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International audience; Agricultural recycling of organic waste (OW) derived from urban, agricultural and agroindustrial sources is an essential sustainable development strategy. Yet repeated application of nutrient-laden OW in crop fields can also drastically boost contaminant levels in soil. This review focuses on the consideration of three categories of OW-borne contaminants, namely trace elements, organic contaminants and pathogens (including antibiotic resistance), in environmental assessments, chiefly involving life cycle assessment (LCA) and risk assessment (RA). The in-depth discussion also focuses on gaps between empirical knowledge and the models underlying these frameworks. Potential improvements to fill the identified gaps are proposed, including novel approaches and uses of existing approaches, while also featuring various levels of “readiness.” Finally, a comprehensive theoretical framework to assess OW recycling scenarios, combining complementary approaches and models, is proposed and exemplified.

Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.

International audience; Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of acute traveler's diarrhea. Adhesins and enterotoxins constitute the major ETEC virulence traits. With the dramatic increase in antibiotic resistance, probiotics are considered a wholesome alternative to prevent or treat ETEC infections. Here, we examined the antimicrobial properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against ETEC H10407 pathogenesis upon co-administration in the TNO gastrointestinal Model (TIM-1), simulating the physicochemical and enzymatic conditions of the human upper digestive tract and preventive treatment in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), integrating microbial populations of the ileum and ascending colon. Interindividual variability was assessed by separate M-SHIME experiments with microbiota from six human individuals. The probiotic did not affect ETEC survival along the digestive tract. However, ETEC pathogenicity was significantly reduced: enterotoxin encoding virulence genes were repressed, especially in the TIM-1 system, and a lower enterotoxin production was noted. M-SHIME experiments revealed that 18-days probiotic treatment stimulate the growth of Bifidobacterium and Lactobacillus in different gut regions (mucosal and luminal, ileum and ascending colon) while a stronger metabolic activity was noted in terms of short-chain fatty acids (acetate, propionate, and butyrate) and ethanol production. Moreover, the probiotic pre-treated microbiota displayed a higher robustness in composition following ETEC challenge compared to the control condition. We thus demonstrated the multi-inhibitory properties of the probiotic S. cerevisiae CNCM I-3856 against ETEC in the overall simulated human digestive tract, regardless of the inherent variability across individuals in the M-SHIME.

Background Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME). Results A loss of ETEC viability was noticed upon gastric digestion, while a growth renewal was found at the end of jejunal and ileal digestion. The remarkable ETEC mucosal attachment helped to maintain luminal concentrations above 6 log10 mL−1 in the ileum and ascending colon up to 5 days post-infection. Seven ETEC virulence genes were monitored. Most of them were switched on in the stomach and switched off in the TIM-1 ileal effluents and in a late post-infectious stage in the M-SHIME ascending colon. No heat-labile enterotoxin production was measured in the stomach in contrast to the ileum and ascending colon. Using 16S rRNA gene-based amplicon sequencing, ETEC infection modulated the microbial community structure of the ileum mucus and ascending colon lumen. Conclusions This study provides a better understanding of the interplay between ETEC and gastrointestinal cues and may serve to complete knowledge on ETEC pathogenesis and inspire novel prophylactic strategies for diarrheal diseases.

