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At least 631 records · Page 35Linked to original sources
PubMed2026

From dysbiosis to resilience: Microbiome engineering for sustainable shrimp aquaculture.

The intensification of shrimp aquaculture has increased exposure to disease, environmental perturbations, and antimicrobial pressure, making microbial stability increasingly relevant to sustainable production. Microbiome stability-encompassing resistance to disturbance and resilience of functional recovery-provides an ecological framework for understanding how shrimp and culture-environment microbial communities respond to intensive farming. This review examines the transition from microbial homeostasis to dysbiosis and evaluates how microbiome engineering could redirect disrupted communities towards resilient states. Evidence is integrated across the intestine, hepatopancreas, rearing water, sediment and biofloc to assess how host genetics, ontogeny, diet, culture conditions, antibiotics and pollutants shape microbiome assembly and destabilization. Disease-associated changes in acute hepatopancreatic necrosis disease, white faeces syndrome, Enterocytozoon hepatopenaei infection, and white spot syndrome virus infection are critically evaluated, with explicit separation of associations, pathogen-induced dysbiosis, and community-level causality. Established and emerging interventions-including probiotics, prebiotics, synbiotics, functional diets, biofloc management, phages, postbiotics, microbiota transplantation and synthetic microbial communities-are assessed according to their capacity to modify microbial function, persistence and recovery rather than taxonomic change alone. We further examine how multi-omics, microbiome-informed breeding, and environmental monitoring could support biomarker development, predictive decision support and context-specific intervention. We argue that progress requires a shift from taxonomic description to function-guided engineering, from endpoint comparisons to direct measurement of resilience, and from laboratory efficacy to reproducible farm-scale validation. Overall, microbiome management may contribute to more disease-resilient and sustainable shrimp production, provided that its effectiveness can be validated under commercial farming conditions.

Dysbiosis↗
PubMed2026

Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.

Cognitive impairment is increasing with global aging, yet mechanisms linking diet, the gut microbiome, and metabolism to cognitive function remain unclear. To investigate a diet-microbiome-metabolome axis associated with cognition, we integrated fecal metagenomics, diet, and multi-platform plasma metabolomics in 505 older adults from four ADRCs. Several microbes broadly associated with circulating metabolites were also linked to multiple measures of cognitive performance. These taxa exhibited coordinated metabolic signatures, with cognition-positive microbes associated with antioxidant, lipid, and microbial-host co-metabolites, and microbes negatively associated with cognition were linked to inflammatory and aromatic amino acid-derived metabolites. Dietary patterns, particularly the Healthy Eating Index Greens and Beans component, were associated with microbial composition and metabolomic structure. Mediation analyses supported a diet-microbe-metabolite-cognition pathway, while metabolites remained associated with cognition after accounting for microbial features. These findings highlight the metabolome as a central integrator of diet, microbial activity, and cognitive function.

Journal Article↗
PubMed2026

Chemo-selective proteomics in microbial systems.

SUMMARYOver the past two decades, the field of bioorthogonal chemistry has transitioned from emerging to an established cornerstone of scientific inquiry. In parallel, advances in microbial and host-microbe research have highlighted the need for functional approaches that extend beyond genomic and transcriptomic analyses to directly interrogate protein-level activity. Despite this need, proteomic strategies capable of resolving dynamic, heterogeneous, and low-abundance protein populations remain underdeveloped in microbial systems. This review highlights the convergence of chemo-selective proteomic technologies with microbial biology, focusing on bioorthogonal non-canonical amino acid tagging (BONCAT), activity- or affinity-based protein profiling, and bioorthogonal post-translational modifications, and comments on possibilities for novel applications for the use of click chemistry-based tools in the functional interrogation of microbial systems. Together, these strategies enable spatiotemporal resolution of protein synthesis, selective profiling of microbial subpopulations, and direct characterization of protein activity and regulation in complex biological contexts, including single-species cultures, host-associated environments, and polymicrobial communities. Continued development and utilization of these technologies will enable deeper mechanistic insight into how microbial systems function and respond to environmental and host-derived cues.

bioorthogonal chemistry↗
PubMed2003

Microbially mediated sulphide production in a thermal, acidic algal mat community in Yellowstone National Park.

