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Results for “microbial competition”

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At least 19 recordsLinked to original sources

PubMed2026

Carbon metabolic homogenization is linked to microbial competition and antimicrobial resistance in soils under forest-to-cropland conversion.

Global agricultural expansion by converting natural forests into croplands often leads to soil functional homogenization and antimicrobial resistance enhancement, threatening ecosystem services. However, the associations between microbial carbon metabolic homogenization and antimicrobial resistance remain largely unknown. Here, we collected 240 paired forest and cropland soil samples from the most intensively farmed Yangtze River Basin in China, and constructed a novel framework based on microbial functional traits to decipher the role of carbon metabolic homogenization on antimicrobial resistance via microbial competition for metabolites. Using genome-scale metabolic models, we found that carbon metabolic homogenization was associated with a shift in microbial interactions from cooperation toward competition, with a 45.6% increase in competitive interactions that coincided with a 35.6% higher antimicrobial resistance gene (ARG) diversity. This shift was accompanied by smaller genome sizes and higher 16S rRNA copy numbers, indicating fast-growing, resource-acquisitive microbial strategies. Metabolic transfer analyses further revealed less cooperation relationships among microbial communities in cropland soils than in forest soils, indicating an intensified battle for communal metabolites and an attenuated exchange for complementary metabolites. Together, these findings provide a new framework to understand the association between carbon metabolic homogenization and soil antimicrobial resistance risks from the perspective of microbial traits and interactions under land use change.

Soil Microbiology↗

PubMed1991

Role of the competitive microbial flora in the radiation-induced enhancement of ochratoxin production by Aspergillus alutaceus var. alutaceus NRRL 3174.

The radiation sensitivity and the toxigenic potential of conidiospores of the fungus Aspergillus alutaceus var. alutaceus were determined after irradiation with 60Co gamma rays and high-energy electrons. Over the pH range of 3.6 to 8.8, the doses required for a 1 log10 reduction in viability based on the exponential portion of the survival curve ranged from 0.21 to 0.22 kGy, with extrapolation numbers (extrapolation of the exponential portion of the survival curve to zero dose) of 1.01 to 1.33, for electron irradiation, and from 0.24 to 0.27 kGy, with extrapolation numbers of 2.26 to 5.13, for gamma irradiation. Nonsterile barley that was inoculated with conidia of the fungus and then irradiated with either electrons or gamma rays and incubated for prolonged periods at 28 degrees C and at a moisture content of 25% produced less ochratoxin A with increasing doses of radiation. Inoculation of barley following irradiation resulted in enhanced ochratoxin levels compared with unirradiated controls. In these experiments, inoculation with 10(2) spores per g produced greater radiation-induced enhancement than inoculation with 10(5) spores per g. There was no radiation-induced enhancement when the barley was surface sterilized by chemical means prior to irradiation. These results are consistent with the hypothesis that a reduction in the competing microbial flora by irradiation is responsible for the enhanced mycotoxin production observed when nonsterile barley is inoculated with the toxigenic fungus A. alutaceus var. alutaceus after irradiation.

Aspergillus ochraceus↗

PubMed2026

Parental niche construction buffers microbial and competitive challenges and drives offspring dependence in burying beetles.

Parents across diverse taxa modify the biotic or abiotic environments of their offspring. Such modifications may constitute ecological inheritance and are central to developmental niche construction, whereby organisms shape developmental conditions and selective pressures experienced by the next generation. Despite its theoretical importance, parental niche construction is often studied under simplified conditions or by focusing on single components of care, limiting our understanding of how multiple parental modifications interact in ecologically relevant contexts, whether they buffer environmental heterogeneity, and how this shapes offspring development and evolutionary trajectories. Using the burying beetle Nicrophorus vespilloides, we investigated how parents jointly modify chemical and microbial properties of vertebrate carcasses, a highly contested resource on which offspring develop. We show that under natural microbial and competitive conditions, prehatch care enhances larval survival and growth, alters cadaveric volatile emissions, and reduces carcass attractiveness to competitors. While soil type shapes carcass-associated microbial communities, parental care buffers these environmental effects, creating a more consistent microbiome and reducing environmentally induced larval mortality. Larvae of the related species Ptomascopus morio, which lacks prehatch carcass preparation, survived equally well on prepared and unmodified carcasses, whereas N. vespilloides larvae showed reduced survival on unmodified carcasses. This contrast is consistent with the hypothesis that N. vespilloides larvae have evolved a reliance on a parentally constructed developmental environment. Together, these findings show that parental care can constitute an integrated form of niche construction that reshapes developmental environments, enhances offspring performance, and may promote evolutionary feedback leading to increased offspring dependence on parental care.

