My Publications
Verschuren LMG, Calus MPL, Jansman AJM, Bergsma R, Knol EF, Gilbert H, Zemb O.
J Anim Sci. 2018 Jul 28. doi: 10.1093/jas/sky268. [Epub ahead of print] No abstract available.
Lisanne and I analyzed the gut microbiota of pigs from TOPIGS NORSWIN submitted to a fiber-rich and a fiber-poor diet. Interestingly some OTUs seemed linked to feed efficiency in the fiber-rich diet only.
Combes S, Massip K, Martin O, Furbeyre H, Cauquil L, Pascal G, Bouchez O, Le Floc'h N, Zemb O, Oswald IP, Gidenne T.
Animal. 2017 May;11(5):854-863. doi: 10.1017/S1751731116002007. Epub 2016 Oct 17.
I participated in this study about feed restriction in rabbits. The impacts were subtle in comparison with the feed restriction in pigs (see publication below).
Direct and correlated responses to selection in two lines of rabbits selected for feed efficiency under ad libitum and restricted feeding: I. Production traits and gut microbiota characteristics,
L. Drouilhet , C.S. Achard, O. Zemb, C. Molette, T. Gidenne, C. Larzul, J. Ruesche, A. Tircazes, M. Segura, T. Bouchez , M. Theau-Clément, T. Joly, E. Balmisse, H. Garreau, H. Gilbert ,
Journal of Animal Science 2016
The microbiota of 2 lines of rabbits selected on their residual feed intake differs. Interestingly the gut microbiota of efficient rabbits also produces more propionate and less hydrogen when fed with predigested feed in vitro under N2/CO2.
Étude des effets de la lignée de l’animal et de celle de la mère sur la croissance et l’efficacité alimentaire dans une lignée sélectionnée sur la consommation résiduelle et la lignée témoin,
Ruesche J., Drouilhet L., Gilbert H., Balmisse E., Benitez F., Richard F., David I., Garreau H., Zemb O.,
Journées de la recherche cunicole 2015
Impact of feed restriction on health, digestion and faecal microbiota of growing pigs housed in good or poor hygiene conditions. Animal.
Le Floc'h-Burban, N., Merlot, E., Montagne, L., Gidenne, T., Knudsen, C., Zemb, O.
Animal (2014)
J'ai analysé le microbiote par séquençage de la région V3V4 du gène codant pour l'ARN 16S. Cette région sert de marqueur d'espèces microbienne. Le résultat majeur est que l'hygiène et la restriction alimentaire interagissent pour aboutir à des communautés microbiennes spécifiques mais ont des effets zootechniques indépendants. Ce résultat est marquant car la fenêtre de dépendance environnementale décrite précédemment était beaucoup plus réduite (4 semaines au lieu de 8 semaines dans notre étude). D'un point de vue de conduite d'élevage, ce résultat signifie que le microbiote des porcs peut encore être influencé après le sevrage (qui intervient généralement à 4 semaines). D'un point de vue technique, ce travail met en oeuvre une nouvelle méthode statistique basée sur l'analyse discriminante. Cette méthode permet d'isoler un signal lié à un traitement même lorsque beaucoup de descripteurs évoluent indépendamment.
Phage adsorption to bacteria in the light of the electrostatics: A case study using E. coli, T2 and flow cytometry.
Zemb O, Manefield M, Thomas F, Jacquet S.
J Virol Methods. 2013 Mar 13;189(2):283-289. doi: 10.1016/j.jviromet.2013.02.007. [Epub ahead of print]
The addition of sodium chloride to freshwater or diluted minimal salt medium increases the adsorption of T2 phages on Escherichia coli. For the first time the adsorption in diluted minimal salt medium was measured by counting unadsorbed phages (i.e. free particles) using flow cytometry, allowing a gentle separation between adsorbed and unadsorbed phages. Flow cytometry was able to detect weakly adsorbed phage that remained undetected using classical centrifugation-based methods and this allowed us to show that increasing ionic strength enhances the phage adsorption to its bacterial host with an extremely low detection limit. A key result was that the adsorption in high ionic strength (i.e. 100mM) reached 4.5±0.1×10-5mL/min which is 1400 fold higher than previously reported values. In order to understand the mechanism underpinning such a weak phage adsorption, the zeta potentials and the diffusion coefficient of the particles were measured by dynamic light scattering. The bacterial cells and the phages had zeta potentials between -60mV and -10mV and -30mV and -10mV, respectively. The diffusion coefficient of the phage was 2.8±0.4×10-12m2s-1 corresponding to a hydrodynamic radius of 104±15nm. However significant adsorption occurs in conditions where the DLVO theory predicts that minimal encounter, suggesting that forces other that electrostatic repulsion and Van der Waals interaction (e.g. potential impurities, particle shape and other biological characteristics) are likely to interplay.