Our objective in this study was to characterize prokaryotic sulphide production within the oxygenic, predominantly eukaryotic algal mat in an acidic stream, Nymph Creek, in Yellowstone National Park (YNP). We used microsensors to examine fluctuations in H2S and O2 concentrations over time through the vertical aspect of the approximately 3 mm mat in a 46-48 degrees C region of the creek. We also used analyses of PCR-amplified 16S rRNA gene sequences obtained from denaturing gradient gels, and PCR-amplified sequences of a functional gene associated with microbial sulphate respiration (dsrA) to characterize the bacterial community in the same region of the mat. During midday, photosynthesis rates were high within the first 500 micro m interval of the mat and high oxygen concentrations (600% air saturation) penetrated deeply (>1800 micro m) into the mat. During early evening and night, oxygen concentrations within the first 1100 micro m of the mat decreased over time from 60% air saturation (a.s) to 12% a.s. A precipitous decline in oxygen concentration occurred at a depth of 1100 micro m in all night measurements and anoxic conditions were present below 1200 micro m. Within this anoxic region, sulphide concentrations increased from nearly 0 micro M at 1200 micro m depth to 100 micro M at 2400 micro m depth. Enrichment cultures inoculated with Nymph Creek mat organisms also produced H2S. Sequence analyses of 16S rRNA and dsrA genes indicated the presence of at least five bacterial genera including species involved in dissimilative sulphate or sulphur reduction.

Eukaryota↗
PubMedDate not supplied

Impact of genetically modified crops on soil- and plant-associated microbial communities.

Transgenic or genetically modified plants possess novel genes that impart beneficial characteristics such as herbicide resistance. One of the least understood areas in the environmental risk assessment of genetically modified crops is their impact on soil- and plant-associated microbial communities. The potential for interaction between transgenic plants and plant residues and the soil microbial community is not well understood. The recognition that these interactions could change microbial biodiversity and affect ecosystem functioning has initiated a limited number of studies in the area. At this time, studies have shown the possibility that transgenes can be transferred to native soil microorganisms through horizontal gene transfer, although there is not evidence of this occurring in the soil. Furthermore, novel proteins have been shown to be released from transgenic plants into the soil ecosystem, and their presence can influence the biodiversity of the microbial community by selectively stimulating the growth of organisms that can use them. Microbial diversity can be altered when associated with transgenic plants; however, these effects are both variable and transient. Soil- and plant-associated microbial communities are influenced not only by plant species and transgene insertion but also by environmental factors such as field site and sampling date. Minor alterations in the diversity of the microbial community could affect soil health and ecosystem functioning, and therefore, the impact that plant variety may have on the dynamics of the rhizosphere microbial populations and in turn plant growth and health and ecosystem sustainability, requires further study.

Bacteria↗
PubMed1993

Biocompatibility: its future in prosthodontic research.

The future of prosthodontic research will involve replacing lost tissues by using scientific methods that evaluate biomaterials and treatment designs based on desired biologic outcomes. The present concept of a biocompatible material is one that elicits an appropriate host response in a specific application. To design optimal biomaterials, three interactive components should be considered: the chemical nature of the surface, the mediating pellicle layer, and microbial and host response. Surface chemistry determines which molecules are selectively absorbed onto a surface from oral fluids. The pellicle-coated surface should be designed to elicit a more desirable host response. Pellicle composition can be altered by chemically changing the surface, precoating surfaces with biological molecules, or using synthetic materials designed to mimic natural tissues. Several surface-sensitive techniques are available to assess these modifications, including vibrational spectroscopy, electron microscopy for chemical analysis, and bioanalytical methods. To develop more biocompatible materials, a further understanding of pellicle formation as a function of surface composition, microbial adhesion to biomaterials, and cellular reaction to implant biomaterials is necessary. This knowledge will facilitate development of new biologically based rationales for treatment modalities in restorative dentistry.

Biocompatible Materials↗
PubMed2006

Microbial community structure and dynamics of dark fire-cured tobacco fermentation.

The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.

Bacteria↗
PubMed2003

The ecological significance of biofilm formation by plant-associated bacteria.

Bacteria associated with plants have been observed frequently to form assemblages referred to as aggregates, microcolonies, symplasmata, or biofilms on leaves and on root surfaces and within intercellular spaces of plant tissues. In a wide range of habitats, biofilms are purported to be microniches of conditions markedly different from those of the ambient environment and drive microbial cells to effect functions not possible alone or outside of biofilms. This review constructs a portrait of how biofilms associated with leaves, roots and within intercellular spaces influence the ecology of the bacteria they harbor and the relationship of bacteria with plants. We also consider how biofilms may enhance airborne dissemination, ubiquity and diversification of plant-associated bacteria and may influence strategies for biological control of plant disease and for assuring food safety. Trapped by a nexus, coordinates uncertain Ever expanding or contracting Cannibalistic and scavenging sorties Excavations through signs of past alliances Consensus signals sound revelry Then time warped by viscosity Genomes showing codependence A virtual microbial beach party With no curfew and no time-out A few estranged cells seeking exit options, Looking for another menagerie. David Sands, Montana State University, Bozeman, February 2003

Bacterial Physiological Phenomena↗
PubMed2001

Infectious diseases: considerations for the 21st century.

