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PubMed2026

Gut microbiota dynamics and metabolic pathways associated with bleomycin-induced pulmonary fibrosis progression.

BACKGROUND: Pulmonary fibrosis (PF) is a progressive respiratory disease characterized by epithelial injury, aberrant repair and excessive extracellular matrix deposition. Although the gut-lung axis is increasingly implicated in respiratory disorders, stage-resolved characterization of gut microbiota taxonomic and functional potential during PF development is limited. METHODS: We established a bleomycin-induced murine PF model and performed cross-sectional shotgun metagenomic sequencing of fecal samples from separate cohorts at three defined stages: baseline (control), day 7 (early fibrosis; M7), and day 14 (established fibrosis; M14). Microbial taxonomy, alpha/beta diversity, and predicted functional capacity were inferred using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZy) annotations; associations were assessed using Procrustes and Spearman correlation analyses. RESULTS: Histopathology and immunohistochemistry confirmed progressive fibrogenesis with increased TGF-β1 and α-SMA expression. Compared with baseline, bleomycin-treated groups exhibited stage-specific shifts in gut microbial composition, including depletion of mucin-associated taxa (e.g., Prevotella, Akkermansia muciniphila) and expansion of Muribaculaceae- and Clostridiaceae-affiliated taxa. Alpha and beta diversity metrics differed across groups. KEGG/CAZy-based annotations revealed predicted, stage-dependent changes in microbial metabolic potential, including early reductions in pathways related to amino acid and glycan metabolism (M7) and later increases in predicted starch/sucrose catabolism, phosphotransferase system (PTS) representation, and secondary bile acid biosynthesis (M14). Correlation analyses linked compositional shifts to these predicted functional changes. CONCLUSION: In a stage-resolved, cross-sectional study, bleomycin-associated pulmonary fibrosis was accompanied by compositional and predicted functional alterations in the gut microbiota. These data identify candidate taxa and predicted pathways for follow-up mechanistic testing, but functional (metabolomic) and causality experiments are required to confirm whether and how microbial changes contribute to PF pathogenesis.

Animals↗

PubMed2007

Modeling the growth and death kinetics of Salmonella in poultry litter as a function of pH and water activity.

Contaminated poultry litter, serving as a reservoir for Salmonella, can be linked to both food safety concerns when contaminated birds enter processing plants and environmental concerns when used as a fertilizer. Predictive modeling allows for the estimation of microbial growth or inactivation as a function of controlling environmental growth factors. A study was conducted to observe the combined effects of pH and water activity (A(w)) at a constant temperature on Salmonella populations in used turkey litter to predict microbial response over time. Litter, first pH-adjusted and then inoculated with a 3-strain Salmonella serovar cocktail to an initial concentration of approximately 10(7) cfu/g, was placed into individual sealed plastic containers with saturated salt solutions for controlling A(w). A balanced design including 3 A(w) values (0.84, 0.91, 0.96), 3 pH values (4, 7, 9), and a constant temperature of 30 degrees C was used, with litter samples periodically removed and analyzed for Salmonella populations, pH, and A(w). At each combination of environmental factors, the Churchill or exponential inactivation mathematical models were used to describe the growth and death of Salmonella over time. Salmonella populations exhibited growth (approximately 2 log) with little decline up to 42 d in litter environments of pH 7 and 9 and a A(w) of 0.96. As litter A(w) and pH levels were reduced, populations declined, with the most drastic reductions (approximately 5 log in 9 h) occurring in low-pH (4) and low-A(w) (0.84) environments. Generalized models for bacterial growth and death under grouped pH environments were successfully developed to predict Salmonella behavior in litter over time. These findings suggest that the best management practices and litter treatments that lower litter A(w) to < or =0.84 and pH to < or =4 are effective in reducing Salmonella populations. The use of a single equation to predict the growth and decline of Salmonella populations as a function of pH and A(w) has potential application for use in the development of effective pathogen control strategies at the farm level.

