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At least 19 recordsLinked to original sources
PubMed2025

Roles of microbial interactions in determining the establishment and function of synthetic consortium inoculants for soil applications.

Synthetic microbial consortium inoculants are emerging nature-based solutions for promoting sustainable agriculture and mitigating environmental challenges. However, despite promising results in simpler lab-scale trials, many inoculants fail to establish or perform satisfactorily in field conditions. One most critical yet least understood factor influencing inoculant effectiveness is the complex microbial interactions, both within consortium inoculants ("within-community" interactions) and between consortium inoculants and native soil communities ("cross-community" interactions). Here, we first discuss major negative and positive "within-community" interactions and highlight the importance to design consortium inoculants with positive interactions for improved stability and functionality. We then examine the bidirectional "cross-community" interactions once introducing consortium inoculants to soils. Soil native communities often create strong resistance to the invasion of inoculants. We discuss major drivers controlling the invasibility of native communities and various strategies increasing the invasiveness of consortium inoculants. We then discuss how consortium inoculants can reshape native communities, with implications for long-term ecosystem resilience and functioning. We propose future research efforts including advancing strategies for harnessing natural species from relatively untapped soil reservoirs and using high-throughput interaction profiling with multi-omics and computational tools to build compatible synthetic consortia with desirable functions; leveraging positive interactions and prebiotics to facilitate inoculant establishment; and assessing fully soil functional resilience over longer terms, including recognizing the importance of rare keystone taxa. By integrating with ecological theory, this review provides a comprehensive insight into microbial interactions to advance the design, application, and monitoring of synthetic consortium inoculants for enhancing soil health and ecosystem sustainability.

establishment↗
PubMed2025

Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.

Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.

Lakes↗
PubMed1992

[Appendicitis: microbial interactions and new pathogens].

The Authors present an exhaustive review on microbial agents of appendicitis by means of literature and personal research data. Thus, a detailed analysis is made on common autochthonous agents and their pathogenetic interactions and on less common exogenous bacterial, viral, mycotic, protozoan and helminthic agents with emphasis to the role of Yersinia enterocolitica. In fact this bacterium seems responsible for 3% to 8% of cases in accordance with literature and personal research data (more detailed, Y. enterocolitica has been isolated in 3.8% of 208 inflamed appendices from both pediatric and adults surgical florentine patients). At the end, the pathogenetic role of "new" other bacteria, like Buttiauxella agrestis, Aeromonas hydrophila, Arizona, Streptococcus lactis, is debated on the basis of a personal study.

Acute Disease↗
PubMed2026

Microbial Interactions with Protein Intake and Preterm Infant Body Composition: Secondary Analysis of a Randomized Trial.

BACKGROUND: Enteral protein supplementation improves preterm infant growth and may impact body composition and the gut microbiota. OBJECTIVES: This study aimed to identify the effects of additional enteral protein supplementation on the gut microbiota and microbial and clinical drivers of body composition. METHODS: Secondary analysis of a masked randomized trial of additional enteral protein vs. standard fortification in preterm infants born at 25 to 28 weeks of gestation (NCT03586102) was conducted. Stool samples at weeks 4 and 8 underwent 16S rRNA sequencing; functional potential was predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Body composition was measured by air-displacement plethysmography at 36 wk postmenstrual age (PMA). Least absolute shrinkage and selection operator (LASSO) regression with multivariable linear regression identified body composition predictors. RESULTS: Among 46 infants, gestational age (P = 0.16) and sex (P = 0.55) did not differ between groups. The protein group had higher week 4 Shannon diversity than standard fortification (median 1.2 vs. 0.87, P = 0.049). Week 4 Shannon diversity was positively correlated with fat-free mass z-score at 36 wk PMA (r2 = 0.34, P = 0.02). Adjusting for covariates, the protein group had higher Peptoniphilus (&#x3b2; = 1.6, Padj = 0.10) and lower Vibrio centered log-ratio abundance (&#x3b2; = -0.98, Padj = 0.10); 62 predicted metabolic pathways were lower in the protein group (false discovery rate < 0.20). In combined LASSO models, Bacillus abundance at week 4 was the strongest predictor of fat-free mass z-score (&#x3b2; = -0.17, P < 0.001; R2 = 0.80) and fat mass z-score (&#x3b2; = -0.31, P < 0.001; R2 = 0.66). CONCLUSIONS: Additional protein supplementation is associated with fat-free mass z-score and alterations to the gut microbiota. Clinical variables and microbial variables are key predictors of body composition, suggesting that nutrition, clinical factors, and the gut microbiota jointly contribute to body composition in extremely preterm infants. This study was registered at clinicaltrials.gov as NCT03586102 https://clinicaltrials.gov/study/NCT03586102 (registered in March 2020).

