Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

Aim: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. Methods and Results: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides ) cluster (27.7%). Conclusion: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. Significance and Impact: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

Tetanus in an adult dog originating from a tooth root abscess

A three-and-a-half-year-old entire male Staffordshire Bull Terrier was presented with a cough and difficulty in swallowing. Two days later the dog was re-presented and a diagnosis of tetanus was made. An abscessed canine tooth was extracted and submitted for culture. Clostridium tetani was cultured from the pulp chamber of the tooth. The dog was treated with tetanus antitoxin, antibiotics and supportive care and made a complete recovery.

Structure of a cellulose degrading bacterial community during anaerobic digestion

It is widely accepted that cellulose is the rate-limiting substrate in the anaerobic digestion of organic solid wastes and that cellulose solubilisation is largely mediated by surface attached bacteria. However, little is known about the identity or the ecophysiology of cellulolytic microorganisms from landfills and anaerobic digesters. The aim of this study was to investigate an enriched cellulolytic microbial community from an anaerobic batch reactor. Chemical oxygen demand balancing was used to calculate the cellulose solubilisation rate and the degree of cellulose solubilisation. Fluorescence in situ hybridisation (FISH) was used to assess the relative abundance and physical location of three groups of bacteria belonging to the Clostridium lineage of the Firmicutes that have been implicated as the dominant cellulose degraders in this system. Quantitation of the relative abundance using FISH showed that there were changes in the microbial community structure throughout the digestion. However, comparison of these results to the process data reveals that these changes had no impact on the cellulose solubilisation in the reactor. The rate of cellulose solubilisation was approximately stable for much of the digestion despite changes in the cellulolytic population. The solubilisation rate appears to be most strongly affected by the rate of surface area colonisation and the biofilm architecture with the accepted model of first order kinetics due to surface area limitation applying only when the cellulose particles are fully covered with a thin layer of cells. (c) 2005 Wiley Periodicals, Inc.

Phenotypic and genotypic characterisation of Clostrum Difficile

Clostridium difficile is at present one of the most common nosocomial infections in the developed world. Hypervirulent strains (PCR ribotype 027) of C. difficile which produce enhanced levels of toxins have also been associated with other characteristics such as a greater rate of sporulation and resistance to fluoroquinolones. Infection due to C. difficile PCR ribotype 027 has also been associated with greater rates of morbidity and mortality. The aim of this thesis was to investigate both the phenotypic and genotypic characteristics of two populations of toxigenic clinical isolates of C. difficile which were recovered from two separate hospital trusts within the UK. Phenotypic characterisation of the isolates was undertaken using analytical profile indexes (APIs), minimum inhibitory concentrations(MICs) and S-layer protein typing. In addition to this, isolates were also investigated for the production of a range of extracellular enzymes as potential virulence factors. Genotypic characterisation was performed using a random amplification of polymorphic DNA(RAPD) PCR protocol which was fully optimised in this study, and the gold standard method, PCR ribotyping. The discriminatory power of both methods was compared and the similarity between the different isolates also analysed. Associations between the phenotypic and genotypic characteristics and the recovery location of the isolate were then investigated. Extracellular enzyme production and API testing revealed little variation between the isolates; with S-layer typing demonstrating low discrimination. Minimum inhibitory concentrations did not identify any resistance towards either vancomycin or metronidazole; there were however significant differences in the distribution of antibiogram profiles of isolates recovered from the two different trusts. The RAPD PCR protocol was successfully optimised and alongside PCR ribotyping, effectively typed all of the clinical isolates and also identified differences in the number of types defined between the two locations. Both PCR ribotyping and RAPD demonstrated similar discriminatory power; however, the two genotyping methods did not generate amplicons that mapped directly onto each other and therefore clearly characterised isolates based on different genomic markers. The RAPD protocol also identified different subtypes within PCR ribotypes, therefore demonstrating that all isolates defined as a particular PCR ribotype were not the same strain. No associations could be demonstrated between the phenotypic and genotypic characteristics observed; however, the location from which an isolate was recovered did appear to influence antibiotic resistance and genotypic characteristics. The phenotypic and genotypic characteristics observed amongst the C. difficile isolates in this study, may provide a basis for the identification of further targets which may be potentially incorporated into future methods for the characterisation of C. difficile isolates.

