Microbial quality of shrimp products of export trade produced from aquacultured shrimp

Bacteriological quality of individually quick frozen (IQF) shrimp products produced from aquacultured tiger shrimp (Penaeus monodon) has been analysed in terms of aerobic plate count (APC), coliforms, Escherichia coli, coagulase-positive staphylococci, Salmonella, and Listeria monocytogenes. Eight hundred forty-six samples of raw, peeled, and deveined tail-on (RPTO), 928 samples of cooked, peeled, and deveined tail-on (CPTO), 295 samples of headless, undeveined shell-on (HLSO), and 141 samples of raw, peeled, and deveined tail-off (RPND) shrimps were analysed for the above bacteriological parameters. Salmonella was isolated in only one sample of raw, peeled tail-on. Serotyping of the strain revealed that it was S. typhimurium. While none of the cooked, peeled tail-on shrimp samples exceeded the aerobic plate count (APC) of 105 colony forming units per gram (cfu/g), 2.5% of raw, peeled, tail-on, 6.4% of raw, peeled tail-off, and 7.5% of headless shell-on shrimp samples exceeded that level. Coliforms were detected in all the products, though at a low level. Prevalence of coliforms was higher in headless shell-on (26%) shrimps followed by raw, peeled, and deveined tail-off (19%), raw, peeled tail-on (10%), and cooked, peeled tail-on (3.8%) shrimps. While none of the cooked, peeled tail-on shrimp samples were positive for coagulase-positive staphylococci and E. coli, 0.6–1.3% of the raw, peeled tail-on were positive for staphylococci and E. coli, respectively. Prevalence of staphylococci was highest in raw, peeled tail-off (5%) shrimps and the highest prevalence of E. coli (4.8%) was noticed in headless shell-on shrimps. L. monocytogenes was not detected in any of the cooked, peeled tail-on shrimps. Overall results revealed that the plant under investigation had exerted good process control in order to maintain superior bacteriological quality of their products

The incidence ,Antibiotic resistence and survival of salmonella and escherichia coli isolated from broiler chicken retail outlets

The incidence of salmonella and escherichia coli in chicken retail outlets in a residential area of coimbatore, Tamilnadu India was studied with the view that accessories may be a source of cross contamination.Accessories like cages,knives ,chopping boards weighing balance trays and the hands of butcher were examined.A toatal of 14 salmonella as well as 31 E.coli were isolated from different sources. The incidence of E.coli was higher than that of Salmonella.The highest incidence of Salmonella was found in chopping boards and the maximum level of E.Coli was detected in cages.

Effect of Delayed Icing on the Microbiological Quality of Hilsa Toli

Effect of delayed icing on the microbial quality and shelf-life of Hilsa toll was studied . Fish iced in rigor condition had a shelf-life of 11 days irrespective of the state of rigor . Fish procured from the landing centre had a shelf-life of only 8 days . It showed the presence of coagulase positive staphylococci, faecal streptococci and E. coli. Total bacterial count was low in all the samples and it increased after spoilage

Molecular Epidemiology of Escherichia coli isolates from Environmental, Food and Clinical Sources

