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Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation
No full textBackground: Accumulating evidence is supporting the protective effect of whole grains against several chronic diseases. Simultaneously, our knowledge is increasing on the impact of gut microbiota on our health and on how diet can modify the composition of our bacterial cohabitants. Herein, we studied C57BL/6J mice fed with diets enriched with rye bran and wheat aleurone, conventional and germ-free C57BL/6NTac mice on a basal diet, and the colonic fermentation of rye bran in an in vitro model of the human gastrointestinal system. We performed 16S rRNA gene sequencing and metabolomics on the study samples to determine the effect of bran-enriched diets on the gut microbial composition and the potential contribution of microbiota to the metabolism of a novel group of betainized compounds.[br/]
Results: The bran-enriched study diets elevated the levels of betainized compounds in the colon contents of C57BL/6J mice. The composition of microbiota changed, and the bran-enriched diets induced an increase in the relative abundance of several bacterial taxa, including Akkermansia, Bifidobacterium, Coriobacteriaceae, Lactobacillus, Parasutterella, and Ruminococcus, many of which are associated with improved health status or the metabolism of plant-based molecules. The levels of betainized compounds in the gut tissues of germ-free mice were significantly lower compared to conventional mice. In the in vitro model of the human gut, the production of betainized compounds was observed throughout the incubation, while the levels of glycine betaine decreased. In cereal samples, only low levels or trace amounts of other betaines than glycine betaine were observed.[br/]
Conclusions: Our findings provide evidence that the bacterial taxa increased in relative abundance by the bran-based diet are also involved in the metabolism of glycine betaine into other betainized compounds, adding another potential compound group acting as a mediator of the synergistic metabolic effect of diet and colonic microbiota
Combinations of non-invasive indicators to detect dairy cows submitted to high starch diet challenge
No full textComparative overview of the mechanisms of action of hormones and endocrine disruptor compounds
No full textEndocrine Disruptor Compounds (EDCs) are synthetic or natural molecules in the environment that promote adverse modifications of endogenous hormone regulation in humans and/or in wildlife animals. In the present paper, we review the potential mechanisms of EDCs and point out the similarities and differences between EDCs and hormones. There was only one mechanism, out of nine identified, in which EDCs acted like hormones (i.e., binding and stimulated hormone receptor activity). In the other eight identified mechanisms of action, EDCs exerted their effects either by affecting endogenous hormone concentration, or its availability, or by modifying hormone receptor turn over. This overview is intended to classify the various EDC mechanisms of action in order to better appreciate when in vitro tests would be valid to assess their risks towards humans and wildlife
A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource
No full textSilver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests
Resource depletion potentials from bottom-up models: Population dynamics and the Hubbert peak theory
No full textLife cycle impact assessment uses so-called characterization factors to address different types of environmental impact (e.g. climate change, particulate matter, land use…). For the topic of resource depletion, a series of proposals was based on heuristic and formal arguments, but without the use of expert-based models from relevant research areas. A recent study in using fish population models has confirmed the original proposal for characterization factors for biotic resources of the nineties. Here we trace the milestones of the arguments and the designs of resource depletion, delivering an ecological-based foundation for the biotic case, and extend it by a novel analysis of the Hubbert peak theory for the abiotic case. We show that the original abiotic depletion potential, used for two decades in life cycle assessment, estimates accurately a marginal depletion characterization factor obtained from a dynamic model of the available reserve. This is illustrated for 29 metal resources using published data
Salivary and urinary metabolome analysis for pre-puberty-related biomarkers identification in porcine
No full textEstrus synchronization is important for optimal management of gilt reproduction in pig farms. Hormonal treatments, such as synthetic progestogens, are used on a routine basis, but there is a growing demand for non-hormonal alternative breeding tools. Before puberty, gilts exhibit a ‘waiting period,’ related to the ovarian development and gonadotrophin secretions, during which external stimulations, such as boar exposure, could induce and synchronize first ovulation. Practical non-invasive tools for identification of this period in farms are lacking. During this period, urinary oestrone levels are high, but urine sampling is difficult in group-housed females. The aim of this work was to search for specific biomarkers of the ‘waiting period’ in saliva and urine. In total, nine 144- to 147-day-old Large White gilts were subjected to trans-abdominal ultrasonography three times a week for 5 weeks until puberty detection (week –5 to week –1 before puberty). Urine and saliva samples were collected for oestrone assay to detect the ‘waiting period’ and for metabolome analysis using 1H-nuclear magnetic resonance spectroscopy to detect potential biomarkers of the ‘waiting period.’ Gilts were slaughtered 7 days after puberty detection for puberty confirmation. Results were consistent with ultrasonography data for six gilts. Urine and saliva samples from these six gilts were analyzed. Urinary estrone concentration significantly increased 2 weeks before puberty detection. Metabolome analysis of urine samples allowed the identification of 78 spectral bins, among them, 42 low-molecular-weight metabolites were identified. Metabolome analysis of salivary samples allowed the identification of 59 spectral bins, among them, 23 low-molecular-weight metabolites were detected and 17 were identified. No potential biomarker was identified in urinary samples. In saliva, butyrate and 2HOvalerate, 5.79 ppm (putatively uridine), formate, malonate and propionate could be biomarker candidates to ascertain the pre-puberty period in gilt reproduction. These results confirm that non-invasive salivary samples could allow the identification of the physiological status of the gilts and presumably the optimal time for application of the boar effect. This could contribute to synchronize puberty onset and hence to develop non-hormonal breeding tools
