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PubMed2003

A thermodynamic interpretation of cell hydrophobicity in aerobic granulation.

Aerobic granulation can be regarded as a microorganism-to-microorganism self-immobilization process, in which cell hydrophobicity could be a decisive parameter in determining the microorganism-to-microorganism interaction and structural compactness of aerobic granules. This study looked into the thermodynamic interpretation of cell hydrophobicity in aerobic granulation; and a model that correlates microbial interaction and relative cell hydrophobicity defined as the ratio of cell hydrophobicity over cell hydrophilicity was derived. This model describes how cell hydrophobic and hydrophilic interactions affect aerobic granulation and offers deep insights into the thermodynamic mechanisms of microbial aggregation. The model prediction was in good agreement with experimental data. Results showed that aerobic granulation was a function of cell hydrophobicity over cell hydrophilicity, i.e. a high cell hydrophobicity strongly favors microbial aggregation and results in a more compact structure.

Aerobiosis↗

PubMed2005

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters.

AIMS: To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air. METHODS AND RESULTS: A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds. CONCLUSIONS: This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems (soils and sediments) where structuring of microbial communities according to depth has been observed.

Air Microbiology↗

PubMed1993

The management of peri-implant breakdown around functioning osseointegrated dental implants.

Peri-implant tissue breakdown can be the result of microbial action as well as of biomechanical and occlusal overload. The long-term goal of the treatment of peri-implant breakdown is to arrest the progression of the disease and to achieve a maintainable site for the patient. Peri-implant bony defects around functioning implants can be treated with either non-surgical or surgical (resective or regenerative) techniques. Bone regeneration is possible in selected peri-implant bony defects of functioning implants if appropriate surgical techniques are utilized and the etiologic cause is eradicated.

Alveolar Bone Loss↗

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↗

PubMed2026

Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.

Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.

Humans↗

PubMed2001

Hypersensitivity pneumonitis in a metal-working environment.

BACKGROUND: An outbreak of lung disease among workers in a metal-working plant included 16 biopsy-confirmed cases of hypersensitivity pneumonitis and additional patients with asthma, bronchiolitis and emphysema, usual interstitial pneumonitis, and sarcoidosis. Study design Clinical examination of patients; cross-sectional questionnaire survey of the outbreak plant and two control plant areas, one with and one without MWF exposures, in a separate facility; industrial hygiene survey with laboratory characterization of microbial flora; and immunological investigation. METHODS: Patients with suspected hypersensitivity pneumonitis underwent a clinical examination including detailed lung function, imaging, and tissue studies. A plant walk-through identified metal-working processes, microbial aerosols, and work practices. Microbial characteristics of the three microbial aerosol-producing processes were characterized. Antibodies to those agents were determined in patient sera. A questionnaire survey was conducted in the case plant and in two areas of a control plant, one with and one without metal-working fluids exposure. RESULTS: Thirty-nine (79.6%) patients described symptoms consistent with work-related lung disease, eight received other diagnoses, and two did not complete their examinations. Sixteen patients had hypersensitivity pneumonitis confirmed on biopsy. Mean decrements in lung forced expiratory volume in 1 s and force vital capacity from before to after work were similar in the 16 biopsy-confirmed cases of hypersensitivity pneumonitis ( - 6.3%; - 7.2%) and the 19 symptomatic patients without biopsies ( - 11.2%, - 10.1%). Symptoms were more common in the case plant than in a non-MWF control plant area. Three sources of water-based aerosols were identified that grew similar microbial flora. Although machining increased airborne bacterial levels, the increase was not related to the concentration of viable bacteria in the sumps. Antibody testing did not identify a specific single organisms. Endotoxin levels were similar in case and MWF control plant. CONCLUSIONS: Lung disease in environments with water-based aerosols may be more common than usually recognized. Patients with HP often present with only subtle abnormalities and may be missed if multiple clinical abnormalities are required to document disease.

Adult↗

PubMed2024

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model.

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Rhizosphere↗

PubMed2003

How not to get bugged by bugs: mechanisms of cellular tolerance to microorganisms.