In the present study diversity of E. coli in the water samples of Cochin estuary were studied for a period of 3 years ranging from January 2010- December 2012. The stations were selected based on the closeness to satellite townships and waste input. Two of the stations (Chitoor and Thevara) were fixed upstream, two in the central part of the estuary namely Bolgatty and Off Marine Science Jetty, and one at the Barmouth. Diversity was assessed in terms of serotypes, phylogenetic groups and genotypes. Two groups of seafood samples such as fish and shellfish collected from the Cochin estuary were used for isolation of E. coli. One hundred clinical E. coli isolates were collected from one public health centre, one hospital and five medical labs in and around Cochin City, Kerala. From our results it was clear that pathogen cycling is occurring through food, water and clinical sources. Pathogen cycling through food is very common and fish and shellfish that harbour these strains might pose potential health risk to consumer. Estuarine environment is a melting pot for various kinds of wastes, both organic and inorganic. Mixing up of waste water from various sources such as domestic, industries, hospitals and sewage released into these water bodies resulting in the co-existence of E. coli from various sources thus offering a conducive environment for horizontal gene transfer. Opportunistic pathogens might acquire genes for drug resistance and virulence turning them to potential pathogens. Prevalence of ExPEC in the Cochin estuary, pose threat to people who use this water for fishing and recreation. Food chain also plays an important role in the transit of virulence genes from the environments to the human. Antibiotic resistant E. coli are widespread in estuarine water, seafood and clinical samples, for reasons well known such as indiscriminate use of antibiotics in animal production systems, aquaculture and human medicine. Since the waste water from these sources entering the estuary provides selection pressure to drug resistant mutants in the environment. It is high time that the authorities concerned should put systems in place for monitoring and enforcement to curb such activities. Microbial contamination can limit people’s enjoyment of coastal waters for contact recreation or shellfish-gathering. E. coli can make people sick if they are present in high levels in water used for contact recreation or shellfish gathering. When feeding, shellfish can filter large volumes of seawater, so any microorganisms present in the water become accumulated and concentrated in the shellfish flesh. If E. coli contaminated shellfish are consumed the impact to human health includes gastroenteritis, urinary tract infections (UTIs), and bacteraemia. In conclusion, the high prevalence of various pathogenic serotypes and phylogenetic groups, multidrug-resistance, and virulence factor genes detected among E. coli isolates from stations close to Cochin city is a matter of concern, since there is a large reservoir of antibiotic resistance genes and virulence traits within the community, and that the resistance genes and plasmid-encoded genes for virulence were easily transferable to other strains. Given the severity of the clinical manifestations of the disease in humans and the inability and/or the potential risks of antibiotic administration for treatment, it appears that the most direct and effective measure towards prevention of STEC and ExPEC infections in humans and ensuring public health may be considered as a priority.

Horizontal nutrient fluxes and production efficiencies in urban and peri-urban crop and livestock husbandry of Niamey, Niger

Urban and peri-urban agriculture (UPA) increasingly supplies food and non-food values to the rapidly growing West African cities. However, little is known about the resource use efficiencies in West African small-scale UPA crop and livestock production systems, and about the benefits that urban producers and retailers obtain from the cultivation and sale of UPA products. To contribute to filling this gap of knowledge, the studies comprising this doctoral thesis determined nutrient use efficiencies in representative urban crop and livestock production system in Niamey, Niger, and investigated potential health risks for consumers. Also assessed was the economic efficiency of urban farming activities. The field study, which was conducted during November 2005 to January 2008, quantified management-related horizontal nutrient flows in 10 vegetable gardens, 9 millet fields and 13 cattle and small ruminant production units. These farms, selected on the basis of a preceding study, represented the diversity of UPA crop and livestock production systems in Niamey. Based on the management intensity, the market orientation and especially the nutrient input to individual gardens and fields, these were categorized as high or low input systems. In the livestock study, high and low input cattle and small ruminant units were differentiated based on the amounts of total feed dry matter offered daily to the animals at the homestead. Additionally, economic returns to gardeners and market retailers cultivating and selling amaranth, lettuce, cabbage and tomato - four highly appreciated vegetables in Niamey were determined during a 6-months survey in forty gardens and five markets. For vegetable gardens and millet fields, significant differences in partial horizontal nutrient balances were determined for both management intensities. Per hectare, average annual partial balances for carbon (C), nitrogen (N), phosphorus (P) and potassium (K) amounted to 9936 kg C, 1133 kg N, 223 kg P and 312 kg K in high input vegetable gardens as opposed to 9580 kg C, 290 kg N, 125 kg P and 351 kg K in low input gardens. These surpluses were mainly explained by heavy use of mineral fertilizers and animal manure to which irrigation with nutrient rich wastewater added. In high input millet fields, annual surpluses of 259 kg C ha-1, 126 kg N ha-1, 20 kg P ha-1 and 0.4 kg K ha-1 were determined. Surpluses of 12 kg C ha-1, 17 kg N ha-1, and deficits of -3 kg P ha-1 and -3 kg K ha-1 were determined for low input millet fields. Here, carbon and nutrient inputs predominantly originated from livestock manure application through corralling of sheep, goats and cattle. In the livestock enterprises, N, P and K supplied by forages offered at the farm exceeded the animals’ requirements for maintenance and growth in high and low input sheep/goat as well as cattle units. The highest average growth rate determined in high input sheep/goat units was 104 g d-1 during the cool dry season, while a maximum average gain of 70 g d-1 was determined for low input sheep/goat units during the hot dry season. In low as well as in high input cattle units, animals lost weight during the hot dry season, and gained weight during the cool dry season. In all livestock units, conversion efficiencies for feeds offered at the homestead were rather poor, ranging from 13 to 42 kg dry matter (DM) per kg live weight gain (LWG) in cattle and from 16 to 43 kg DM kg-1 LWG in sheep/goats, pointing to a substantial waste of feeds and nutrients. The economic assessment of the production of four high value vegetables pointed to a low efficiency of N and P use in amaranth and lettuce production, causing low economic returns for these crops compared to tomato and cabbage to which inexpensive animal manure was applied. The net profit of market retailers depended on the type of vegetable marketed. In addition it depended on marketplace for amaranth and lettuce, and on season and marketplace for cabbage and tomato. Analysis of faecal pathogens in lettuce irrigated with river water and fertilized with animal manure indicated a substantial contamination by Salmonella spp. with 7.2 x 104 colony forming units (CFU) per 25 g of produce fresh matter, while counts of Escherichia coli averaged 3.9 x 104 CFU g-1. In lettuce irrigated with wastewater, Salmonella counts averaged 9.8 x 104 CFU 25 g-1 and E. coli counts were 0.6 x 104 CFU g-1; these values exceeded the tolerable contamination levels in vegetables of 10 CFU g-1 for E. coli and of 0 CFU 25 g-1 for Salmonella. Taken together, the results of this study indicate that Niamey’s UPA enterprises put environmental safety at risk since excess inputs of N, P and K to crop and livestock production units favour N volatilisation and groundwater pollution by nutrient leaching. However, more detailed studies are needed to corroborate these indications. Farmers’ revenues could be significantly increased if nutrient use efficiency in the different production (sub)systems was improved by better matching nutrient supply through fertilizers and feeds with the actual nutrient demands of plants and animals.