Animals↗

PubMed2026

From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.

Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.

Microbiota↗

PubMed1992

The effects of agitation, sediment, and competition on the persistence and efficacy of Bacillus thuringiensis var. israelensis (Bti).

The persistence and efficacy of Bacillus thuringiensis var. israelensis (Bti) were examined in aquatic microcosms under varying conditions of agitation, sediment content, and microbial competition. Agitation was found to be the most important factor in maintaining persistence of Bti cells and the bioavailability of Bti toxin. Sediment acted to decrease efficacy by increasing settling of the toxic particles, but did not decrease the persistence of Bti cells were found, but efficacy of the Bti endotoxin was adversely affected.

Animals↗

PubMed1989

Molecular approaches to problems in biogeochemical cycling.

By using molecular probe techniques in combination with activity and expression measurements, it is possible to estimate bacterial populations in nature. This information can be exploited to study a number of important environmental problems. For instance, it will be possible to study ecosystem perturbation and microbial competition, by altering an ecosystem or a laboratory model of an ecosystem, and assessing corresponding changes in key activities and populations. In addition, regulation of activities in the laboratory can be compared to the response of activities and populations in situ, to develop an understanding of the key parameters that control these processes in nature. These types of approaches are important steps for determining the role of microorganisms in geochemical cycling, in both specific habitats and on a global basis.

Antigens, Bacterial↗

PubMed1976

Survival of coliform bacteria in sewage sludge applied to a forest clearcut and potential movement into groundwater.

Anaerobically digested dewatered sludge (10 to 15 cm thick) was applied to a forest clearcut as a fertilizer source in northwest Washington on gravelly glacial outwash soil. This sludge is not microbiologically sterile and may contain pathogenic organisms. Fecal coliform bacterial counts in sludge applied in summer (July) fell from 1.08 X 10(5) to 358/g in 204 days and to 0/g in 267 days. Dieoff appeared more rapid in winter (January)-applied sludge, when colnts fell from 1.2 X 10(5) to 20/g in 162 days. Initial death rates were related to sludge temperature, moisture, pH, physical composition, and microbial competition. Aftergrowth of fecal coliforms occurred in warm summer and fall months, but counts were of similar magnitude to background levels in forest soils, where a maximum count of 54/g was recorded. Total coliform counts in fresh sludge ranged from 1.4 X 10(4) to 1.9 X 10(6)/g. Numbers stabilized at 10(3) to 10(4)/g in spring, fall, and summer, with lower numbers in winter. Both total and fecal bacteria moved from the sludge to the soil beneath, but few penetrated past the first 5 cm. The soil acts as an effective biological filter. Few fecal coliform bacteria were recorded in the groundwater, generally being less than 5/100 ml and mostly 0/100 ml. A maximum count of 52/100 ml was recorded. Groundwater contamination from vertical movement of potential pathogens appears unlikely, but hazards from surface runoff and direct handling in the first year may arise.

Escherichia coli↗

PubMed1989

Improvement of DNA transfer frequency and transposon mutagenesis of Erwinia carotovora subsp. betavasculorum.

The production of antibiotics and their role in microbial competition under natural conditions can be readily studied by the use of transposon mutants. Several antibiotic-producing strains of Erwinia carotovora subsp. betavasculorum were unable to accept foreign DNA. A plasmid delivery system was developed, using ethyl methanesulfonate mutagenesis, which entailed isolating E. carotovora subsp. betavasculorum mutants able to accept foreign DNA and transfer it to other strains. This enabled transposon mutagenesis of a wild-type antibiotic-producing strain of E. carotovora subsp. betavasculorum. Twelve antibiotic-negative mutants were isolated, and one of these showed a reduction in antibiotic production in vitro. Many of these mutants also showed a reduction in their ability to macerate potato tissue. The mutants were classified into four genetic groups on the basis of their genetic and phenotypic characteristics, indicating that several genes are involved in antibiotic biosynthesis by E. carotovora subsp. betavasculorum.

Anti-Bacterial Agents↗

PubMed1992

Data for the properties of Listeria strains (a review).

