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PubMed1998

Highly virulent pathogens--a post antibiotic era?

The spectrum of infectious diseases is changing rapidly. Emerging infectious agents present an intriguing constellation of nosocomial challenges. Antimicrobial resistance results in increased morbidity, mortality and costs of health care. Resistance to antimicrobial agents has been recorded since 1940 with penicillin resistant Escherichia coli (E coli) (Abraham and Chain 1940). A similar pencillin resistance was reported in 1944 in Staphylococus aureus (S. aureus) (Kirby 1944) Even before the widespread global use of penicillin, resistance had already been detected in both gram-positive and gram-negative organisms. The 1990s herald the era of multiple drug resistance. To grasp further the enormity and complexity of our modern antimicrobial resistance problem, one only needs to think about how many--how fast--and in how many settings (hospitals, clinics, outpatients nursing and long term facilities, etc), these pathogens have developed antimicrobial resistance: Multiple drug-resistant Mycobacterium tuberculosis, penicillin-resistant Streptococcus pneumonia, fluconzole-resistant Candida, methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococci (VRE) and now S. aureus with reduced susceptibility to vancomycin. Given the dramatic increase in the incidence of multiple drug-resistant organisms--and now--the mounting evidence of resistance transfer from one organism to another, we will certainly witness a combined growth of nosocomial pathogens, for which there are no antibiotic solutions. Appropriate infection control measures for such resistant strains depend, in part, on the mechanisms of genetic information exchanged among micro-organisms. Clearly we need to strengthen the basic tenets of infection prevention and control; hygiene, engineering and microbial barriers, to prevent transinfection. We need to control horizontal nosocomial transmission of organisms. Contaminated environmental surfaces are a reservoir for resistant organisms such as MRSA (Boyce et al 1997) and VRE (Karanfil et al 1992). Stringent infection control policies need to be developed and implemented. A comprehensively applied infection control programme will reduce the dissemination of resistant strains. Each patient care setting must examine its current practices and review the outcome efficacy. A consensus development conference to develop centres for disease control (CDC) formal guidelines against vancomycin intermediate-level resistant staphylococcus aureus (VISA) and vancomycin-resistant staphylococcus aureus (VRSA) may take a year or more to convene. This paper will examine the basic considerations currently offered by the CDC which may be valuable starting points for the enhancement of current infection control practices. Perspectives of the Society for Healthcare Epidemiology of America (SHEA) will also be included.

Anti-Bacterial Agents↗
PubMed1994

Survival and respiratory activity of genetically engineered Pseudomonas spp. exposed to antimicrobial agents in broth and soil.

The effectiveness of seven chemical disinfectants were tested against genetically engineered Pseudomonas spp. under optimal growth conditions. Each chemical was tested to determine how quickly 10(8) cells/ml Pseudomonas fluorescens C5t (containing Bacillus thuringiensis endotoxin gene) were killed in King's B broth at 30 degrees C. The minimal bactericidal concentrations (MBC) for calcium hypochlorite, benzalkonium chloride, Germiphene and Spectrum Clear Bath were 0.06% (w/v), 0.01% (w/v), 0.08% (v/v) and 0.044 (v/v), respectively. Virocidin X and CanLab Neutral did not kill P. fluorescens C5t at concentrations up to 20% (v/v). Baxter Bacdown was ineffective as a killing agent at concentrations up to 10% (v/v). These agents were also tested on P. aureofaciens RNL11 (lacZY), P. putida strains PaW8 and PaW340 (containing the plasmid pLV1013 encoding the xylE gene) and P. aeruginosa UG2L (lacZY and luxAB). All strains were killed by similar disinfectant concentrations with the exception of P. aeruginosa UG2L. The MBCs for this strain were double the MBCs for P. fluorescens C5t with all disinfectants used except for Spectrum Clear Bath, which was similar. Oxygen consumption and carbon dioxide evolution were used to assess the activity of P. fluorescens C5t inoculated in non-sterile soil in the presence of antimicrobial agents. Concentrations chosen were 0.1 and 1.0% (w/v) calcium hypochlorite, 0.01 and 0.1% (w/v) benzalkonium chloride, 0.1 and 1.0% (v/v) Germiphene and 0.1 and 1.0% (v/v) Spectrum Clear Bath. Over a 15-day period, the antimicrobial agents did not reduce respiratory activity of P. fluorescens C5t and indigenous soil micro-organisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Containment of Biohazards↗
PubMed1987

Problems and potential for in situ treatment of environmental pollutants by engineered microorganisms.