Effects of Different Feeding Regimes on the Digestibility and Faecal Excretion of Nitrogen, Soluble Carbohydrates and Fibre Fractions in Water Buffaloes kept under Subtropical Conditions

In the course of the ‘Livestock Revolution’, extension and intensification of, among others, ruminant livestock production systems are current phenomena, with all their positive and negative side effects. Manure, one of the inevitable secondary products of livestock rearing, is a valuable source of plant nutrients and its skillful recycling to the soil-plant interface is essential for soil fertility, nutrient - and especially phosphorus - uses efficiency and the preservation or re-establishment of environmentally sustainable farming systems, for which organic farming systems are exemplarily. Against this background, the PhD research project presented here, which was embedded in the DFG-funded Research Training Group 1397 ‘Regulation of soil organic matter and nutrient turnover in organic agriculture ’ investigated possibilities to manipulate the diets of water buffalo (Bubalus bubalis L.) so as to produce manure of desired quality for organic vegetable production, without affecting the productivity of the animals used. Consisting of two major parts, the first study (chapter 2) tested the effects of diets differing in their ratios of carbon (C) to nitrogen (N) and of structural to non-structural carbohydrates on the quality of buffalo manure under subtropical conditions in Sohar, Sultanate of Oman. To this end, two trials were conducted with twelve water buffalo heifers each, using a full Latin Square design. One control and four tests diets were examined during three subsequent 7 day experimental periods preceded each by 21 days adaptation. Diets consisted of varying proportions of Rhodes grass hay, soybean meal, wheat bran, maize, dates, and a commercial concentrate to achieve a (1) high C/N and high NDF (neutral detergent fibre)/SC (soluble carbohydrate) ratio (HH), (2) low C/N and low NDF/SC ratio (LL); (3) high C/N and low NDF/SC ratio (HL) and (4) low C/N and high NDF/SC (LH) ratio. Effects of these diets, which were offered at 1.45 times maintenance requirements of metabolizable energy, and of individual diet characteristics, respectively, on the amount and quality of faeces excreted were determined and statistically analysed. The faeces produced from diets HH and LL were further tested in a companion PhD study (Mr. K. Siegfried) concerning their nutrient release in field experiments with radish and cabbage. The second study (chapter 3) focused on the effects of the above-described experimental diets on the rate of passage of feed particles through the gastrointestinal tract of four randomly chosen animals per treatment. To this end, an oral pulse dose of 683 mg fibre particles per kg live weight marked with Ytterbium (Yb; 14.5 mg Yb g-1 organic matter) was dosed at the start of the 7 day experimental period which followed 21 days of adaptation. During the first two days a sample for Yb determination was kept from each faecal excretion, during days 3 – 7 faecal samples were kept from the first morning and the first evening defecation only. Particle passage was modelled using a one-compartment age-dependent Gamma-2 model. In both studies individual feed intake and faecal excretion were quantified throughout the experimental periods and representative samples of feeds and faeces were subjected to proximate analysis following standard protocols. In the first study the organic matter (OM) intake and excretion of LL and LH buffaloes were significantly lower than of HH and HL animals, respectively. Digestibility of N was highest in LH (88%) and lowest in HH (74%). While NDF digestibility was also highest in LH (85%) it was lowest in LL (78%). Faecal N concentration was positively correlated (P≤0.001) with N intake, and was significantly higher in faeces excreted by LL than by HH animals. Concentrations of fibre and starch in faecal OM were positively affected by the respective dietary concentrations, with NDF being highest in HH (77%) and lowest in LL (63%). The faecal C/N ratio was positively related (P≤0.001) to NDF intake; C/N ratios were 12 and 7 for HH and LL (P≤0.001), while values for HL and LH were 11.5 and 10.6 (P>0.05). The results from the second study showed that dietary N concentration was positively affecting faecal N concentration (P≤0.001), while there was a negative correlation with the faecal concentration of NDF (P≤0.05) and the faecal ratios of NDF/N and C/N (P≤0.001). Particle passage through the mixing compartment was lower (P≤0.05) for HL (0.033 h-1) than for LL (0.043 h-1) animals, while values of 0.034 h-1 and 0.038 h-1 were obtained for groups LH and HH. At 55.4 h, total tract mean retention time was significantly (P≤0.05) lower in group LL that in all other groups where these values varied between 71 h (HH) and 79 h (HL); this was probably due to the high dietary N concentration of diet LL which was negatively correlated with time of first marker appearance in faeces (r= 0.84, P≤0.001), while the dietary C concentration was negatively correlated with particle passage through the mixing compartment (r= 0.57, P≤0.05). The results suggest that manure quality of river buffalo heifers can be considerably influenced by diet composition. Despite the reportedly high fibre digestion capacity of buffalo, digestive processes did not suppress the expression of diet characteristics in the faeces. This is important when aiming at producing a specific manure quality for fertilization purposes in (organic) crop cultivation. Although there was a strong correlation between the ingestion and the faecal excretion of nitrogen, the correlation between diet and faecal C/N ratio was weak. To impact on manure mineralization, the dietary NDF and N concentrations seem to be the key control points, but modulating effects are achieved by the inclusion of starch into the diet. Within the boundaries defined by the animals’ metabolic and (re)productive requirements for energy and nutrients, diet formulation may thus take into account the abiotically and biotically determined manure turnover processes in the soil and the nutrient requirements of the crops to which the manure is applied, so as to increase nutrient use efficiency along the continuum of the feed, the animal, the soil and the crop in (organic) farming systems.

Effects of tubers of the Jerusalem artichoke (Helianthus tuberosus) and potatoes (Solanum tuberosum) on the intestinal microbiota of pigs and evaluation of a procedure for quantification of microbial mass in pig faeces

