Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity

Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very common for similar habitats to be described by different terms, which makes them hard to compare automatically, e.g. intestine and gut. The use of a common reference to standardize these habitat descriptions as claimed by (Ivana et al., 2010) is a necessity. We propose the ontology called OntoBiotope that we have been developing since 2010. The OntoBiotope ontology is in a formal machine-readable representation that enables indexing of information as well as conceptualization and reasoning.Comment: 5 page

Les gaz et l'aliment. Les éléments déterminant de l'efficacité des gaz vis-à-vis des microorganismes : Les phénomènes de solubilité et de transfert des gaz et les données disponibles dans les aliments

Les gaz et l'aliment. Les éléments déterminant de l'efficacité des gaz vis-à-vis des microorganismes. Les phénomènes de solubilité et de transfert des gaz et les données disponibles dans les aliments. Efficacité des atmosphères modifiées sur la qualité microbiologique des aliment

Modelling and characterization of gas transfer (O2/CO2) in packaging / food related reactions of microbial growth (predictive microbiology)

Un des rôles de l'emballage est de limiter les réactions de dégradation des aliments : pour cela, il contrôle les transferts de gaz (O2, CO2, N2) entre l'atmosphère extérieure et l'espace de tête. Dans le cas des Emballages sous Atmosphère Modifiée (EAM), la composition gazeuse est judicieusement choisie afin de limiter la croissance microbienne (en général faible teneur en O2 et forte concentration en CO2). L'objectif de ce travail est d'étudier et modéliser l'impact des transferts de gaz (O2/CO2/N2) dans le système EAM sur la croissance microbienne. Des modèles existants de microbiologie prévisionnelle ont été couplés avec ceux développés concernant les transferts de gaz via un système d'Equations Différentielles Ordinaires. La perméation au travers de l'emballage, la solubilisation et la diffusion des gaz (O2/CO2) dans les aliments ont été prises en compte. La solubilité et diffusivité de l'O2 et du CO2 dans les aliments solides sont indispensables pour les modèles de transferts. Devant le peu de données concernant ces paramètres, leur caractérisation expérimentale s'est avérée nécessaire. Des méthodologies ont été spécifiquement développées afin de pouvoir accéder à ces deux coefficients, solubilité et diffusivité, dans les aliments solides modèles (fromage emprésuré, miglyols) et réels (jambon, beurre) pour les deux gaz d'études, O2 et CO2. Les méthodologies d'acquisition de la diffusivité et solubilité de l'oxygène reposent sur l'utilisation de capteurs par extinction de luminescence, quant à celles utilisées pour le CO2, se basent sur la titration chimique. La loi de Henry, qui relie concentration dissoute et pression partielle en CO2 dans l'espace de tête a été validée dans les différents produits analysés. La diffusion de l'O2 dans les milieux lipidiques modèles a été étudiée avec une analyse de l'impact de la viscosité et de la température. Ainsi, l'énergie d'activation de la diffusion de l'O2 dans un milieu modèle (Miglyol 812) est de 25 kJ.mol-1 entre 5 et 30°C. Un modèle de transfert de gaz pour le système emballage/aliment a été développé, basé sur la description fickienne des transferts de matière et a été couplé à des modèles de microbiologie prévisionnelle existants dans la littérature. Ce modèle a été confronté aux résultats expérimentaux obtenus sur fromage emprésuré artificiellement contaminé par Listeria monocytogenes à une concentration de 10^3 CFU.g-1. Ce travail a permis d'approfondir les connaissances générales sur la solubilité et la diffusion de l'O2 et du CO2 dans les matrices alimentaires solides, de comprendre et quantifier l'effet des transferts de gaz dans le système emballage/aliment sur la croissance des micro-organismes et de construire les bases essentielles pour un outil d'aide à la décision de choix d'EAM en fonction de l'aliment.Packaging is a key player on reducing food losses, by defining around the food, via the mass transfer of gases (O2, CO2, N2) through the packaging, a headspace atmosphere whose composition is able to reduce physical-chemical (namely oxidation), microbial and physiological (for respiring foods) food degradation rate. In Modified Atmosphere Packaging (MAP) of fresh produce, the gaseous composition of the headspace is chosen in order to prevent microorganism growth (usually low O2 and high CO2 concentrations are chosen). This work aimed at initiating and developing a generalised approach permitting to study and quantitatively model the impact of gas transfer (O2/CO2/N2) occurring in the food packaging system on microbial growth. In this purpose, existing models of predictive microbiology will be coupled to mass transfers (permeation through packaging and solubilisation/diffusion within food) using numerical methods such as ODE (Ordinary Differential Equation) solvers. If the permeation is relatively well known, the two other parameters, O2 and CO2 solubilities and diffusivities, required in mass transfer models are less known, especially for solid food matrices. Experimental acquisition of these parameters was thus required. Some dedicated methodologies have been developed in the framework of this study in order to gain missing data of solubility and diffusivity in solid food matrices for the two studied gases, O2 and CO2. The methods of O2 diffusivity and solubility measurement relied on the use of luminescence-based sensors while for CO2, the methodologies were based on chemical titration. A processed cheese was used as solid model food and the O2 and CO2 solubilities and diffusivities were characterized in this model food as in other real food products: cooked ham and butter. A peculiar attention was paid on the validation of Henry's law in the case of CO2 that links CO2 partial pressure to the dissolved content into the product. The O2 diffusion within lipid-based model materials was studied with a deep analysis of the impact of temperature and viscosity. The energy of activation of oxygen diffusivity in model matrix (Miglyol 812) was found equal to 25 kJ mol-1 for temperature ranging from 5 to 30°C. A mathematical model of gas transfer was developed for the overall food/packaging system and was coupled to existing equations of predictive microbiology. This generalised model was compared with experimental data obtained in the case of mono-directionnal transfers, on the mass transfer and microbiological part (on processed cheese voluntarily contaminated by Listeria monocytogenes with an initial biomass equal to 10^3 UFC g-1). This work had permitted to increase knowledge on the behaviour of O2 and CO2 solubilities and diffusivities into solid food products, to understand and quantify the impact of gas transfers in the food/packaging system on the microorganism growth and to build basements for a new decision support system aiming at helping the user in the choice and design of MAP for a given application