The extension of urban and peri-urban areas and the related artificialization of soils drastically impacts the water cycle as well as biogeochemical cycles. In particular, the sealing of soils with impervious surfaces such as roads increases runoff and decreases concomitant infiltration. At the catchment scale, more significant amounts of stormwater must be collected and managed to prevent from flooding urban areas and mitigate discharge to the environment. Sustainable Urban Drainage Systems (SUDS) were developed to alleviate these problems. These systems allow the restoration of one of the main functions of urban and peri-urban soils, i.e., infiltrating stormwater. They simultaneously reduce the risk of flooding and increase groundwater recharge. Another essential service must be ensured and optimized: the removal of pollutants from infiltrating water by the soil, to avoid the degradation of the quality of the groundwater.The INFILTRON project aims to design a methodology for the assessment of infiltration and filtration of pollutants by SUDS. The project is a collaboration of many partners, with expertise in soil physics, urban hydrology, nanoparticle engineering, and modeling, to engineer a specific device for the simultaneous monitoring of water infiltration and pollutant filtration. This infiltration device both infiltrates water and injects nanoparticles (NPs) into the soil. It was sized to account for preferential flow, which is known to have a significant impact on infiltration and pollutant transfer. The engineered NPs were designed to be detectable in the ground using ground-penetrating radar (GPR) and to mimic the transfer of nano-pollutants (emerging pollutants, bacteria, etc.) commonly found in real stormwater. An infiltration-filtration model was developed to interpret the experimental data and to quantify two indicators for the assessment of water infiltration and pollutant filtration. INFILTRON will provide a very interesting toolbox for practitioners and stakeholders for the evaluation of the infiltration and filtration functions of not only SUDS within the framework of stormwater management, but also anthropized soils within the management of urban and peri-urban areas.

International audience; Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA)q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.

Background Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. Results Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota’s inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. Conclusion In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3957-2) contains supplementary material, which is available to authorized users.

Aims To construct and validate the recombinase-based in vivo expression technology (R-IVET) tool in Streptococcus thermophilus (ST). Methods and Results The R-IVET system we constructed in the LMD-9 strain includes the plasmid pULNcreB allowing transcriptional fusion with the gene of the site-specific recombinase Cre and the chromosomal cassette containing a spectinomycin resistance gene flanked by two loxP sites. When tested in M17 medium, promoters of the genes encoding the protease PrtS, the heat-shock protein Hsp16 and of the lactose operon triggered deletion of the cassette, indicating promoter activity in these conditions. The lactose operon promoter was also found to be activated during the transit in the murine gastrointestinal tract. Conclusions The R-IVET system developed in ST is relatively stable, functional, very sensitive and can be used to assay activity of promoters, which are specifically active in in vivo conditions. Significance and Impact of the Study This first adaptation of R-IVET to ST provides a highly valuable tool allowing an exploration of the physiological state of ST in the GIT of mammals, fermentation processes or dairy products.

International audience; AbstractThe acquisition of prtS by Streptococcus thermophilus strains allowed hydrolysis of caseins into peptides and then to increase their growth in milk. This leads to faster milk acidification, which is important in dairy industry. However, some strains harboring the same allele of prtS present different acidification rates, which could be explained by a difference in the regulation of prtS expression. We chose two strains with the same allele of prtS (including the same promoter region): one, PB302, is with high acidification rate while the other, PB18O, is without. They exhibited similar growth in M17, but not in milk, where PB302 showed better growth. The expression of prtS and activity of PrtS were lower in PB18O, in the two media tested. We demonstrated that other genes known to be involved in carbon and nitrogen metabolism were overexpressed in PB302. Interestingly, these genes were overexpressed in milk compared to M17. Nearly all these genes possessed a putative CodY-box in their promoter region. Taken together, difference of gene expression detected in PB302 between milk (low-peptide medium) and M17 (rich-peptide medium) and presence of a putative CodY-box is a feature of the transcriptional pattern of CodY-regulated genes. Altogether, our results propose that acquisition of prtS is not enough in certain strains to achieve rapid milk acidification. High transcriptional level of dtpT, amiF, ilvC, ilvB, bcaT, livJ, ackA, codY, and prtS in fast acidifying strain suggests that this transcriptional pattern could be required for fast milk acidification in Streptococcus thermophilus.

