Byproducts Of Microbial Metabolism Research Articles

Research advances in microfluidic collection and detection of virus, bacterial, and fungal bioaerosols.

Bioaerosols are airborne suspensions of fine solid or liquid particles containing biological substances such as viruses, bacteria, cellular debris, fungal spores, mycelium, and byproducts of microbial metabolism. The global Coronavirus disease 2019 (COVID-19) pandemic and the previous emergence of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza have increased the need for reliable and effective monitoring tools for bioaerosols. Bioaerosol collection and detection have aroused considerable attention. Current bioaerosol sampling and detection techniques suffer from long response time, low sensitivity, and high costs, and these drawbacks have forced the development of novel monitoring strategies. Microfluidic technique is considered a breakthrough for high performance analysis of bioaerosols. In recent years, several emerging methods based on microfluidics have been developed and reported for collection and detection of bioaerosols. The unique advantages of microfluidic technique have enabled the integration of bioaerosol collection and detection, which has a higher efficiency over conventional methods. This review focused on the research progress of bioaerosol collection and detection methods based on microfluidic techniques, with special attention on virus aerosols and bacterial aerosols. Different from the existing reviews, this work took a unique perspective of the targets to be collected and detected in bioaerosols, which would provide a direct index of bioaerosol categories readers may be interested in. We also discussed integrated microfluidic monitoring system for bioaerosols. Additionally, the application of bioaerosol detection in biomedicine was presented. Finally, the current challenges in the field of bioaerosol monitoring are presented and an outlook given of future developments.

Transport of metformin metabolites by guanidinium exporters of the small multidrug resistance family.

Proteins from the small multidrug resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in the metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid-supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologs. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologs, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homolog, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homolog Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.

Rational Modification of Human Gut Microbiome and Metabolites By Dietary Resistant Starch in Allogeneic Hematopoietic Stem Cell Transplantation: A Feasibility Study

Allogeneic hematopoietic stem cell transplantation (allo-HCT) is limited by acute graft versus host disease (GVHD). GVHD is the principal cause of non-relapse mortality (NRM) and a major cause of morbidity after allo-HCT. Recent published experimental data demonstrated that altering the microbiome-metabolite axis regulates acute GVHD severity. Specifically, short chain fatty acid (SCFA) butyrate was significantly decreased in the intestinal epithelial cells (IECs) of mice experiencing GVHD, while restoring butyrate levels by increasing intestinal butyrate-producing bacteria, reduced experimental acute GI GVHD severity and mortality. Prebiotics usually refer to indigestible carbohydrates that are metabolized by the intestinal microbiota to produce microbial metabolites, such as SCFAs, that serve as nutrients for IECs. Administration of defined quantities of resistant potato starch (RPS), as a prebiotic, to normal healthy human volunteers promoted increase in butyrogenic bacteria and increased intestinal levels of SCFA butyrate to a greater extent than other commercially available resistant starch preparations tested. These data form the rationale for this study and led to prospectively study the clinical feasibility and impact of the administration of RPS as a prebiotic dietary intervention on the intestinal microbiota and its dependent metabolites in allo-HCT recipients. Adults undergoing human leukocyte antigen-matched, related-donor myeloablative allo-HCT were recruited and received RPS orally daily from day -7 to day 100 after allo-HCT. Stool samples were collected in the OMNIgene-Gut® (DNA Genotek) collection kit. Fecal samples were subjected to 16S rRNA gene sequencing to determine microbiota composition and quantification of fecal SCFAs was performed by liquid chromatography. Blood specimens were collected using standardized protocols. The effect of RPS on plasma SCFAs and > 200 other metabolites was longitudinally assessed using targeted and global metabolomic analyses. Mass spectrometry was utilized for quantification of plasma metabolites. The primary objective was to assess the feasibilty and test the effect of RPS on the structure of the patients' intestinal microbiome. Metrics for the feasibility of this dietary intervention were prespecified by setting a target for ≥ 60 % of patients to adhere to ≥ 70% of scheduled doses. We hypothesized that RPS would be feasible and increase stool butyrate levels as a byproduct of microbial metabolism. Key secondary objectives were to longitudinally evaluate plasma metabolites in recipients of RPS compared to historical controls as well as assess tolerability of RPS in allo-HCT recipients. Ten subjects were enrolled. The primary endpoint was met. Feasibility exceeded the preset goal of ≥ 70% adherence to scheduled dosages in ≥ 60 % of patients as 8 of the 10 patients (80%) received ≥ 70 % of scheduled doses. Intestinal butyrate levels were significantly higher while participants were on RPS as compared to when they were not on RPS (p < 0.0001) (fig. 1A). We observed longitudinal changes in plasma metabolites post allo-HCT compared to baseline independent of whether allo-HCT recipients received RPS (p < 0.0001) (fig. 1B). In RPS recipients, the dominant plasma metabolites were, however, much more stable across timepoints when compared to historic controls suggesting a greater equilibrium in their production and consumption (fig. 1C). The median age of participants was 57 years (range 52-62 years). All subjects received standard GVHD prophylaxis with tacrolimus and methotrexate as well as standard antibiotic prophylaxis with levaquin, and standard neutropenic fever treatment with IV cefepime (90%) or IV vancomycin, No adverse effects/toxicities attributed to RPS were observed and longitudinal specimens were collected successfully (table 1). This study showed that a dietary intervention using RPS in allo-HCT recipients is feasible, and was able to rationally alter the salutary intestinal microbial metabolite SCFA butyrate, despite the utilization of several HCT related medications, including antibiotics. These data demonstrate translation of fundamental discoveries in mouse allo-HCT studies, to testing RPS in healthy humans, to showing that RPS is a feasible microbiome-modifying intervention in allo-HCT recipients, and that a prebiotic strategy can now be applied and tested to mitigate acute GVHD in allo-HCT.