Gram-positive infections in patients with end-stage renal disease

Gram-positive microorganisms, specifically coagulase-negative staphylococci are the most common species recovered from clinical culture specimens of patients with end-stage renal disease. The propensity of coagulase-negative staphylococci (CNS) to cause infection in this patient group has been widely debated. However, it is still unclear how this usually avirulent commensal microorganism produces infection that contributes to high rates of morbidity and mortality in patients with end-stage renal disease. The aim of this thesis was to investigate the rate, geographical distribution, molecular and phenotypic mechanisms of Gram-positive microorganisms associated with infection in renal dialysis patients. In addition, it sought to assess the value of early serological diagnosis of dialysis catheter-associated infection and the effect of antimicrobial treatment regimens on the faecal carriage of enteric microorganisms. In this study, the incidence of haemodialysis catheter-associated infection was established with the Meditrend audit tool. This tool was used to assess the infection outcomes of catheter insertion and management procedures until the catheter was explanted. Introduction of a catheter management protocol decreased the incidence of catheter-related infection. Staphylococcal species recovered from episodes of haemodialysis catheter-associated infection and continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis were genotyped by determination of macrorestriction profiles with pulsed-field gel electrophoresis. This highlighted horizontal transfer of microorganisms between different patients and the environment. The phenotypic characteristics of these strains were also investigated to determine characteristics that could be used as markers for dialysis catheter-associated infection. The expression of elastase, lipase and esterase by CNS was significantly associated with infection. A rapid enzyme-linked immunosorbent assay incorporating a novel staphylococcal antigen (lipid S) was used to evaluate the early detection of anti-staphylococcal immunoglobulin gamma in patient sera. The comparison of culture positive and culture negative patients demonstrated a steady state of immune activation in both groups. However anti-lipid S serum antibody titres > 1000 were found to be a predictor of infection. The effect on faecal carriage of vancomycin resistant enterococci (VRE) and Clostridium difficile toxins in patients treated with CAPD when empiric cephalosporin therapy was substituted for piperacillin/tazobactam was investigated. The introduction of piperacillin/tazobactam demonstrated a decrease in the faecal carriage of VRE.

Multiple component patient safety intervention in English hospitals:controlled evaluation of second phase