Die Mikrobiota im Gastrointestinaltrakt (GIT) spielt eine bedeutende Rolle beim Fermentationsprozess im Bezug auf die Nährstoffversorgung sowie die Gesundheit des Darms und des gesamten Organismus. Inulin und resistente Stärke (RS) konnten als präbiotisch wirksame Substanzen identifiziert werden und sind jeweils auch in den Knollen der Topinamburpflanze (Helianthus tuberosus) und in Kartoffeln (Solanum tuberosum) enthalten. Da sie ebenfalls energiereiche Futtermittel für Schweine sind, war es das Ziel der ersten beiden Studien, die Auswirkungen der Aufnahme von Topinamburknollen und Kartoffeln auf die intestinale Mikrobiota und Parameter des Immunsystems bei Endmastschweinen zu bestimmen. In der dritten Studie wurde die mikrobielle Biomasse quantitativ mit einem Verfahren zur Isolation von Bakterien in einer Flüssigkeit durch Hochgeschwindigkeits-Zentrifugation erfasst und der bakteriell gebundene Stickstoff (MP-N) mit dem bakteriellen und endogenem Kotstickstoff (BEDN) verglichen. Im ersten Versuch wurden 72 Endmastschweine in einem Freilandhaltungssystem in eine Kontroll- (CT), die mit Kraftfutter entsprechend des Bedarfs der Tiere für ein Leistungsniveau von 700 g täglichem Lebendmassezuwachs versorgt wurde, und eine Versuchsvariante (ET) aufgeteilt. In der Versuchsvariante erhielten die Tiere nur 70% der Kraftfuttermenge der Kontrollvariante, hatten aber Zugang zu einer abgeteilten Fläche, auf der Topinamburknollen angebaut waren. Die freie Aufnahme von Topinamburknollen wurde auf 1•24 kg Trockenmasse (TM)/Tag bestimmt, entsprechend einer Inulinaufnahme von durchschnittlich 800 g/Tag. Während sich die Wachstumsleistung in der Kontrollvariante auf 0•642 ± 0•014 kg/Tag belief, war sie in der Versuchsvariante mit 0•765 ± 0•015 kg/Tag (P=0•000) höher. Die freie Verfügbarkeit von Inulin und Fructo-oligosacchariden (FOS) im GIT der Schweine erhöhte die Keimzahlen der anaeroben Bakterien (P=0•000), Laktobazillen (P=0•046) und Hefen (P=0•000) signifikant und verringerte das Vorkommen von Clostridium perfringens im Schweinekot erheblich von lg 5•24 ± 0•17 kolonie-bildende Einheiten pro g Frischmasse (KbE/ g FM) in der Kontrollvariante auf lg 0•96 ± 0•20 KbE/ g FM in der Versuchsvariante (P=0•000). C-reaktives Protein (CRP) und Antikörper gegen Lipopolysaccharide (LPS) von Escherichia coli J5 ließen keine Unterschiede zwischen den Fütterungsvarianten erkennen. In der zweiten Untersuchung wurden 58 Endmastschweine einer Kontrollvariante (CT), die bedarfsgerecht mit einer Kraftfuttermischung für ein Leistungsniveau von 700 g Tageszunahmen gefüttert wurde, und zwei Versuchsvarianten zugeteilt. Die Versuchsvarianten erhielten eine Menge von 1•2 kg TM gedämpften Kartoffeln (potato treatment, PT) oder gedämpften und einsilierten Kartoffeln (silage treatment, ST) pro Tag und nur 46% bzw. 43% der Menge des Kraftfutters der Kontrollvariante. Die Wachstumsleistung und Schlachtkörperzusammensetzung ließen keine signifikanten Unterschiede zwischen