Sediment-Derived Dissolved Organic Matter Stimulates Heterotrophic Prokaryotes Metabolic Activity in Overlying Deep Sea in the Ulleung Basin, East Sea

The effects of benthic dissolved organic carbon (DOC) flux on the dynamics of DOC in the deep continental margins (200 – 2000 m depth) is poorly understood. We investigated heterotrophic prokaryotes (hereafter bacteria) production (BP) and the bio-reactive properties of sediment-derived dissolved organic matter (SDOM) to elucidate microbially mediated cause-effect relationships regarding the rapid consumption of dissolved oxygen (DO) and accumulation of humic-like fluorescent DOM (FDOMH) in the deep-water column (750 – 2000 m depth range) of the Ulleung Basin (UB) in the East Sea. BP in the deep water (2.2 μmol C m-3 d-1) of the UB was among the highest reported for various deep-sea sites. The high DOC concentration (55 μM) likely supported the high BP seen in the deep-water column of the UB. Concentrations of DOC and C1 component of the FDOMH, which is indicative of microbial metabolic by-products, were 13-fold and 20-fold greater, respectively, in pore water than in the overlying bottom water, indicating that the sediment in the continental margins is a significant source of DOM in the overlying water column. Fine-scale water sampling revealed that BP near the sediment (0 – 30 m above the seafloor; 2.78 μmol C m-3 d-1) was 1.67 times higher than that measured in the water column above (30 – 100 m above the seafloor; 1.67 μmol C m-3 d-1). In addition, BP increased in the bottom water incubation amended with SDOM-containing pore water (PW). The results demonstrated that SDOM contains bio-reactive forms of DOM that stimulate heterotrophic microbial metabolism at the expense of oxygen in the bottom water layer. The accumulation of C1 component in both PW-amended and unamended bottom water incubation (i.e., without an extra DOM supply from sediment) further indicated that refractory DOM is produced autochthonously in the water column via heterotrophic metabolic activity. This explains in part the microbially mediated accumulation of excess FDOMH in the deep-water column of the UB. Overall results suggest that the benthic release of bio-reactive DOM may be of widespread significance in controlling microbial processes in the deep-water layer of marginal seas.