It seems that taxonomy of listeriae is in a fluid stage. Between beta-haemolytic property and virulence of these bacteria a strong relationship has been demonstrated. These characters are coded by hlyA gene which seems to belong to a monocistronic unit. Virulent Listeria strains possess specific surface antigens and can enter as well as multiply in host cells. Their exact human virulence is not known. Listeriae can grow from around 0 to 42 degrees C and can survive either the effect of frost or of temperature of 48 degrees C. They may form biofilm on different surfaces. Their growth kinetics, persistance and heat resistance can be influenced by many factors (type of growth environment, pH, acidulants, salts, chemicals, antibiotics, plant substances, enzymes, humidity, atmosphere, temperature, prior temperature-effects, microbial competition and the length of influences). Radiation sensitivity of Listeria is usual. Plasmid mediated antibiotic resistant mutant of Listeria monocytogenes is verified.

Food Microbiology↗

PubMed1977

Competition for mixed substrates by microbial populations.

A model for the growth of an organism on multiple substrates was developed, assuming that each substrate has a competitive inhibition effect on the uptake of other substrates. The model was extended to examine mixed substrates, showing that the coexistence of several species at steady state in continuous cultures is possible, even when all the organisms all strongly prefer the one substrate. The diversity of nutrient sources in a real system may be a key factor in supporting a heterogeneous microbial population.

Bacteria↗

PubMed1991

Microbial polysaccharide, HS-142-1, competitively and selectively inhibits ANP binding to its guanylyl cyclase-containing receptor.

During the search for ANP receptor ligands of microbial origin, we isolated a novel polysaccharide, HS-142-1, from culture broth of Aureobasidium sp. HS-142-1 inhibited [125I]-rANP binding to ANP receptor in rabbit kidney cortex membranes with an IC50 of 0.3 mu g/ml, but gave no effects on specific binding of [125I]-Endothelin nor [125I]-Angiotensin II to their respective receptors in bovine lung membranes. HS-142-1 competitively and selectively inhibited ANP binding to its guanylyl cyclase-containing receptor purified from solubilized bovine adrenocortical membranes and blocked cGMP production elicited by ANP. HS-142-1 is the first non-peptide antagonist selective for ANP functional receptor and will be a powerful tool to elucidate the physiological functions of ANP.

Adrenal Cortex↗

PubMed2026

ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.

UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes. IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.

Metagenomics↗

PubMed2025

The Gfr Uptake System Provides a Context-Dependent Fitness Advantage to Salmonella Typhimurium SL1344 During the Initial Gut Colonization Phase.

Salmonella enterica serovar Typhimurium (S. Tm) is a major cause of foodborne diarrhea. However, in healthy individuals, the microbiota typically restricts the growth of incoming pathogens, a protective mechanism termed colonization resistance (CR). To circumvent CR, Salmonella strains can utilize private nutrients that remain untapped by the resident microbiota. However, the metabolic pathways and environmental niches promoting pathogen growth are still not completely understood. Here, we investigate the significance of the gfr operon in gut colonization of S. Tm, which is essential for the utilization of fructoselysine (FL) and glucoselysine (GL). These Amadori compounds are present in heated foods with high protein and carbohydrate contents. We detected FL in both mouse chow and the intestinal tract of mice and showed that gfr mutants are attenuated during the initial phase of colonization in the murine model. Experiments in gnotobiotic mice and competition experiments with Escherichia coli suggest that gfr-dependent fitness advantage is context-dependent. We conclude that dietary Amadori products like FL can support S. Tm gut colonization, depending on the metabolic capacities of the microbiota.

Salmonella typhimurium↗

PubMed2026

Computational mass spectrometry and genome mining guided discovery of metallophores produced by Microbulbifer.

Iron is an essential component of cellular biology. Thus, iron's low bioavailability is a key evolutionary pressure guiding microbial dynamics in the marine environment. Among marine bacteria, Microbulbifer is a chemically underexplored and functionally versatile bacterial genus, which is commonly associated with sponges, algae, corals, and sediments. Previously, genome analyses have revealed that Microbulbifer spp. can degrade polymers and synthesize natural products. Despite their recognized potential to produce secondary metabolites, siderophores are yet to be identified in Microbulbifer, and their iron acquisition strategies remain largely unknown. Here, we developed a comprehensive mass spectrometry-based query language code to determine siderophore production by Microbulbifer spp. in mono- and mixed cultures. Using this workflow, we discovered a new metallophore, which we named bulbichelin, as well as a suite of previously unreported petrobactins containing an unprecedented longer chain length acylation on the central spermidine moiety. We applied genome mining methods to describe the biosynthesis of these compounds. Using metal infusion mass spectrometry, we show that bulbichelins bind a variety of metals. Notably, neither of these compounds were produced in a co-culture of Microbulbifer with coral-derived pathogen Vibrio coralliilyticus Cn52-H1. Understanding how siderophores shape interspecies interactions between Microbulbifer spp. and other marine organisms will aid in unraveling the chemical and catalytic versatility of this genus and adaptation in nutrient deplete marine environment.

