Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios.

Background: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.

Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence.

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth's climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability.

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia.

Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance.

Application of a path-modelling approach for deciphering causality relationships between microbiota, volatile organic compounds and off-odour profiles during meat spoilage.

Microbiological spoilage of meat is considered as a process which involves mainly bacterial metabolism leading to degradation of meat sensory qualities. Studying spoilage requires the collection of different types of experimental data encompassing microbiological, physicochemical and sensorial measurements. Within this framework, the objective herein was to carry out a multiblock path modelling workflow to decipher causality relationships between different types of spoilage-related responses: composition of microbiota, volatilome and off-odour profiles.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol.

Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited.

Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere.

Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon.

Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products.

Objectives: Sequencing of 16S rDNA V3-V4 region is widely applied for food community profiling. However, two different universal forward primers (named here MUYZER-primer1 and KLINDWORTH-primer2) targeting an identical conservative sequence upstream of the V3 region of 16S rRNA gene, and only distinguished by a single mismatch are both used. This study was carried out to compare whether the accuracy of food microbiota analysis would depend on the choice of one of these two primers.

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.

Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase.

Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics.

Data in this article provide detailed information on the microbial dynamics during inhibition of anaerobic digestion by phenol and ammonia. Ten concentrations of both inhibitors were tested in triplicates. Data include the operational conditions and degradation performance measurements, as well as microbial community analysis, by 16S rRNA gene sequencing, at different time points for the different conditions (96 samples).

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics.

Data in this article provide detailed information on the microbial dynamics within digesters supplemented with different support media (two types of zeolites, two types of activated carbons, one type of chitosan, one control) in presence of different inhibitory conditions (control without inhibitor, 1.3 g/L of phenol and 19 g/L of total ammonia nitrogen). Data include the operational conditions and degradation performance measurements, as well as microbial community analysis, by 16S rRNA gene sequencing, at different time points for the different conditions (samples).

Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage.

In this study, we present the draft genome sequences of nine strains from various psychrotrophic species identified in meat products and being recognized as important emerging food spoilers. Many of these species have only one or few strains being sequenced, and this work will contribute to the improvement of the overall genomic knowledge about them.

Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects.

A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate.

Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities.

This study aimed at providing a better understanding of the influence of support media (10g/L of zeolites, 10g/L of activated carbons, and 1g/L of chitosan) on key phylotypes steering anaerobic digestion (AD) performance in presence of 19g/L of Total Ammonia Nitrogen (TAN) within batch digesters. Support media did not influence TAN concentration. However, both zeolites and activated carbon 1 reduced methanization lag phase by 47% and 25%, respectively.

Acclimation strategy to increase phenol tolerance of an anaerobic microbiota.

A wide variety of inhibitory substances can induce anaerobic digester upset or failure. In this work the possibility to improve the resistance of an anaerobic microbiota to a common pollutant, the phenol, was evaluated in a lab-scale semi-continuous bioreactor. An acclimation strategy, consisting in a regular step-wise adaptation of the microbiota to stressful condition was employed.

Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators?

Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L.

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes.

Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0g/L at 35°C.

Schizophrenia patients with polydipsia and water intoxication are characterized by greater severity of psychotic illness and a more frequent history of alcohol abuse.

Polydipsia and water intoxication (PWI) are relatively frequent among schizophrenic subjects, particularly in institutional settings and may lead to severe complications. However, little is known on their association with other characteristics of psychosis. Hence, we took advantage of a cohort of 114 subjects extensively assessed on natural history and clinical variables to examine the correlates of PWI in chronic schizophrenia.

A factor analysis of the Strauss and Carpenter revised outcome criteria scale: a validation of the French translation.

This article seeks to validate the French translation of the Strauss and Carpenter revised outcome criteria scale (SCOCS-R) through the study of its interrater reliability, its convergent validity, and its factor structure. Using a sample of 113 DSM-IV schizophrenic subjects, we assessed the interrater reliability of the SCOCS-R and its convergent validity with an already validated scale (Social and Occupational Functioning Assessment Scale). The factor structure of the SCOCS-R was assessed using a principal components analysis.