Waste-based hydrothermal carbonization aqueous phase substitutes urea for rice paddy return: Improved soil fertility and grain yield

Hydrothermal carbonization is an emerging and efficient technology for utilizing wet waste. However, the utilization of hydrothermal carbonization aqueous phase (HAP), a carbon-rich liquid product containing massive quantities of nutrient elements, has been largely unexplored. In this study, HAP produced by hydrothermal carbonization of sewage sludge (SHAP) and pig manure (PHAP) at 180 °C and 260 °C was applied as a substitute for partial (9.1–55.9%) urea in rice paddy field. Results showed that HAP increased the abundance of humic acid-like substances and microbial metabolic by-products in soil dissolved organic matter (DOM) by 3.3–7.2 times and 42.1–101.6%, respectively, compared to the control treatment without HAP addition (CK). Meanwhile, HAP significantly increased soil fluorescence and humification index of soil DOM by 28.5–41.9% and 12.3–26.8%, respectively, in comparison with CK. Soil fertilized with SHAP260 had greater mineral nitrogen, total organic carbon and Olsen-P compared to CK. HAP increased the grain N uptake by 34.0–58.8% and rice yield by 6.3–34.1% with essential amino acids in grains improved by 8.6–20.9% compared to CK. This study stated that HAP as a substitute of partial urea for rice paddy return has positive effects on soil fertility and grain yields.

Modulating the Microbiota as a Therapeutic Intervention for Type 2 Diabetes.

Mounting evidence suggested that the gut microbiota has a significant role in the metabolism and disease status of the host. In particular, Type 2 Diabetes (T2D), which has a complex etiology that includes obesity and chronic low-grade inflammation, is modulated by the gut microbiota and microbial metabolites. Current literature supports that unbalanced gut microbial composition (dysbiosis) is a risk factor for T2D. In this review, we critically summarize the recent findings regarding the role of gut microbiota in T2D. Beyond these associative studies, we focus on the causal relationship between microbiota and T2D established using fecal microbiota transplantation (FMT) or probiotic supplementation, and the potential underlying mechanisms such as byproducts of microbial metabolism. These microbial metabolites are small molecules that establish communication between microbiota and host cells. We critically summarize the associations between T2D and microbial metabolites such as short-chain fatty acids (SCFAs) and trimethylamine N-Oxide (TMAO). Additionally, we comment on how host genetic architecture and the epigenome influence the microbial composition and thus how the gut microbiota may explain part of the missing heritability of T2D found by GWAS analysis. We also discuss future directions in this field and how approaches such as FMT, prebiotics, and probiotics supplementation are being considered as potential therapeutics for T2D.

166 Altering the ruminal microbiota in dairy calves using rumen contents dosing

Abstract A major goal in dairy research is to improve milk production efficiency (MPE). With the advent of next-generation sequencing, efforts are underway to improve MPE by manipulating the rumen microbiota. MPE correlates to ruminal bacterial community composition (BCC), but the adult rumen microbiota is highly stable and returns to a baseline BCC after heavy perturbation. We seek to influence rumen BCC by early intervention in pre-weaning calves. Two cannulated Holstein donors of disparate MPE were selected. Three cohorts of 6 bull calves were established and dosed by gavage with a rumen inoculum sourced from the high-efficiency donor (HE), the low-efficiency donor (LE), or an autoclaved 50:50 mix as a microbe-free control (C). Dosing occurred at birth, then biweekly through 6 weeks. Feces were collected at each dosing. Daily preweaning intake of calf starter, which correlates to downstream feed efficiency, was greatest in HE calves and lowest in C calves (P < 0.05), though preweaning average daily gain did not differ between cohorts (P = 0.210). Calves were sacrificed at 8 weeks to access rumen contents and rumen wall sections were collected to assess papillation. Fecal and rumen samples were subjected to 16S rRNA amplicon sequencing. BCC differed by cohort in fecal and rumen samples (P < 0.05), with HE calf samples most similar to adult rumen samples and C calves least similar. Additionally, HE calves tended to have elongated papillae (P =0.062), the development of which is dependent on byproducts of microbial metabolism in the rumen and which points to differences in potential absorptive capacity of the epithelium. These data demonstrate that the rumen BCC can be influenced by early intervention. Future work includes expansion of this dosing protocol to a cohort of 60 female calves, following rumen BCC development and the impact on MPE in through the first lactation.

