The use of analysis of variance (ANOVA) in applied microbiology

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the number of replications required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the DF of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for each error term of the ANOVA. Finally, it is important to consider the design of the experiment because this determines the appropriate ANOVA to use. Some of the most common experimental designs used in the biosciences and their relevant ANOVAs are discussed by. If there is doubt about which ANOVA to use, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Statistical analysis in microbiology:statnotes

This book is aimed primarily at microbiologists who are undertaking research and who require a basic knowledge of statistics to analyse their experimental data. Computer software employing a wide range of data analysis methods is widely available to experimental scientists. The availability of this software, however, makes it essential that investigators understand the basic principles of statistics. Statistical analysis of data can be complex with many different methods of approach, each of which applies in a particular experimental circumstance. Hence, it is possible to apply an incorrect statistical method to data and to draw the wrong conclusions from an experiment. The purpose of this book, which has its origin in a series of articles published in the Society for Applied Microbiology journal ‘The Microbiologist’, is an attempt to present the basic logic of statistics as clearly as possible and therefore, to dispel some of the myths that often surround the subject. The 28 ‘Statnotes’ deal with various topics that are likely to be encountered, including the nature of variables, the comparison of means of two or more groups, non-parametric statistics, analysis of variance, correlating variables, and more complex methods such as multiple linear regression and principal components analysis. In each case, the relevant statistical method is illustrated with examples drawn from experiments in microbiological research. The text incorporates a glossary of the most commonly used statistical terms and there are two appendices designed to aid the investigator in the selection of the most appropriate test.

Pig producer perspectives on the use of meat inspection as an animal health and welfare diagnostic tool in the Republic of Ireland and Northern Ireland

Background
Currently, there is growing interest in developing ante and post mortem meat inspection (MI) to incorporate measures of pig health and welfare for use as a diagnostic tool on pig farms. However, the success of the development of the MI process requires stakeholder engagement with the process. Knowledge gaps and issues of trust can undermine the effective exchange and utilisation of information across the supply chain. A social science research methodology was employed to establish stakeholder perspectives towards the development of MI to include measures of pig health and welfare. In this paper the findings of semi-structured telephone interviews with 18 pig producers from the Republic of Ireland and Northern Ireland are presented.

Results
Producers recognised the benefit of the utilisation of MI data as a health and welfare diagnostic tool. This acknowledgment, however, was undermined for some by dissatisfaction with the current system of MI information feedback, by trust and fairness concerns, and by concerns regarding the extent to which data would be used in the producers’ interests. Tolerance of certain animal welfare issues may also have a negative impact on how producers viewed the potential of MI data. The private veterinary practitioner was viewed as playing a vital role in assisting them with the interpretation of MI data for herd health planning.

Conclusions
The development of positive relationships based on trust, commitment and satisfaction across the supply chain may help build a positive environment for the effective utilisation of MI data in improving pig health and welfare. The utilisation of MI as a diagnostic tool would benefit from the development of a communication strategy aimed at building positive relationships between stakeholders in the pig industry.

Carcass and meat quality characteristics of Arsi-Bale goats supplemented with different levels of air-dried Moringa stenopetala leaf

This study was conducted to assess the effect of air-dried Moringa stenopetala leaf (MSL) supplementation on carcass components and meat quality in Arsi-Bale goats. A total of 24 yearling goats with initial body weight of 13.6+/-0.25 kg were randomly divided into four treatments with six goats each. All goats received a basal diet of natural grass hay ad libitum and 340 g head^(−1) d^(−1) concentrate. The treatment diets contain a control diet without supplementation (T1) and diets supplemented with MSL at a rate of 120 g head^(−1) d^(−1) (T2), 170 g head^(−1) d^(−1) (T3) and 220 g head^(−1) d^(−1) (T4). The results indicated that the average slaughter weight of goats reared on T3 and T4 was 18.2 and 18.3 kg, respectively, being (P<0.05) higher than those of T1 (15.8 kg) and T2 (16.5 kg). Goats fed on T3 and T4 diets had higher (P<0.05) daily weight gain compared with those of T1 and T2. The hot carcass weight in goats reared on T3 and T4 diets was 6.40 and 7.30 kg, respectively, being (P<0.05) higher than those of T1 (4.81 kg) and T2 (5.06 kg). Goats reared on T4 had higher (P<0.05) dressing percentage than those reared in other treatment diets. The rib-eye area in goats reared on T2, T3 and T4 diets was higher (P<0.05) than those of T1. The protein content of the meat in goats reared on T3 and T4 was 24.0 and 26.4%, respectively being significantly higher than those of T1 (19.1%) and T2 (20.1%). In conclusion, the supplementation of MSL to natural grass hay improved the weight gain and carcass parts of Arsi-Bale goats indicating Moringa leaves as alternative protein supplements to poor quality forages.