Humans↗
PubMed1992

Microbial interaction with animal cell surface carbohydrates.

Microbes have selected primarily carbohydrates for attachment to host animal cells. Recent studies have revealed essential characteristics in the recognition of receptor carbohydrates. Of importance is the property of recognizing also sequences placed inside an oligosaccharide chain, which differs from most animal antibodies. This is the basis for series of isoreceptors with the minimum receptor sequence in common but with separate neighbouring groups. There are families of microbial ligands that show different preferences for members within one series of isoreceptors, indicating only slight differences in the complementary binding sites of the proteins. Such differences may explain shifts in the selectivity of separate host tissues for infection. A second characteristic is the low affinity interaction often found where simple receptor-containing saccharides are unable to inhibit attachment. Technical possibilities are rapidly developing for the design of synthetic receptor analogues to be used in the therapy of clinical infections. This is urgently needed in cases where no rational therapy exists today.

Adhesins, Escherichia coli↗
PubMed2025

Pseudomonas aeruginosa phenazines dictate site-specific competitive interactions with Klebsiella pneumoniae.

Pseudomonas aeruginosa and Klebsiella pneumoniae are Gram-negative opportunistic pathogens that frequently colonize the human body and are major causes of infection. These bacteria are often co-isolated in polymicrobial urinary tract and lung infections, the latter of which is associated with increased disease severity and worse clinical outcomes. Despite their overlapping niches and clinical relevance, little is known about how these two pathogens interact and how those interactions influence human health. Given the growing recognition that microbial interactions are key drivers of disease, we investigated how P. aeruginosa and K. pneumoniae influence one another. We discovered an antagonistic interaction in which P. aeruginosa restricts the growth of K. pneumoniae. This inhibition is driven by phenazine production in P. aeruginosa, specifically the secondary metabolites pyocyanin and pyorubin, which are both necessary and sufficient to suppress K. pneumoniae growth. Using a diverse set of clinical isolates, we found that this antagonism is strain dependent. Both the susceptibility of K. pneumoniae to phenazines and the ability of P. aeruginosa to restrict K. pneumoniae growth varies between strains. Moreover, the necessity of phenazine production is specific to the site of infection. Together, these findings demonstrate that strain background and environmental context are critical determinants of pathogen interactions. Our work underscores the importance of considering these variables when investigating how microbial interactions influence infection and disease outcomes.

Journal Article↗
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&#xa0;mm, DFT) and Xiaofen (5&#xa0;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&#xa0;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↗
PubMed2026

Cooperative anaerobic catabolism of chlorinated organic compounds: implications for sustainable bioremediation.

Biodegradation research historically followed a reductionist approach focused on axenic (pure) cultures capable of catabolizing the specific contaminant(s) of interest. While this approach has substantially advanced our understanding of the microbiology, physiology, biochemistry, and genetics of contaminant degradation under laboratory conditions, it does not capture the complexity of natural and engineered environments. During in situ bioremediation, microbiomes are exposed to mixtures of contaminants, and microbial interactions profoundly influence contaminant transformation and fate. In anoxic environments, degradation of chlorinated compounds is often sustained by metabolic cooperation among taxonomically and physiologically distinct microorganisms. Through the exchange of metabolites such as hydrogen, formate, acetate, and other nutrients, microbial populations establish interdependent networks that overcome thermodynamic and physiological constraints, enabling self-sustaining systems of contaminant transformations that would be inefficient or impossible with individual organisms. We highlight examples of microbial interactions that underpin anaerobic catabolism of chlorinated contaminants, including systems resulting in self-sustained anaerobic bioremediation.