Global transcriptional profiling of tyramine and d-glucuronic acid catabolism in Salmonella

Salmonella has evolved various metabolic pathways to scavenge energy from the metabolic byproducts of the host gut microbiota, however, the precise metabolic byproducts and pathways utilized by Salmonella remain elusive. Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and d-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolic pathways of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and construct the regulatory circuits for the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis approaches. We report that TYR induced differential expression of 319 genes (172 up-regulated and 157 down-regulated) when Salmonella was grown in the presence of TYR as a sole energy source. These included the genes originally predicted to be involved in the classical TYR catabolic pathway. TYR also induced expression of majority of genes involved in the acetaldehyde degradation pathway and aided identification of a few new genes that are likely involved in alternative pathway for TYR catabolism. In contrast, DGA induced differential expression of 71 genes (58 up-regulated and 13 down-regulated) when Salmonella was grown in the presence of DGA as a sole energy source. These included the genes originally predicted to be involved in the classical pathway and a few new genes likely involved in the alternative pathway for DGA catabolism. Interestingly, DGA also induced expression of SPI-2 T3SS, suggesting that DGA may also influence nutritional virulence of Salmonella. In summary, this is the first report describing the global transcriptional profiling of TYR and DGA catabolic pathways of Salmonella. This study will contribute to the better understanding of the role of TYR and DGA in metabolic adaptation and virulence of Salmonella.

Dietary Synbiotic Supplementation Protects Barrier Integrity of Hepatocytes and Liver Sinusoidal Endothelium in a Mouse Model of Chronic-Binge Ethanol Exposure.

Alcohol overconsumption disrupts the gut microbiota and intestinal barrier, which decreases the production of beneficial microbial metabolic byproducts and allows for translocation of pathogenic bacterial-derived byproducts into the portal-hepatic circulation. As ethanol is known to damage liver sinusoidal endothelial cells (LSEC), here we evaluated dietary supplementation with a previously studied synbiotic on gut microbial composition, and hepatocyte and LSEC integrity in mice exposed to ethanol. We tested a chronic-binge ethanol feeding mouse model in which C57BL/6 female mice were fed ethanol (5% vol/vol) for 10 days and provided a single ethanol gavage (5 g/kg body weight) on day 11, 6 h before euthanasia. An ethanol-treatment group also received oral supplementation daily with a synbiotic; and an ethanol-control group received saline. Control mice were pair-fed and isocalorically substituted maltose dextran for ethanol over the entire exposure period; they received a saline gavage daily. Ethanol exposure decreased gut microbial abundance and diversity. This was linked with diminished expression of adherens junction proteins in hepatocytes and dysregulated expression of receptors for advanced glycation end-products; and this coincided with reduced expression of endothelial barrier proteins. Synbiotic supplementation mitigated these effects. These results demonstrate synbiotic supplementation, as a means to modulate ethanol-induced gut dysbiosis, is effective in attenuating injury to hepatocyte and liver endothelial barrier integrity, highlighting a link between the gut microbiome and early stages of acute liver injury in ethanol-exposed mice.

Unaccounted risk of cardiovascular disease: the role of the microbiome in lipid metabolism.