The discipline of infectious diseases will assume added prominence in the 21st century in both developed and developing nations. To an unprecedented extent, issues related to infectious diseases in the context of global health are on the agendas of world leaders, health policymakers, and philanthropies. This attention has focused both on scientific challenges such as vaccine development and on the deleterious effects of infectious diseases on economic development and political stability. Interest in global health has led to increasing levels of financial support, which, combined with recent technological advances, provide extraordinary opportunities for infectious disease research in the 21st century. The sequencing of human and microbial genomes and advances in functional genomics will underpin significant progress in many areas, including understanding human predisposition and susceptibility to disease, microbial pathogenesis, and the development new diagnostics, vaccines, and therapies. Increasingly, infectious disease research will be linked to the development of the medical infrastructure and training needed in developing countries to translate scientific advances into operational reality.

Bioterrorism↗
PubMed2000

Special feature for the Olympics: effects of exercise on the immune system: exercise-induced modulation of macrophage function.

Macrophages are important effector cells involved in phagocytosis, microbial killing and antitumour activity. Macrophages also display accessory cell function, in that they can present antigen to foster the development of T lymphocyte-mediated immunity. Recent work, including studies from this group, has demonstrated that acute and chronic exercise can affect many facets of macrophage biology. Manifestation of these effects depends on exercise intensity and duration, the function measured, the timing of measurement in relation to exercise and the concentration of the macrophage-activating stimulus. Exercise has potent stimulatory effects on phagocytosis, antitumour activity, reactive oxygen and nitrogen metabolism, and chemotaxis. Indeed, it has been shown that exercise training can increase macrophage antitumour activity in mice of different ages. However, not all functions are enhanced by exercise. Exercise-induced reductions in macrophage MHC II expression and antigen-presentation capacity have been documented. These findings bring up the possibility that exercise, and perhaps other stressors, activate macrophages for effector functions while downregulating accessory cell functions. To a large extent, the mechanisms responsible for the exercise-induced changes in macrophage function remain unknown, but may depend on exercise-induced changes in neuroendocrine factors. Future studies need to explore the effects in a mechanistic way and provide documentation as to their physiological significance.

Animals↗
PubMedDate not supplied

[Distribution and activity of microorganisms in the deep repository for liquid radioactive waste at the Siberian Chemical Combine].

The physicochemical conditions, composition of microbial communities, and the rates of anaerobic processes in the deep sandy horizons used as a repository for liquid radioactive wastes (LRW) at the Siberian Chemical Combine (Seversk, Tomsk oblast), were studied. Formation waters from the observation wells drilled into the production horizons of the radioactive waste disposal site were found to be inhabited by microorganisms of different physiological groups, including aerobic organotrophs, anaerobic fermentative, denitrifying, sulfate-reducing, and methanogenic bacteria. The density of microbial population, as determined by cultural methods, was low and usually did not exceed 10(4) cells/ml. Enrichment cultures of microorganisms producing gases (hydrogen, methane, carbon dioxide, and hydrogen sulfide) and capable of participation in the precipitation of metal sulfides were obtained from the waters of production horizons. The contemporary processes of sulfate reduction and methanogenesis were assayed; the rates of these terminal processes of organic matter destruction were found to be low. The denitrifying bacteria from the underground repository were capable of reducing the nitrates contained in the wastes, provided sources of energy and biogenic elements were available. Biosorption of radionuclides by the biomass of aerobic bacteria isolated from groundwater was demonstrated. The results obtained give us insight into the functional structure of the microbial community inhabiting the waters of repository production horizons. This study indicates that the numbers and activity of microbial cells are low both inside and outside the zone of radioactive waste dispersion, in spite of the long period of waste discharge.

Bacteria↗
PubMed2006

Identification of population dynamics in sulfate-reducing consortia on exposure to sulfate.