den Varianten erkennen. Im PT und ST waren gegenüber dem CT im Kot der pH-Wert sowie die Gehalte von TM, Neutral-Detergenz-Faser (NDF), unverdautem Futterstickstoff (UDN) und teilweise von Säure-Detergenz-Faser (ADF) signifikant niedriger (P=0•000) und die von Ammonium (NH4) und Ammoniumstickstoff (NH4-N) signifikant höher (P=0•000). Das hohe Angebot von hitzebehandelten Kartoffeln führte zu einer erheblichen Verringerung von E. coli (P=0•000), C. perfringens (P=0•000) und Immunoglobulin A gegen LPS von E. coli J5 (P=0•001). Darüber hinaus waren in der ersten Versuchsperiode im ST die aeroben und anaeroben Gesamtkeimzahlen sowie die Laktobazillen und Hefen gegenüber dem PT signifikant erhöht. Die Unterschiede in der Mikrobiota zwischen der Kontroll- und Versuchsvarianten weisen auf die positiven Auswirkungen von Topinamburknollen und hitzebehandelten Kartoffeln auf die Mikrobiota im hinteren Darmabschnitt hin. Das Ziel der dritten Untersuchung war die Modifizierung des Verfahrens zur Isolation von Bakterien in einer Flüssigkeit mittels verschiedener Zentrifugationsschritte, um ein mikrobielles Pellet (MP) zu erhalten, welches die quantitative Abtrennung und Erfassung der Bakterien in Schweinekot ermöglicht. Zusätzlich wurde der BEDN Anteil sowie die Gehalte der Aminozucker Galactosamin, Glucosamin, Mannosamin und Muraminsäure im Kot und im MP bestimmt. Die untersuchten Kotproben stammten von Schweinen eines Phosphor (P) Stoffwechselversuch. Zehn männlich-kastrierte Schweine mit einem durchschnittlichen Lebendgewicht von 51•1 ± 8•5 kg wurden einzeln in Stoffwechselkäfigen gehalten. Die Tiere wurden fünf Fütterungsvarianten zugeteilt, die dem Bedarf der Tiere für ein Leistungsniveau von 700 g Tageszunahmen entsprachen, in den Rationen 2 bis 5 jedoch eine P-Gehalt unter dem Tagesbedarf der Tiere aufwiesen und in den Rationen 3 bis 5 mit abgestuften Gehalten von 50, 100 sowie 200 mg/kg einer experimentellen Phytase ergänz waren. Die Absenkung des P Gehaltes im Futter verringerte den Asche- (P=0•024) und Trockenmassegehalt im Kot (P=0•017) sowie die P Konzentration im MP (P=0•000) signifikant. Die mikrobielle Biomasse im Kot wurde durch die Wiegung des MP auf durchschnittlich 467 g/kg TM bestimmt. Der Stickstoffgehalt im Kot betrug im Mittel 46•1 g/kg TM und der in die Bakterienmasse eingebaute Stickstoffanteil 27•1 g/kg TM bzw. 58% vom Gesamtstickstoffgehalt im Kot. Die BEDN Fraktion wurde auf 73% am Kotstickstoff bestimmt. Der P-Gehalt im Kot sowie der N Gehalt im MP mit durchschnittlichen 10•4 und 57•9 g/kg TM lagen im Bereich von Literaturangaben. Die P Gehalte im MP schwankten in Abhängigkeit von der Zugabe von Phytase signifikant (P=0•000) von 1•8 bis 4•8 g/kg TM. Die Aminozucker wiesen keine signifikanten unterschiede zwischen Fütterungsvarianten auf und lagen im Bereich von Werten von Rinderkot. Ergebnisse weisen darauf hin, dass die angewandte Methode zur direkten Quantifizierung der mikrobiellen Biomasse geeignet ist.

