, microbial infection induces a wave of production of a new DC subtype. The functional implications of this shift in the DC network remain to be determined.

Animals↗
PubMed2005

Toll-like receptors: sentinels of host defence against bacterial infection.

Innate immunity provides a first line of host defence against infection through microbial recognition and killing while simultaneously activating a definitive adaptive immune response. Toll-like receptors (TLRs) are principal mediators of rapid microbial recognition and function mainly by detection of structural patterns that do not exist in the host. TLR2 and TLR4 were the first members of this innate immune receptor family to be strongly implicated in antibacterial host defence. Following the initial description of the mammalian TLR family, susceptibility to infection with numerous human microbial pathogens has been intensively studied using mice with engineered deletions of each of these molecules. While it has become quite clear that TLR activation is necessary for optimal host defence, a comprehensive understanding of the mechanisms by which this family of pattern recognition receptors engages protective immunity, particularly the adaptive response, is still evolving.

Adaptor Proteins, Signal Transducing↗
PubMed2026

MetagenomicKG: a knowledge graph for metagenomic applications.

MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored. RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction. CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

Metagenomics↗
PubMedDate not supplied

Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes.

It is suggested that genomes found in any form of cellular life contain potentially size-variable repetitive DNA moieties. In eukaryotes, large proportions of the multi-chromosomal genome consist of various classes of repetitive DNA. Also in archaeal genomes, repetitive DNA is encountered and, as is the case for the eukaryotes as well, little or no function is at present attributable to most of it. For prokaryotes, elegant experiments have highlighted so-called slipped strand nucleotide mispairing (SSM) as a basic and causal mechanism, giving rise to repeat unit number variation at a distinct locus. Illegitimate base pairing in regions of repetitive DNA during replication, in association with defective DNA repair and enhanced nuclease susceptibility of replication intermediates, in the end gives rise to deletion or addition of repeat units. Prokaryotic short sequence repeats (SSRs) harbour arrays of short repeat units, between one and approximately 20 nucleotides in length. SSRs are involved in various mechanisms of microbial gene expression regulation. Promoter strength can be affected by altering the spacing between important structural domains as can the integrity of open reading frames. In the present communication the literature on microbial SSRs harbouring repeat units that are five nucleotides in length will be briefly reviewed. Examples of these SSRs with discrete functionality are encountered in bacterial species such as Haemophilus influenzae, Neisseria gonorrhoeae, and Pasteurella haemolytica. In addition, several of the currently known bacterial and archaeal whole genome sequences were scanned for the presence of novel examples of potential five-nucleotide SSRs (and others) in order to gather additional knowledge on the propensity and putative functions of this type of potential genetic switch.

Base Sequence↗
PubMed2000

Life at the oxic-anoxic interface: microbial activities and adaptations.

Molecular oxygen is one of the most important reactants in biogeochemical cycles. Due to its low solubility in water, the consumption of oxygen leads to the development of oxic-anoxic interfaces, which separate aerobic from anaerobic processes in virtually all environments, ranging in scale from oceanic sediments to the fecal pellets of a small soil invertebrate. Three case studies were selected to illustrate the basic situation and the specific characteristics of oxic-anoxic interfaces: sediments, the rhizosphere of aquatic plants, and the intestinal tract of insects. Each system is governed by the same general principles, but striking differences arise from, e.g., the nature of the major microbial activities and the mechanisms controlling metabolite fluxes. Also scale and dimensional differences as well as the consequences of temporal fluctuations are of fundamental importance. Recent developments in microbial ecology, which often combine traditional and modern approaches, have significantly furthered our understanding of the specific microniches and the metabolic and behavioral adaptations of microorganisms to life at the oxic-anoxic interface. New concepts help to define the targets of future studies: the spatial organization of microbial populations, their microenvironments and in situ activities, and the functional interactions within structured microbial communities.

Adaptation, Physiological↗
PubMed2005

Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassa.

Phytochromes (Phys) comprise a superfamily of red-/far-red-light-sensing proteins. Whereas higher-plant Phys that control numerous growth and developmental processes have been well described, the biochemical characteristics and functions of the microbial forms are largely unknown. Here, we describe analyses of the expression, regulation, and activities of two Phys in the filamentous fungus Neurospora crassa. In addition to containing the signature N-terminal domain predicted to covalently associate with a bilin chromophore, PHY-1 and PHY-2 contain C-terminal histidine kinase and response regulator motifs, implying that they function as hybrid two-component sensor kinases activated by light. A bacterially expressed N-terminal fragment of PHY-2 covalently bound either biliverdin or phycocyanobilin in vitro, with the resulting holoprotein displaying red-/far-red-light photochromic absorption spectra and a photocycle in vitro. cDNA analysis of phy-1 and phy-2 revealed two splice isoforms for each gene. The levels of the phy transcripts are not regulated by light, but the abundance of the phy-1 mRNAs is under the control of the circadian clock. Phosphorylated and unphosphorylated forms of PHY-1 were detected; both species were found exclusively in the cytoplasm, with their relative abundances unaffected by light. Strains containing deletions of phy-1 and phy-2, either singly or in tandem, were not compromised in any known photoresponses in Neurospora, leaving their function(s) unclear.

Alternative Splicing↗
PubMed2026

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗
PubMed2005

The metagenomics of soil.

Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.

DNA↗
PubMed1999

The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.

Bacteria↗
PubMedDate not supplied

The role of molecular methods in evaluating biological treatment processes.