The microbial population structure and function of a mixed culture of sulfate-reducing bacteria (SRB) maintained in anaerobic continuous bioreactors were tracked before and after a major perturbation, which involved the addition of sulfate to the influent of a bioreactor when operated at steady state at 35 degrees C, pH 7.8 and a 2.5 day residence time with feed stream containing 10 and 15 kg m(-3) sulfate as terminal electron acceptor and 19.6 and 29.4 kg m(-3) ethanol as carbon source and electron donor, respectively. The population structure determined by fluorescence in situ hybridization (FISH), by using 16S rRNA-targeted oligonucleotide probes, was linked to the functional performance of the SRB in the reactor. Hybridization analysis using these 16S rRNA-targeted oligonucleotide probes revealed that a high concentration of sulfate was toxic for Desulfobacterium and Desulfobulbus. On the other hand, the Desulfococcus group was found to be the most dominant group of SRB in the feed stream containing 15 kg m(-3) sulfate as terminal electron acceptor and 29.4 kg m(-3) ethanol as carbon source and electron donor.

Bioreactors↗
PubMed2006

Functional analysis of human MUC7 mucin gene 5'-flanking region in lung epithelial cells.

The human MUC7 gene encodes a low-molecular-mass mucin glycoprotein that functions in modulation of microbial flora in the oral cavity and respiratory tracts. MUC7 gene expression is tissue- and cell-specific, with dominant expression in salivary gland acinar cells. To begin to understand the molecular mechanisms responsible for controlling MUC7 gene expression, we analyzed the promoter activity of MUC7 5'-flanking region in a human lung epithelial cell line A549. We demonstrated that MUC7 gene is expressed constitutively in this cell line and is upregulated by TNF-alpha stimulation. The promoter activities of a 2,762-bp fragment of the human genomic DNA (-2,732/+30 bp) and its deletion series, subcloned into a luciferase reporter vector, were characterized at the basal level and under stimulation by TNF-alpha. The results indicated that the minimal functional MUC7 promoter is in the region of -138/+30 bp. This region also revealed the greatest increase in the promoter activity upon TNF-alpha stimulation. Two putative AP1-binding elements and one NF-kappaB-binding element were identified within the proximal promoter. Further analyses demonstrated that mutations of these elements dramatically reduced specific DNA-protein binding ability and reporter gene expression. AP1 elements played an essential role in the constitutive expression, while the NF-kappaB element was crucially important in the response to TNF-alpha stimulation, demonstrating that TNF-alpha activates MUC7 transcription via NF-kappaB signaling pathway.

5' Flanking Region↗
PubMed1999

Mechanisms and assessment of lectin-mediated mitogenesis.

The discovery of lectin-mediated mitogenesis by Nowell in 1960 stimulated interest in the properties of lectins while advancing knowledge of immunology. Although some lectins are polyclonal activators both in vitro and in vivo, others may display a broad range of activities toward human lymphocytes. Indeed, the same lectin (e.g., wheat germ agglutinin or Datura lectin) may be mitogenic, comitogenic, or antimitogenic, depending on the experimental conditions. An individual lectin may bind to several glycoproteins on the lymphocyte surface, resulting in interactions that may or may not be functionally relevant, and that may have opposing effects. Studies with lectins and with monoclonal antibodies (MAbs) have established that a surprisingly large variety of cell-surface molecules can influence the initiation and regulation of lymphocyte activation and proliferation. Interactions between lymphocytes and accessory cells are crucial; some signals are cell-mediated, but others depend on soluble cytokines. Mitogenic lectins presumably bind to the T-cell receptor complex and also promote a positive costimulatory signal leading to the synthesis of interleukin 2 and interleukin 2 receptors (IL-2R). Nonmitogenic, comitogenic, and antimitogenic lectin activities also probably act via accessory molecules involved in costimulation. Plant lectin-animal lymphocyte interactions presumably have no physiological significance, but it is suggested that the former mimics microbial superantigens, which may function in the colonization of host cells. Mitogenic stimulation of lymphocytes can be assessed in several ways. The standard technique measures [3H]-thymidine incorporation into DNA, but nonradioactive procedures are also available.

Animals↗
PubMed2000

New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress.