Caractérisation et modélisation des transferts de gaz (O2 /CO2) dans le système emballage/aliment en lien avec les réactions de croissance microbienne (microbiologie prévisionnelle)

Packaging is a key player on reducing food losses. In Modified Atmosphere Packaging (MAP) of fresh produce, the gaseous composition of the headspace is chosen in order to prevent microorganism growth (usually low O2 and high CO2 concentrations are chosen). This work aimed at initiating and developing a generalised approach permitting to study and quantitatively model the impact of gas transfer (O2 /CO2 /N2 ) occurring in the food packaging system on microbial growth. In this purpose, existing models of predictive microbiology will be coupled to mass transfers (permeation through packaging and solubilisation/diffusion within food) using numerical methods such as ODE (Ordinary Differential Equation) solvers. If the permeation is relatively well known, the two other parameters, O2 and CO2 solubilities and diffusivities, required in mass transfer models are less known, especially for solid food matrices. Experimental acquisition of these parameters was thus required. Some dedicated methodologies have been developed in the framework of this study in order to gain missing data of solubility and diffusivity in solid food matrices for the two studied gases, O2 and CO2 . The methods of O2 diffusivity and solubility measurement relied on the use of luminescence-based sensors while for CO2 , the methodologies were based on chemical titration. A processed cheese was used as solid model food and the O2 and CO2 solubilities and diffusivities were characterized in this model food as in other real food products: cooked ham and butter. A peculiar attention was paid on the validation of Henry’s law in the case of CO2 that links CO2 partial pressure to the dissolved content into the product. The O2 diffusion within lipid-based model materials was studied with a deep analysis of the impact of temperature and viscosity. The energy of activation of oxygen diffusivity in model matrix (Miglyol 812) was found equal to 25 kJ. mol -1 for temperature ranging from 5 to 30°C. A mathematical model of gas transfer was developed for the overall food/packaging system and was coupled to existing equations of predictive microbiology. This generalised model was compared with experimental data obtained in the case of mono-directionnal transfers, on the mass transfer and microbiological part (on processed cheese voluntarily contaminated by Listeria monocytogenes with an initial biomass equal to 10^3 UFC g -1 ). This work had permitted to increase knowledge on the behaviour of O2 and CO2 solubilities and diffusivities into solid food products, to understand and quantify the impact of gas transfers in the food/packaging system on the microorganism growth and to build basements for a new decision support system aiming at helping the user in the choice and design of MAP for a given application.Un des rôles de l’emballage est de limiter les réactions de dégradation des aliments. Dans le cas des Emballages sous Atmosphère Modifiée (EAM), la composition gazeuse est judicieusement choisie afin de limiter la croissance microbienne (en général faible teneur en O2 et forte concentration en CO2 ). L’objectif de ce travail est d’étudier et modéliser l’impact des transferts de gaz (O2 /CO2 /N2 ) dans le système EAM sur la croissance microbienne. Des modèles existants de microbiologie prévisionnelle ont été couplés avec ceux développés concernant les transferts de gaz via un système d’Equations Différentielles Ordinaires. La perméation au travers de l’emballage, la solubilisation et la diffusion des gaz (O2 /CO2 ) dans les aliments ont été prises en compte. La solubilité et diffusivité de l’O2 et du CO2 dans aliments solides sont indispensables pour les modèles de transferts. Devant le peu de données concernant ces