Molecular mechanisms underlying microbial disease control in intercropping
No full textMany reports indicate that intercropping, which usually consists in growing two species next to each other, reduces the incidence of microbial diseases. Besides mechanisms operating at the field level like inoculum dilution, there is recent evidence that plant-centered mechanisms with identified plant molecules and pathways are also involved. First, plants may trigger the induction of resistance in neighboring plants by the well-known mechanism of induced resistance. Second, molecules produced by one plant, either above or below ground, can directly inhibit pathogens or indirectly trigger resistance through the induction of the plant immune system in neighboring plants. Third, competition for resources like light or nutrients may indirectly modify the expression of the plant immune system. The conceptual frameworks of non-kin/stranger recognition and competition may be useful to further investigate the molecular mechanisms underlying crop protection in interspecific plant mixtures
Assessing sustainability of different forms of farm organization: adaptation of IDEA method to rubber family farms in Thailand
No full textWith increasing concerns on the sustainability of agricultural systems, many tools have been developed to assess farm sustainability. The main objective of this study was to assess and compare the sustainability of different forms of family farm organization. A second objective was to test the relevance of the IDEA method (Indicateurs de Durabilité des Exploitations Agricoles or Farm Sustainability Indicators) to compare tree-crop-based family farms in tropical areas. Percentages of sustainability were calculated based on individual interviews conducted with 25 rubber farmers representing three different types of farm (typology based on the labor used for farming activities), using three scales and 10 components. The socio-territorial scale was the weak point of the rubber farms. In contrast, the economic scale was relatively the best asset on all farms. The factor that most differentiated the three types of farm was the agro-ecological scale followed by the socio-territorial scale. The economic scale did not discriminate. Moreover, only the diversity of production and efficiency components showed a notable difference between the different types of farm. Overall, the three types of farm with contrasting forms of farm organization were not much different in terms of sustainability performance. Family business farms with managerial family labor appeared to be the least sustainable. Thus, as family business farms are becoming more and more important in Thai agriculture, if these results are confirmed on a broader scale, this represents an issue for the sustainability of the Thai rubber sector that would require government intervention.Les préoccupations croissantes concernant la durabilité des systèmes agricoles ont conduit au développement de nombreux outils pour l’évaluer. L’objectif principal de cette étude était d’évaluer et comparer la durabilité de différentes formes d’organisation de l’agriculture familiale. Un deuxième objectif était de tester la pertinence de la méthode IDEA (Indicateurs de Durabilité des Exploitations Agricoles) pour comparer des exploitations familiales à base de plantes pérennes en zone tropicale. À partir d’entretiens individuels conduits avec 25 planteurs d’hévéa représentant trois types d’exploitations agricoles (typologie basée sur le travail mobilisé pour les activités agricoles), des pourcentages de durabilité ont été calculés sur trois échelles et 10 composantes. L’échelle socio-territoriale était le point faible des exploitations hévéicoles. À l’inverse, l’échelle économique était le point fort pour toutes les exploitations. L’échelle agro-écologique est celle qui discriminait le mieux les trois types d’exploitations, suivie par l’échelle socio-territoriale. L’échelle économique n’était pas discriminante. De plus, les seules composantes présentant des différences entre les trois types d’exploitation étaient la diversité des productions et l’efficience des exploitations. Les trois types d’exploitation représentant des formes contrastées d’organisation de la production agricole ne sont finalement pas apparus très différents en termes de durabilité. Les exploitations familiales patronales avec la famille seulement impliquée dans la gestion seraient les moins durables. Pourtant, les exploitations patronales occupent une place croissante dans l’agriculture en Thaïlande. Si ces résultats sont confirmés à plus grande échelle, cela représente un problème pour la durabilité de l’hévéaculture en Thaïlande qui demanderait une intervention du gouvernement
Puumala Hantavirus Genotypes in Humans, France, 2012-2016
No full textThe analysis of the nucleoprotein gene of 77 Puumala hantavirus strains detected in human samples in France during 2012-2016 showed that all belonged to the Central European lineage. We observed 2 main clusters, geographically structured; one included strains with the Q64 signature and the other strains with the R64 signature
Crystal structure of the multidrug resistance regulator RamR complexed with bile acids
No full textDuring infection, Salmonella senses and responds to harsh environments within the host. Persistence in a bile-rich environment is important for Salmonella to infect the small intestine or gallbladder and the multidrug efflux system AcrAB-TolC is required for bile resistance. The genes encoding this system are mainly regulated by the ramRA locus, which is composed of the divergently transcribed ramA and ramR genes. The acrAB and tolC genes are transcriptionally activated by RamA, whose encoding gene is itself transcriptionally repressed by RamR. RamR recognizes multiple drugs; however, the identity of the environmental signals to which it responds is unclear. Here, we describe the crystal structures of RamR in complexes with bile components, including cholic acid and chenodeoxycholic acid, determined at resolutions of 2.0 and 1.8 Å, respectively. Both cholic and chenodeoxycholic acids form four hydrogen bonds with Tyr59, Thr85, Ser137 and Asp152 of RamR, instead of π-π interactions with Phe155, a residue that is important for the recognition of multiple compounds including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G. Binding of these compounds to RamR reduces its DNA-binding affinity, resulting in the increased transcription of ramA and acrAB-tolC. Our results reveal that Salmonella senses bile acid components through RamR and then upregulates the expression of RamA, which can lead to induction of acrAB-tolC expression with resulting tolerance to bile-rich environments