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International audience; Hubbell’s neutral model has become a major paradigm in ecology. Whereas the steady-state structure is well understood, results about the dynamical aspects of the model are scarce. Here we derive dynamical equations for the Simspon diversity index. Both mean and variance of the diversity are proven to satisfy stable linear system dynamics. We show that in the stationary limit we indeed recover previous results, and we supplement this with numerical simulations to validate the dynamical part of our analytical computations. These .ndings are especially relevant for experiments in microbial ecology, where the Simpson diversity index can be accurately measured as a function of time.

Feed restriction could be a relevant strategy to preserve gut health, reduce systemic inflammatory response and finally limit antibiotic use. This study assessed the effect of feed restriction on growing pigs submitted to a moderate inflammatory challenge induced by the degradation of the environmental hygiene that is known to alter growth rate. The experiment was run on 80 pigs selected at 7 weeks of age according to a 2×2 factorial design: two feeding levels, ad libitum (AL) and feed restricted (FR) at 60% of AL, and two conditions of environmental hygiene, clean and dirty. Pigs were housed individually throughout the experiment. From 61 to 68 days of age (day 0 to 7), pigs were housed in a post weaning unit and feed restriction was applied to half of the pigs from day 0 to day 29. At 68 days of age (day 7 of the experiment), pigs were transferred in a growing unit where half of FR and half of AL pigs were housed in a dirty environment (poor hygiene) and the other half in a clean environment (good hygiene) until day 42. Growth performance was recorded weekly. Blood and faeces samples were collected to measure indicators of inflammation, nutrient digestibility and microbiota composition. Faecal consistency was monitored daily to detect diarrhoeas. Feed restriction decreased daily weight gain (-35% to -50%, P

International audience; Chloroform (CF, CHCl3) is a recalcitrant and toxic environmental pollutant. In this communication we report for the first time a microbial community capable of complete CF dechlorination by metabolic processes. Cultures derived from subsurface soil (3.5 m) could sustain complete dechlorination of CF at levels of least 360 mu M at a rate of 40 mu M per day. Scrutiny of CF dechlorination revealed two metabolic processes at work. First, CF was respired to dichloromethane (DCM, CH2Cl2), which was then fermented to acetate, hydrogen and carbon dioxide. Elevated hydrogen partial pressures were found to inhibit the fermentation process. Interspecies hydrogen transfer was observed in the form of methanogenesis and acetogenesis. This suggests that the dechlorination process required syntrophic partners to maintain low hydrogen partial pressures. C-13-labelled DCM was employed to help elucidate the chemistry of the process and identify bacterial community members involved. CF respiring cultures, where emulsified vegetable oil was supplied as the electron donor and DCM fermenting cultures, where DCM was supplied as the sole organic carbon source were studied separately. Pyrosequencing of these cultures revealed Dehalobacter lineages as a predominant community member in both. Subsequent growth experiments confirmed that the proliferation of Dehalobacter was linked directly to both the dehalorespiration and dehalofermentation processes.

International audience; Nonylphenols (NP) have estrogenic potential because of their phenolic ring, but the organisms involved in the degradation of this alkylated phenol remain unidentified. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP) and a new method based on pyrosequencing, we identified the bacteria involved in the degradation of the aromatic ring of [U-ring-13C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5 d−1. Single strand conformation polymorphism of density-separated labeled and unlabeled 16S rRNA showed significant differences and enabled selection of four representative fractions for pyrosequencing. Nineteen phylotypes showed a significant enrichment in the heavy fraction in the labeled pulse. The relative abundances of these phylotypes were combined with the RNA concentration of each fraction to yield a simple model of the distribution of each phylotype across the gradient. This model was used to estimate the percentage of labeling for each phylotype. The sequences showing the highest labeling (11%) were closely related to Afipia sp. but represented only 2 % of the RNA in the heavy fraction of the labeled pulse. The sequences representing the largest proportion of the RNA in the heavy fraction were related to Propionibacterium acnes and Frateuria aurantia, which are known to possess enzymes for phenol degradation. The model shows that despite Afipia having the highest 13C enrichment, other species encoding phenol degradation pathways are responsible for more 13C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% 13C above natural abundance.

International audience; In the past decade, an increasing number of methods in microbial ecology have been developed that address the questions of which microbes exist in the environment, what their roles are and, to some extent, what their abundance is. In the present paper, we propose and describe the proof of principle of a novel method for analysing shifts in microbial community composition that uses small RNA fragments directly derived from 16S rRNA. Community fingerprints are generated on the basis of sequence-dependent conformational differences of rRNA fragments. We applied this method to profile artificial and natural communities and to detect changes in community structure in enrichment cultures. This method constitutes a PCR-free alternative to microbial community characterisation and can provide information on the relative abundance of rRNA from individual phylotypes in low diversity samples.

International audience; A reactive iron barrier in a contaminated aquifer with low pH was found to dechlorinate 1,2-dichloroethane (1,2-DCA) in situ. This chlorinated ethane is known to resist abiotic reduction by zero valent iron. Samples taken up-gradient and within the barrier were used to inoculate anaerobic batch cultures amended with various electron donors. Cultures inoculated with groundwater from within the reactive iron barrier reduced 1,2-DCA to ethene. The same effect could be achieved by simultaneously supplying hydrogen while neutralising pH. The presence of iron or hydrogen at neutral pH had negligible effects on 1,2-DCA reduction in cultures inoculated with groundwater sampled up-gradient of the barrier. Molecular microbial community characterisation revealed that Dehalobacter species were more abundant in groundwater sampled from within the barrier. These findings suggest reactive iron barriers represent a remediation technology for 1,2-DCA degradation acting through in situ recruitment of 1,2-DCA reducing bacteria such as Dehalobacter.