19th Meeting of the Club of Lactic Acid Bacteria, Bordeaux, FRANCE, OCT 16-18, 2013; International audience; Streptococcus thermophilus, a lactic acid bacterium used to produce yogurts and cheeses is more and more considered for its potential probiotic properties. This implies that additional information should be obtained regarding its survival and metabolic activity in the human Gastro-Intestinal Tract (GIT). In this study, we screened 30 S. thermophilus strains for urease, small heat shock protein, and amino-acid decarboxylase functions which may play a role in survival in the upper part of the GIT. The survival kinetics of 4 strains was investigated using the TIM, a physiologically relevant in vitro dynamic gastric and small intestinal model. The three strains LMD9, PB18O and EBLST20 showed significantly higher survival than CNRZ21 in all digestive compartments of the TIM, which may be related to the presence of urease and heat shock protein functions. When LMD9 bacterial cells were delivered in a fermented milk formula, a significant improvement of survival in the TIM was observed compared to non-fermented milk. With the RIVET (Recombinase In Vivo Expression Technology) method applied to the LMD9 strain, a promoter located upstream of hisS, responsible for the histidyl-transfer RNA synthesis, was found to be specifically activated in the artificial stomach. The data generated on S. thermophilus survival and its adaptation capacities to the digestive tract are essential to establish a list of biomarkers useful for the selection of probiotic strains.

Enterohemorrhagic Escherichia coli (EHEC) are major foodborne pathogens that constitute a serious public health threat, mainly in young children. Shiga toxins (Stx) are the main virulence determinants of EHEC pathogenesis but adhesins like intimin (eae) and Long polar fimbriae (Lpf) also contribute to infection. The TNO GastroIntestinal Model (TIM) was used for a comparative study of EHEC O157:H7 survival and virulence under adult and child digestive conditions. Survival kinetics in the in vitro digestive tract were determined by plating while bacterial viability was assessed by flow cytometry analysis. Expression of stx, eae, and lpf genes was followed by reverse transcriptase-quantitative PCR (RT-qPCR) and Stx production was measured by ELISA (enzyme-linked immunosorbent assay). Upon gastrointestinal passage, a higher amount of viable cells was found in the simulated ileal effluents of children compared to that of adults (with 34 and 6% of viable cells, respectively). Expression levels of virulence genes were up to 125-fold higher in children. Stx was detected only in child ileal effluents. Differences in digestive physicochemical parameters may partially explain why children are more susceptible to EHEC infection than adults. Such data are essential for a full understanding of EHEC pathogenesis and would help in designing novel therapeutic approaches.

In silk analysis of the genome of Streptococcus thermophilus LMD-9 revealed that this strain has a potential new peptide/nickel ABC transporter. We named this system OTS for Oligopeptide Transporter of S. thermophilus. It is composed of a peptide/nickel binding protein OtsA, two permeases OtsB and OtsC and a double ATPase OtsD. This system was presumably acquired by horizontal transfer from Actinobacteria or distant species like Lactococcus raffinolactis or Enterococcus asini may be via an intermediate like Lactococcus lactis or its ancestor. RT-PCR experiments proved that OTS gene cluster is transcribed and that at least the otsB, otsC, and otsD genes constitute an operon. A mutant LMD-9 Delta ots partially deleted for the otsA and otsB genes was constructed. Growth of LMD-9 and LMD-9 Delta ots strains was monitored in the presence of different nitrogen sources and in the presence of urea and nickel. Results revealed that OTS is not implicated in nickel transport but constitutes a new characterized transporter of peptides of small size, possibly di- and tripeptides in S. thermophilus. (C) 2016 Published by Elsevier Ltd.

