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Finely laminated (cm–μm scale) metalliferous precipitates are widespread in the surficial environment, especially around mineral deposits and reflect biogeochemical processes that can pervade near-surface environments on a larger scale. Examples in this paper involve precipitates of the transition metals Fe, Cu and Mn with minor Co, Ni, V and Zn; the metalloids As and Sb; and authigenic Au. Mobility and re-precipitation are driven primarily by geochemical disequilibrium, especially with respect to pH and redox states, that arises from complex interactions between biological processes, geological processes, and variations in the surrounding environment. Different degrees of chemical disequilibrium arise on small spatial scales on time scales of days to millennia. Interactions between biota, waters and rocks in these small near-surface settings affect the biogeochemical environments. Sulfur- and iron-oxidising bacteria are common biogeochemical agents associated with sulfide-bearing lithologies, but localised reductive environments can also develop, leading to gradients in pH and redox state and differential metal mobility. In general, there is commonly a spatial separation of Fe-rich precipitates from those with Cu and Mn, and other transition metals also follow Cu and Mn rather than Fe. Metalloids As and Sb have a strong affinity for Fe under oxidising conditions, but not under more reducing conditions. However, complex biogeochemical parageneses of laminated metalliferous deposits preclude prediction of finer formation details. The textures, mineral species, and metal associations within these deposits are likely to be encountered in all facets of mineral deposit development: initial exploration activity of near-surface locations, mining of shallow portions of orebodies, especially supergene zones, and downstream environmental management with respect to discharging metalliferous waters.
Primary deficit schizophrenia (DS) is characterized by enduring negative symptoms and represents a qualitatively different disease entity with respect to non-deficit schizophrenia (NDS). No studies investigated the association between the enzyme paraoxonase 1 (PON1) and DS and its phenomenology.
In this case-control study, Thai women and men, aged 18 to 65 years, were divided in DS (n = 40) and NDS (n = 40) and were compared to controls (n = 40). PON1 activities against 4-(chloromethyl)phenyl acetate (CMPA) and phenylacetate were determined. Moreover, subjects were genotyped for their PON1 Q192R polymorphism and immunoglobulin A (IgA) levels responses directed to Gram-negative bacteria were measured.
DS is significantly associated with the QQ genotype and the Q allele as compared with NDS and controls. PON1 activities are significantly and inversely associated with negative symptoms, formal thought disorders, psychomotor retardation, excitation and DS. The presence of the Q allele is associated with increased IgA responses to Pseudomonas aeruginosa, Morganella morganii, and Pseudomonas putida as compared with RR carriers.
The PON1 Q allele and lower PON1 activities especially against CMPA are associated with DS, indicating lowered quorum quenching abilities as well as lowered defenses against lipoperoxidation and immune activation. It is suggested that lowered PON1 activity in DS constitutes an impairment in the innate immune system which together with lowered natural IgM may cause lower immune regulation thereby predisposing toward greater neurotoxic effects of immune-inflammatory, oxidative and nitrosative pathways and Gram-negative microbiota.
Changed spatial configurations at sowing have been investigated as a strategy to minimize interspecific competition and improve the establishment and persistence of multi-species plantings in pastures, but the impact of this practice on the soil microbiome has received almost no previous research attention. Differences in populations of bacteria and fungi in the surface 10 cm of soil in the third year following pasture establishment were quantified using quantitative polymerase chain reaction and terminal restriction fragment length polymorphism methods. Populations were compared on, and between, drill rows sown to either the perennial grass phalaris (Phalaris aquatica L.), perennial legume lucerne (alfalfa; Medicago sativa L.) or the annual legume subterranean clover (Trifolium subterraneum L.). Results showed that soil microbial abundance and diversity were related to plant distribution across the field at the time of sampling and to soil chemical parameters including total carbon (C), mineral nitrogen (N), pH, and available phosphorus (P), potassium (K) and sulfur (S). Despite the 27-month lag since sowing, pasture species remained concentrated around the original drill row with very little colonization of the inter-row area. The abundance and diversity of bacterial and fungal populations were consistently greater under drill rows associated with higher total C concentrations in the surface soil compared with the inter-row areas. Our results showed that the pH and available nutrients were similar between the subterranean clover drill row and the inter-row, suggesting that soil microbial populations were not impacted directly by these soil fertility parameters, but rather were related to the presence or absence of plants. The abundance of bacteria and fungi were numerically lower under phalaris rows compared to rows sown to legumes. The richness and diversity of fungal populations were lowest between rows where lucerne was planted. Possible explanations for this observation include a lower C:N ratio of lucerne roots and/or a lack of fibrous roots at the soil surface compared to the other species, illustrating the influence of contrasting plant types on the soil microflora community. This study highlights the enduring legacy of the drill row on the spatial distribution of plants well into the pasture phase of a cropping rotation and discusses the opportunity to enhance the microbiome of cropping soils on a large scale during the pasture phase by increasing plant distribution across the landscape.