Methods derived from molecular biology provide powerful new tools to analyze biological treatment processes. Because molecular methods can be used to directly interrogate genetic information about the microbial community, they can provide the fine detail that is impossible with the blunt, nondiscriminating information usually obtained from more traditional measures such as biochemical oxygen demand and volatile suspended solids. Molecular methods allow tracking of critical groups of microorganisms, such as ammonia oxidizers, that comprise a small fraction of the total biomass. Molecular methods also allow tracking of specific metabolic reactions or other functions that are key to the satisfactory performance of a system. Despite their power, molecular methods do not provide sufficient information when used alone. Aggregated measures and quantitative modeling remain necessary to establish mass balances, quantify the function of the microbial community, and connect the results of molecular assays to practice. Several examples involving nitrifying bacteria in activated sludge illustrate the fine detail available with molecular methods and how they can be linked to traditional and quantitative analyses. Other manuscripts in this special issue also provide examples of the value of using molecular tools in combination with traditional methods.

Biomass↗
PubMed2004

Is the nectar redox cycle a floral defense against microbial attack?

Many angiosperms use a remarkable reproductive strategy that relies on attracting animals (insect, avian or mammalian pollinators) to transfer pollen between plants. Relying on other organisms for sexual reproduction seems evolutionarily untenable, but the great diversity of angiosperms illustrates how highly successful this strategy is. To attract pollinators, plants offer a variety of rewards. Perhaps the primary floral reward is floral nectar. Plant nectar has long been considered a simple sugar solution but recent work has demonstrated that nectar is a complex biological fluid containing significant and important biochemistry with the potential function of inhibiting microbial growth. These results lead the way to novel insights into the mechanisms of floral defense and the co-evolution of angiosperms and their pollinators.

Bacteria↗
PubMed1983

Impaired macrophage functions as a possible basis of immunomodification by microbial agents, tilorone and dimethyldioctadecylammonium bromide.

Four microbial and two chemically defined immunomodulating agents namely viable BCG, killed Mycobacterium butyricum, killed Lactobacillus plantarum, zymosan, tilorone, and dimethyldioctadecylammonium bromide (DDA) were studied for their effects on macrophage functions in vitro and in vivo. All agents induced a dose-dependent mortality of macrophages as determined by trypan blue exclusion. DDA and especially tilorone were rather toxic for macrophages in vitro. All agents except tilorone and DDA inhibited phagocytosis of yeast cells and uptake of acridine orange in vitro at doses which killed up to about 30% of the macrophages. DDA and tilorone had no effect at similar doses. All agents but zymosan inhibited the spreading of macrophages. No interference with the fusion of lysosomes and yeast cell-containing phagosomes could be observed. The activity of the mononuclear phagocytic system (MPS) in vivo as measured by carbon clearance was stimulated by all substances within twenty-four hours. All agents but DDA and tilorone enhanced non-specific bacterial resistance. As demonstrated previously for DDA, tilorone could serve as adjuvant for induction of specific resistance to Listeria monocytogenes. The results are discussed in relation to other data on influencing of macrophage functions and on immunomodification. It is concluded that hampered antigen destruction by local macrophage suppression attended with MPS stimulation might be a basic mechanism for adjuvanticity exerted by these agents.

Adjuvants, Immunologic↗
PubMed2026

Electron shuttles facilitate methane-dependent arsenate reduction in paddy soils.

Methane-dependent arsenate reduction (M-AsR) occurs widely in paddy soils and can substantially enhance arsenic mobilization, posing potential ecological risks. However, the role of electron shuttles in this process remains poorly understood. In this study, we investigated the influence of anthraquinone-2,6-disulfonate (AQDS) on M-AsR in paddy soils. Fourteen-day incubation showed that 1 mmol/L AQDS facilitated 50.88 % of arsenate reduction and 31.31 % of methane oxidation. Quantitative polymerase chain reaction analysis revealed that AQDS significantly increased the abundance of functional genes associated with arsenate reduction (arrA, arsC) and anaerobic methane oxidation (mcrA) (P < 0.05). Microbial community analysis revealed that AQDS addition enriched Cloacibacterium, Sphingorhabdus, and Methylocystis, while decreasing the relative abundance of Methylobacter and Methylomonas. These findings indicate that electron shuttles facilitate M-AsR by modulating functional microbial populations, providing valuable insights into arsenic biogeochemistry and the coupled cycling of methane and arsenic in paddy soils.

Methane↗
PubMed2006

Correlation of functional instability and community dynamics in denitrifying dispersed-growth reactors.

Understanding the relationship between microbial community dynamics and functional instability is an important step towards designing reliable biological water treatment systems. In this study, the community dynamics of two dispersed-growth denitrifying reactors were examined during periods of functional stability and instability. In both reactors during the period of functional instability, the effluent chemistry changed over time, with periods of high nitrate concentrations followed by periods of fluctuating nitrite concentrations. Community structure was examined by clone library analysis of the 16S rRNA gene. Community dynamics were investigated with terminal restriction fragment (T-RF) length polymorphism, and the functional diversity represented by T-RFs was assessed through nitrate reduction assays of representative isolates. During the period of functional instability, the community structure changed considerably, and the dynamics correlated significantly with effluent chemistry. The nitrite concentration was significantly correlated with the relative abundances of the nitrate-reducing Delftia- and Achromobacter-like T-RFs. The isolate representing the Acidovorax-like T-RF reduced nitrate directly to nitrogen in batch assays without the accumulation of any intermediates. The Acidovorax-like T-RF relative abundance was significantly negatively correlated with nitrite concentration, indicating that it was associated with good functional performance. The results of this study reveal a clear relationship between community dynamics and functional instability and the importance of diversity among nitrate-reducing populations within a denitrifying community.

Bacteria↗