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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↗
PubMed2004

Microbial-gut interactions in health and disease. Epithelial cell responses.

Intestinal epithelial cells are unique in that they represent the only host cells that are constantly interacting with a very large bacterial population in the lumen. The single monolayer of epithelial cells consists of subpopulations with distinct functions that include protection against luminal microorganisms. Although the microbial flora remains to be fully characterized, its normal relationship with the host intestinal epithelial cells appears to be predominantly symbiotic or commensal. The molecular complexity of the epithelial-microbial relationship has been shown in studies that have examined the establishment of the resident bacteria in germ-free mice. Recent work has also demonstrated the ability of resident bacteria to enhance epithelial protective responses. The mechanisms by which epithelial cells may avoid pro-inflammatory responses to resident microorganisms, while retaining the capacity to respond to pathogens, are also being characterized.

Enterobacteriaceae↗
PubMed2004

Microbial-gut interactions in health and disease. Interactions between dendritic cells and bacteria in the regulation of intestinal immunity.

Dendritic cells (DCs) are immunoregulatory antigen-presenting cells. DCs can be potent activators of naïve T cells and influence the generation and homing of effector lymphocytes; they can also induce regulatory mechanisms and maintain non-responsiveness. In part, these different outcomes are influenced by exposure of the DC to microbial products. The regulatory role of DCs is of particular importance at mucosal surfaces such as the intestine, where the immune system exists in intimate association with the external antigenic environment. Much of what we know about DCs has come from studies on the cells outside the gastrointestinal tract but information about gut DCs and their contribution to the specialized immune environment of the gut is now emerging. Here, we review current knowledge on gut DCs, suggest models for interactions between DCs and the commensal microflora in health and disease, and discuss gut DCs as targets for probiotic therapies.

Dendritic Cells↗
PubMed2001

Microbes and microbial toxins: paradigms for microbial-mucosal interactions. VIII. Pathological consequences of rotavirus infection and its enterotoxin.

Rotaviral infection in neonatal animals and young children leads to acute self-limiting diarrhea, but infected adults are mainly asymptomatic. Recently, significant in-roads have been made into our understanding of this disease: both viral infection and virally manufactured nonstructural protein (NSP)4 evoke intracellular Ca(2+) ([Ca(2+)]i) mobilization in native and transformed gastrointestinal epithelial cells. In neonatal mouse pup mucosa models, [Ca(2+)]i elevation leads to age-dependent halide ion movement across the plasma membrane, transepithelial Cl(-) secretion, and, unlike many microbial enterotoxins, initial cyclic nucleotide independence to secretory diarrhea. Similarities between rotavirus infection and NSP4 function suggest that NSP4 is responsible for these enterotoxigenic effects. NSP4-mediated [Ca(2+)]i mobilization may further facilitate diarrhea by signaling through other Ca(2+)-sensitive cellular processes (cation channels, ion and solute transporters) to potentiate fluid secretion while curtailing fluid absorption. Apart from these direct actions in the mucosa at the onset of diarrhea, innate host-mediated defense mechanisms, triggered by either or both viral replication and NSP4-induced [Ca (2+)]i mobilization, sustain the diarrheal response. This secondary component appears to involve the enteric nervous system and may be cyclic nucleotide dependent. Both phases of diarrhea occur in the absence of significant inflammation. Thus age-dependent rotaviral disease represents an excellent experimental paradigm for understanding a noninflammatory diarrhea.

Animals↗
PubMed2005

Utilising the synergy between plants and rhizosphere microorganisms to enhance breakdown of organic pollutants in the environment.