Molecular microbial ecology could provide tools for studying the structure and function of biodegradative microbial communities useful for in situ removal of environmental pollutants. Detection and monitoring of released organisms in the environment is required and DNA:DNA colony hybridization seems to be one of the highly sensitive and accurate technologies available for achieving this goal. A realistic and pragmatic view is required for analysis of the risks of environmental release of genetically-modified or engineered organisms.

Bacteria↗
PubMed2026

Optimizing eco-engineering pedogenesis of bauxite residues: Synergistic effects of humus and FeSO4/sulfur on microbial community and function.

Eco-engineered pedogenesis represents a promising approach for soil amelioration of bauxite residues (BRs) through exogenous organic matter. However, the role of humus in mediating this process remains poorly understood, significantly impeding the eco-engineering rehabilitation of BRs. In this study, we conducted pot experiments and subsequent microbial analysis to evaluate the individual improvement of humic acid (HA), fulvic acid (FA), and corn straw (SWZ) on the BRs' pedogenesis. High-throughput sequencing analysis revealed that both FA and SWZ were more effective than HA in steering microbial community assembly, as community diversity, dominant taxa enrichment, and species' interaction were all significantly higher (p < 0.05) in the FA/SWZ treatments than in HA treatments. Notably, the combination of FA with FeSO4 specifically enriched halophilic taxa, while FA coupled with sulfur (S) significantly improved the connectivity and complexity of the microbial network, as the average connection degree increasing from 1.008 to 1.113. Hydrolytic enzyme activity assays further indicated that FA, especially when combined with S, was the most effective treatment in restoring microbial function during BR pedogenesis. These findings highlight FA as a critical driver of microbial restructuring and functional recovery in BRs. Moreover, its efficacy can be enhanced by co-amendment with FeSO4 or S. This study provides important theoretical and practical insights for optimizing organic-inorganic amendment strategies to accelerate the eco-engineering pedogenesis of bauxite residues.

Humic Substances↗
PubMed2001

Comparative effects of a genetically engineered insect virus and a growth-regulating insecticide on microbial communities in aquatic microcosms.

The effects of a genetically engineered insect baculovirus on indigenous aquatic microbial communities were determined in closed, recirculating aquatic microcosms, and compared with the effects of a natural strain of the virus and of a growth-regulating insecticide, Dimilin. The recombinant virus was a nuclear polyhedrosis virus (NPV) of the spruce budworm (Choristoneura fumiferana (Cf)) with a lacZ marker gene inserted into the egt region of the CfNPV. The natural virus was Ireland strain CfNPV. Microbial measurement endpoints included decomposition activity (mass loss of organic material), respiration on two different substrates (O2 consumption), heterotrophic bacterial abundance (plate counts), and microbial community metabolic profiles (carbon source utilization patterns in Biolog GN microplates). Viral DNA of both the natural strain and the recombinant viruses, detected by polymerase chain reaction techniques, settled out of the microcosm water and accumulated on bottom substrates within 3 days of the microcosm inoculations. The viral DNA persisted in bottom substrates for the duration of the 21-day experimental period, although there was some evidence that the recombinant virus was less stable than the natural strain in particulate organic matter. No significant changes in microbial decomposition or respiration activity, bacterial abundance, or average metabolic responses were detected by a time trend analysis in microcosms inoculated with either the lacZ recombinant virus or the natural Ireland strain CfNPV. Significant effects on microbial decomposition and respiration activity were detected in microcosms treated with the growth-regulating insecticide at, and above, the expected environmental concentrations. Despite significant effects on microbial community functional attributes in Dimilin-treated microcosms, there were no detectable changes in community structure in terms of metabolic profiles or bacterial abundance.

