Products Of Microbial Metabolism Research Articles

Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras.

Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEAc]) and assessing the relative placement of common sponge species in bivariate (δ13C and δ15N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.

Bio-economics of melanin biosynthesis using electromagnetic field resistant Streptomyces sp.-EF1 isolated from cave soil

Moving charges due to electric current create electromagnetic waves, which generate electromagnetic fields (EMFs). The low frequency EMFs are unlikely to cause adverse effects on living organisms; however, health-related incidents have prompted researchers to investigate the biochemical characteristics in microorganisms. We hypothesized that a diverse variety of microorganisms, i.e., bacteria, will respond to EMF and bio-stimulate microbial metabolic products of commercial significance. An EMF generator that produces a 10-mT-strength magnetic field was built in-house to investigate the magnetic response of microbial communities from cave soil samples. 16S rRNA sequencing was employed to identify three EMF-responsive isolates: Streptomyces sp., Arthrobacter sp., and Lysinibacillus sphaericus, designated as EF1, EF2, and EF3, respectively. Streptomyces sp.-EF1 showed a dark brown pigment identified as melanin on nutrient agar plates supplemented with 0.4 % L-tyrosine and L-DOPA. We also investigated the bio-economics of melanin biosynthesis, which revealed that waste shredded paper ($33.29 /g melanin) followed by starch ($256.03 /g melanin) were among suitable substrates for melanin biosynthesis under non-EMF condition. The most time-efficient melanin formation was achieved by starch under submerged fermentation (3.52 h/μg/mL) conditions. Shredded, laser-printer paper was noticed to be a cost-efficient process ($33.29 /g melanin) for melanin biosynthesis.

Bacterial metabolites of diet-derived lignans and isoflavones inversely associate with asthma and wheezing

Lignans and isoflavones are plant-derived chemicals with potent anti-inflammatory and antioxidant effects.1 Lignans are ubiquitous in Western diets, with flaxseeds containing the greatest amounts, while isoflavones are most abundant in soybeans (see Table E1 in this article's Online Repository at www.jacionline.org). The end product(s) of gut microbial metabolism of lignans is enterolactone2; metabolism of the isoflavone daidzein gives rise to equol and O-desmethylangolensin (O-DMA). Human studies demonstrate inverse associations between lignans and isoflavones and hormone-dependent cancers, cardiovascular disease, and osteoporosis,1 and improvements in asthma control are reported in those with high soy consumption.

The role of lactate on the immunomodulatory properties of the nonbacterial fraction of kefir

The identification of components responsible for the bioactive properties of functional foods is of central interest in the food industry. In particular, fermented dairy products that are of a health benefit to the consumer may exert those salutary effects through the constituent microorganisms per se and/or through other bioactive components. Kefir is a beverage obtained by the fermentation of milk with kefir grains containing different lactic- and acetic-acid bacteria plus yeasts. We studied the immunomodulatory capacity of the nonbacterial fraction of kefir through approaches involving biochemistry and cell biology. Lactate, a major microbial metabolic product, was identified as the component responsible for the modulation of certain innate immune epithelial response: At the concentrations found in kefir-fermented milk, lactate inhibits the activation of intestinal epithelial cells triggered by interleukin-1β, tumor necrosis factor-α, or flagellin. Lactate treatment furthermore abrogates NF-κB signaling in the cells, whose action could be responsible for the observed modulation of the inflammatory response. These findings provide a new perspective in the analysis of the biologic properties of kefir-fermented-milk products.

Irritable bowel syndrome, inflammatory bowel disease and the microbiome

Purpose of reviewThe review aims to update the reader on current developments in our understanding of how the gut microbiota impact on inflammatory bowel disease and the irritable bowel syndrome. It will also consider current efforts to modulate the microbiota for therapeutic effect.Recent findingsGene polymorphisms associated with inflammatory bowel disease increasingly suggest that interaction with the microbiota drives pathogenesis. This may be through modulation of the immune response, mucosal permeability or the products of microbial metabolism. Similar findings in irritable bowel syndrome have reinforced the role of gut-specific factors in this ‘functional’ disorder. Metagenomic analysis has identified alterations in pathways and interactions with the ecosystem of the microbiome that may not be recognized by taxonomic description alone, particularly in carbohydrate metabolism. Treatments targeted at the microbial stimulus with antibiotics, probiotics or prebiotics have all progressed in the past year. Studies on the long-term effects of treatment on the microbiome suggest that dietary intervention may be needed for prolonged efficacy.SummaryThe microbiome represents ‘the other genome’, and to appreciate its role in health and disease will be as challenging as with our own genome. Intestinal diseases occur at the front line of our interaction with the microbiome and their future treatment will be shaped as we unravel our relationship with it.