Not all of the risk of cardiovascular disease can be explained by diet and genetics, and the human microbiome, which lies at the interface of these two factors, may help explain some of the unaccounted risk. This review examines some of the well established links between the microbiome and cardiovascular health, and proposes relatively unexplored associations. Byproducts of microbial metabolism are associated with health and disease: Trimethylamine N oxide is associated with atherosclerosis; whereas short-chain fatty acids are associated with decreased inflammation and increased energy expenditure. More broadly, a large number of association studies have been conducted to explore the connections between bacterial taxa and metabolic syndrome. In contrast, the relationship between the microbiome and triglycerides levels remains poorly understood. We suggest that deeper understanding of the molecular mechanisms that drive linkages between the microbiome and disease can be determined by replacing 16S rRNA gene sequencing with shotgun metagenomic sequencing or other functional approaches. Furthermore, to ensure translatability and reproducibility of research findings, a combination of multiple different complementary '-omic' approaches should be employed.

Microbial Short-Chain Fatty Acids and Blood Pressure Regulation.

Microbial short-chain fatty acids (SCFAs) are byproducts of microbial metabolism which can be absorbed into the bloodstream of the host, where they exert effects on host physiology. SCFAs have been known to influence several aspects of host physiology, including the regulation of blood pressure. In this review, we will consider recent studies linking SCFAs to blood pressure regulation. Several recent studies have found that changes in blood pressure often coordinate with expected changes in SCFAS. Efforts are now well underway to dissect and better understand this potential connection. One way that SCFAs can influence host cells is by interacting with host GPCRs, including Gpr41 and Olfr78, among others. Intriguingly, mice null for Olfr78 are hypotensive, whereas mice null for Gpr41 are hypertensive, implying that these pathways may be physiologically important links between SCFAs and host blood pressure control. In sum, these studies demonstrate that there does indeed appear to be a link between SCFAs and blood pressure, which likely involves host GPCRs, at least in part; however, the details and intricacies of these interactions are not yet fully understood and will greatly benefit from further studies.

Unique microbial-derived volatile organic compounds in portal venous circulation in murine non-alcoholic fatty liver disease

Background and aimsNon-alcoholic fatty liver disease is now the leading liver disease in North America. The progression of non-alcoholic fatty liver disease to the inflammatory condition, non-alcoholic steatohepatitis is complex and currently not well understood. Intestinal microbial dysbiosis has been implicated in the development of non-alcoholic fatty liver disease and progression of non-alcoholic steatohepatitis. Volatile organic compounds are byproducts of microbial metabolism in the gut that may enter portal circulation and have hepatotoxic effects contributing to the pathogenesis of non-alcoholic steatohepatitis. To test this hypothesis, we measured volatile organic compounds in cecal luminal contents and portal venous blood in a mouse model of non-alcoholic steatohepatitis. MethodsGas chromatography–mass spectrometry analysis was conducted on cecal content and portal vein blood for volatile organic compound detection from mice fed a methionine and choline deficient diet, which induces non-alcoholic steatohepatitis. The colonic microbiome was studied by 16S rRNA gene amplification using the Illumina MiSeq platform. ResultsSixty-eight volatile organic compounds were detected in cecal luminal content, a subset of which was also present in portal venous blood. Importantly, differences in portal venous volatile organic compounds were associated with diet-induced steatohepatitis establishing a biochemical link between gut microbiota-derived volatile organic compounds and increased susceptibility to non-alcoholic steatohepatitis. ConclusionOur model creates a novel tool to further study the role of gut-derived volatile organic compounds in the pathogenesis of non-alcoholic steatohepatitis.

Bioregeneration of hyper-cross-linked polymeric resin preloaded with phenol

In this study, the preliminary feasibility of bio-regeneration of a hyper-cross-linked polymeric resin NDA-802 preloaded with phenol was investigated. As compared to the abiotic experiments, phenol preloaded with NDA-802 could be effectively desorbed and biodegraded, and the bioregenerated NDA-802 could be employed for multiple use. The concentration gradient hypothesis could interpret such bioregeneration process reasonably. A slight drop in adsorption capacity of NDA-802 after bioregeneration possibly resulted from the mesopore blockage by microbial metabolic by-products. In general, bioregeneration could serve as a potential choice for the exhausted hyper-cross-linked polymeric resin in wastewater treatment.