BACKGROUND: Phytoremediation is a promising technology for the cleanup of polluted environments. The technology has so far been used mainly to remove toxic heavy metals from contaminated soil, but there is a growing interest in broadening its applications to remove/degrade organic pollutants in the environment. Both plants and soil microorganisms have certain limitations with respect to their individual abilities to remove/breakdown organic compounds. A synergistic action by both rhizosphere microorganisms that leads to increased availability of hydrophobic compounds, and plants that leads to their removal and/or degradation, may overcome many of the limitations, and thus provide a useful basis for enhancing remediation of contaminated environments. MAIN FEATURES: The review of literature presented in this article provides an insight to the nature of plant-microbial interactions in the rhizosphere, with a focus on those processes that are relevant to the breakdown and/or removal of organic pollutants. Due consideration has been given to identify opportunities for utilising the plant-microbial synergy in the rhizosphere to enhance remediation of contaminated environments, RESULTS AND DISCUSSION: The literature review has highlighted the existence of a synergistic interaction between plants and microbial communities in the rhizosphere. This interaction benefits both microorganisms through provision of nutrients by root exudates, and plants through enhanced nutrient uptake and reduced toxicity of soil contaminants. The ability of the plant-microbial interaction to tackle some of the most recalcitrant organic chemicals is of particular interest with regard to enhancing and extending the scope of remediation technologies. CONCLUSIONS: Plant-microbial interactions in the rhizosphere offer very useful means for remediating environments contaminated with recalcitrant organic compounds. OUTLOOK: A better knowledge of plant-microbial interactions will provide a basis for improving the efficacy of biological remediations. Further research is, however, needed to investigate different feedback mechanisms that select and regulate microbial activity in the rhizosphere.

Biodegradation, Environmental↗
PubMed2002

Streptococcus pneumoniae evades complement attack and opsonophagocytosis by expressing the pspC locus-encoded Hic protein that binds to short consensus repeats 8-11 of factor H.

Streptococcus pneumoniae is an important cause of upper and lower respiratory tract infections, meningitis, peritonitis, bacterial arthritis, and sepsis. Here we have studied a novel immune evasion mechanism of serotype 3 pneumococci, which are particularly resistant to phagocytosis. On their surfaces the bacteria express the factor H-binding inhibitor of complement (Hic), a protein of the pneumococcal surface protein C family. Using radioligand binding, microtiter plate assays, surface plasmon resonance analysis, and recombinant constructs of factor H, we located the binding site of Hic to short consensus repeats (SCRs) 8-11 in the middle part of factor H. This represents a novel microbial interaction region on factor H. The only other ligand known so far for SCRs 8-11 of factor H is C-reactive protein (CRP), an acute phase protein that binds to the pneumococcal C-polysaccharide. The binding sites of Hic and CRP within the SCR8-11 region were different, however, because CRP did not inhibit the binding of Hic and required calcium for binding. Binding of factor H to Hic-expressing pneumococci promoted factor I-mediated cleavage of C3b and restricted phagocytosis of pneumococci. Thus, virulent pneumococci avoid complement attack and opsonophagocytosis by recruiting functionally active factor H with the Hic surface protein. Hic binds to a previously unrecognized microbial interaction site in the middle part of factor H.

Bacterial Proteins↗
PubMed2002

Antibiotic production by bacterial biocontrol agents.

Interest in biological control of plant pathogens has been stimulated in recent years by trends in agriculture towards greater sustainability and public concern about the use of hazardous pesticides. There is now unequivocal evidence that antibiotics play a key role in the suppression of various soilborne plant pathogens by antagonistic microorganisms. The significance of antibiotics in biocontrol, and more generally in microbial interactions, often has been questioned because of the indirect nature of the supporting evidence and the perceived constraints to antibiotic production in rhizosphere environments. Reporter gene systems and bio-analytical techniques have clearly demonstrated that antibiotics are produced in the spermosphere and rhizosphere of a variety of host plants. Several abiotic factors such as oxygen, temperature, specific carbon and nitrogen sources, and microelements have been identified to influence antibiotic production by bacteria biocontrol agents. Among the biotic factors that may play a determinative role in antibiotic production are the plant host, the pathogen, the indigenous microflora, and the cell density of the producing strain. This review presents recent advances in our understanding of antibiotic production by bacterial biocontrol agents and their role in microbial interactions.

Anti-Bacterial Agents↗
PubMedDate not supplied

Epidemiology of Clostridium difficile-induced intestinal disease.

The epidemiology of Clostridium difficile-induced intestinal disease is an intriguing subject about which there are few answers but many remaining questions. Although it is accepted that altered intestinal microecology (usually the result of antimicrobial therapy) is a major predisposition to disease, the details of microbial interactions are not yet known and clearly involve more than simple overgrowth of a resistant member of the resident flora. A variety of reservoirs of C. difficile are recognized. These include endogenous carriage, environmental contamination, and zoonoses, but the relative epidemiologic importance of these varied sources is yet to be determined. Because minor variations in methods for cultivation of C. difficile can markedly affect the ability to detect the organism, even the prevalence of endogenous carriage by various populations is not fully defined. There is good evidence for nosocomial acquisition of disease, but the frequency of this event and the usefulness of preventive measures need to be determined. The development of a typing system would provide a valuable tool for investigating many of the remaining questions. Finally, in addition to the recognized risk factors, which include the apparently predisposing alteration in intestinal microecology and exposure to C. difficile, there appear to be other, as yet undefined, variables that help to determine whether disease will occur. Perhaps the elucidation of the details of the pertinent microbial interactions as well as an understanding of the relevant host-pathogen relationships will provide important insights into the epidemiology of C. difficile-induced disease.