Objective: To independently evaluate the impact of the second phase of the Health Foundation's Safer Patients Initiative (SPI2) on a range of patient safety measures. Design: A controlled before and after design. Five substudies: survey of staff attitudes; review of case notes from high risk (respiratory) patients in medical wards; review of case notes from surgical patients; indirect evaluation of hand hygiene by measuring hospital use of handwashing materials; measurement of outcomes (adverse events, mortality among high risk patients admitted to medical wards, patients' satisfaction, mortality in intensive care, rates of hospital acquired infection). Setting: NHS hospitals in England. Participants: Nine hospitals participating in SPI2 and nine matched control hospitals. Intervention The SPI2 intervention was similar to the SPI1, with somewhat modified goals, a slightly longer intervention period, and a smaller budget per hospital. Results: One of the scores (organisational climate) showed a significant (P=0.009) difference in rate of change over time, which favoured the control hospitals, though the difference was only 0.07 points on a five point scale. Results of the explicit case note reviews of high risk medical patients showed that certain practices improved over time in both control and SPI2 hospitals (and none deteriorated), but there were no significant differences between control and SPI2 hospitals. Monitoring of vital signs improved across control and SPI2 sites. This temporal effect was significant for monitoring the respiratory rate at both the six hour (adjusted odds ratio 2.1, 99% confidence interval 1.0 to 4.3; P=0.010) and 12 hour (2.4, 1.1 to 5.0; P=0.002) periods after admission. There was no significant effect of SPI for any of the measures of vital signs. Use of a recommended system for scoring the severity of pneumonia improved from 1.9% (1/52) to 21.4% (12/56) of control and from 2.0% (1/50) to 41.7% (25/60) of SPI2 patients. This temporal change was significant (7.3, 1.4 to 37.7; P=0.002), but the difference in difference was not significant (2.1, 0.4 to 11.1; P=0.236). There were no notable or significant changes in the pattern of prescribing errors, either over time or between control and SPI2 hospitals. Two items of medical history taking (exercise tolerance and occupation) showed significant improvement over time, across both control and SPI2 hospitals, but no additional SPI2 effect. The holistic review showed no significant changes in error rates either over time or between control and SPI2 hospitals. The explicit case note review of perioperative care showed that adherence rates for two of the four perioperative standards targeted by SPI2 were already good at baseline, exceeding 94% for antibiotic prophylaxis and 98% for deep vein thrombosis prophylaxis. Intraoperative monitoring of temperature improved over time in both groups, but this was not significant (1.8, 0.4 to 7.6; P=0.279), and there were no additional effects of SPI2. A dramatic rise in consumption of soap and alcohol hand rub was similar in control and SPI2 hospitals (P=0.760 and P=0.889, respectively), as was the corresponding decrease in rates of Clostridium difficile and meticillin resistant Staphylococcus aureus infection (P=0.652 and P=0.693, respectively). Mortality rates of medical patients included in the case note reviews in control hospitals increased from 17.3% (42/243) to 21.4% (24/112), while in SPI2 hospitals they fell from 10.3% (24/233) to 6.1% (7/114) (P=0.043). Fewer than 8% of deaths were classed as avoidable; changes in proportions could not explain the divergence of overall death rates between control and SPI2 hospitals. There was no significant difference in the rate of change in mortality in intensive care. Patients' satisfaction improved in both control and SPI2 hospitals on all dimensions, but again there were no significant changes between the two groups of hospitals. Conclusions: Many aspects of care are already good or improving across the NHS in England, suggesting considerable improvements in quality across the board. These improvements are probably due to contemporaneous policy activities relating to patient safety, including those with features similar to the SPI, and the emergence of professional consensus on some clinical processes. This phenomenon might have attenuated the incremental effect of the SPI, making it difficult to detect. Alternatively, the full impact of the SPI might be observable only in the longer term. The conclusion of this study could have been different if concurrent controls had not been used.

Isolation and characterisation of bacteria associated with flying insects in hospitals, with particualr emphasis on Clostridum difficile

Clostridium difficile is a bacterial healthcare-associated infection, which houseflies Musca domestica may transfer due to their synanthropic nature. The aims of this thesis were to determine the ability of M. domestica to transfer C. difficile mechanically and to collect and identify flying insects in UK hospitals and classify any associated bacteria. M. domestica exposed to independent suspensions of vegetative cells and spores of C. difficile were able to mechanically transfer the bacteria on to agar for up to 4 hours following exposure. C. difficile could be recovered from fly excreta for 96hrs and was isolated from the M. domestica alimentary canal. Also confirmed was the carriage of C. difficile by M. domestica larvae, although it was not retained in the pupae or in the adults that subsequently developed. Flying insects were collected from ultra-violet light flytraps in hospitals. Flies (order Diptera) were the most commonly identified. Chironomidae were the most common flies, Calliphora vicina were the most common synanthropic fly and ‘drain flies’ were surprisingly numerous and represent an emerging problem in hospitals. External washings and macerates of flying insects were prepared and inoculated onto a variety of agars and following incubation bacterial colonies identified by biochemical tests. A variety of flying insects, including synanthropic flies (e.g. M. domestica and C. vicina) collected from UK hospitals harboured pathogenic bacteria of different species. Enterobacteriaceae were the group of bacteria most commonly isolated, followed by Bacillus spp, Staphylococci, Clostridia, Streptococci and Micrococcus spp. This study highlights the potential for M. domestica to contribute to environmental persistence and spread of C. difficile in hospitals. Also illustrated is the potential for flying insects to contribute to environmental persistence and spread of other pathogenic bacteria in hospitals and therefore the need to implement pest control as part of infection control strategies.

Fluorescent probe for detection of bacteria:conformational trigger upon bacterial reduction of an azo bridge

Using biomimetic chemical reduction or Clostridium perfringens cell extract containing azoreductase, the dimer-fluorescent probe 2,4-O-bisdansyl-6,7- diazabicyclooct-6-ene, which possesses a conformationally constrained cis-azo bridge, is reduced to the tetra-equatorial 2,4-O-bisdansyl-cyclohexyl-3,5- bisammonium salt which exhibits fluorescence indicative of a dansyl monomer. © 2012 The Royal Society of Chemistry.