Urban and peri-urban agricultural production along railway tracks: a case study from the Mumbai Metropolitan Region

Urban and peri-urban agriculture (UPA) contributes to food security, serves as an opportunity for income generation, and provides recreational services to urban citizens. With a population of 21 Million people, of which 60 % live in slums, UPA activities can play a crucial role in supporting people’s livelihoods in Mumbai Metropolitan Region (MMR). This study was conducted to characterize the railway gardens, determine their role in UPA production, and assess potential risks. It comprises a baseline survey among 38 railway gardeners across MMR characterized by different demographic, socio-economic, migratory, and labour characteristics. Soil, irrigation water, and plant samples were analyzed for nutrients, heavy metals, and microbial load. All the railway gardeners practiced agriculture as a primary source of income and cultivated seasonal vegetables such as lady’s finger (Abelmoschus esculentus L. Moench), spinach (Spinacia oleracea L.), red amaranth (Amaranthus cruentus L.), and white radish (Raphanus sativus var. longipinnatus) which were irrigated with waste water. This irrigation water was loaded with 7–28 mg N l^(−1), 0.3–7 mg P l^(−1), and 8–32 mg K l^(−1), but also contained heavy metals such as lead (0.02–0.06 mg Pb l^(−1)), cadmium (0.03–0.17 mg Cd l^(−1)), mercury (0.001–0.005 mg Hg l^(−1)), and pathogens such as Escherichia coli (1,100 most probable number per 100 ml). Levels of heavy metals exceeded the critical thresholds in surface soils (Cr, Ni, and Sr) and produce (Pb, Cd, and Sr). The railway garden production systems can substantially foster employment and reduce economic deprivation of urban poor particularly slum dwellers and migrant people. However this production system may also cause possible health risks to producers and consumers.