DNA, Viral↗
PubMedDate not supplied

Metabolic engineering of propanediol pathways.

Microbial fermentation is an important technology for the conversion of renewable resources to chemicals. In this paper, we describe the application of metabolic engineering for the development of two new fermentation processes: the microbial conversion of sugars to 1,3-propanediol (1,3-PD) and 1,2-propanediol (1,2-PD). A variety of naturally occurring organisms ferment glycerol to 1,3-PD, but no natural organisms ferment sugars directly to 1,3-PD. We first describe the fed-batch fermentation of glycerol to 1,3-PD by Klebsiella pneumoniae. We then present various approaches for the conversion of sugars to 1,3-PD, including mixed-culture fermentation, cofermentation of glycerol and glucose, and metabolic engineering of a "sugars to 1,3-PD" pathway in a single organism. Initial results are reported for the expression of genes from the K. pneumoniae 1,3-PD pathway in Saccharomyces cerevisiae. The best naturally occurring organism for the fermentation of sugars to 1,2-PD is Thermoanaerobacterium thermosaccharolyticum. We describe the fermentation of several different sugars to 1,2-PD by this organism in batch and continuous culture. We report that Escherichia coli strains engineered to express either aldose reductase or glycerol dehydrogenase convert glucose to (R)-1,2-PD. We then analyze the ultimate potential of fermentation processes for the production of propanediols. Linear optimization studies indicate that, under aerobic conditions, propanediol yields that approach the theoretical maximum are possible and CO2 is the primary coproduct. Without the need to produce acetate, final product titers in the range of 100 g/L should be possible; the high titers and low coproduct levels should make product recovery and purification straightforward. The examples given in this paper illustrate the importance of metabolic engineering for fermentation process development in general.

Biotechnology↗
PubMed2003

Microbially influenced corrosion as a model system for the study of metal microbe interactions: a unifying electron transfer hypothesis.

The general term biomineralisation refers to biologically induced mineralisation in which an organism modifies its local microenvironment creating conditions such that there is chemical precipitation of mineral phases extracellularly. Most usually this results from an oxidation or reduction carried out by some microbial species, with the formation of a recognised biomineralised product. These reactions play a major role in microbial physiology and ecology, and are of central importance to such engineering consequences as microbial mining and microbially influenced corrosion. This paper will examine metal microbe interactions, both in naturally occurring microbial ecosystems and in two particular cases of biocorrosion, with the objective of putting forward a unifying hypothesis relevant to the understanding of each of these apparently disparate processes.

Anaerobiosis↗
PubMed2026

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom&#xa0;3 improved the neutral detergent fiber degradation (NDFD) by 20.39%&#xa0;averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom&#xa0;3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF,&#xa0;+&#x2009;11.47%). Genomic analysis revealed that the SynCom&#xa0;3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals↗
PubMed2026

Microbial diversity: the essential foundation for life on our planet.

The biological basis of life on Earth is microbial diversity that ensures human health, agricultural productivity, ecological balance, and ecosystem functioning. Microorganisms enable ecosystem restoration through bioremediation, maintain soil fertility, support plant growth, manage vital biogeochemical cycles, and contribute to climate resilience. Precision probiotics, postbiotics, faecal microbiota transplantation, and personalized microbiome medicine are the examples of emerging microbiome-based therapies that offer promising therapeutic opportunities. In humans, the gut microbial community is essential for immune regulation, metabolism, and disease prevention. In terrestrial ecological systems, interactions between plants, fungi, bacteria, and other soil microorganisms improve carbon sequestration, nutrient cycling, stress resilience, and sustainable agricultural productivity in the given effects of climate change. Emerging uses in agriculture, environmental restoration, and medicine are made possible by advancements in multi-omic techniques, synthetic microbial genomes, microbiome engineering, and artificial intelligence. Considering these developments, issues with ecological complexity, long-term validation, standardization, and field scale application still exist. Therefore, preserving microbial diversity is important for conserving ecological resilience and strengthening the One Health framework, which highlights the mutual dependance of health of animal, human, plant, and environment. This review summarizes what has been discovered about ecological and biomedical relevance of microbiome, identifies important research gaps, highlighting emerging technologies, and evaluates potential future directions for using microbiome to support planetary sustainability.