Avaliação da Capacidade Antioxidante e da Estabilidade Após Embalamento a Vácuo de Hambúrgueres de Pata-roxa (Scyliorhinus canicula).

Toneladas de pescado são desperdiçadas diariamente aquando do processamento do peixe e o hambúrguer de pata-roxa foi desenvolvido para reaproveitar esse pescado subvalorizado e para ser uma fonte nutricional rica em antioxidantes. No presente trabalho, pretendeu-se comprovar o potencial antioxidante antes e após o tratamento térmico do hambúrguer de pata-roxa, e o potencial citotóxico e antiproliferativo sobre um modelo celular do cancro da mama (MCF-7). Foi também observada a estabilidade do hambúrguer de pata-roxa embalado a vácuo e refrigerado. A extração dos compostos fitoquímicos foi realizada com solventes de polaridade distinta (água, metanol e diclorometano) e com diferentes durações do processo (12h e 24h). O tratamento térmico aplicado foi vinte minutos a 180ºC. O potencial antioxidante foi avaliado pela capacidade de redução do radical livre 1,1-difenil-2-picrilhidrazil (DPPH) e pela capacidade de redução de radicais de oxigénio (ORAC), e através da quantificação total de polifenóis (QTP) pelo método de Folin-Ciocalteu (FC). O potencial citotóxico e antiproliferativo foi avaliado na linha celular MCF-7, cujos resultados foram revelados por ensaios espectrofotométricos (método do brometo de 3- (4,5-dimetiltiazol-2-il)-2,5-difenil tetrazólio (MTT)) e fluorimétricos (método de acetoxi-metil éster de calceína (calceína-AM)). A estabilidade do hambúrguer de pataroxa em vácuo e refrigerado foi avaliada através do estudo microbiológico com metodologias de referência (contagens de “totais” e produtores de sulfureto de hidrogénio (H2S) aeróbios e anaeróbios, esporos de Clostridium sulfitos-redutores, enterobactérias, Escherichia coli e pesquisa de Salmonella spp.), da determinação do índice de ácido tiobarbitúrico (TBA) e da avaliação da cor do hambúrguer pelo sistema CIE-L*a*b*. Os ensaios de DPPH e ORAC comprovaram a atividade antioxidante do extrato de hambúrguer de pata-roxa (metanol, 12h) com 79,5% de redução do DPPH e 8603,01μmol ET/100g para amostras sem tratamento térmico, e 87,4% de redução do DPPH e 2567,27μmol ET/100g para amostras com tratamento térmico. Quanto ao conteúdo fenólico, os extratos (metanol, 12h) revelaram 17,13mg EAG/100g do hambúrguer cru e 31,81mg EAG/100g do hambúrguer cozinhado. A extração de 24 horas não aumentou a quantidade de compostos fitoquímicos presentes no extrato. O hambúrguer apenas revelou ainda um potencial citotóxico in vitro relevante na linha celular MCF-7 (1mg/mL, 24h).Apesar do abuso observado na temperatura de armazenamento em refrigeração (temperatura média de 10,3ºC), o hambúrguer de pata-roxa cru, quando submetido ao embalamento a vácuo, apresentou um aumento no período de vida útil de prateleira de 4 dias relativamente à pata-roxa. Foi detetada a presença de esporos de Clostridium sulfito-redutores e 1,0x101ufc E. coli por 1g de hambúrguer de pata-roxa. Não foi detetada a presença de Salmonella spp. O índice de TBA manteve-se estável, mas o hambúrguer de pata-roxa sofreu uma perda na vivacidade (Cab) e na tonalidade (hab) da cor ao fim de 6 dias em refrigeração. É necessário continuar o estudo para melhorar o novo produto alimentar funcional, mas o presente trabalho permitiu concluir que o hambúrguer de pata-roxa reúne as condições para ter um elevado potencial antioxidante, apresentar maior estabilidade em armazenamento e, em simultâneo, constituir uma solução para o desperdício de pescado.

The cellular lipids of Romboutsia.