The effects of powdered activated carbon or ferric chloride on sludge characteristics and microorganisms in a membrane bioreactor

AbstractIn this study, the effects of two different additives, powdered activated carbon (PAC) and ferric chloride (FeCl3) were evaluated on the characteristics of wastewater treatment sludge. The sludge activity was quantified by the measurement of the specific oxygen uptake rate (SOUR), dehydrogenase activity (DHA), microbial metabolic products including extracellular polymeric substances (EPS) and soluble microbial products (SMP), and by the quantification of the microbial diversity. In a 60-d period of PAC addition (PAC-MBR), average SOUR was 6.11 ± 1.02 mg O2/g VSS h, and SOUR remained relatively stable. Average SOUR was 7.55 ± 2.40 mg O2/g VSS h, but it presented greater variability during the FeCl3 runs (Fe-MBR). During PAC-MBR, DHA was higher than during Fe-MBR and increased significantly with chemical oxygen demand; however, this correlation was low in Fe-MBR. Compared with PAC-MBR, EPS, and SMP in Fe-MBR showed a slowly decreasing trend. DGGE profiles of microbial diversity showed more total ban...

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

BackgroundConsistent compositional shifts in the gut microbiota are observed in IBD and other chronic intestinal disorders and may contribute to pathogenesis. The identities of microbial biomolecular mechanisms and metabolic products responsible for disease phenotypes remain to be determined, as do the means by which such microbial functions may be therapeutically modified.ResultsThe composition of the microbiota and metabolites in gut microbiome samples in 47 subjects were determined. Samples were obtained by endoscopic mucosal lavage from the cecum and sigmoid colon regions, and each sample was sequenced using the 16S rRNA gene V4 region (Illumina-HiSeq 2000 platform) and assessed by UPLC mass spectroscopy. Spearman correlations were used to identify widespread, statistically significant microbial-metabolite relationships. Metagenomes for identified microbial OTUs were imputed using PICRUSt, and KEGG metabolic pathway modules for imputed genes were assigned using HUMAnN. The resulting metabolic pathway abundances were mostly concordant with metabolite data. Analysis of the metabolome-driven distribution of OTU phylogeny and function revealed clusters of clades that were both metabolically and metagenomically similar.ConclusionsThe results suggest that microbes are syntropic with mucosal metabolome composition and therefore may be the source of and/or dependent upon gut epithelial metabolites. The consistent relationship between inferred metagenomic function and assayed metabolites suggests that metagenomic composition is predictive to a reasonable degree of microbial community metabolite pools. The finding that certain metabolites strongly correlate with microbial community structure raises the possibility of targeting metabolites for monitoring and/or therapeutically manipulating microbial community function in IBD and other chronic diseases.

Fecal microbiome and metabolites differ between breast and formula‐fed human infants

Herein, an integrated analysis of the fecal microbiota, microbiome and metabolites of 3‐month‐old breast‐ (BF; n=6) or formula‐fed (FF; n=6) infants was performed. Microbial composition and functional microbiome were accessed by 16S rDNA amplicon and shotgun metagenomic pyrosequencing, respectively. Fecal metabolites were measured by gas chromatography/mass spectrometry. Distance‐based redundancy analysis distinguished the microbiota of BF from FF. BF infants harbored more Bacteroidetes, while FF had more Firmicutes and Verrucomicrobia (p<0.05). The microbiomes of BF and FF infants contained higher proportions of protein/amino acid vs. carbohydrate metabolism genes, respectively. Partial least‐squares discriminant analysis discriminated fecal metabolomic profiles of BF vs. FF. The major metabolites enriched in BF infants were 15‐methylhexadecanoic acid, galactitol and maltose. The metabolites associated with FF were beta‐alanine, dodecanoic acid, glycolic acid, decanoic acid and tyramine. Thus, early nutrition impacts the composition of the fecal microbiota, as well as the complement of microbial genes and metabolic products. (BMS Freedom to Discover Award).Grant Funding Source: BMS Freedom to Discover Award