Regulation of antimicrobial peptide gene expression by nutrients and by-products of microbial metabolism

Antimicrobial peptides (AMPs) are synthesized and secreted by immune and epithelial cells that are constantly exposed to environmental microbes. AMPs are essential for barrier defense, and deficiencies lead to increased susceptibility to infection. In addition to their ability to disrupt the integrity of bacterial, viral and fungal membranes, AMPs bind lipopolysaccharides, act as chemoattractants for immune cells and bind to cellular receptors and modulate the expression of cytokines and chemokines. These additional biological activities may explain the role of AMPs in inflammatory diseases and cancer. Modulating the endogenous expression of AMPs offers potential therapeutic treatments for infection and disease. The present review examines the published data from both in vitro and in vivo studies reporting the effects of nutrients and by-products of microbial metabolism on the expression of antimicrobial peptide genes in order to highlight an emerging appreciation for the role of dietary compounds in modulating the innate immune response. Vitamins A and D, dietary histone deacetylases and by-products of intestinal microbial metabolism (butyrate and secondary bile acids) have been found to regulate the expression of AMPs in humans. Vitamin D deficiency correlates with increased susceptibility to infection, and supplementation studies indicate an improvement in defense against infection. Animal and human clinical studies with butyrate indicate that increasing expression of AMPs in the colon protects against infection. These findings suggest that diet and/or consumption of nutritional supplements may be used to improve and/or modulate immune function. In addition, by-products of gut microbe metabolism could be important for communicating with intestinal epithelial and immune cells, thus affecting the expression of AMPs. This interaction may help establish a mucosal barrier to prevent invasion of the intestinal epithelium by either mutualistic or pathogenic microorganisms.

The Importance of Termites to the CH4 Balance of a Tropical Savanna Woodland of Northern Australia

Termites produce methane (CH4) as a by-product of microbial metabolism of food in their hindguts, and are one of the most uncertain components of the regional and global CH4 exchange estimates. This study was conducted at Howard Springs near Darwin, and presents the first estimate of CH4 emissions from termites based on replicated in situ seasonal flux measurements in Australian savannas. Using measured fluxes of CH4 between termite mounds and the atmosphere, and between soil and the atmosphere across seasons we determined net CH4 flux within a tropical savanna woodland of northern Australia. By accounting for both mound-building and subterranean termite colony types, and estimating the contribution from tree-dwelling colonies it was calculated that termites were a CH4 source of +0.24 kg CH4-C ha−1 y−1 and soils were a CH4 sink of −1.14 kg CH4-C ha−1 y−1. Termites offset 21% of CH4 consumed by soil resulting in net sink strength of −0.90 kg CH4-C ha−1 y−1 for these savannas. For Microcerotermes nervosus (Hill), the most abundant mound-building termite species at this site, mound basal area explained 48% of the variation in mound CH4 flux. CH4 emissions from termites offset 0.1% of the net biome productivity (NBP) and CH4 consumption by soil adds 0.5% to the NBP of these tropical savannas at Howard Springs.

Biological Iron‐Monosulfide Production for Efficient Electricity Harvesting from a Deep‐Sea Metal‐Reducing Bacterium