Intestinal microbiology in Crohn's disease: a study of Escherichia coli as a potential etiologic agent

La malaltia de Crohn és una malaltia inflamatòria intestinal crònica d'etiologia encara desconeguda. Actualment es pensa que hi participen factors genètics i immunològics que confereixen una susceptibilitat a l'hoste, i factors externs o ambientals, com serien els microorganismes i/o l'estil de vida. L'objectiu principal d'aquest treball ha estat descriure les poblacions bacterianes associades especialment als malalts de Crohn, amb la intenció d'identificar possibles agents etiològics. Els resultats d'aquest treball coincideixen amb investigacions prèvies que descriuen l'alteració bacteriana present en els malalts de Crohn (disbiosi) i recolzen la hipòtesi que implica el recentment descrit patovar "Adherent- Invasive Escherichia coli" (AIEC) en l'etiologia d'aquesta malaltia inflamatòria intestinal. A més, contribuïm a la descripció de les poblacions d'E. coli associades a la mucosa intestinal aportant dades sobre aspectes ecològics i patogènics. Finalment, descrivim nous aspectes fenotípics d'AIEC que podrien estar relacionats amb la seva patogènia, com seria la capacitat de formar biofilms.

Low cost eye tracking for human-machine interfacing

One of the main challenges for developers of new human-computer interfaces is to provide a more natural way of interacting with computer systems, avoiding excessive use of hand and finger movements. In this way, also a valuable alternative communication pathway is provided to people suffering from motor disabilities. This paper describes the construction of a low cost eye tracker using a fixed head setup. Therefore a webcam, laptop and an infrared lighting source were used together with a simple frame to fix the head of the user. Furthermore, detailed information on the various image processing techniques used for filtering the centre of the pupil and different methods to calculate the point of gaze are discussed. An overall accuracy of 1.5 degrees was obtained while keeping the hardware cost of the device below 100 euros.

Promoting microbial immobilization of soil nitrogen during restoration of abandoned agricultural fields by organic additions

Application of organic materials to soils to enhance N immobilization into microbial biomass, thereby reducing inorganic N concentrations, was studied as a management option to accelerate the reestablishment of the native vegetation on abandoned arable fields on sandy soils the Kiskunsag National Park, Hungary. Sucrose and sawdust were used at three different topographic sites over 4 years. N availability and extractable inorganic N concentrations were significantly reduced in all sites. Soil microbial biomass C and microbial biomass N increased significantly following C additions, but the microbial C to microbial N ratio remained unaffected. It is concluded that the combined application of the rapidly utilized C source (sucrose) promoted N immobilization, whereas the addition of the slowly utilized C source (sawdust) maintained the elevated microbial biomass C and microbial biomass N in the field.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