Research on the biogenic-specific polymorphism and morphology of carbonate has been gaining momentum in the fields of biomineralization and industrial engineering in recent years. We report the nucleation of carbonate particles on bacterial cell templates to produce a novel dumbbell-like morphology which was assembled by needle-like crystals of magnesium calcite or aragonite radiating out from both ends of the template bacterium. Mature dumbbell-like structures had a tendency to break apart in the central template region, which was made up mostly of weak amorphous carbonate. Further crystal growth, especially at the template region, transformed the broken pieces into spherulites. Rod-like cell templates were essential for the formation of dumbbell-like morphologies, and we propose a possible formation mechanism of the dumbbell-like morphology. Our findings provide new perspectives on the morphological formation mechanism in biomineralization systems and may have a potential significance in assembling composite materials suitable for industrial applications.
Slow-release urea (SRU) can substitute dietary protein sources in the diet of feedlotting ruminant species . However, different SRU structures show varying results of productive performance. This study was conducted to investigate the effect of different sources of nitrogen on performance, blood parameter, ruminal fermentation and relative population of rumen microorganisms in male Mehraban lambs. Thirty-five male lambs with an average initial BW of 34.7 ± 1.8 kg were assigned randomly to five treatments. Diets consisted of concentrate mixture and mineral and vitamin supplements plus (1) alfalfa and soybean meal, (2) wheat straw and soybean meal, (3) wheat straw and urea, (4) wheat straw and Optigen® (a commercial SRU supplement) and (5) wheat straw and SRU produced in the laboratory. No statistical difference was observed in animal performance and DM intake among treatments. The mean value of ruminal pH and ammonia was higher (P < 0.05) for the SRU diet compared with WU diet. The difference in pH is likely to be due to the higher ammonia level as VFAs concentrations were unchanged. The level of blood urea nitrogen (BUN) was different among treatments (P = 0.065). The highest concentration of BUN was recorded in Optigen diet (183.1 mg/l), whereas the lowest value was recorded in wheat straw-soybean meal diet (147 mg/l). The amount of albumin and total protein was not affected by the treatments. The relative population of total protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens and Ruminococcus albus in the SRU treatment was higher (P < 0.01) than that in urea treatment at 3 h post-feeding. During the period of lack of high-quality forage and in order to reduce dietary costs, low-quality forage with urea sources can be used in the diet. Results of microbial populations revealed that SRU can be used as a nitrogen source which can sustainably provide nitrogen for rumen microorganism without negative effects on the performance of feedlotting lambs.
The first chapter, “Pathogens and Parasites,” introduces the major helminthic, protozoal, viral, and bacterial intestinal disease agents, and it provides estimates of their current prevalence and contribution to the burden of human disease. The chapter discusses the biological and social determinants of infectious intestinal disease transmission, and it makes the point that, although a range of hygienic practices can have a significant influence on transmission, owing to a range of ecological and cultural variables, few universal rules apply. It discusses some recent findings from the microbiome project that provide new ways of thinking about infectious intestinal disease, and it makes the case that a deeper understanding of the historical epidemiology of infectious intestinal diseases can potentially improve the public health outcomes from contemporary interventions.
Mycoplasma gallisepticum causes disease in poultry and emerged as a novel pathogen in house finches resulting in a mycoplasmal conjunctivitis epidemic across North America after a single successful host jump from poultry to house finches. The rapid spread of the epidemic across eastern North America, causing a decline in host abundance, has been documented. Once established, disease prevalence showed regular seasonal variation: a late summer/early autumn peak, a mid-December minimum, followed by a late winter peak and a breeding season minimum, which requires seasonal reproduction (providing an autumn pulse of naïve hosts) and winter social aggregation as well as partial immunity of recovered birds. Virulence evolved rapidly: in eastern populations it increased once the disease had become endemic. In western North America the established strain was of much lower virulence, but once established also increased in virulence. We show that virulence may evolve in opposite directions depending on selection pressures. A detailed study showed that disease decreased survival and mobility and a high proportion of birds recovered; also that re-observation rates of clinically diseased birds are often different from those of asymptomatic birds; only calculations which include this effect allow an accurate estimate of disease prevalence.