Aim: To isolate viruses of specific heterotrophic bacterial strains from marine environments using a host addition/virus amplification protocol (HAVAP) for use in phage/host systems. Methods and Results: Bacteria-free seawater samples containing natural viruses assemblages were inoculated with a single laboratory grown bacterial host of interest in a nutrient-enriched [peptone, Fe(III) and yeast extract] seawater suspension. These conditions enhanced the replication of only those virus(s) capable of infecting the host bacterium. After incubation, free viruses were recovered at concentrations ranging 105–1010 infectious virus particles per ml of seawater. Using this approach, 15 viruses were isolated and represented 12 unique phage/host systems. Two of the hosts tested were infected by more than one virus. Conclusions: Isolation of high concentrations of specific viruses is possible even if their initial concentrations in native waters are low. This approach allows the recovery of phage/host systems that may not be numerically dominant. Significance and Impact of the Study: This host enrichment protocol for virus detection and isolation is well-suited for aquatic viral ecology studies that require phage/host systems.

International audience; The program safum provides a smart interface to import, visualize and compare fingerprinting profiles, especially on capillary electrophoresis single strand conformation polymorphism data, in conjunction with basic statistical analysis tools. It includes principal component analysis, two- or three-dimensional representations, dendrograms based on Euclidean distance, and easily exportable files for subsequent applications. safum is useful for the analysis of spatial or temporal sequences of microbial community fingerprints obtained with an ABI prism sequencer.

Summary The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns (denaturing gradient electrophoresis (DGE), single- strand conformation polymorphism (SSCP)) provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500 000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the sim- ulation inputs. Diversity results in experimental pat- terns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.

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International audience; The objective of this study was to evaluate the impact of chronic heat stress (HS) on microbiota composition of gestating sows and of their female offspring. There were two environmental conditions: thermoneutral (TN; cyclic 18 to 24 °C) and HS (cyclic 28 to 34 °C). Pregnant sows were exposed to either TN (PTN; n=12) or HS (PHS; n=12) conditions from d 9 to 109 of gestation. During the finishing period, two female offspring per sow were allotted to either a growing TN (GTN; n=24) or HS (GHS; n=24) environment. All pigs were fed the same diet all throughout the experiment. From 75 to 140 d of age, GTN pigs (n=24) were in TN conditions, while GHS pigs (n=24) were in TN conditions from 75 to 81 d of age and in GHS conditions from 82 to 140 d of age. Spot faecal samples were collected on d 4 and d 105 of gestation in the sows, and on 78 and 136 d of age in the growing pigs for 16S rRNA analyses of microbiota composition. In both sows and offspring, exposure to HS increased rectal (+0.16 and +0.30 °C, respectively; P

Improving feed efficiency (FE) is a major preoccupation for pig production. The FE is a complex trait dealing with lots of functions in pig. The intestinal microbiota is known to play a key role in host metabolism and health with subsequent impact on its performance. The PhD program aimed at studying the modifications of the intestinal microbiota composition on pigs exposed to several environmental perturbations and to evaluate the relationships between digestive microbiota composition and the host performance. Data from three experimental studies conducted on growing-finishing pigs (60 to 1.200 depending on the study) which were exposed to different perturbations [high fiber diet, diet contaminated by mycotoxin (DON), or exposed to acute or chronic heat stress] have been used. The microbiota analysis was based on fecal samples collected before and after the perturbations. Phenotypes directly or indirectly related to FE were measured to evaluate and to quantifythe relationships between the host performance and its microbiota. A detailed bioinformatic and statistical analysis of the microbial data demonstrated that the environmental perturbations affect the fecal microbiota composition but these effects were generally transient. Depending on the nature of the challenge (standard or high fiber diet, exposition to a chronic or acute heat stress, or DON-contaminated diet), the impact on fecal microbiota composition seemed to differ. In this PhD program, the relative abundance of the OTU does not allow to implement quantitative prediction models of pig performance. Functional; L’amélioration de l’efficacité alimentaire (EA) est un enjeu important pour la filière porcine. L’EA est un phénotype complexe faisant intervenir un grand nombre de fonctions chez le porc. Au travers son rôle dans le métabolisme de son hôte et le maintien de sa santé, le microbiote intestinal est susceptible d’impacter les performances de l’hôte et en particulier son EA. Ce travail de thèse vise à étudier les modifications de composition du microbiote intestinal du porc soumis à différents facteurs environnementaux et à évaluer les relations entre cette composition microbienne et les performances de l’hôte. Pour cela, les données de trois études réalisées sur des porcs en croissance-finition (entre 60 et 1 200 porcs par étude) soumis à des perturbations de natures différentes (aliment riche en fibres, aliment contaminé par des mycotoxines (DON) ou exposition à un stress thermique chronique ou aigu) ont été utilisées. L’analyse du microbiote a été réalisée sur la base de prélèvements dede fèces obtenus avant et après les perturbations. Parallèlement, des phénotypes en lien avec l’EA de l’hôte ont été mesurés afin d’évaluer et quantifier les relations entre les performances du porc et son microbiote intestinal. L’analyse bio-informatique et statistique approfondie des données microbiennes a montré que les perturbations environnementales impactent la composition du microbiote fécal mais que cet effet n’est généralement que transitoire. Selon la nature du challenge (régime alimentaire standard vs. riche en fibre, exposition à un stress thermique chronique ou aigu, et aliment

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