Micro-organisms inhabit a broad range of natural environments through the exploitation of multiple metabolic strategies and are able to perform most thermodynamically possible redox reactions to obtain energy for their growth. Present concerns about the depletion of natural resources has increased the need to understand inherent microbial ingenuities, and search for methodologies for utilizing (or replicating) their metabolism to harness renewable sources of energy. Herein, we report the biological production of single-phase iron monosulfide (mackinawite) for efficient harvesting of bacterial metabolized electrons in electrochemical cells. Iron sulfides (FeS), such as mackinawite, greigite, marcasite, and pyrite, are ubiquitous and abundant minerals in anoxic marine environments formed as by-products of microbial metabolism or a consequence of geothermal activity. Several biogeochemical processes associated with microbial interaction with FeSs have been reported, with the discovery of highly active biospheres around hydrothermal vents illustrating the significance of FeSs as an energy source for microbial activities in environments isolated from solar irradiation. Moreover, a number of biological functions of FeSs, including structural support, antimicrobial agents, and magnetic-, optical-, and gravity-sensing devices, have been identified; this highlights the diverse microbial mechanisms that exist for harnessing cell-surface-associated nanosized FeSs. Although the biomineralization of nanosized FeSs is a wellknown phenomenon, only a few previous studies have considered its biological function from the view point of electron-conducting properties. FeSs have a wide range of compositions and structures, fulfilling the diverse electrochemical functionalities required for solid-state batteries, electrocatalysis, photovoltaics, and other industrial applications. In an effort to further explore microbial ingenuity and understand the importance of FeSs in microbial metabolism and electron transfer, we examined the biomineralization of FeSs by the Fereducing bacterium Shewanella loihica PV-4, which was originally isolated from iron-rich microbial mats near a deep-sea hydrothermal vent (1325 m below sea level). This study demonstrated that S. loihica PV-4 has the ability to exploit the Fe 3d electrons of biologically synthesized iron monosulfide (FeS) as extracellular long-distant electron-transfer conduits. Self-organizing, electrically conducting cell–FeS assemblies enabled the generation of a microbial current two orders of magnitude higher than in cell cultures lacking the biogenic minerals. S. loihica PV-4 cells were cultured anaerobically at 25 8C in a medium containing both ferric ions (FeCl3) and thiosulfate (Na2S2O3) as terminal electron acceptors, and lactate as a carbon source and electron-donating compound. The cell suspension instantly turned from yellow to brown, and a black precipitate was generated after approximately 5 h of inoculation. The X-ray diffraction (XRD) pattern of the yellow precipitate present before the addition of cells showed a broad undefined region with no significant peaks (Figure 1, bottom). Upon incubation with cells, however, several peaks appeared in the XRD pattern, which were assigned to elemental sulfur (S), goethite (a-FeOOH), and mackinawite (FeS; Figure 1, 1 day). The peak intensities for both elemental sulfur and goethite decreased with increasing incubation times, while a concomitant increase in the peaks assigned to mackinawite was observed. SEM observations (Figure 2) combined with confocal microscopy on GFP-labeled cells (Figure S2) showed populations of rod-shaped cells surrounded by nanosized FeS colloids, with the nanocolloids serving to interconnect the cells (Figure 2, bottom). The black precipitate was not observed in the suspension lacking cells ; this confirms that the formation of mackinawite was a consequence of the microbial reduction of ferric ions and thiosulfate. Mackinawite is one of the major constituents of black sedimentary minerals in anoxic marine systems and has a struc-

Effects of probiotics and commensals on intestinal epithelial physiology: implications for nutrient handling

Eukaryotes and prokaryotes have developed mutually beneficial relationships over millennia of evolutionary adaptation. Bacteria in our gut rely on our diet and the protected environment of our bodies just as our health depends on byproducts of microbial metabolism. Microorganisms of the gut microbiota ferment carbohydrates into short-chain fatty acids, convert dietary and endogenous nitrogenous compounds into ammonia and microbial protein, and synthesize and activate B vitamins and vitamin K. The benefit from their activity is multiplex and translates into increased energy for the gut epithelial cells, balanced absorption of salt and water, nitrogen recycling, breakdown of complex lipids and cholesterol, and detoxification of waste compounds.

Post-harvest biology of sugarcane

Cutting of the sugarcane stalk at harvest disrupts the physiology of the plant. The altered balance amongst plant functions that results from cutting leads to changes in the composition of the stalk, many of which are undesirable. These negative effects are worsened by increased duration of the period between harvest and sucrose extraction, as well as by high ambient temperature. In addition to physiological changes within the stalk, damage to the stalk during harvesting provides entry points for microbes (bacteria and fungi) that occur naturally in the environment. Many of these microbes grow well in the sucrose-rich stalk, using the sugars as an energy source, while producing metabolic by-products that cause processing problems in the mill and refinery. Post-harvest physiology and microbiology of the sugarcane stalk are currently being studied at the South African Sugarcane Research Institute (SASRI) to determine the effects of harvesting on sucrose and hexose (glucose and fructose) levels, the growth of microbes in the stalk and the appearance of undesirable by-products of microbial metabolism. The information will ultimately be used in the development of mathematical models to quantify and predict the effects of harvest-to-crush delays on stakeholder profitability.