Biodegradation, Environmental↗
PubMed1992

The ES-242s, novel N-methyl-D-aspartate antagonists of microbial origin, interact with both the neurotransmitter recognition site and the ion channel domain.

ES-242-1 approximately 5 are novel microbial bioxanthracenes which do not contain nitrogen. The ES-242s inhibited the binding of [3H]TCP and [3H]CGS19755 to the N-methyl-D-aspartate (NMDA) receptor complex. They had no effect on the binding of the specific ligands for the non-NMDA receptor. The biochemical and pharmacological properties of ES-242-1 were fully examined since it is the most potent of the five compounds. ES-242-1 is highly specific for the NMDA receptor; it has no effect on other receptors. Kinetic analyses indicated that ES-242-1 inhibited the binding of [3H]TCP and [3H]CGS19755 in a competitive manner, respectively, suggesting that ES-242-1 interacts with both the transmitter recognition site and the channel domain. ES-242-1 selectively inhibited NMDA-induced Ca2+ influx in primary cultures of mouse hippocampal neurons. ES-242-1 also specifically blocked the increase in cyclic GMP accumulation induced by NMDA or L-glutamate in rat cerebellar slices. In a concentration range of 0.1-1.0 microM, ES-242-1 was as potent as MK-801 in preventing glutamate-induced neurotoxicity in primary cultures of mouse hippocampal neurons. These results show that ES-242-1 is a potent and specific antagonist for the NMDA receptor. The antagonistic properties of the ES-242s appear to be due to a novel mechanism of action at the NMDA receptor.

Animals↗
PubMed2025

Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus.

Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging (MSI) revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface. Integration of LC-MS/MS and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with Brachybacterium, and experiments with purified penicillic acid showed inhibition of a range of cheese rind bacteria. These findings show that A. westerdijkiae deploys a context-dependent arsenal of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.

Aspergillus westerdijkiae↗
PubMed2025

Metabolism and gene expression models for the microbiome reveal how diet and metabolic dysbiosis impact disease.

The gut microbiome plays a critical role in human health, spurring extensive research using multi-omic technologies. Although these tools offer valuable insights, they often fall short in capturing the complexity of microbial interactions that associate with disease onset, progression, and treatment. Thus, integration of multi-omics datasets with metabolic models is needed to predict associations between microbial activity and disease. Here, we automated the reconstruction of 495 metabolic and gene expression models (ME-models), overcoming the main limitation preventing the wide use of this approach. We integrated them with multi-omics data from patients with inflammatory bowel disease (IBD), identifying taxa associated with variations in amino acids, short-chain fatty acids, and pH in the gut of IBD patients. In general, this approach provides testable hypotheses of the metabolic activity of the gut microbiota, and the automated pipeline opens the opportunity to study microbial interactions in other biologically relevant settings using ME-models.

Humans↗
PubMed1976

Interaction of microbial DNA with cultured mammalian cells. Binding of the donor DNA to the cell surface.

Cultured fibroblasts grown in monolayer were incubated for a short time with radioactively labeled microbial DNA and diethylaminoethyl-dextran (DEAE-dextran), poly-L-lysine, or calcium phosphate, agents previously demonstrated by others to markedly enhance transfection. Immediately after such treatment of 1 by 10(-6)-1.5 by 10(6) cells with DNA, approx. 0.05-0.15 mug of donor DNA representing 10-30% of the input DNA became cell associated. In contrast, when the cells are similarly treated with only a DNA solution approx. 0.5-5% of the donor DNA was retained by the cells. More than 95% of the cell-associated donor DNA was shown to be bound to the surface of cells treated with polycation. It was also shown that in the absence of polycation treatment, most of the cell-associated donor DNA was bound to the cell surface.

Animals↗