PURPOSE OF REVIEW: Advances in the characterization of the receptors and signaling pathways involved in the response to infection have led to a more detailed understanding of cellular tolerance to endotoxin and other microbial components. This review summarizes recent progress in the field, particularly in relation to the molecular mechanisms that underlie the development of tolerance to microorganisms. RECENT FINDINGS: The identification of Toll-like receptors as major sensors of microbial molecules has led to numerous studies of their function in tolerant cells. Decreased Toll-like receptor expression, altered interactions between the Toll-like receptors and intracellular signal transducers, and decreased expression or activity of downstream signaling molecules have all been implicated. Upregulation of specific proteins that inhibit Toll-like receptor signaling has also been described. Apart from these general mechanisms, special features of the intestinal microenvironment and its resident cells also contribute to making the gut hyporesponsive to microorganisms. SUMMARY: The application of gene knockout technology has highlighted the importance of macrophage tolerance in regulating innate immunity to microbial infection. Such studies have indicated that the failure of tolerance can lead to exaggerated inflammatory responses to intestinal bacteria, raising the possibility that defects in tolerance may be linked to conditions such as inflammatory bowel disease. Further characterization of this link will help in elucidating the pathogenesis of such conditions and in devising new approaches to treatment.

Journal Article↗

PubMed2004

Anatomical and functional evidence for a role of arginine-vasopressin (AVP) in rat olfactory epithelium cells.

The olfactory epithelium (OE) is composed of olfactory sensory neurons (OSNs) and sustentacular cells; it lies in the nasal cavity where it is protected by a thin mucus layer. The finely regulated composition of this mucus provides OSN with a suitable ionic environment. To maintain the functional integrity of the epithelium despite permanent physical, chemical and microbial aggressions, both OSNs and surrounding sustentacular cells are continuously renewed from globose basal cells. Moreover, the sense of smell is involved in so numerous behaviours (feeding, reproduction, etc.) that it has to cross-talk with the endocrine and neuroendocrine systems. Thus, besides its sensory function, the olfactory epithelium is thought to undergo a lot of complex regulatory processes. We therefore studied the effects of various neuropeptides on primary cultures of Sprague-Dawley rat olfactory epithelium cells. We found that arginine-vasopressin (AVP) triggered a robust, dose-dependent calcium increase in these cells. The cell response was essentially ascribed to the V1a AVP receptor, whose presence was confirmed by RT-PCR and immunolabelling. In the culture, V1a but not V1b receptors were present, mainly localized in neurons. In the epithelium, both subtypes were found differentially distributed. V1a-R were localized mainly in globose basal cells and at the apical side of the epithelium, in the area of the dendritic knobs of OSNs. V1b-R were strongly associated with Bowman's gland cells and globose basal cells. These localizations suggested potential multifaceted roles of a hormone, AVP, in the olfactory epithelium.

Animals↗

PubMed1992

The Jeremiah Metzger Lecture. Microbial defenses against killing by phagocytes.

Phagocytes are a key feature of defense against microorganisms. Phagocyte function is a complex system with many intricately involved components. Each of these components provides microorganisms with a target for countermeasures against phagocytes. We have discussed examples and purported mechanisms for microbial defenses against the steps involved in killing by phagocytes. Understanding the interplay of these host and pathogen factors leads to a better understanding of both normal host defenses and pathogenesis of disease.

Animals↗

PubMed2003

Epidermal Langerhans cells efficiently mediate CD1a-dependent presentation of microbial lipid antigens to T cells.

Langerhans cells are a critical component of skin immunity, capable of capturing protein antigens in the epidermis and presenting them to specific T cells in the context of major histocompatibility complex class II molecules. Recently, a major histocompatibility complex independent pathway of lipid antigen presentation has been identified and is mediated by molecules of the CD1 family (CD1a, CD1b, CD1c, and CD1d). Because Langerhans cells are professional antigen-presenting cells and express CD1a molecules prominently, we hypothesized that Langerhans cells might play a role in T cell responses directed against not only peptide antigens but also lipid antigens. Here, we show that freshly isolated immature Langerhans cells as well as mature Langerhans cells that have migrated from the epidermis are efficient in presenting foreign microbial lipid antigens to specific T cells whereas dermal dendritic cells express much less CD1a molecules and function inefficiently. Further, we found that Langerhans cells migrating from epidermal sheets that were exposed to microbial lipid antigens expressed lipid-antigen-loaded CD1a molecules on the cell surface, resulting in activation of specific T cells. These results underscore an outstanding ability of Langerhans cells to mediate CD1a-dependent lipid antigen presentation. Thus, Langerhans-cell-mediated skin immunity may involve T cell recognition of both peptide and lipid antigens.

Antigen Presentation↗

PubMed1995

Vitamin B12 in health and disease: part I--inherited disorders of function, absorption, and transport.