We have examined the lipids of three isolates, Romboutsia lituseburensis, Romboutsia ilealis, and Romboutsia sp. strain FRIFI, of the newly described genus Romboutsia by two-dimensional thin-layer chromatography (2D-TLC) and by liquid chromatography/mass spectrometry (LC/MS). We have found three phospholipids, phosphatidylglycerol (PG), cardiolipin and phosphatidic acid in all three species. A fourth phospholipid, lysyl-PG, was found in R. lituseburensis and strain FRIFI. Polyprenyl-phosphates were identified in the lipid extracts of all three species. Three glycolipids, mono-, di- and tri-hexosyldiacylglycerol, were common to all three species. An additional glycolipid, tetrahexosyl-diacylglycerol was identified in strain FRIFI. Acylated trihexosyldiacylglycerol and acyl-tetrahexosydiacylglycerol were also found in R. ilealis and strain FRIFI. Remarkably, no alk-1-enyl ether lipids (plasmalogens) were present in Romboutsia as distinct from bacteria of the related genus Clostridium in which these ether lipids are common. We have compared the lipidome of Romboutsia with that recently described for Clostridium difficile, which has plasmalogens, no lysyl-PG, and no tetrahexosyl-diacylglycerol. According to 16S rRNA gene sequencing, Romboutsia spp. and C. difficile are closely related (>95% sequence identity).

Energy requirements for the continuous biohydrogen production from Spirogyra biomass in a sequential batch reactor

The current energy market requires urgent revision for the introduction of renewable, less-polluting and inexpensive energy sources. Biohydrogen (bioH2) is considered to be one of the most appropriate options for this model shift, being easily produced through the anaerobic fermentation of carbohydrate-containing biomass. Ideally, the feedstock should be low-cost, widely available and convertible into a product of interest. Microalgae are considered to possess the referred properties, being also highly valued for their capability to assimilate CO2 [1]. The microalga Spirogyra sp. is able to accumulate high concentrations of intracellular starch, a preferential carbon source for some bioH2 producing bacteria such as Clostridium butyricum [2]. In the present work, Spirogyra biomass was submitted to acid hydrolysis to degrade polymeric components and increase the biomass fermentability. Initial tests of bioH2 production in 120 mL reactors with C. butyricum yielded a maximum volumetric productivity of 141 mL H2/L.h and a H2 production yield of 3.78 mol H2/mol consumed sugars. Subsequently, a sequential batch reactor (SBR) was used for the continuous H2 production from Spirogyra hydrolysate. After 3 consecutive batches, the fermentation achieved a maximum volumetric productivity of 324 mL H2/L.h, higher than most results obtained in similar production systems [3] and a potential H2 production yield of 10.4 L H2/L hydrolysate per day. The H2 yield achieved in the SBR was 2.59 mol H2/mol, a value that is comparable to those attained with several thermophilic microorganisms [3], [4]. In the present work, a detailed energy consumption of the microalgae value-chain is presented and compared with previous results from the literature. The specific energy requirements were determined and the functional unit considered was gH2 and MJH2. It was possible to identify the process stages responsible for the highest energy consumption during bioH2 production from Spirogyra biomass for further optimisation.

Avaliação da anchoita (engraulis anchoita) salgada maturada acondicionada em atmosfera modificada

A anchoita foi capturada e acondicionada a bordo sob-resfriamento a 0°C com gelo em escamas. Após o recebimento, o pescado foi processado na forma salgado-maturado. Após a maturação foram processadas e embaladas em sacos de polietileno e armazenadas sob-refrigeração a 5°C durante 84 dias. As amostras foram divididas grupos: (1) sob pressão atmosfera normal, (2) vácuo, (3) atmosfera modificada com 50% CO2 + 20% O2 + 30% N2 e (4) 60% CO2 + 10% O2 + 30% N2, em embalagens de polietileno e aluminizadas, termo-seladas e armazenadas sob-refrigeração a 5°C. Os valores de textura tiveram uma redução de 2277,8 N (Kg.m/s2 ) para 821,90 N (Kg.m/s2 ) para o tratamento controle. A qualidade inicial do pescado atendeu aos padrões legais vigentes, apresentando ausência Salmonella sp e enumerações aceitáveis aos padrões de Staphylococcus coagulase positiva, Clostridium sulfito redutores, coliforme totais e a 45ºC. Com relação ao pH, houve diferenças significativas durante o tempo de processamento (p<0,05), o valor passou de 6,3 (início) para 6,4 (final). Com relação aos resultados correspondentes aos parâmetros L*, a* e b* (cor), em todos os tratamentos e ao longo do tempo de processamento (ambas as embalagens), ocorreram diferenças significativas (p<0,05). Os valores de L* variaram de 34,80 para 18,00 (controle) 23,00 (vácuo), 20,21 (T3) e 22,00 (T4) embalagens de polietileno. Nas embalagens de alumínio os valores de L* variaram de 34,00 para 25,00 (controle), 29,00(vácuo), 22,10 (T3) e 26,00 (T4).