Incorporation and mineralization of TNT and other anthropogenic organics by natural microbial assemblages from a small, tropical estuary

2,4,6-Trinitrotoluene (TNT) metabolism was compared across salinity transects in Kahana Bay, a small tropical estuary on Oahu, HI. In surface water, TNT incorporation rates (range: 3-121μgCL(-1)d(-1)) were often 1-2 orders of magnitude higher than mineralization rates suggesting that it may serve as organic nitrogen for coastal microbial assemblages. These rates were often an order of magnitude more rapid than those for RDX and two orders more than HMX. During average or high stream flow, TNT incorporation was most rapid at the riverine end member and generally decreased with increasing salinity. This pattern was not seen during low flow periods. Although TNT metabolism was not correlated with heterotrophic growth rate, it may be related to metabolism of other aromatic compounds. With most TNT ring-carbon incorporation efficiencies at greater than 97%, production of new biomass appears to be a more significant product of microbial TNT metabolism than mineralization.

The gut microbial metabolome: modulation of cancer risk in obese individuals

Obesity is a critical health concern and although genetic factors may predispose an individual to become obese, changes in diet and lifestyle over the last few decades are likely to be significant contributors. Even so, it has been suggested that the causes of the current obesity crisis are not simply explained by changes in eating and exercise habits. Evidence suggests that the gut microbiota may play an important role in obesity and may be a factor in the development of associated disease including diabetes, CVD, non-alcoholic fatty liver disease and cancer. There have been tremendous advances in knowledge regarding the composition of human gut microbiota, but less is known about their function and role within the human host. It is becoming widely accepted that the products of microbial metabolism influence human health and disease, particularly with respect to immune response and inflammation. However, in most cases, the products of microbial metabolism are uncharacterised and their mechanism of action remains unknown. This review addresses the role of the metabolites produced by gut microbiota in cancer and obesity. It is clear that only if the link between microbial diversity and metabolic functionality is firmly established, will the mechanism by which gut microbiota maintains health or contributes to disease development be elucidated.

Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products

Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In this work, Nuclear Magnetic Resonance measurements of relaxation rates and molecular diffusion, useful for probing pore structure and transport dynamics in porous systems, were used to physically characterize the unfrozen vein network structure in ice and its response to the presence of metabolic products produced by V3519-10, a cold tolerant microorganism isolated from the Vostok ice core. Recent research has found microorganisms that can remain viable and even metabolically active within icy environments at sub-zero temperatures. One potential mechanism of survival for V3519-10 is secretion of an extracellular ice binding protein that binds to the prism face of ice crystals and inhibits ice recrystallization, a coarsening process resulting in crystal growth with ice aging. Understanding the impact of ice binding activity on the bulk vein network structure in ice is important to modeling of frozen geophysical systems and in development of ice interacting proteins for biotechnology applications, such as cryopreservation of cell lines, and manufacturing processes in food sciences. Here, we present the first observations of recrystallization inhibition in low porosity ice containing V3519-10 extracellular protein extract as measured with Nuclear Magnetic Resonance and Magnetic Resonance Imaging.

Biobeneficiation of Iron Ores

Utilization of aerobic and anaerobic microorganisms in iron ore beneficiation is discussed. Microorganisms such as Paenibacillus polymyxa, Bacillus subtilis, Saccharomyces cerevisiae (yeast) and Desulfovibrio desulfuricans (SRB) are capable of significantly altering the surface chemical behavior of iron ore minerals such as hematite, corundum, calcite, quartz and apatite. Differing mineral surface affinities of microbial cells and metabolic products such as proteins and polysaccharides can be utilized to induce their flotation or flocculation. Mineral-specific bioreagents such as proteins are generated when bacteria and yeast were grown in the presence of hematite, corundum, calcite, quartz and apatite. This study has demonstrated the utility and amenability of microbially-induced mineral beneficiation of iron ores through bacterial and yeast cells and their metabolic byproducts.