All of vitamin B12 in nature is of microbial origin. Cobalamin, as vitamin B12 should correctly be termed, is a large polar molecule that must be bound to specialized transport proteins to gain entry into cells. Entry from the lumen of the intestine under physiological conditions occurs only in the ileum and only when bound to intrinsic factor. It is transported into all other cells only when bound to another transport protein, transcobalamin II. Congenital absence or defective synthesis of intrinsic factor or transcobalamin II result in megaloblastic anemia. The Immerslund-Graesbeck syndrome, a congenital defect in the transcellular transport of cobalamin through the ileal cell during absorption, also presents with megaloblastic anemia, but with accompanying albuminuria. In most bacteria and in all mammals, cobalamin regulates DNA synthesis indirectly through its effect on a step in folate metabolism, the conversion of N5-methyltetrahydrofolate to tetrahydrofolate, which in turn is linked to the conversion of homocysteine to methionine. This reaction occurs in the cytoplasm, and it is catalyzed by methionine synthase, which requires methyl cobalamin (MeCbl), one of the two coenzyme forms of the vitamin, as a cofactor. Defects in the generation of MeCbl (cobalamin E and G diseases) result in homocystinuria; affected infants present with megaloblastic anemia, retardation, and neurological and ocular defects. 5'-Deoxyadenosyl cobalamin (AdoCbl), the other coenzyme form of cobalamin, is present within mitochondria, and it is an essential cofactor for the enzyme Methylmalonyl-CoA mutase, which converts L-methylmalonyl CoA to succinyl CoA. This reaction is in the pathway for the metabolism of odd chain fatty acids via propionic acid, as well as that of the amino acids isoleucine, methionine, threonine, and valine. Impaired synthesis of AdoCbl (cobalamin A or B disease) results in infants with methylmalonic aciduria who are mentally retarded, hypotonic, and who present with metabolic acidosis, hypoglycemia, ketonemia, hyperglycinemia, and hyperammonemia. Megaloblastic anemia does not develop in these children because adequate amounts of MeCbl are present, but the effect of methylmalonic acid on marrow stem cells may give rise to pancytopenia. Congenital absence of reductases in the cytoplasm, which normally reduce the cobalt atom in cobalamin from its oxidized to its reduced state (cobalamin C and D diseases), results in impaired synthesis of both MeCbl and AdoCbl. Both methylmalonic aciduria and homocystinuria therefore develop in these children, and they present with megaloblastosis, mental retardation, a host of neurological and ocular disorders, and failure to thrive; however, they do not have hyperglycinemia or hyperammonemia. A similar biochemical profile and clinical presentation is also seen in cobalamin F disease, which results from a defect in the release of cobalamin from lysosomes, following receptor-mediated endocytosis of the transcobalamin II-cobalamin complex into cells. It is important to recognize these inborn errors of cobalamin absorption, transport, or function as soon after birth as possible, because most respond (in some patients more fully than others) to parenteral administration of cobalamin. Delays in diagnosis can lead to grave clinical consequences.

Biological Transport↗

PubMed2006

[Microbial nucleic acids in the pathogenesis of glomerulonephritis].

Recent advances in the understanding of innate pathogen recognition revealed that nucleic acids have immunomodulatory functions in inflammation. A set of Toll-like pattern-recognition receptors recognize various types of microbial nucleic acids, i.e. double-stranded viral RNA (TLR3), single-stranded viral RNA (TLR7 and TLR8), and viral and bacterial CpG-DNA (TLR9). All of these TLRs are differentially expressed in the healthy and diseased kidney and TLR ligation was shown to initiate and modulate experimental glomerulonephritis. In this review we summarize the arising evidence in this field and discuss new hypotheses for the pathogenesis of kidney diseases that are triggered by infectious organisms.

Bacterial Outer Membrane Proteins↗

PubMedDate not supplied

Immunoregulation of murine leishmaniasis by interleukin-12.

Distinct phenotypic outcomes following infection of mice with Leishmania major are closely linked to the emergence of functionally dissimilar Th1 or Th2 CD4+ T-cell responses early in the course of disease. This model of T-cell-dependent microbial pathology has proven useful for the study of cytokine regulatory and effector functions in vivo. To this end, the causal relationships linking synthesis of IFN gamma to cure and of IL4 to disease exacerbation have already been well characterized. IL12 also has a defined role in shaping the immune response against L. major. Early treatment with recombinant IL12, or vaccination using IL12 as an adjuvant, protects genetically susceptible hosts from progressive infection. Protective mechanisms include both suppression of deleterious Th2 cell responses and amplification of beneficial Th1 cell activities. Although Leishmania are poor stimuli for macrophage-derived IL12 when compared to bacteria and other protozoa, in vivo production during infection can be indirectly demonstrated by the worsening of leishmaniasis that follows anti-IL12 injection in normally resistant mice. Whether IL12 production during infection represents constitutive or regulated synthesis by infected macrophages is unresolved and deserves further exploration.