Streptococcus thermophilus (ST) is a lactic acid bacterium widely used in dairy industry and displays several properties which could be beneficial for host. The objective of this study was to investigate, in vitro, the implication of sortase A (SrtA) and sortase-dependent proteins (SDPs) in the adhesion of ST LMD-9 strain to intestinal epithelial cells (IECs) and resistance to bile salt mixture (BSM; taurocholoate, deoxycholate, and cholate). The effect of mutations in prtS (protease), mucBP (MUCin-Binding Protein), and srtA genes in ST LMD-9 in these mechanisms were examined. The HT29-MTX, HT29-CL.16E, and Caco-2 TC7 cell lines were used. HT29-MTX and HT29-CL.16E cells express different mucins found in the gastro intestinal tract; whereas, Caco-2 TC7 express cell surface proteins found in the small intestine. All mutants showed different adhesion profiles depending on cell lines. The mutation in genes srtA and mucBP leads to a significant decrease in LMD-9 adhesion capacity to Caco-2 TC7 cells. A mutation in mucBP gene has also shown a significant decrease in LMD-9 adhesion capacity to HT29-CL.16E cells. However, no difference was observed using HT29-MTX cells. Furthermore, ST LMD-9 and srtA mutant were resistant to BSM up to 3 mM. Contrariwise, no viable bacteria were detected for prtS and mucBP mutants at this concentration. Two conclusions could be drawn. First, SDPs could be involved in the LMD-9 adhesion depending on the cell lines indicating the importance of eukaryotic-cell surface components in adherence. Second, SDPs could contribute to resistance to bile salts probably by maintaining the cell membrane integrity.

International audience; The influence on the hydrolysis of isracidin of cell-associated extracellular aminopeptidase and X-prolyl dipeptidyl peptidase activities in addition to protease PrtS of Streptococcus thermophilus strains was investigated. S. thermophilus LMD-9 (PrtS(+) phenotype) efficiently hydrolyzed the isracidin mainly through the PrtS activity, whereas strain CNRZ1066 (PrtS(-) phenotype) and two mutant strains LMD-9-Delta prtS and LMD-9-Delta prtS-Delta htrA also displayed substrate hydrolysis, but different from that of the wild type strain LMD-9. Identification by mass spectrometry of breakdown products of isracidin revealed the existence of novel cell-associated extracellular carboxypeptidase and peptidyl dipeptidase activities in all PrtS(-) strains, besides known cell-associated extracellular aminopeptidase and X-prolyl dipeptidyl peptidase activities. Both aminopeptidase and peptidyl dipeptidase activities were not able to cleave the isracidin at peptide bonds with proline residues. No hydrolysis of isracidin was detected in cell free filtrate for all the strains studied, indicating that no cell lysis had occurred. Taken together, these results suggested the presence of cell-associated extracellular peptidase activities in S. thermophilus strains that could be vital for the growth of PrtS(-) strains.

The consumption of raw milk cheese can expose populations to Shiga toxin-producing Escherichia coli (STEC). We report here the genome sequence of an E. coli O26:H11 strain isolated from humans during the first raw milk cheese outbreak described in France (2005).

International audience; PrtS is the sole cell envelope protease ((CEP) characterized in Streptococcus thermophilus. It is believed that it is anchored to the cell wall by sortase A ((SrtA) through the LPXTG motif present at its C-terminus. Two soluble proteases corresponding to PrtS in its proenzyme and mature form were detected in the supernatant of S. thermophilus strain 4F44. In this strain, 60% of the PrtS molecules are anchored to the cell wall and 40% released in the medium. Such a release might result from a partial deficiency in the strain 4F44 of SrtA, even if its sequence slightly differs from that of S. thermophilus strain LMD-9, in which PrtS is anchored. Indeed, the presence of an intact LPXTG motif at the C-terminus of the released proteases showed that the linking process driven by SrtA did not occur and these proteases were not released by proteolysis after their anchoring.

Proteolytic and acidifying properties of Streptococcus thermophilus strains isolated from yoghurt or cheeses were evaluated. Among 30 strains tested, 12 exhibited cell envelope-associated proteinase activity (PrtS + ), three displayed a slight PrtS activity (PrtS +/− ) and 15 were PrtS − , despite the presence of the corresponding gene ( prtS ) in eight of them. Sequencing of the prtS gene in four PrtS − and one PrtS + strains revealed that the absence of PrtS activity in the PrtS − strain probably results from an alteration of the prtS regulation. The strains displaying the highest acidifying capacities were all PrtS + . All but one PrtS + strains were phylogenetically close, as shown by the sequencing of their rDNA internal transcribed spacer (ITS) 16S-23S. More specifically, the high proteolytic and acidifying capacities are associated with the presence of a type II-ITS.