Animals↗

PubMed2001

Ubiquitous expression of the calcitonin-i gene in multiple tissues in response to sepsis.

Calcitonin precursors (CTpr), including procalcitonin, are important markers and also potentially harmful mediators in response to microbial infections. The source and function of CTpr production in sepsis, however, remains an enigma. In the classical view, the transcription of the CT-I gene is restricted to neuroendocrine cells, in particular the C cells of the thyroid. To better understand the pathophysiology of CTpr induction in sepsis, we used an animal model analog to human sepsis, in which bacterial infection is induced in hamsters by implanting Escherichia coli pellets ip. Compared with control hamsters, levels of CTpr were elevated several fold in septic plasma and in nearly all septic hamster tissues analyzed. Unexpectedly, CT-messenger RNA was ubiquitously and uniformly expressed in multiple tissues throughout the body in response to sepsis. Notably, the transcriptional expression of CT-messenger RNA seemed more widely up-regulated in sepsis than were classical cytokines (e.g. tumor necrosis factor-alpha and interleukin-6). Our findings, which describe a potentially new mechanism of host response to a microbial infection mediated by CTpr, introduce a new pathophysiological role for the CT-I gene.

Animals↗

PubMed2001

Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.

Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer phytoplankton bloom.

Journal Article↗

PubMed2005

Distribution and stability of sulfate-reducing prokaryotic and hydrogenotrophic methanogenic assemblages in nutrient-impacted regions of the Florida Everglades.

Although the influence of phosphorus loading on the Everglades ecosystem has received a great deal of attention, most research has targeted macro indicators, such as those based on vegetation or fauna, or chemical and physical parameters involved in biogeochemical cycles. Fewer studies have addressed the role of microorganisms, and these have mainly targeted gross informative parameters such as microbial biomass, enzymatic activities, and microbial enumerations. The objectives of this study were to characterize the dynamics of sulfate-reducing and methanogenic assemblages using terminal restriction fragment length polymorphism (T-RFLP) targeting the dissimilatory sulfite reductase (dsrA) and methyl coenzyme M reductase (mcrA) genes, respectively, and assess the impact of nutrient enrichment on microbial assemblages in the northern Everglades. T-RFLP combined with principal component analysis was a powerful technique to discriminate between soils from sites with eutrophic, transitional, and oligotrophic nutrient concentrations. dsrA T-RFLP provided a higher level of discrimination between the three sites. mcrA was a relatively weaker system to distinguish between sites, since it could not categorically discriminate between eutrophic and transition soil samples, but may be useful as an early indicator of phosphorus loading which is altering hydrogenotrophic methanogenic community in the transition zones, making them more similar to eutrophic zones. Clearly, targeting a combination of different microbial communities provides greater insight into the functioning of this ecosystem and provides useful information for understanding the relationship between eutrophication effects and microbial assemblages.

Biodegradation, Environmental↗

PubMed2006

Plant stomata function in innate immunity against bacterial invasion.

Microbial entry into host tissue is a critical first step in causing infection in animals and plants. In plants, it has been assumed that microscopic surface openings, such as stomata, serve as passive ports of bacterial entry during infection. Surprisingly, we found that stomatal closure is part of a plant innate immune response to restrict bacterial invasion. Stomatal guard cells of Arabidopsis perceive bacterial surface molecules, which requires the FLS2 receptor, production of nitric oxide, and the guard-cell-specific OST1 kinase. To circumvent this innate immune response, plant pathogenic bacteria have evolved specific virulence factors to effectively cause stomatal reopening as an important pathogenesis strategy. We provide evidence that supports a model in which stomata, as part of an integral innate immune system, act as a barrier against bacterial infection.

Abscisic Acid↗

PubMed2003

A method for multiple sequential analyses of macrophage functions using a small single cell sample.