Mastitis is one of the most prevalent and costly diseases in dairy cattle. Key components for adequate mastitis control are the detection of early stages of infection, as well as the selection of appropriate management interventions and therapies based on the causal pathogens associated with the infection. The objective was to characterize the pattern of electrical conductivity (EC) in milk during intramammary infection, considering specific mastitis-causing pathogen groups involvement. Cows (n = 200) identified by an in-line mastitis detection system with a positive deviation ≥15% in the manufacturer’s proprietary algorithm for EC (high electrical conductivity (HEC)) were considered cases and enrolled in the study at the subsequent milking. One control (CON) cow, within normal ranges for EC, was matched to each case. A composite milk sample was collected aseptically from each cow for bacteriological culture. Milk yield (MY) and EC were recorded for each milking during ±7 days relative to enrollment. Milk cultures were categorized into gram positive (GP), gram negative (GN), other (OTH) and no growth (NOG). Data were submitted for repeated-measures analysis with EC as the dependent variable and EC status at day −1, bacteriological culture category, parity number, stage of lactation and days relative to sampling as main independent variables. Average (± standard error (SE)) EC was greater in HEC than in CON cows (12.5 ± 0.5 v. 10.8 ± 0.5 mS/cm) on the day of identification (day −1). Milk yield on day −1 was greater in CON than in HEC (37.6 ± 5.1 v. 33.5 ± 5.2 kg). For practical management purposes, average EC on day −1 was similar for the different bacteriological culture categories: 11.4 ± 0.6, 11.7 ± 0.5, 12.3 ± 0.8 and 11.7 ± 0.5 mS/cm in GN, GP, OTH and NOG, respectively. Parity number was only associated with day −1 EC in HEC group, with the greatest EC values in parity 3 (12.3 ± 0.3 mS/cm), followed by parity 2 (11.9 ± 0.2 mS/cm), parity >3 (11.6 ± 0.5 mS/cm) and primiparous cows (11.2 ± 0.2 mS/cm). An effect on EC for the interaction of day relative to identification by pathogen gram category was observed. The same interaction effect was observed on daily MY. Overall, the level of variation for MY and EC between- and within-cows was substantial, and as indicated by the model diagnostic procedures, the magnitude of the variance in the cows in the CON group resulted in deviations from normality in the residuals. We concluded that characteristic temporal patterns in EC and MY in particular pathogen groups may provide indications for differentiation of groups of mastitis-causing pathogens. Further research to build detection models including EC, MY and cow-level factors is required for accurate differentiation.
The evidence supporting the efficacy of antibiotic therapy in the treatment of chronic rhinosinusitis is not compelling. A limited number of studies show that the changes in the nasal microbiome in patients following drug therapy are unpredictable and variable. The evidence for the impact of oral antibiotics on the gut microbiota is stronger, possibly as a result of differences in drug distribution to various sites around the body. There are few studies on sinus mucosal and mucus levels of oral antibiotics used in the treatment of chronic rhinosinusitis. The distribution dependent effects of antibiotics on the sinonasal microbiome is unclear.
This review highlights that relative drug concentrations and their efficacy on microbiota at different sites is an important subject for future studies investigating chronic rhinosinusitis.
Microbial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host–parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites–microbiota–host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host–microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host–microbe interactions in both human health and disease.
The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, ‘Are intestinal microbiota effects measurable and meaningful?’ and ‘What research methods and variables are influenced by intestinal microbiota effects?’. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.
Mars is considered to be one of the most favourable places in the Solar System to search for past and present life. In the past Mars was warmer and wetter, so terrestrial halophiles can be regarded as analogues of hypothetical ancient Martian halophiles. In this study we used microorganisms from unique Altai region (Russia) to estimate the capability of terrestrial bacteria and archaea to survive at low temperatures and high concentration of salts and metals, similar to the Martian environment. The current report demonstrates that both halophilic archaea and halotolerant bacteria from saline lakes of the Altai region may be considered as analogues of ancient Martian organisms, since they are able to withstand conditions that hypothetically existed in subsurface layers of the early Mars (low temperatures, salt solutions with a high content of NaCl) with only slight decrease in viability. We also found that the studied microorganisms can use some organic substances found in meteorites. We consider that transfer of unicellular halophiles from Earth to Mars was possible, and, moreover, they could successfully survive and grow on early Mars. Adjusting our growth media to the chemical composition of the lakes, from which the studied strains were isolated, resulted in significant increase in survival and growth rates. Certain strains could survive several freeze–thaw cycles at −70 °C typical for Martian nights.