paramètres, leur caractérisation expérimentale s’est avérée nécessaire. Des méthodologies ont été spécifiquement développées afin de pouvoir accéder à ces deux coefficients, solubilité et diffusivité, dans les aliments solides modèles (fromage emprésuré, miglyols) et réels (jambon, beurre) pour les deux gaz d’études, O2 et CO2 . Les méthodologies d’acquisition de la diffusivité et solubilité de l’oxygène reposent sur l’utilisation de capteurs par extinction de luminescence, quant à celles utilisées pour le CO2 , se basent sur la titration chimique. La loi de Henry, qui relie concentration dissoute et pression partielle en CO2 dans l’espace de tête a été validée dans les différents produits analysés. La diffusion de l’O2 dans les milieux lipidiques modèles a été étudiée avec une analyse de l’impact de la viscosité et de la température. Ainsi, l’énergie d’activation de la diffusion de l’O2 dans un milieu modèle (Miglyol 812) est de 25 kJ.mol -1 entre 5 et 30°C. Un modèle de transfert de gaz pour le système emballage/aliment a été développé, basé sur la description Fickienne des transferts de matière et a été couplé à des modèles de microbiologie prévisionnelle existants dans la littérature. Ce modèle a été confronté aux résultats expérimentaux obtenus sur fromage emprésuré artificiellement contaminé par Listeria monocytogenes à une concentration de 10^3 CFU.g -1 . Ce travail a permis d’approfondir les connaissances générales sur la solubilité et la diffusion de l’O2 et du CO2 dans les matrices alimentaires solides, de comprendre et quantifier l’effet des transferts de gaz dans le système emballage/aliment sur la croissance des micro-organismes et de construire les bases essentielles pour un outil d’aide à la décision de choix d’EAM en fonction de l’aliment

Evaluation of O2 transfer in the food/packaging system for a better shelf life evaluation of modified atmosphere food packaging.

Modified Atmosphere Packaging (MAP) relies on modification of the atmosphere inside the package in order to extend food shelf life by reducing oxidation and microbial degradation rate. In the peculiar case of inert products (e.g. meat- or fish-based food products) MAP is achieved by the interplay of two processes: (1) the transfer of gases through the packaging and (2) either the gas depletion (gain) process (gas flush or absorber). To preserve the quality of a food, MAP maintains duration of a given O2/CO2 mixture by using high barrier packaging materials. Currently, to evaluate the impact of gases on microorganisms growth, the “pack and pray” empirical methodology is used: different gases mixtures (mainly O2/CO2/N2) are successively tested on the product until the right combination (O2/CO2 ratio, package surface/volume, mass of food, etc.) is found. The use of mass transfer models concomitantly with predictive microbiology would be a more appropriate method to allow a correct design and sizing of modified atmosphere packaging systems by minimizing the number of experiments. However, this kind of tool combining mass transfer and predictive microbiology does not yet exist. Gases transfer phenomena in solid food matrix are characterised with two parameters, a thermodynamic one (solubility), and a kinetic one (diffusivity), both indispensible in mathematical models of mass transfer. The main bottleneck in the evaluation of O2 solubility and diffusivity is the quantification of dissolved oxygen in solid food matrix. This work that takes place in the context of the MAP’OPT project, funded by the French National Research Agency, aims at developing innovative, rapid and non-destructive methodologies to determine O2 solubility and diffusivity in liquid and solid food matrices. These methods are based on the use of oxygen sensors permitting quantification of O2 partial pressure by quenching of luminescence. Methodologies and first preliminary results will be presented here