Microbial pathogens such as bacillus Calmette-Guérin (BCG) induce the activation of macrophages. Activated macrophages can be characterized by the increased production of reactive oxygen and nitrogen metabolites, generated via NADPH oxidase and inducible nitric oxide synthase, respectively, and by the increased expression of major histocompatibility complex class II molecules (MHC II). Multiple microassays have been developed to measure these parameters. Usually each assay requires 2-5 x 10(5) cells per well. In some experimental conditions the number of cells is the limiting factor for the phenotypic characterization of macrophages. Here we describe a method whereby this limitation can be circumvented. Using a single 96-well microassay and a very small number of peritoneal cells obtained from C3H/HePas mice, containing as little as <=2 x 10(5) macrophages per well, we determined sequentially the oxidative burst (H2O2), nitric oxide production and MHC II (IAk) expression of BCG-activated macrophages. More specifically, with 100 micro l of cell suspension it was possible to quantify H2O2 release and nitric oxide production after 1 and 48 h, respectively, and IAk expression after 48 h of cell culture. In addition, this microassay is easy to perform, highly reproducible and more economical.

Animals↗

PubMed1999

Gammadelta T cells and Mycobacterium tuberculosis.

Since the first descriptions of mycobacterial reactivity for gammadelta T cells in 1989, studies of gammadelta T-cell responses to M. tuberculosis in humans and animal models have increased our understanding of the complex role(s) of this T-cell subset not only in the immune response to M. tuberculosis, but also to microbial pathogens in general. Although CD4+ T cells remain the dominant and critical T-cell subset in protection against M. tuberculosis, gammadelta T cells appear to have an important complementary role, which may be primarily expressed in and around maturing granulomas. This is a difficult area to study in humans. Gammadelta T cells are potent sources of IFN-gamma and competent cytotoxic effector cells, but differ from CD4+ T cells in the antigens they recognize and the manner in which M. tuberculosis-infected macrophages process and present antigens to these two subsets. One of the most fascinating features of Vgamma9/Vgamma2+ gammadelta T cells is their responsiveness to non-peptidic molecules. Solving the mechanism(s) of antigen recognition and presentation of these molecules to gammadelta T cells should help determine whether gammadelta T cells are responding to universal 'supernatigen'-like motifs expressed by a broad range of microbes or in fact discriminate among a diversity of peptidic and nonpeptidic microbial antigens. Enhanced understanding of the function of and antigen recognition by Vgamma9+/Vgamma2+ T cells is not only important for immunity to M. tuberculosis but also for T-cell responses to microbial pathogens in general.

Animals↗

PubMed2005

Regulation and signal transduction of toll-like receptors in human chorioncarcinoma cell lines.

PROBLEM: Toll-like receptors (TLRs) are expressed on placental cells. The aim of this study is to analyze signaling components activated in placenta cells after TLR ligand engagement. METHODS OF STUDY: In chorioncarcimoma cell lines the regulation of TLRs was determined by real time polymerase chain reaction as well as by fluorescence-activated cell sorter analysis. Activation of NF-kappaB was determined in a reporter assay system and the activation of the mitogen-activated protein kinase signaling pathways by immunoblot analysis. RESULTS: Both lipopolysaccharide (LPS) and DNA oligonucleotides containing unmethylated CpG motifs (CpG) induced the enhanced expression of TLR2 mRNA as well as a TLR2 surface protein expression. Functionally, incubation of JAR cells with microbial stimuli such as LPS activated NF-kappaB, as well as the phosphorylation of ERK1/2 and p38 MAP kinases and secretion of interleukin-8. CONCLUSION: The functional expression of TLRs on placental cells may play an important role in the initiation of an immune response in the developing fetus.

Cell Line, Tumor↗

PubMed2024

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater.

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Groundwater↗

PubMed1992

[The role of iron in immunologic processes].

Iron, apart a for long time well-known function connected with: transportation (hemoglobin), storage (myoglobin), and utilize (cytochromes, cytochrome oxidase) oxygen for respiration, has a critical role in host-pathogen interactions. Iron is essential for microbial growth, but also for immune function. The role of iron in infection, thermoregulation, acute lymphocytic leukemia, neoplasia, rheumatoid arthritis, stimulation of free radical reactions, and studies with iron chelation therapy are discussed.