Microbiology of the Gut of the Kola Nut Weevil,Balanogastris kolae

Reports have shown that many insects have microbes in their gut system. Gut microbes are very important for insect vitality and much of their nutrition is derived from products of microbial metabolism. The habitat of Balanogastris kolae (Desbrocher des Loges) (Coleoptera: Curculionidae) suggests that they possess the ability to digest varieties of sugars particularly starch and protein materials present in the kola nut, Cola nitida Schott & Endlicher (Malvales: Malvaceae). The aim of this study was to characterize the gut bacterial communities of the kola weevil, B. kolae. To ascertain this, the gut bacterial community of a kola nut-feeding weevil, B. kolae was characterized using culture-dependent methods. The bacterial counts in the foregut, midgut and hindgut were 7.14 ± 0.11 × 106cfu ml-1, 2.68 ± 0.13 × 107 cfu ml-1 and 1.43 ± 0.20 × 106 cfu ml-1 respectively. There were no significant differences in the total bacterial count of the foregut, midgut and hindgut. The bacterial species were identified to be Fusobacterium nucleatum, Staphylococcus aureus, Bacillus subtilis, Corynebacterium fascians, Arthrobacter globiformis, Serratia marcescens, Bacillus brevis, Vibrio haemolyticus and Flavobacterium breve. The majority of these isolates were demonstrated to have both proteolytic and amylolytic activities.

Functional analysis of colonic bacterial metabolism: relevant to health?

With the use of molecular techniques, numerous studies have evaluated the composition of the intestinal microbiota in health and disease. However, it is of major interest to supplement this with a functional analysis of the microbiota. In this review, the different approaches that have been used to characterize microbial metabolites, yielding information on the functional end products of microbial metabolism, have been summarized. To analyze colonic microbial metabolites, the most conventional way is by application of a hypothesis-driven targeted approach, through quantification of selected metabolites from carbohydrate (e.g., short-chain fatty acids) and protein fermentation (e.g., p-cresol, phenol, ammonia, or H(2)S), secondary bile acids, or colonic enzymes. The application of stable isotope-labeled substrates can provide an elegant solution to study these metabolic pathways in vivo. On the other hand, a top-down approach can be followed by applying metabolite fingerprinting techniques based on (1)H-NMR or mass spectrometric analysis. Quantification of known metabolites and characterization of metabolite patterns in urine, breath, plasma, and fecal samples can reveal new pathways and give insight into physiological regulatory processes of the colonic microbiota. In addition, specific metabolic profiles can function as a diagnostic tool for the identification of several gastrointestinal diseases, such as ulcerative colitis and Crohn's disease. Nevertheless, future research will have to evaluate the relevance of associations between metabolites and different disease states.

Dietary conjugated linoleic acid supplementation of laying hens: effects on egg fatty acid composition and quality

Conjugated linoleic acid (CLA) is a common term for a group of positional and geometric isomers of linoleic acid; the most commonly found in natural products is cis-9, trans-11-octadecanoic acid. Naturally occurring CLA is produced as an intermediate product of microbial metabolism of linoleic acid in the rumen. For this reason the CLA concentration is higher in ruminant products, such as milk, cheese and meat compared to products derived from monogastrics, particularly chicken meat and egg yolk. Recent investigations suggest that CLA have anticarcinogenic properties, antiatherosclerotic and antioxidant activity (Ip et al., 1995; Nicolosi et al., 1997; Du et al., 2001)...

Probiotics in Inflammatory Bowel Diseases and Associated Conditions

A complex set of interactions between the human genes encoding innate protective functions and immune defenses and the environment of the intestinal mucosa with its microbiota is currently considered key to the pathogenesis of the chronic inflammatory bowel diseases (IBD). Probiotics offer a method to potentially alter the intestinal microbiome exogenously or may provide an option to deliver microbial metabolic products to alter the chronicity of intestinal mucosal inflammation characterizing IBD. At present, there is little evidence for the benefit of currently used probiotic microbes in Crohn’s disease or associated conditions affecting extra-intestinal organs. However, clinical practice guidelines are now including a probiotic as an option for recurrent and relapsing antibiotic sensitive pouchitis and the use of probiotics in mild ulcerative colitis is provocative and suggests potential for benefit in select patients but concerns remain about proof from trials.