CO2 kinetics in cheese matrix at 20°C position from interface (mm) A new methodology to monitor CO 2 transfer and determine its diffusivity and solubility in solid food

Carbon dioxide is the most important gas in Modified Atmosphere Packaging (MAP) systems, usually intentionally added for its bacteriostatic properties for increasing shelf life of non-respiring fresh products. For example, CO2 level between 20 to 30% are usually used for MAP of meat product. In such case of high CO2 headspace concentration, a CO2 transfer from the food and packaging headspace toward external atmosphere occurs, which rate depends on respectively CO2 diffusivity within food and packaging CO2 permeability. Solubility parameter determines the maximal CO2 quantity that could dissolve in the product and CO2 diffusivity, the rate at which this molecule migrates in the product. Historically, dissolved CO2 in the food matrix was calculated using Henry’s law considered only the solubilisation in the aqueous fraction. Recent studies have shown that this shortcut was not relevant for fatty products because CO2 significantly dissolves in the fat fraction. Experimental measurements of CO2 solubility were thus necessary. Furthermore, CO2 diffusivity was scarcely accurately measured, this parameter being almost always neglected in MAP dimensioning. However, both parameters, solubility and diffusivity, are required in mathematical models to predict mass transfer in the food/packaging system and consequently, food shelf life. In this work, an original experimental set-up was proposed to perform CO2 solubility measurement based on chemical titration of dissolved CO2. This methodology was adapted and used for monitoring CO2 diffusion in solid matrix as a function of the position in the food in order to obtain distribution profile of dissolved CO2 in the product. From these experimental profiles, accurate values of CO2 diffusivity could be then identified. This work takes place in the context of the MAP’OPT project (2011-2015), funded by the French National Research Agency, whose title is “Equilibrium gas composition in modified atmosphere packaging and food quality

Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity

Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very common for similar habitats to be described by different terms, which makes them hard to compare automatically, e.g. intestine and gut. The use of a common reference to standardize these habitat descriptions as claimed by (Ivana et al., 2010) is a necessity. We propose the ontology called OntoBiotope that we have been developing since 2010. The OntoBiotope ontology is in a formal machinereadable representation that enables indexing of information as well as conceptualization and reasoning

Text mining tools for extracting information about microbial biodiversity in food

Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & MethodsWe propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, we analyzed terms that designate Microbial and Habitat entities in text. Microorganism names were predicted using the NCBI taxonomy. Habitat entities were detected using the syntactic structure of the terms and the OntoBiotope ontology. This ontology has been specifically enriched for the recognition of food terms in text. In a second time, we predicted links between microorganisms and their habitats (labeled “Lives_in” relationships) using pattern and machine-learning based methods. The results of text-mining predictions are indexed and presented in a semantic search engine. Result The AlvisIR search engine for microbe literature gives online access to 1.2 million PubMed abstracts in 2015, among which 13% are specific to food. This tool makes it possible to use text-mining results to search for information on bacterial biodiversity. It covers all types of microbial habitats to help understand the origin of microbial presence in food. Significance This work presents the first semantic search engine dedicated to better understand microbial food biodiversity from text

Performance of a non-invasive methodology for assessing oxygen diffusion in liquid and solid food products

Based on the measurement of local oxygen partial pressure kinetic, a non-invasive methodology was proposed to assess O2 diffusivity ( D O 2 ) in liquid, viscous and solid matrices. This new method was compared with a previous invasive method, developed by the same group, based on the same principle. The new method has proven to be essential to measure D O 2 in solid food matrices where invasive methods usually failed. It was successfully used to obtain D O 2 of cooked ham and processed cheese which were found respectively equal to 0.450 ± 0.004 × 10−9 m2·s−1 and 1.15 ± 0.11 × 10−9 m2·s−1 at 20 °C. D O 2 was also evaluated as a function of temperature (from 5 to 30 °C) and viscosity in lipid-based matrices. These results have permitted to determine activation energy of the diffusion and have revealed that increasing viscosity of the lipid matrices tested did not impact their D O 2 values

Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity

International audienceMicrobiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very common for similar habitats to be described by different terms, which makes them hard to compare automatically, e.g. intestine and gut. The use of a common reference to standardize these habitat descriptions as claimed by (Ivana et al., 2010) is a necessity. We propose the ontology called OntoBiotope that we have been developing since 2010. The OntoBiotope ontology is in a formal machinereadable representation that enables indexing of information as well as conceptualization and reasoning