Bioremediation↗
PubMed2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes.

UNLABELLED: Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome. IMPORTANCE: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems.

Panicum↗
PubMed2001

Introduction to advantages and problems of shaken cultures.

Shaking bioreactors are the most frequently used reaction vessels in biotechnology and have been so for many decades. In spite of their large practical importance, very little is known about the characteristic properties of shaken cultures from an engineering point of view. The few publications available contain to some extent contradicting statements and conflicting advice concerning the correct operating conditions of shaking bioreactors. Depending on the investigated microbial system, the engineering parameters may more or less significantly influence the experimental results in a quantitative as well as in a qualitative manner. Unfortunately, these kind of interactions are often overlooked or ignored by scientists. Precise knowledge about the controlling hydrodynamic phenomena in shaking bioreactors and quantitative information about the physical parameters influencing the cultures are needed to assure reproducible and meaningful operating conditions. In this introduction, the state of the art of culturing microorganisms in shaking bioreactors is reviewed and some issues of their practical application in screening and process development projects are addressed.

Journal Article↗
PubMed2026

Microbial decaprenoxanthin: From understanding an extremophile-derived C50 carotenoid to its bioprocessing for large-scale applications.

Decaprenoxanthin (DPXT) is an unusual bacterial C50 carotenoid that has historically received limited attention despite its well-defined structure. For decades, carotenoid research and industrial development have been dominated by C40 carotenoids, leaving longer-chain carotenoids largely overlooked. Recent discoveries, particularly from microorganisms inhabiting Antarctic and other extreme environments, have repositioned DPXT as an adaptive pigment shaped by intense environmental pressures. Its extended polyene chain and membrane-associated behavior suggest roles in membrane stabilization and protection against ultraviolet radiation and oxidative stress, features that may hold relevance for food and biotechnological applications. This review integrates historical and recent knowledge on DPXT, covering its structural characteristics, biosynthetic pathways, ecological function, and emerging technological relevance. Special attention is given to microbial sources, particularly Actinomycetota from extreme environments, and to recent advances in microbial genomics, metabolic engineering, and sustainable bioprocess development that enable the production and exploration of C50 carotenoids beyond their native extremophilic context. The analysis highlights DPXT as a representative example of stress-resilient carotenoids, with physicochemical and membrane-interacting properties that may offer advantages for future food and biotechnological systems. Although significant challenges remain in cultivation strategies, yield optimization, and downstream recovery, advances in microbial cell factories and green extraction technologies open new opportunities for valorizing C50 carotenoids. This review bridges extremophile microbiology, carotenoid biochemistry, and sustainable food innovation, positioning DPXT as an emerging molecule that may expand the functional and structural landscape of carotenoids relevant to food science.

Carotenoids↗
PubMed1994

Computer aided microbial safety design of food processes.

To reduce the time required for product development, to avoid expensive experimental tests, and to quantify safety risks for fresh products and the consequence of processing there is a growing interest in computer aided food process design. This paper discusses the application of hybrid object-oriented and rule-based expert system technology to represent the data and knowledge of microbial experts and food engineers. Finite element models for heat transfer calculation routines, microbial growth and inactivation models and texture kinetics are combined with food composition data, thermophysical properties, process steps and expert knowledge on type and quantity of microbial contamination. A prototype system has been developed to evaluate changes in food composition, process steps and process parameters on microbiological safety and textual quality of foods.

Computer-Aided Design↗
PubMed1982

Fate in model ecosystems of microbial species of potential use in genetic engineering.

