Stress responses and digestive tract robustness of Lactobacillus plantarum

Lactobacillus plantarumis one of the most versatile lactic acid bacteria that can successfully inhabit a variety of environmental niches. It is a common inhabitant of the human and animal gastrointestinal (GI) tract and it is used as starter culture in various fermentation processes for different food raw-materials, including milk, fruits, vegetables, and meat. Moreover, L. plantarum is marketed as a health-promoting culture, i.e. a probiotic. In these different environments and processes the bacteria encounter stress conditions, such as heat, cold, acid, salt, and oxygen stress. Since starter cultures and probiotics require metabolic activity to contribute to the taste and texture of the fermented products, and/or viability to exert their in situ beneficial effect on the consumer, it is important to understand and improve the gene-regulatory adaptation that sustains their function and viability under these challenging conditions. Nowadays, genomic approaches are available that enable the global, genome-wide analysis of stress responses in lactic acid bacteria. The work presented in this thesis employs such tools and also developed some novel strategies to understand stress responses in L. plantarum. During wine fermentation, L. plantarum is exposed to ethanol and global transcriptome profiling demonstrated the gene expression adaptation of this microorganism upon short and long term exposure to sublethal levels of this solvent. The results suggested that the ethanol induced activation of the CtsR-related stress regulon contributes to its adaptation to ethanol exposure which also provides cross-protection against heat stress. Transcriptome analyses under different growth conditions of gene deletion derivatives of the L. plantarum WCFS1 strain that lack the genes encoding the stress response regulators ctsR and/or hrcA, enabled the refinement of the gene regulation repertoire that is controlled by these central regulators of stress responses in this species. Notably, the deletion of both stress-regulators, elicited transcriptome changes that affected a large variety of additional gene-functions in a temperature-dependent manner, which prominently included genes related to cell-envelope remodelling. Culturing of L. plantarum WCFS1 under different fermentation conditions led to large differences in GI-tract survival and robustness, which was addressed using a simple in vitro survival assay. Enhanced GI-tract survival and robustness could be associated with low salt and low pH conditions during the fermentations. The transcriptomes obtained for each of the fermentation conditions employed, were correlated with the observed GI-tract survival rates, enabling the identification of candidate genes involved in the robustness phenotype, including a transcription regulator involved in capsular polysaccharide remodelling (Lp_1669), a penicillin-binding protein (Pbp2A) involved in peptidoglycan biosynthesis, and a Na+/H+ antiporter (NapA3). A role of these candidate genes in actual survival in the GI-tract assay could be confirmed by mutation analysis, further confirming their contribution to GI-tract stress robustness in L. plantarum. This thesis also describes the use of a novel, next-generation sequencing-based method, for the assessment of the in vivo GI-tract persistence of different L. plantarum strains that were administered to healthy human volunteers in specifically designed strain-mixtures. A remarkable consistency of the strain-specific in vivo persistence curves was observed when comparing data obtained from different volunteers. Moreover, a striking congruency was observed between the strain-specific in vivo persistence curves and the predicted GI-tract survival based on the simple in vitro assay. Finally, evolutionary adaptation of L. plantarum WCFS1 to the murine GI-tract was studied by extended exposure of the strain to the mice digestive tract through consecutive rounds of (re)feeding of the longest persisting bacterial colonies. Re-sequencing of the genomes of more persistent derivatives of the original strain, and the evaluation of the genomic modifications identified, implied that genes encoding cell envelope-associated functions and energy metabolism play an important role in the determination of GI-tract persistence in L. plantarum. The results described in this thesis strive to obtain an improved understanding of the gene-regulatory adaptations of L. plantarum that allow its survival under stress conditions, including those associated with residence in the gastrointestinal tract of animals and humans, with the intention to exploit such understanding to rationally improve the robustness of these bacteria.</p

Congruent Strain Specific Intestinal Persistence of Lactobacillus plantarum in an Intestine-Mimicking In Vitro System and in Human Volunteers

BACKGROUND: An important trait of probiotics is their capability to reach their intestinal target sites alive to optimally exert their beneficial effects. Assessment of this trait in intestine-mimicking in vitro model systems has revealed differential survival of individual strains of a species. However, data on the in situ persistence characteristics of individual or mixtures of strains of the same species in the gastrointestinal tract of healthy human volunteers have not been reported to date. METHODOLOGY/PRINCIPAL FINDINGS: The GI-tract survival of individual L. plantarum strains was determined using an intestine mimicking model system, revealing substantial inter-strain differences. The obtained data were correlated to genomic diversity of the strains using comparative genome hybridization (CGH) datasets, but this approach failed to discover specific genetic loci that explain the observed differences between the strains. Moreover, we developed a next-generation sequencing-based method that targets a variable intergenic region, and employed this method to assess the in vivo GI-tract persistence of different L. plantarum strains when administered in mixtures to healthy human volunteers. Remarkable consistency of the strain-specific persistence curves were observed between individual volunteers, which also correlated significantly with the GI-tract survival predicted on basis of the in vitro assay. CONCLUSION: The survival of individual L. plantarum strains in the GI-tract could not be correlated to the absence or presence of specific genes compared to the reference strain L. plantarum WCFS1. Nevertheless, in vivo persistence analysis in the human GI-tract confirmed the strain-specific persistence, which appeared to be remarkably similar in different healthy volunteers. Moreover, the relative strain-specific persistence in vivo appeared to be accurately and significantly predicted by their relative survival in the intestine-mimicking in vitro assay, supporting the use of this assay for screening of strain-specific GI persistence

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km &lt;sup&gt;2&lt;/sup&gt; resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km &lt;sup&gt;2&lt;/sup&gt; pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2&nbsp;m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0\u20135 and 5\u201315&nbsp;cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10\ub0C (mean&nbsp;=&nbsp;3.0&nbsp;\ub1&nbsp;2.1\ub0C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6&nbsp;\ub1&nbsp;2.3\ub0C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler ( 120.7&nbsp;\ub1&nbsp;2.3\ub0C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Beheersen van Listeria : Risicoproducten onder de loep

Zeer geregeld worden producten vanwege een besmetting met Listeria uit de markt teruggeroepen. Uit data van het RIVM blijkt dat ook het aantal gevallen van listeriose in Nederland toeneemt. Wat zijn de achterliggende oorzaken? En hoe richt je de productie zo in dat Listeria geen probleem wordt