Globin-like oxygen-binding proteins occur in bacteria, yeasts and other fungi, and protozoa. The simplest contain protohaem as sole prosthetic group, but show considerable variation in their similarity to the classical animal globins and plant globins. Flavohaemoglobins comprise a haem domain homologous to classical globins and a ferredoxin-NADP+ reductase (FNR)-like domain that converts the globin into an NAD(P)H-oxidizing protein with diverse reductase activities. In Escherichia coli, the prototype flavohaemoglobin (Hmp) is clearly involved in responses to nitric oxide (NO) and nitrosative stress: (i) the structural gene hmp is upregulated by NO and nitrosating agents; (ii) purified Hmp binds NO avidly, but also converts it to nitrate (aerobically) or nitrous oxide (anaerobically); (iii) hmp mutants are hypersensitive to NO and nitrosative stresses. Here, we review recent advances in E. coli and the growing number of microbes in which globins are known, draw particular attention to the essential chemistry of NO and related reactive species and their interactions with globins, and suggest that microbial globins have additional functions unrelated to 'NO' stresses.

Animals↗
PubMed2001

The effect of long-term mercury pollution on the soil microbial community.

The effect of long-term exposure to mercury on the soil microbial community was investigated in soil from three different sites along a pollution gradient. The amount of total and bioavailable mercury was negatively correlated to the distance from the center of contamination. The size of the bacterial and protozoan populations was reduced in the most contaminated soil, whereas there was no significant difference in fungal biomass measured as chitinase activity. Based on the number of colony morphotypes, moreover, the culturable bacterial population was structurally less diverse and contained a higher proportion of resistant and fast-growing forms. The profiles of amplified 16S rDNA sequences obtained from community DNA by denaturating gradient gel electrophoresis (DGGE) also reflected the altered community structure and decreased diversity along the mercury gradient as expressed in terms of the number and abundance of bands. The functional potential of the microbial population measured as sole carbon source utilization by Ecoplates((R)) differed between the soils, but there was no change in the number of substrates utilized. The observed changes in the different soil microbial populations are probably a combination of both direct and indirect effects of the mercury contamination.

Journal Article↗
PubMed1999

Acetogenic and sulfate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the sea grass Halodule wrightii.

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizospheres that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacteria and clostridia were enriched in sediments colonized by the sea grasses Halodule wrightii and Thalassia testudinum compared to an adjacent unvegetated sediment. Most-probable-number analyses found that in contrast to butyrate-producing clostridia, acetogens and acetate-utilizing sulfate reducers were enriched by an order of magnitude in rhizosphere sediments. Although sea grass roots are oxygenated in the daytime, colorimetric root incubation studies demonstrated that acetogenic O-demethylation and sulfidogenic iron precipitation activities were tightly associated with washed, sediment-free H. wrightii roots. This suggests that the associated anaerobes are able to tolerate exposure to oxygen. To localize and quantify the anaerobic microbial colonization, root thin sections were hybridized with newly developed (33)P-labeled probes that targeted (i) low-G+C-content gram-positive bacteria, (ii) cluster I species of clostridia, (iii) species of Acetobacterium, and (iv) species of Desulfovibrio. Microautoradiography revealed intercellular colonization of the roots by Acetobacterium and Desulfovibrio species. Acetogenic bacteria occurred mostly in the rhizoplane and outermost cortex cell layers, and high numbers of sulfate reducers were detected on all epidermal cells and inward, colonizing some 60% of the deepest cortex cells. Approximately 30% of epidermal cells were colonized by bacteria that hybridized with an archaeal probe, strongly suggesting the presence of methanogens. Obligate anaerobes within the roots might contribute to the vitality of sea grasses and other aquatic plants and to the biogeochemistry of the surrounding sediment.

Acetates↗
PubMed2002

Relationship of the glyoxylate pathway to the pathogenesis of Cryptococcus neoformans.

Functional genomics has become a major focus in the study of microbial pathogenesis. This study used a functional genomic tool, differential display reverse transcription-PCR, to identify a transcriptional profile of Cryptococcus neoformans cells as they produced meningitis in an immunosuppressed host. This serial global gene expression during infection allowed for the identification of up- and down-regulated genes during infection. During this profiling, a single gene for the enzyme isocitrate lyase (ICL1) was found to be up regulated at 1 week of infection in a rabbit meningitis model and during a time of maximum host cellular response. The finding suggested that this enzyme and the glyoxylate shunt pathway are important to this yeast's energy production during infection. However, site-directed icl1 mutants had no apparent virulence defect in two animal models and no growth defect within macrophages. These observations suggest that although the yeast responded to a certain environmental cue(s) by an increase in ICL1 expression during infection, this gene was not necessary for progression of a C. neoformans infection. Compounds that specifically target only ICL1 are unlikely to cripple C. neoformans growth in vivo.

Amino Acid Sequence↗