Capillary electrophoresis ribosomal RNA single-stranded conformation polymorphism: a new approach for characterization of low-diversity microbial communities
Nai, Yi H.; Zemb, Oliver; Gutierrez-Zamora, Maria-Luisa; et al.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY Volume: 404 Issue: 6-7 Pages: 1897-1906 DOI: 10.1007/s00216-012-6268-0 Published: OCT 2012
Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal sample requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from individual phylotypes in low-diversity samples. As a gel-based method, it has a long analysis time and relatively large reagent and sample requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the sample requirement by ten-fold. The combination of fast analysis time, low sample requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low-diversity microbial communities.
Complete chloroform dechlorination by organochlorine respiration and fermentation
Lee, Matthew; Low, Adrian; Zemb, Olivier; et al.
ENVIRONMENTAL MICROBIOLOGY Volume: 14 Issue: 4 Pages: 883-894 DOI: 10.1111/j.1462-2920.2011.02656.x Published: APR 2012
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.
Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge.
Zemb, O; Lee, M; Gutierrez-Zamora, M L; Hamelin, J; Coupland, K; Hazrin-Chong, N H; Taleb, I; Manefield, M
Water research 46 3 601 10 2012-Mar-1 2012
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-(13)C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5d(-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 (13)C enrichment, other species encoding phenol degradation pathways are responsible for more (13)C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% (13)C above natural abundance. Download 0 1879-2448 MEDLINE:22154106
Bacterial and fungal community composition over time in chicken litter with high or low moisture content
Wadud, S.; Michaelsen, A.; Gallagher, E.; et al.
BRITISH POULTRY SCIENCE Volume: 53 Issue: 5 Pages: 561-569 DOI: 10.1080/00071668.2012.723802 Published: 2012
1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production.
2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter.
3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.
Direct rRNA Fingerprinting, a Novel Method to Profile Low Diversity Microbial Communities
Gutierrez-Zamora, Maria-Luisa; Zemb, Olivier; Manefield, Mike
MICROBIAL ECOLOGY 62 1 177 187 10.1007/s00248-011-9877-9 JUL 2011 2011
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. 0 0 0095-3628 WOS:000293030400016
Reactive iron barriers: a niche enabling microbial dehalorespiration of 1,2-dichloroethane
Zemb, Olivier; Lee, Matthew; Low, Adrian; Manefield, Mike
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 88 1 319 325 10.1007/s00253-010-2740-y SEP 2010 2010
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. Download 0 2 0175-7598 WOS:000280914900033
Effect of a transient perturbation on marine bacterial communities with contrasting history
Zemb, O.; West, N.; Bourrain, M.; Godon, J. J.; Lebaron, P.
JOURNAL OF APPLIED MICROBIOLOGY 109 3 751 762 10.1111/j.1365-2672.2010.04706.x SEP 2010 2010
Aims:To evaluate the importance of the bacterial composition on the resilience of the organic matter assimilation in the sea.Methods and Results:Chemostats were inoculated with coastal and offshore bacterial communities. Bacterial density and protein synthesis increased before stabilizing, and this response to confinement was more marked in the offshore chemostats. Before the toluene perturbation the community structure in the coastal chemostats remained complex whereas the offshore chemostats became dominated by Alteromonas sp. After the perturbation, bacterial protein synthesis was inhibited before peaking briefly at a level fivefold to that observed before the perturbation and then stabilizing at a level comparable to that before the perturbation. Alteromonas dominated both the coastal and the offshore communities immediately after the perturbation and the coastal communities did not recover their initial complexity.Conclusions:Cell lysis induced by the toluene perturbation favoured the growth of Alteromonas which could initiate growth rapidly in response to the nutrient pulse. Despite their different community structure in situ, the resilience of protein synthesis of coastal and offshore bacterial communities was dependent on Alteromonas, which dominated in the chemostats.Significance and Impact of the Study:Here we show that although Alteromonas sp. dominated in artificial offshore and coastal communities in chemostats, their response time to the shock was different. This suggests that future perturbation studies on resilience in the marine environment should take account of ecosystem history. 0 0 1364-5072 WOS:000280979700002
Efficient method to isolate and purify viruses of bacteria from marine environments
Zemb, O.; Urios, L.; Coetsier, C.; Lebaron, P.