Validation of stress indicators for the assessment of animal welfare and prediction of pork meat quality variation at commercial level

Les procédures appliquées avant l’abattage des animaux influencent directement la qualité de la viande en modulant l’état physiologique des porcs; ainsi, l’augmentation de la température corporelle, les taux élevés de lactate sanguin et l’épuisement des réserves de glycogène entre autres, occasionnent la majorité des baisses de qualité. L’objectif de cette thèse était de valider des outils indicateurs de stress porcin pour les fermes et les abattoirs. Ceux-ci seraient appliqués à la surveillance du bien-être animal et à la prédiction de variation de qualité de la viande porcine au niveau commercial. Premierement, les résultats de la thèse ont permis de conclure qu’un des outils développés (analyseur portatif de lactate) mesure la variation du niveau de lactate sanguin associé à l’état physiologique des porcs dans la phase péri-mortem et aide à expliquer la variation de la qualité de la viande chez le porc à l’abattoir, en particulier dans les muscles du jambon. Deuxièmement, les résultats des audits du bien-être animal appliqués de la ferme à l’abattoir ont démontré que la qualité du système d’élevage à la ferme d’origine et les compétences du chauffeur de camion sont d’importants critères affectant la réponse comportementale des porcs à la manipulation avant l’abattage. Ces résultats ont également démontré que les conditions de logement à la ferme (la faible densité et l’enrichissement dans les enclos), le comportement des porcs en période pré-abattage (glissade), ainsi que les interventions du manipulateur (utilisation du bâton électrique) dans la zone d’étourdissement de l’abattoir affectent négativement la variation de la qualité de la viande. L’application des protocoles d’audits dans la filière porcine a également démontré que le respect des critères de bien-être animal fixés par un outil de vérification est primordiale et permet de contrôler les conditions de bien-être des porcs à chaque étape de la période pré-abattage, de produire une viande de qualité supérieure et de réduire les pertes. Les audits de bien-être animal sont donc un outil qui apporte des resultats très pertinents pour aider a éviter les variations de la qualité de la viande chez le porc. Troisièmement, la thermographie infrarouge s’est avéré être une technique prometteuse permettant d’évaluer la variation de température corporelle de l’animal pendant et après un stress physique, en particulier lorsque cette mesure est prise derrière les oreilles. En conclusion, les outils validés à travers cette thèse représentent des méthodologies non invasives et potentiellement complémentaires à d’autres approches d’évaluation de l’état physiologique et du bien-être animal par rapport au stress, permettant de réduire les pertes de qualité de viande (par exemple en utilisation conjointe avec le niveau de lactate sanguin et les indicateurs de stress comportemental, entre autres).

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189 +/- 58 operational taxonomic units (OTUs) but dropped to 27 +/- 12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

From the farm to the fork: fungal occupational exposure in the swine meat supply chain

Feed production, swine and slaughterhouses were already reported as occupational environments with high fungal contamination. This condition can ultimately lead to the development of several health conditions. This study aimed to characterize the occupational exposure to fungal burden in three different settings: swine feed unit, swine units and slaughterhouse.

Development of a long-life vacuum-packaged ready-to-eat meat product based on a traditional Portuguese seasoned meat

Carne do alguidar is a Portuguese traditional pork fried meat, usually manufactured for self-consumption purposes. This study developed a ready-to-eat (RTE) meat product, to meet today's consumers’ convenience, manufactured at the industrial scale evaluating its quality and shelf-life, assessing the effect of vacuum packaging and the use of an antioxidant (50 ppm BHT) to enhance oxidative stability. Physicochemical and microbiological parameters were assessed and a sensory analysis was performed. Interestingly, no significant differences were recorded between control (non-BHT) and antioxidant (BHT) samples. Microbiological counts remained at low levels throughout the storage period, ensuring the product’s required microbiological quality. At later storage stages, higher values of thiobarbituric acid reactive substances arose and off flavours and aromas were perceived. Still, overall appreciation was not affected until 12 months storage and a significant depreciation was perceived only after 15 months. Fibrousness and rising of off flavours were negatively correlated with overall appreciation.

Feeding low protein diets to meat chickens: Effects on emissions of toxic and odorous metabolites

Low protein diet and odour emissions in meat chickens

137Cs in the meat of wild boars: a comparison of the impacts of Chernobyl and Fukushima

The impact of Chernobyl on the 137Cs activities found in wild boars in Europe, even in remote locations from the NPP, has been much greater than the impact of Fukushima on boars in Japan. Although there is great variability within the 137Cs concentrations throughout the wild boar populations, some boars in southern Germany in recent years exhibit higher activity concentrations (up to 10,000 Bq/kg and higher) than the highest 137Cs levels found in boars in the governmental food monitoring campaign (7900 Bq/kg) in Fukushima prefecture in Japan. The levels of radiocesium in boar appear to be more persistent than would be indicated by the constantly decreasing 137Cs inventory observed in the soil which points to a food source that is highly retentive to 137Cs contamination or to other radioecological anomalies that are not yet fully understood.

Food Microbiology Laboratory Overview of food analysis

Introduction to microorganisms and foodborne diseases. Activities in a Food Microbiology Laboratory.