Anti-Bacterial Agents↗
PubMed1996

The diet and gut microflora influence the distribution of enteroendocrine cells in the rat intestine.

Several functions of the gut are locally influenced by peptides and biogenic amines released from enteroendocrine cells. The aim of the present study was to assess whether the luminal stimulus of diet or microbial flora or diet-microbial interactions have an influence on the distribution of enteroendocrine cells along the crypt-surface axes of the small and large intestine. The effects of diet and indigenous flora were investigated by comparing the numbers of argyrophil and serotonin immunoreactive cells in the jejunum and colon of germ free and conventional rats fed either a purified diet containing fine ingredients or a commercial diet containing crude fibre of cereal origin. The effect of human flora were analysed in germ-free rats inoculated with human faecal organisms. 1. Feeding the commercial diet reduced the number of argyrophil endocrine cells in the jejunum and serotonin immunoreactive cells in the colon of germ-free animals but increased the serotonin immunoreactive cells in the colon of conventional animals. 2. The rat flora increased the serotonin immunoreactive cells in the colon of animals fed a commercial diet and decreased in those fed a purified diet. 3. Inoculation of human flora increased the numbers of serotonin immunoreactive cells both in the jejunum and colon. The results provide evidence that the dietary changes and diet-microbial interactions can affect the regional number of enteroendocrine cells.

Animals↗
PubMed2003

Interaction of microbial populations in Steinernema (Steinernematidae, Nematoda) infected Galleria mellonella larvae.

Infection of Galleria mellonella larvae with the entomopathogenic nematodes Steinernema feltiae (A21 and R strains) and Steinernema glaseri (Dongrae) resulted in several species of bacteria, including the respective bacterial symbiont, Xenorhabdus spp., growing in the infected insect cadavers. These other bacteria were Enterococcus in all three nematode infections studied and Acinetobacter in the S. feltiae infections. The respective populations of these bacteria changed with time. Following infection of G. mellonella larvae with any one of the Steinernema sp., only Enterococcus bacteria were detected initially in the dead larvae. Between 30 and 50h post-infection Xenorhabdus bacteria were detected and concurrent with this Enterococcus population declined to zero. This was probably due to secondary metabolites with antibacterial properties that were produced by Xenorhabdus. In the S. feltiae (both R and A21 strains) infections a third bacterium, Acinetobacter, appeared at about 130h (in S. feltiae A21 infections) or 100h (in S. feltiae R infections) and increased in population size to approximately that of Xenorhabdus. It was demonstrated that Enterococcus, orginating from the G. mellonella digestive tract, was sensitive to the organically soluble antimicrobials produced by Xenorhabdus but Acinetobacter, which was carried by the nematode, was not.

Acinetobacter↗
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↗
PubMed1987

Substrate-inhibitor cooperative interactions with microbial dihydrofolate reductases.