Alternative methodologies - stretching the in vitro box

Current gas-based in vitro evaluation systems are extremely powerful research techniques. However they have the potential to generate a great deal more than simple fermentation dynamics. Details from four experiments are presented in which adaptation, and novel application, of an in vitro system allowed widely differing objectives to be examined. In the first two studies, complement methodologies were utilised. In such assays, an activity or outcome is inferred through the occurrence of a secondary event rather than by direct observation. Using an N-deficient incubation medium, the increase in starch fermentation, when supplemented with individual amino acids (i.e., known level of N) relative to that of urea (i.e., known quantity and N availability), provided an estimate of their microbial utilisation. Due to the low level of response observed with some arnino acids (notably methionine and lysine), it was concluded, that they may not need to be offered in a rumen-inert form to escape rumen microbial degradation. In another experiment, the extent to which degradation of plant cell wall components was inhibited by lipid supplementation was evaluated using fermentation gas release profiles of washed hay. The different responses due to lipid source and level of inclusion suggested that the degree of rumen protection required to ameliorate this depression was supplement dependent. That in vitro inocula differ in their microbial composition is of little interest per se, as long as the outcome is the same (i.e., that similar substrates are degraded at comparable rates and end-product release is equivalent). However where a microbial population is deficient in a particular activity, increasing the level of inoculation will have no benefit. Estimates of hydrolytic activity were obtained by examining fermentation kinetics of specific substrates. A number of studies identified a fundamental difference between rumen fluid and faecal inocula, with the latter having a lower fibrolytic activity, which could not be completely attributed to microbial numbers. The majority of forage maize is offered as an ensiled feed, however most of the information on which decisions such as choice of variety, crop management and harvesting date are made is based on fresh crop measurements. As such, an attempt was made to estimate ensiled maize quality from an in vitro analysis of the fresh crop. Fermentation profiles and chemical analysis confirmed changes in crop composition over the growing season, and loss of labile carbohydrates during ensiling. In addition, examination of degradation residues allowed metabolizable energy (ME) contents to be estimated. Due to difficulties associated with starch analysis, the observation that this parameter could be predicted by difference (together with an assumed degradability), allowed an estimate of ensiled maize ME to be developed from fresh material. In addition, the contribution of the main carbohydrates towards ME showed the importance of delaying harvest until maximum starch content has been achieved. (c) 2005 Elsevier B.V. All rights reserved.

Farm-level risk factors for fluoroquinolone resistance in E-coli and thermophilic Campylobacter spp. on finisher pig farms

Logistic regression, supported by other statistical analyses was used to explore the possible association of risk factors with the fluoroquinolone (FQ)-resistance status of 108 pig finisher farms in Great Britain. The farms were classified as 'affected' or 'not affected' by FQ-resistant E. coli or Campylobacter spp. on the basis of isolation of organisms from faecal samples on media containing 1 mg/l FQ. The use of FQ was the most important factor associated with finding resistant E. coli and/or Campylobacter, which were found on 79% (FQ-resistant E. coli) and 86% (FQ-resistant Campylobacter) of farms with a history of FQ use. However, resistant bacteria were also found on 19% (FQ-resistant E. coli) and 54% (FQ-resistant Campylobacter) of farms with no history of FQ use. For FQ-resistant E. coli, biosecurity measures may be protective and there was strong seasonal variation, with more farms found affected when sampled in the summer. For FQ-resistant Campylobacter, the buying-in of grower stock may increase risk and good on-farm hygiene may be protective. The findings suggest that resistant organisms, particularly Campylobacter, may spread between pig farms.

Reversible phase variation in the phnE gene, which is required for phosphonate metabolism in Escherichia coli K-12

It is known that Escherichia coli K-12 is cryptic (Phn(-)) for utilization of methyl phosphonate (MePn) and that Phn(+) variants can be selected for growth on MePn as the sole P source. Variants arise from deletion via a possible slip strand mechanism of one of three direct 8-bp repeat sequences in phnE, which restores function to a component of a putative ABC type transporter. Here we show that Phn(+) variants are present at the surprisingly high frequency of >10(-2) in K-12 strains. Amplified-fragment length polymorphism analysis was used to monitor instability in phnE in various strains growing under different conditions. This revealed that, once selection for growth on MePn is removed, Phn(+) revertants reappear and accumulate at high levels through reinsertion of the 8-bp repeat element sequence. It appears that, in K-12, phnE contains a high-frequency reversible gene switch, producing phase variation which either allows ("on" form) or blocks ("off" form) MePn utilization. The switch can also block usage of other metabolizable alkyl phosphonates, including the naturally occurring 2-aminoethylphosphonate. All K-12 strains, obtained from collections, appear in the "off" form even when bearing mutations in mutS, mutD, or dnaQ which are known to enhance slip strand events between repetitive sequences. The ability to inactivate the phnE gene appears to be unique to K-12 strains since the B strain is naturally Phn(+) and lacks the inactivating 8-bp insertion in phnE, as do important pathogenic strains for which genome sequences are known and also strains isolated recently from environmental sources.