Animals↗

PubMed2006

Separate pathways for O acetylation of polymeric and monomeric sialic acids and identification of sialyl O-acetyl esterase in Escherichia coli K1.

O acetylation at carbon positions 7 or 9 of the sialic acid residues in the polysialic acid capsule of Escherichia coli K1 is catalyzed by a phase-variable contingency locus, neuO, carried by the K1-specific prophage, CUS-3. Here we describe a novel method for analyzing polymeric sialic acid O acetylation that involves the release of surface sialic acids by endo-N-acetylneuraminidase digestion, followed by fluorescent labeling and detection of quinoxalinone derivatives by chromatography. The results indicated that NeuO is responsible for the majority of capsule modification that takes place in vivo. However, a minor neuO-independent O acetylation pathway was detected that is dependent on the bifunctional polypeptide encoded by neuD. This pathway involves O acetylation of monomeric sialic acid and is regulated by another bifunctional enzyme, NeuA, which includes N-terminal synthetase and C-terminal sialyl O-esterase domains. A homologue of the NeuA C-terminal domain (Pm1710) in Pasteurella multocida was also shown to be an esterase, suggesting that it functions in the catabolism of acetylated environmental sialic acids. Our combined results indicate a previously unexpected complexity in the synthesis and catabolism of microbial sialic and polysialic acids. These findings are key to understanding the biological functions of modified sialic acids in E. coli K1 and other species and may provide new targets for drug or vaccine development.

Acetylation↗

PubMed2005

Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE).

To study the structure of microbial communities in the biological hydrogen production reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gradient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. and Ethanologenbacterium sp.), beta-proteobacteria (Acidovorax sp.), gamma-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase of Ethanologenbacterium sp., Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types of Clostridium sp. Acidovorax sp., Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the co-metabolism of microbial community played a great role of biohydrogen production in the reactors.

Bacteroides↗

PubMedDate not supplied

[Current aspects of the physiopathology of the infectious process. II. Cybernetic elements in the pathogenetic structure of infectious diseases].

The authors discuss the applicability of general cybernetic principles (the theory of systems and self-regulated mechanisms based on inversed connections) to the pathophysiologic structure of infections. With reference to concrete examples they outline the following elements: the appartenance of the infectious process to the notion of system (as conceived in the theory of systems), the previsible character of the functional potential of the structured system in the components of infection, and the sequental correspondence between system dynamics and the dynamics of the infectious process. Starting from the mechanism of action of the main microbial toxins, the aptitude of the latter to act upon the functional code of the macroorganism, altering the cellular and supracellular self-regulated biosystems, is demonstrated. Finally, the practical implications of assimilating cybernetic processes in the pathophysiology of infectious diseases are analyzed.

Bacterial Infections↗

PubMed2006

Development of AFLP-derived, functionally specific markers for environmental persistence studies of fungal strains.

The ability to rapidly identify and quantify a microbial strain in a complex environmental sample has widespread applications in ecology, epidemiology, and industry. In this study, we describe a rapid method to obtain functionally specific genetic markers that can be used in conjunction with standard or real-time polymerase chain reaction (PCR) to determine the abundance of target fungal strains in selected environmental samples. The method involves sequencing of randomly cloned AFLP (amplified fragment length polymorphism) products from the target organism and the design of PCR primers internal to the AFLP fragments. The strain-specific markers were used to determine the fate of three industrially relevant fungi, Aspergillus niger, Aspergillus oryzae, and Chaetomium globosum, during a 4 month soil microcosm experiment. The persistence of each of the three fungal strains inoculated separately into intact soil microcosms was determined by PCR analyses of DNA directly extracted from soil. Presence and absence data based on standard PCR and quantification of the target DNA by real-time PCR showed that all three strains declined after inoculation (approximately 14-, 32-, and 4-fold for A. niger, A. oryzae, and C. globosum, respectively) but remained detectable at the end of the experiment, suggesting that these strains would survive for extended periods if released into nature.

Aspergillus niger↗