Arthritis, Rheumatoid↗

PubMed2004

Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens.

The gastrointestinal tract is a complex ecosystem that associates a resident microbiota and cells of various phenotypes lining the epithelial wall expressing complex metabolic activities. The resident microbiota in the digestive tract is a heterogeneous microbial ecosystem containing up to 1 x 10(14) colony-forming units (CFUs) of bacteria. The intestinal microbiota plays an important role in normal gut function and maintaining host health. The host is protected from attack by potentially harmful microbial microorganisms by the physical and chemical barriers created by the gastrointestinal epithelium. The cells lining the gastrointestinal epithelium and the resident microbiota are two partners that properly and/or synergistically function to promote an efficient host system of defence. The gastrointestinal cells that make up the epithelium, provide a physical barrier that protects the host against the unwanted intrusion of microorganisms into the gastrointestinal microbiota, and against the penetration of harmful microorganisms which usurp the cellular molecules and signalling pathways of the host to become pathogenic. One of the basic physiological functions of the resident microbiota is that it functions as a microbial barrier against microbial pathogens. The mechanisms by which the species of the microbiota exert this barrier effect remain largely to be determined. There is increasing evidence that lactobacilli and bifidobacteria, which inhabit the gastrointestinal microbiota, develop antimicrobial activities that participate in the host's gastrointestinal system of defence. The objective of this review is to analyze the in vitro and in vivo experimental and clinical studies in which the antimicrobial activities of selected lactobacilli and bifidobacteria strains have been documented.

Animals↗

PubMed2006

Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.

UNLABELLED: The analysis of protein function is a challenge and a major bottleneck towards well-annotated and analysed microbial genomes. In particular, bacterial surface proteins present an opportunity for pharmacological intervention and vaccine development. We present Augur, an automatic prediction pipeline that integrates major surface prediction algorithms and enables comparative analysis, classification and visualization for gram-positive bacteria on a genomic scale. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/augur

Algorithms↗

PubMed1999

Recombinant microbial lipases for biotechnological applications.

Lipases, mainly of microbial origin, represent the most widely used class of enzymes in biotechnological applications and organic chemistry. Modern methods of genetic engineering combined with an increasing knowledge of structure and function will allow further adaptation to industrial needs and exploration of novel applications. Production of such tailored lipases requires their functional overexpression in a suitable host. Hence, this article describes the functional heterologous production of commercially important microbial lipases. Based on the knowledge of different lipases' substrate binding sites, the most suitable lipase for a particular application may be selected.

Bacillus↗

PubMed1986

Scanning electron microscopy of isolated epithelium of the murine gastrointestinal tract: morphology of the basal surface and evidence for paracrinelike cells.

By using the method of Bjerknes and Cheng, isolated murine gastrointestinal epithelial sheets were prepared for scanning electron microscopy. Examination of isolated epithelium from fundic stomach revealed numerous branched gastric glands. Parietal cells were easily detected bulging from the basal surface of the glandular epithelium. The basal surface membrane of parietal cells appeared smooth, with only sparse microvilluslike projections, whereas adjacent glandular cells had numerous 1- to 2-micron fingerlike projections which interdigitated laterally with similar processes from adjacent cells. Occasionally, paracrinelike cells having long cytoplasmic processes ranging from 10 to 20 micron in length were observed on the basal epithelial surface of the stomach and the colon, but not the small intestine. In isolated intestinal epithelia, the basal surface of crypt epithelial cells showed extensive cytoplasmic interdigitations, but no distinct morphology permitting recognition of individual cell types. Various stages of intestinal crypt bifurcation were seen. Craterlike spaces in the basal surface of crypt epithelium, presumably due to migrating leukocytes, were also numerous. Examination of the luminal surface of the isolated intestinal epithelium revealed that intimate associations between epithelium and mucosal-associated microorganisms were maintained, thus suggesting that minimal alterations in surface morphology were incurred by epithelial isolation. These observations on epithelial structure suggest that isolated gastrointestinal epithelia may be well suited for physiological studies of epithelial function and interactions with the microbial flora.