MassQL↗

PubMed1986

[Peptide inhibitors of a bacterial collagenase].

The properties of the cleavage site of collagen by collagenases remain discussed. The authors report their studies on the active site of the collagenase of a bacteria, achromobacter, based on two types of methods. The first type uses synthetic substrates, the second one enzymatic inhibitors. The results of both methods are reviewed. The inhibitors seem more sensitive than substrates to study the relation between structure and activity of the enzyme.

Alcaligenes↗

PubMed1992

The growth of pure and simple microbial competitors in a moving distributed medium.

The dynamics of pure and simple competition between two microbial species are examined for the case of interaction arising in a distributed and nonstagnant environment. The environment is modeled as a tubular reactor. It is shown that for relatively small values of the dispersion coefficient (i.e., for small, but nonzero, backmixing of the medium), the two competing populations can coexist in a stable steady state. It has been assumed that the species grow uninhibited and that if there are maintenance requirements they are satisfied from endogenous sources. From numerical studies it has been found that a necessary condition for coexistence is that the net specific growth rate curves of the two competitors cross each other at a positive value of the concentration of the rate-limiting substrate. The model equations have been numerically solved by using the methods of orthogonal and spline collocation.

Animals↗

PubMed2026

Cross-Kingdom Siderophores: Biosynthesis, Ecology, and Biotechnological Applications.

Microbial siderophores are high-affinity iron-binding compounds which are produced by bacteria, fungi, and actinomycetes to obtain iron and survive and interact with different species in an iron-deficient environment. While the conventional research on siderophore systems deals mainly with the study within the same taxa, modern researchers have increased their inclination toward cross-kingdom integration of siderophore behavior and their impact on host-associated environments. This can be largely attributed to differences in biosynthetic gene clusters, receptor systems, and regulatory networks, which produce distinct genotype-to-phenotype results determining microbial cooperation and competition. Current advancements in genomic research, together with omics studies like transcriptomics, proteomics, and metabolomics, have created newer insights into how siderophores function. However, the present literature evidences multiple major gaps in multi-omics data because the link between genomes and metabolomes remains weak due to inconsistent regulatory data sets and failure in identifying producer-consumer relationships in polymicrobial systems. Additionally, major constraints like molecular instability, delivery system limitations, host toxicity, limitations in upscaling, and regulatory issues delimit the use of siderophores in medical treatment, agricultural practices, and environmental biotechnology. This review aims to bridge the existing knowledge about siderophore biochemistry, biosynthesis, ecological functions, and genetic regulation across kingdoms while integrating multi-omics outlook with translational considerations. Thus, by connecting molecular mechanisms with evolutionary cross-talk, this study aims to provide a system-level framework in the world of siderophore-mediated iron uptake and therefore shapes future directions in emerging fields of microbial engineering, precision therapies, and sustainable biotechnology.

Fur regulation↗

PubMed1986

Iron transport-mediated antagonism between plant growth-promoting and plant-deleterious Pseudomonas strains.

Both plant growth-promoting Pseudomonas B10 and its yellow-green, fluorescent iron transport agent (siderophore) pseudobactin enhance potato growth and biologically control certain soil-borne fungal diseases in part by depriving specific root-colonizing endemic microorganisms including phytopathogens of iron(III), thus inhibiting their growth. The present study examines this mode of iron deprivation. The growth inhibition of certain bean-deleterious fluorescent pseudomonads by specific bean-beneficial fluorescent pseudomonads is due in part to the inability of susceptible strains to utilize siderophores from beneficial strains to transport iron(III). Conversely, deleterious strains which were able to utilize siderophores from beneficial strains were not inhibited. The ability of a given pseudomonad to utilize another pseudomonad's siderophore may depend upon its possessing a specific outer membrane receptor protein for that pseudomonad's ferric siderophore. Siderophore-mediated competition for iron in microbial systems appears to be a widespread phenomenon.

Binding, Competitive↗