Salt marsh pore water geochemistry does not correlate with microbial community structure

Spatial and temporal trends in pore water geochemistry and sediment microbial community structure are compared at three intertidal sites of a saltmarsh on Sapelo Island, GA. The sites include a heavily bioturbated, unvegetated creek bank, a levee with dense growth of Spartina alterniflora, and a more sparsely vegetated ponded marsh site. The redox chemistry of the pore waters ranges from sulfide-dominated at the ponded marsh site to suboxic at the creek bank site. At the three sites, the vertical redox stratification of the pore waters is more compressed in summer than in winter. The trends in redox chemistry reflect opposing effects of sediment respiration and pore water irrigation. Intense and deep burrowing activity by fiddler crabs at the creek bank site results in the efficient oxidation of reduced byproducts of microbial metabolism and, hence, the persistence of suboxic conditions to depths of 50 cm below the sediment surface. Increased supply of labile organic substrates at the vegetated sites promotes microbial degradation processes, leading to sharper redox gradients. At the levee site, this is partly offset by the higher density and deeper penetration of roots and macrofaunal burrows. Surprisingly, the microbial community structure shows little correlation with the variable vertical redox zonation of the pore waters across the saltmarsh. At the three sites, the highest population densities of aerobic microorganisms, iron- plus manganese-reducing bacteria, and sulfate reducers coexist within the upper 10 cm of sediment. The absence of a clear vertical separation of these microorganisms is ascribed to the high supply of labile organic matter and intense mixing of the topmost sediment via bioturbation.

Carbohydrates in hot water extracts of soil aggregates as influenced by long-term management

Microbial carbohydrates are immediate by-products of microbial metabolism and play an important role in the formation and stabilization of soil structure. The effect of long-term management on soil carbohydrate content and monosaccharide composition was investigated in five Danish sandy loams under organic and conventional management with animal manure and mineral fertilizers. Hot-water (80°C) extraction was used to measure the distribution and composition of carbohydrates in aggregate size. Carbohydrates released to hot water were determined after hydrolysis as reducing sugars equivalent to glucose. The monosaccharide composition in hot-water extracts was analyzed as the corresponding alditol acetates. Sites with a history of long-term continuos management practices were used. Three treatments from the >100 year Askov long-term field experiment were used to show results of contrasting fertilization on soil carbohydrate content. These were all grown to a four-course crop rotation. Total carbohydrate content was significantly influenced by long-term management practices, with a significantly higher carbohydrate content in soils fertilized with either mineral fertilizers or animal manure (1200 to 800 mg C kg− 1 DM aggregate) than in an unfertilized soil (600 to 500 mg C kg− 1 DM aggregate). These results were as true for micro-aggregates (<0.25 mm) as for the 0.5–1.0 mm and 4.0–8.0 mm fractions. The organically managed soil (>40 years) was sited at a commercial farm with forage crop rotations, organic manure and no use of crop protection chemicals. These results showed significantly higher levels of carbohydrate both in micro-aggregate and macro-aggregates (1200 to 900 mg C kg− 1 DM aggregate) than an adjacent conventionally managed soil with annual cash crop, mineral fertilizers and use of crop protection chemicals (960 to 760 mg C kg− 1 DM aggregate). Carbohydrate C content generally increased as aggregate size decreased in both soils. Monosaccharide distribution was generally similar among three aggregate size classes studied. In all soils the content of monosaccharide was highest in microaggregates and lowest in macro-aggregates. Mannose and galactose were normally the most common monosaccharides in the hot-water extracts of aggregate fractions, indicating a predominantly microbial origin.