Metabolic production of a novel polymer feedstock, 3-carboxy muconate, from vanillin

Vanillin can be produced on a commercial scale by depolymerising renewable lignin. One product of microbial metabolism of vanillin by common soil microbes, such as Acinetobacter baylyi, is a tricarboxylic acid with a butadiene backbone known as 3-carboxy muconate (3CM). Three enzymes, 4-hydroxy benzaldehyde dehydrogenase, vanillate monooxygenase and protocatechuate 3,4-dioxygenase, catalyse the biotransformation of vanillin to 3CM. These three enzymes were metabolically engineered into an Escherichia coli host, giving a biocatalyst that converted vanillin into 3CM. The biocatalyst was found to give 100% yield of 3CM from 1 mM of vanillin after 39 h. The rate-limiting reaction was identified as the conversion of vanillate to 3,4-dihydroxybenzoate catalysed by vanillate monooxygenase. Low expression of the reductase subunit of this enzyme was identified as contributing to the reduced rate of this reaction. Proof of principle of a novel application for 3CM was demonstrated when it was converted into a trimethyl ester derivative and copolymerised with styrene.

Differences in gut microbial metabolism are responsible for reduced hippurate synthesis in Crohn's disease

BackgroundCertain urinary metabolites are the product of gut microbial or mammalian metabolism; others, such as hippurate, are mammalian-microbial 'co-metabolites'. It has previously been observed that Crohn's disease (CD) patients excrete significantly less hippurate than controls. There are two stages in the biosynthesis of this metabolite: 1) gut microbial metabolism of dietary aromatic compounds to benzoate, and 2) subsequent hepatorenal conjugation of benzoate with glycine, forming hippurate. Differences in such urinary co-metabolites may therefore reflect systemic consequences of altered gut microbial metabolism, though altered host metabolic pathways may also be involved.MethodsIt was hypothesised that reduced hippurate excretion in CD patients was due to alterations in the gut microbiota, and not differences in dietary benzoate, nor defective host enzymatic conjugation of benzoate. 5 mg/kg sodium benzoate were administered orally to 16 CD patients and 16 healthy controls on a low-benzoate diet. Baseline and peak urinary hippurate excretion were measured.ResultsBaseline hippurate levels were significantly lower in the CD patients (p = 0.0009). After benzoate ingestion, peak urinary levels of hippurate did not differ significantly between the cohorts. Consequently the relative increase in excretion was significantly greater in CD (p = 0.0007).ConclusionsLower urinary hippurate levels in CD are not due to differences in dietary benzoate. A defect in the enzymatic conjugation of benzoate in CD has been excluded, strongly implicating altered gut microbial metabolism as the cause of decreased hippurate levels in CD.

Neurotoxicity of Fungal Volatile Organic Compounds in Drosophila melanogaster

Many volatile organic compounds (VOCs) are found in indoor environment as products of microbial metabolism. In damp indoor environments, fungi are associated with poor air quality. Some epidemiological studies have suggested that microbial VOCs have a negative impact on human health. Our study was designed to provide a reductionist approach toward studying fungal VOC-mediated toxicity using the inexpensive model organism, Drosophila melanogaster, and pure chemical standards of several important fungal VOCs. Low concentrations of the following known fungal VOCs, 0.1% of 1-octen-3-ol and 0.5% of 2-octanone; 2,5 dimethylfuran; 3-octanol; and trans-2-octenal, caused locomotory defects and changes in green fluorescent protein (GFP)- and antigen-labeled dopaminergic neurons in adult D. melanogaster. Locomotory defects could be partially rescued with L-DOPA. Ingestion of the antioxidant, vitamin E, improved the survival span and delayed the VOC-mediated changes in dopaminergic neurons, indicating that the VOC-mediated toxicity was due, in part, to generation of reactive oxygen species.

Biodiscovery from microbial resources: Actinomycetes leading the way

Biodiscovery from microbial resources can be defined as the exploration of microbial metabolic products to detect, identify and evaluate their potential for medicinal, agricultural and biotechnological operations. Microbial resource centres house microbial compounds produced under different physical and nutritional parameters to maximise the production of metabolites and are subsequently tested in different bioassays to define targeted activity.