Cooperativity in the binding of two substrates to an enzyme is a now well-established phenomenon. The x-ray crystallographic structure of the E. coli DHFR binary TMP complex compared with the ternary enzyme-NADPH-TMP complex suggests without too imaginative extrapolation, that the conformational changes resulting from the binding of one ligand aid in favorably positioning potential binding sites for the second ligand. Of greater importance is the fact that the extent to which inhibitor binding is enhanced by the binding of NADPH varies from species to species. To a significant extent, for example, the selectivity of TMP is enhanced by the increase in its binding to the E. coli enzyme when NADPH is present as compared with several mammalian enzymes. The reverse, negative cooperativity (a decrease in binding of a substance when moving from the binary to a ternary complex), is perhaps less common and certainly less well studied. The present paper deals with one such enzyme, the DHFR from C. albicans, and by reference to another, that from S. cerevisiae, where it is shown that the binding of substrates exhibit strong negative cooperativity. It was of interest also to determine the relationship between inhibitor/NADPH cooperativity and the relative insensitivity of N. gonorrhoeae to TMP. Equilibrium studies show that the binding of TMP in binary complex with this enzyme is exceedingly poor and that a 2,200-fold cooperative effect brings the gonococcal enzyme Ki within one order of magnitude of the E. coli enzyme Ki. Even so, it takes synergism of another sort (with sulfamethoxazole) and high doses to make co-trimoxazole therapy feasible for treating gonorrhoeae. The comparative results on the gonococcal enzyme for a family of near relatives of TMP are of interest also for the reason that the structure-activity relationships with this enzyme are quite different from those of the E. coli and other microbial enzymes. Finally, it should be pointed out that although the negative cooperativity found for the candida and saccharomyces enzymes is relatively large, it is the values of the substrate Michaelis constants that are physiologically relevant. The Km values of the yeast enzymes are within the range for other DHFR and therefore the intracellular activity of the enzymes should not be compromised.

Candida albicans↗
PubMed2004

Microbial-gut interactions in health and disease. Antibiotic-associated diarrhoea.

Most cases of antibiotic-associated diarrhoea (AAD) are directly or indirectly due to the alteration of gut microflora by antibiotics. 'Functional' diarrhoea, usually limited to a mild and brief change in stool frequency, is considered as the most frequent pattern of AAD. Reduced carbohydrate fermentation and impaired metabolism of bile acids have been claimed as the potential causes of this transient digestive discomfort but a critical analysis of the data supporting these theories is necessary. Alternatively, changes in the gut flora ecosystem allow pathogens to proliferate. Clostridium difficile is responsible for approximately 10% of cases of AAD and almost all cases of antibiotic-associated pseudomembranous colitis. The level of evidence which supports the potential responsibility of other candidate pathogens (Klebsiella oxytoca, enterotoxin-producing Clostridium perfringens and Staphylococcus aureus, Candida) needs to be appreciated according to the updated postulates of causality relationships between a bacterium and a disease.

Anti-Bacterial Agents↗
PubMed2004

Microbial-gut interactions in health and disease. Gastrointestinal cancer.

A combination of both environmental and genetic factors contributes to the vast majority of human cancers and in particular cancers of the gastrointestinal tract, including the stomach, colon and rectum. The mechanisms associated with cancer causation or prevention are largely unknown and the subject of much research. Many of these mechanisms implicate the metabolic activities of the bacterial flora normally resident in the gastrointestinal tract. This paper examines both the detrimental and beneficial consequences of bacterial activity of the gastrointestinal tract, focusing in particular on the stomach and large intestine.

Animals↗
PubMed2004

Microbial-gut interactions in health and disease. Probiotics.

The definition of probiotics has evolved from a live active culture which improves the balance of the gut microbiota composition to specific effects, in particular, the immunomodulatory potential of clearly defined strains. The strains with beneficial properties, potential sources of probiotics, most frequently belong to the genera Bifidobacterium and Lactobacillus, and some of these strains exhibit powerful anti-inflammatory properties. Indeed, probiotic therapy has attracted research interest in human infectious, inflammatory and allergic disease. The most fully documented disease altering the gut microbiota is acute infectious diarrhoea in childhood. Current probiotic research aims to provide safe but sufficient bacterial stimulus in order to avert deviant immune responsiveness related to allergic and inflammatory diseases. However, further rigorous scientific efforts are required to characterize the immunomodulatory potential of specific probiotic strains for these targets.

Bifidobacterium↗
PubMed2004

Microbial-gut interactions in health and disease. Epithelial cell responses.

Pathogenic bacteria use many strategies to secure their survival within the host. Enteropathogens exploit intestinal epithelial cells in many ways, including the manipulation of normal cellular functioning, or of cellular structural components, or by the induction of signalling pathways, such as the production of pro-inflammatory cytokines. However, the enterocyte warns the host of impending danger and, in turn, elicits a protective response. Pathogens are detected by epithelial cells owing to their vast array of surface antigens and secreted products. Epithelial cells have developed both extracellular and intracellular sensing proteins that function as a first line of defence against pathogens; this is followed by acquired immunity, namely IgA, which is used as reinforcement. Thus, in a game of constant attack and defence, the pathogen and the enterocyte aim to outsmart each other in an effort to survive.

Enterobacteriaceae↗