Animals↗

PubMed2005

Morphological engineering of Streptomyces hygroscopicus var. geldanus: regulation of pellet morphology through manipulation of broth viscosity.

Actinomycetes, especially members of the genus Streptomyces, are responsible for producing the majority of known antibiotics. The production of antibiotics by filamentous organisms is often dependent on the morphology and size distribution of the pellet population within the culture. Particle interaction and subsequent pellet formation are primarily dependent on the rate of collision of particles in culture, which is in turn, a function of fluid turbulence. The microbial polysaccharide xanthan gum was used to artificially regulate the apparent viscosity (mu(a)) of S. hygroscopicus fermentation broths with the aim of controlling particle interaction, aggregation and hence pellet formation. An increase in both pellet count and biomass concentration from approximately 2,000 to 8,000 pellets ml(-1) and 0.9-2.1 g l(-1) dry weight of biomass, as well a decrease in the mean pellet volume from 0.014 to 0.004 mm(3) was observed in cultures supplemented with 3 g l(-1) xanthan gum. The addition of xanthan gum significantly alters fluid rheology by increasing the mu(a). Counter-intuitively, an increase in the mu(a) within the experimental range examined resulted in an increase in the rate of gas-liquid mass transfer. This was attributed to the predominantly diffusive nature of oxygen transfer in shake flask cultures.

Culture Media↗

PubMed2006

Influence of the diet components on the symbiotic microorganisms community in hindgut of Coptotermes formosanus Shiraki.

Artificial diet was developed for rearing of lower termites (workers) Coptotermes formosanus. C. formosanus was fed with either wood powder of Japanese red pine, cellulose, cellobiose, or glucose for 30 days. The effect of carbon sources in the diet on the structure and function of the symbiotic intestinal microbial community and on the physiological activity of C. formosanus was studied. Three symbiont protozoa, Pseudotrichonympha grassi, Holomastigotoides hartmanni, and Spirotrichonympha leidyi, were found in the hindgut of C. formosanus that fed on the diets containing carbon sources with high molecular weight (MW). However, when artificial diets containing carbohydrate with low MW were used, both P. grassi and H. hartmanni disappeared, and only few S. leidyi were alive. This suggested that both P. grassi and H. hartmanni play important roles in the digestion and utilization of carbohydrate with high MW. The denaturing gradient gel electrophoresis analysis of bacterial community in the hindgut of termites showed that the similarity between intestinal bacteria community in termites fed with diets containing high-MW carbon sources and those with low MW was only about 40%. It was apparent that changes in diets resulted to changes in intestinal microbial community, and this in turn affected cellulase activity in C. formosanus.

Animals↗

PubMed1991

Molecular cross talk between epithelial cells and pathogenic microorganisms.

The conference brought together epithelial cell biologists and molecular microbiologists and emphasized that these seemingly diverse disciplines are intricately intertwined. The model systems discussed throughout the meeting emphasized the novel approaches available to address key issues and begin to understand the molecular details of responses triggered at the microbial-epithelial interface. For example, co-crystallization of native ligand-receptor complexes as well as biologically or chemically altered forms of these complexes will allow fine details of receptor-ligand interactions to be determined. This approach is critical in development of new generation antimicrobial agents. Furthermore, transfection techniques that allow receptor expression in model epithelia, development of representative animal model systems, and development of transgenic mouse strains will aid in dissecting microbial-epithelial interactions and will provide further advances in studies on pathogenesis and tissue and host tropism. We are only beginning to uncover the nature of the bidirectional regulatory signals that occur between microbes and hosts. We know little about how these signals relate to the disease state, to microbial virulence, or to immune function. Clearly the cross talk between cell biologists and microbiologists is an important step in unraveling the events occurring between microbes and eukaryotic cells.

Animals↗