Eight ruminally-fistulated wethers were used to examine the temporal effects of afternoon (PM; 1600h) v. morning (AM; 0800 h) allocation of fresh spring herbage from a perennial ryegrass (Lolium perenne L.)-based pasture on fermentation and microbial community dynamics. Herbage chemical composition was minimally affected by time of allocation, but daily mean ammonia concentrations were greater for the PM group. The 24-h pattern of ruminal fermentation (i.e. time of sampling relative to time of allocation), however, varied considerably for all fermentation variables (P⩽0.001). Most notably amongst ruminal fermentation characteristics, ammonia concentrations showed a substantial temporal variation; concentrations of ammonia were 1.7-, 2.0- and 2.2-fold greater in rumens of PM wethers at 4, 6 and 8h after allocation, respectively, compared with AM wethers. The relative abundances of archaeal and ciliate protozoal taxa were similar across allocation groups. In contrast, the relative abundances of members of the rumen bacterial community, like Prevotella 1 (P=0.04), Bacteroidales RF16 group (P=0.005) and Fibrobacter spp. (P=0.008) were greater for the AM group, whereas the relative abundance of Kandleria spp. was greater (P=0.04) for the PM group. Of these taxa, only Prevotella 1 (P=0.04) and Kandleria (P<0.001) showed a significant interaction between time of allocation and time of sampling relative to feed allocation. Relative abundances of Prevotella 1 were greater at 2h (P=0.05), 4h (P=0.003) and 6h (P=0.01) after AM allocation of new herbage, whereas relative abundances of Kandleria were greater at 2h (P=0.003) and 4h (P<0.001) after PM allocation. The early post-allocation rise in ammonia concentrations in PM rumens occurred simultaneously with sharp increases in the relative abundance of Kandleria spp. and with a decline in the relative abundance of Prevotella. All measures of fermentation and most microbial community composition data showed highly dynamic changes in concentrations and genus abundances, respectively, with substantial temporal changes occurring within the first 8h of allocating a new strip of herbage. The dynamic changes in the relative abundances of certain bacterial groups, in synchrony with a substantial diurnal variation in ammonia concentrations, has potential effects on the efficiency by which N is utilised by the grazing ruminant.
The contamination of the environment, ambulance equipment, and staff hands consequently are major factors which create nosocomial infections in emergency patients. The contamination of equipment and devices plays an important role in nosocomial infections.
The aim of this study was to determine the effectiveness of a disinfectant on the rate of microbial contamination of ambulances in Qom Emergency Medical Services (EMS), Qom, Iran.
This is a quasi-experimental study with a before-after design in order to determine microbial contaminations at the rear and front cabin of ambulances, as well as medical equipment being utilized in Qom EMS. Saya sept-HP-2% solution was used for disinfection. Bacteriological standard methods were used to identify the contaminations.
The contamination rates before and after use of disinfection solution were 52% and eight percent, respectively. Coagulase-negative staphylococci were the most commonly isolated bacterial agent from the equipment (53%). In all equipment, the contamination level has shown a significant reduction after applying disinfectant.
In spite of the fact that the rate of infection from ambulance equipment is high, the results showed that the use of the suitable disinfectant had an effective role in the reduction of bacteria.
FarhadlooR, Goodarzi FarJ, AzadehMR, ShamsS, Parvaresh-MasoudM.Evaluation of Bacterial Contamination on Prehospital Ambulances Before and After Disinfection. Prehosp Disaster Med. 2018;33(6):602–606.
Understanding the rumen microbial ecosystem requires the identification of factors that influence the community structure, such as nutrition, physiological condition of the host and host–microbiome interactions. The objective of the current study was to describe the rumen microbial communities before, during and after a complete rumen content transfer. The rumen contents of one donor cow were removed completely and used as inoculum for the emptied rumen of the donor itself and three acceptor cows under identical physiological and nutritional conditions. Temporal changes in microbiome composition and rumen function were analysed for each of four cows over a period of 6 weeks. Shortly after transfer, the cows showed different responses to perturbation of their rumen content. Feed intake depression in the first 2 weeks after transfer resulted in short-term changes in milk production, methane emission, fatty acid composition and rumen bacterial community composition. These effects were more pronounced in two cows, whose microbiome composition showed reduced diversity. The fermentation metrics and microbiome diversity of the other two cows were not affected. Their rumen bacterial community initially resembled the composition of the donor but evolved to a new community profile that resembled neither the donor nor their original composition. Descriptive data presented in the current paper show that the rumen bacterial community composition can quickly recover from a reduction in microbiome diversity after a severe perturbation. In contrast to the bacteria, methanogenic communities were more stable over time and unaffected by stress or host effects.