Avaliação de alguns parâmetros da qualidade da anchoita (Engraulis anchoita) enlatada em óleo de girassol e em molho de tomate

O consumo de pescado no Brasil cresceu 40% nos últimos 7 anos passando de 6,46 para 9,03 kg/habitante/ano, valor que se aproxima do recomendado pela Organização Mundial de Saúde. A razão está relacionada com a subutilização de determinadas espécies e a falta de diversificação da indústria processadora para a produção de alimentos com maior valor agregado. Considerando o esgotamento de determinadas espécies com a utilização da sobrepesca, é possível o emprego da anchoita na forma de conservas através da utilização de meios de cobertura como molho de tomate e óleo comestível. Este trabalho teve como objetivo elaborar conservas de anchoita (Engraulis anchoita) com a utilização de 2 meios de cobertura: molho de tomate e óleo de girassol, submetidas a tempos de salmouragem diferenciados, 2 e 5 min e com o emprego ou não de pré-cozimento. De acordo com os padrões estabelecidos, as amostras de pescado fresco utilizadas para a execução dos enlatados apresentaram resultados físico químicos adequados comprovando o frescor do pescado envolvido no processo, ou sejam: 16,29 mg/100 g amostra para N-BVT, 7,90 mg/100 g amostra para N-TMA e pH 6,5. As conservas em molho de tomate submetidas a operação de salmouragem durante 2 min, com e sem pré-cozimento apresentaram, respectivamente, 16,57 e 16,24% proteínas, 3,94 e 4,66% lipídios, 73,0 e 73,28% umidade, 3,22 e 3,67% cinzas, 0,17 e 0,19% de cloretos (NaCl). As conservas com molho de tomate, utilizando anchoita eviscerada salmourada por 5 min, com e sem pré-cozimento, apresentaram respectivamente, 15,94 e 15,31% proteínas, 3,15 e 4,90 lipídios%, 73,70 e 73,98% umidade, 3,80 e 4,10% cinzas, 0,21 e 0,24% cloretos (NaCl). Para as conservas de anchoita em óleo de girassol, utilizando tempo de salmouragem de 2 min, com e sem pré-cozimento, apresentaram 16,97 e 16,76% proteínas, 7,68 e 5,70% lipídios, 65,87 e 68,74% umidade, 3,16 e 3,28% cinzas, 0,10 e 0,12% cloretos (NaCl), respectivamente. As conservas utilizando o pescado previamente submetido a salmouragem por 5 min e posteriormente enlatado com a adição de óleo de girassol, com e sem pré-cozimento apresentaram respectivamente, 15,97 e 15,89% proteínas, 7,91 e 5,19% lipídios, 66,26 e 68,23% umidade, 3,78 e 3,87% cinzas, 0,13 e 0,21% NaCl. As análises microbiológicas das conservas submetidas aos diferentes tratamentos mostraram ausência de Salmonella spp, Staphylococcus coagulase positiva e Clostridium sulfito-redutor, resultados estes, de acordo com o estabelecido pela legislação higiênico-sanitária brasileira. Nos testes de esterilidade comercial não foram constatadas alterações visíveis nos enlatados submetidos a incubação por 5 dias a 36 ± 1°C (determinação de micro-organismos aeróbios viáveis) e a 7-10 dias a 55 ± 1°C (termófilos). Considerando as quantidades de pescado enlatado (80, 90 e 100g), o rendimento para todas as amostras apresentaram, no mínimo, 50% de pescado em relação ao peso líquido. A avaliação sensorial realizada por teste de ordenação para a avaliação da preferência não apresentou diferenças significativas entre as amostras.