The changes in populations of Staphylococcus aureus, Bacillus subtilis, Salmonella typhimurium, Klebsiella pneumoniae, Agrobacterium tumefaciens, Rhizobium meliloti, and Saccharomyces cerevisiae were measured after their introduction into samples of sewage, lake water, and soil. Enumeration of small populations was possible because the strains used were resistant to antibiotics in concentrations and combinations such that few species native to these ecosystems were able to grow on agar containing the inhibitors. Fewer than 2 cells per ml of sewage or lake water and 25 cells per g of soil could be detected. A. tumefaciens and R. meliloti persisted in significant numbers with little decline, but S. aureus, K. pneumoniae, S. typhimurium, S. cerevisiae, and vegetative cells of B. subtilis failed to survive in samples of sewage and lake water. In sterile sewage, however, K. pneumoniae, B. subtilis, S. typhimurium, A. tumefaciens, and R. meliloti grew; S. cerevisiae populations were maintained at the levels used for inoculation; and S. aureus died rapidly. In sterile lake water, the population of S. aureus and K. pneumoniae and the number of vegetative cells of B. subtilis declined rapidly, R. meliloti grew, and the other species maintained significant numbers with little or a slow decline. The populations of S. aureus, K. pneumoniae, A. tumefaciens, B. subtilis, and S. typhimurium declined in soil, but the first four species grew in sterile soil. It is suggested that some species persist in environments in which they are not indigenous because they tolerate abiotic stresses, do not lose viability readily when starved, and coexist with antagonists. The species that fails to survive need only be affected by one of these factors.

Bacillus subtilis↗
PubMed2003

Engineering a mevalonate pathway in Escherichia coli for production of terpenoids.

Isoprenoids are the most numerous and structurally diverse family of natural products. Terpenoids, a class of isoprenoids often isolated from plants, are used as commercial flavor and fragrance compounds and antimalarial or anticancer drugs. Because plant tissue extractions typically yield low terpenoid concentrations, we sought an alternative method to produce high-value terpenoid compounds, such as the antimalarial drug artemisinin, in a microbial host. We engineered the expression of a synthetic amorpha-4,11-diene synthase gene and the mevalonate isoprenoid pathway from Saccharomyces cerevisiae in Escherichia coli. Concentrations of amorphadiene, the sesquiterpene olefin precursor to artemisinin, reached 24 microg caryophyllene equivalent/ml. Because isopentenyl and dimethylallyl pyrophosphates are the universal precursors to all isoprenoids, the strains developed in this study can serve as platform hosts for the production of any terpenoid compound for which a terpene synthase gene is available.

Alkenes↗
PubMedDate not supplied

Compartmentalization of metals within the diverse colloidal matrices comprising activated sludge microbial flocs.

Activated sludge floc from a wastewater treatment system was characterized, with regard to principal structural, chemical, and microbiological components and properties, in relation to contaminant-colloid associations and settling. Multiscale analytical microscopies, in conjunction with multimethod sample preparations, were used correlatively to characterize diverse colloidal matrices within microbial floc. Transmission electron microscopy, in conjunction with energy dispersive spectroscopy (EDS), revealed specific associations of contaminant heavy metals with individual bacterial cells and with extracellular polymeric substances (EPS). Floc structure was mapped from the level of gross morphology down to the nano-scale, and flocs were described with respect to settling properties, size, shape, density, porosity, bound water content, and EPS chemical composition; gross surface properties were also measured for correlation with principal floc features. Compartmentalization results based on 171 EDS analyses and representative high-resolution images showed that nano-scale agglomerations of (i) silver (100%) and (ii) zinc (91%) were confined almost entirely to EPS matrices while (iii) Pb (100%) was confined to intracellular granules and (iv) aluminum was partitioned between EPS matrices (41%) and intracellular matrices (59%). The results suggest that engineered changes in microbial physiology and/or in macromolecular EPS composition may influence metal removal efficiencies.

Flocculation↗