Bacterial infection is a common finding in acute sialadenitis and may play a role in the chronicity of the condition. This study investigated if bacterial biofilm is present in submandibular chronic obstructive sialadenitis.
A descriptive case–control study was conducted that compared 10 histological sections of submandibular glands with chronic obstructive sialadenitis, to 10 histological sections of the healthy part of submandibular glands with pleomorphic adenoma. Fluorescence in situ hybridisation and confocal laser scanning microscopy visualised evidence of bacterial biofilm.
In the chronic obstructive sialadenitis group, 5 out of 10 histological sections showed morphological evidence of bacterial biofilm. In the control group, there was no sign of bacterial biofilm formation.
Morphological evidence of bacterial biofilm was found in the submandibular gland sections from patients with chronic sialadenitis and suggests a role in the chronicity of submandibular chronic obstructive sialadenitis.
Although bats are increasingly recognised as potential reservoir hosts of human zoonotic pathogens, bacteria in bats are still poorly studied. To investigate the DNA faecal prevalence of the bacterium Anaplasma phagocytophilum, we sampled 23 lesser horseshoe bat (Rhinolophus hipposideros) maternity colonies located in buildings (churches, barns) in rural villages of eastern France. A total of 552 faecal samples were collected from 278 individuals. Anaplasma phagocytophilum DNA was detected in the faeces of 63 individuals (22.7%). Such high prevalence might suggest persistent infection in bats and/or a frequent consumption of insect preys carrying bacteria. Faecal DNA prevalence varied highly among colonies but was not related to the colony size. Faecal DNA prevalence was the highest in the Jura Department, where the density of ticks is known to be the highest across the study area. Because the sampled bats live in close proximity to humans, we discuss how concerning the presence of A. phagocytophilum DNA in bat guano is for humans frequenting places of worship that shelter bats. We also advocate future research to understand what a high faecal DNA prevalence in bat guano really implicates in terms of bacteria transmission.
Nitrification potential of a tropical vertisol saturated with water was estimated during sequential reduction of nitrate (NO3−), ferric iron (Fe3+), sulphate (SO42−) and carbon dioxide (CO2) in terminal electron-accepting processes (TEAPs). In general, the TEAPs enhanced potential nitrification rate (PNR) of the soil. Nitrification was highest at Fe3+ reduction followed by SO42− reduction, NO3− reduction and lowest in unreduced control soil. Predicted PNR correlated significantly with the observed PNR. Electron donor Fe2+ stimulated PNR, while S2− inhibited it significantly. Terminal-restriction fragment length polymorphism targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) highlighted population dynamics during the sequential reduction of terminal electron acceptors. Only the relative abundance of AOA varied significantly during the course of soil reduction. Relative abundance of AOB correlated with NO3− and Fe2+. Linear regression models predicted PNR from the values of NO3−, Fe2+ and relative abundance of AOA. Principal component analysis of PNR during different reducing conditions explained 72.90% variance by PC1 and 19.52% variance by PC2. Results revealed that AOA might have a significant role in nitrification during reducing conditions in the tropical flooded ecosystem of a vertisol.
The following experiment evaluated the inhibitory activity of a resin acids-based product (RAP) to bacterial pathogens. Clostridium perfringens isolated from chickens, turkeys and pigs, Staphylococcus aureus from chickens, pigs and cattle, and Escherichia coli O149 isolated from pigs were tested. Two different methods were used, a broth dilution method (BDM) using 0.01%, 0.1% and 0.5% resin acid, and an agar diffusion method (ADM) using 0.01%, 0.1%, 0.5%, 1% and 5% resin acid. For the BDM, C. perfringens was inhibited completely at all concentrations. S. aureus was inhibited completely at 0.5%, but only slightly at 0.1% and not at all at 0.01%. The E. coli strains showed no or little inhibition at 0.5%. For the ADM, narrow inhibition zones evolved around the concentration of 0.5% (8–10 mm), 1% (8.0–12.0 mm), and 5% (9.0–19.5 mm) on the C. perfringens strains, while the inhibition zones for S. aureus were smaller and E. coli developed no inhibition zones. Overall, the RAP inhibited C. perfringens at all concentrations of the product, S. aureus at 0.1%, 0.5%, 1% and 5% concentrations, and E. coli O149 only at 0.5% concentrations, although some strain variation was recorded.