Effect of time and diet change on the bacterial community structure throughout the gastrointestinal tract and in faeces of the northern brown bandicoot, Isoodon macrourus

A significant gap, in not only peramelid nutritional physiology but marsupial nutrition as a whole, is the lack of information relating to microorganisms of the gastrointestinal tract. This research is a preliminary investigation that will provide a baseline for comparisons among peramelids. The high degree of 16S rRNA gene clones identified in this research that are closely related to culturable bacteria suggests that additional research will enable a more complete description of the gastrointestinal bacteria of I. macrourus. Most identifiable clones belonged to Clostridium and Ruminococcus. This research has confirmed that the hindgut of I. macrourus, the caecum, proximal colon and distal colon, are the main sites for microbial activity.

Metabolomics as a tool to explore the staphylococcal biofilm

Orthopaedic infections can be polymicrobial existing as a microbiome. Infections often incorporate staphylococcal species, including Staphylococcus aureus. Such infections can lead to life threatening illness and implant failure. Furthermore, biofilm formation on the implant surface can occur, increasing pathogenicity, exacerbating antibiotic resistance and altering antimicrobial mechanism of action. Bacteria change dramatically during the transition to a biofilm growth state: phenotypically; transcriptionally; and metabolically, highlighting the need for research into molecular mechanisms involved in biofilm formation. Metabolomics can provide a tool to analyse metabolic changes which are directly related to the expressed phenotype. Here, we aimed to provide greater understanding of orthopaedic infection caused by S. aureus and biofilm formation on the implant surface. Through metagenome analysis by employing: implant material extraction; DNA extraction; microbial enrichment; and whole genome sequencing, we present a microbiome study of the infected prosthesis to resolve the causative species of orthopaedic hip infection. Results highlight the presence of S. aureus as a primary cause of orthopaedic infection along with Enterococcus faecium and the presence of secondary pathogen Clostridium difficile. Although results were hindered by the presence of host contaminating DNA even after microbial enrichment, conclusions could be made over the potential increased pathogenicity caused by the presence of a secondary pathogen and highlight method and sample preparation considerations when undertaking such a study. Following this finding, studies were focused on an orthopaedic clinical isolate of S. aureus and a metabolome extraction method for staphylococcal biofilms was developed using cell lysis through bead beating and solvent metabolome extraction. The method was found to be reproducible when coupled with liquid chromatography-mass spectrometry (LC-MS) and bioinformatics, allowing for the detection of significant changes in metabolism between planktonic and biofilm cultures to be identified and drug mechanism of actions (MOA) to be studied. Metabolomics results highlight significant changes in a number of metabolic pathways including arginine biosynthesis and purine metabolism between the two cell populations, evidence of S. aureus responding to their changing environment, including oxygen availability and a decrease in pH. Focused investigations on purine metabolism looking for biofilm modulation effects were carried out. Modulation of the S. aureus biofilm phenotype was observed through the addition of exogenous metabolites. Inosine increased biofilm biomass while formycin B, an inosine analogue, showed a dispersal effect and a potential synergistic effect in biofilm dispersal when coupled with gentamycin. Changes in metabolism between planktonic cells and biofilms highlight the requirement for antimicrobial testing to be carried out against planktonic cells and biofilms. Untargeted metabolomics was used to study the MOA of triclosan in S. aureus. The triclosan target and MOA in bacteria has already been characterised, however, questions remain over its effects in bacteria. Although the use of triclosan has come under increasing speculation, its full effects are still largely unknown. Results show that triclosan can induce a cascade of detrimental events in the cell metabolism including significant changes in amino acid metabolism, affecting planktonic cells and biofilms. Results and conclusions provide greater understanding of orthopaedic infections and specifically focus on the S. aureus biofilm, confirming S. aureus as a primary cause of orthopaedic infection and using metabolomic analysis to look at the changing state of metabolism between the different growth states. Metabolomics is a valuable tool for biofilm and drug MOA studies, helping understand orthopaedic infection and implant failure, providing crucial insight into the biochemistry of bacteria for the potential for inferences to be gained, such as the MOA of antimicrobials and the identification of novel metabolic drug targets.