LETTERS IN APPLIED MICROBIOLOGY 47 1 41 45 10.1111/j.1472-765X.2008.02381.x JUL 2008 2008
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 10(5)-10(10) 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. Download 0 0 0266-8254 WOS:000256724700008
Dynamics of neutral biodiversity
Vanpeteghem, Dimitri; Zemb, Olivier; Haegeman, Bart
MATHEMATICAL BIOSCIENCES 212 1 88 98 10.1016/j.mbs.2008.01.002 MAR 2008 2008
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 Simpson 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 findings are especially relevant for experiments in microbial ecology, where the Simpson diversity index can be accurately measured as a function of time. (c) 2008 Elsevier Inc. All rights reserved. 8 8 0025-5564 WOS:000254730600005
Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean
West, Nyree J.; Obernosterer, Ingrid; Zemb, Olivier; Lebaron, Philippe
ENVIRONMENTAL MICROBIOLOGY 10 3 738 756 10.1111/j.1462-2920.2007.01497.x MAR 2008 2008
One of the first comparisons of a natural iron fertilized bloom with a high-nutrient low-chlorophyll (HNLC) site was undertaken during the Kerguelen ocean and plateau compared study (KEOPS) cruise. To understand better the bacteria-phytoplankton relationship in the context of natural iron fertilization, bacterial diversity and activity was investigated in the bloom and in the adjacent HNLC region by 16S rDNA clone libraries and by single strand conformation polymorphism (SSCP) analysis. Both libraries were dominated by Alphaproteobacteria, Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cluster analysis at 99% sequence similarity yielded several microdiverse clusters and revealed striking differences between the two libraries. In the bloom, the dominant operational taxonomic units (OTUs) were the Roseobacter NAC11-7 cluster, SAR92 and a Cytophaga-Flavobacteria-Bacteroides cluster related to the agg58 group, whereas in the HNLC region, SAR11, Roseobacter RCA and Polaribacter dominated. SSCP analysis of 16S rDNA and 16S rRNA revealed contrasting dynamics of three different Roseobacter OTUs. Roseobacter NAC11-7 and NAC11-6 had higher relative abundances and activities in the bloom compared with the HNLC site and NAC11-6 was only detected at the decline of the bloom concomitant with a shift in phytoplankton composi tion. In contrast, Roseobacter RCA was relatively abundant and active both inside and outside of the bloom. These results suggest that the different OTUs within the Roseobacter group represent functional groups that each play an important role in the cycling of carbon. 39 40 1462-2912 WOS:000252712300018
SAFUM: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators
Zemb, O.; Haegeman, B.; Delgenes, J. P.; Lebaron, P.; Godon, J. J.
MOLECULAR ECOLOGY NOTES 7 5 767 770 10.1111/j.1471-8286.2007.01882.x SEP 2007 2007
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. Download 26 26 1471-8278 WOS:000249193000007
SAFUM is a 2007 Matlab script providing a user-interface to work with CE-SSCP fingerprints (single strand conformation), but it can be used for any spectra or matrix by using a excel spreadsheet to import data.Please check the Files exchange for research for the latest version as Matlab script.
If you just want to use Safum in its executable version , you need 2 files on your windows machine :
1) MCRInstaller.exe (Run it to get the Matlab Libraries on your PC. Note that this is free but that it doesn't mean that you'll have the "real" Matlab )
This file is available at http://www.mediafire.com/download.php?jl5elcaxx0vh2lo
2) Run Safum.exe (it will start the main menu)
This file is availble at http://www.mediafire.com/download.php?3omrckibgl9cdu7
Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
Loisel, P; Harmand, J; Zemb, O; Latrille, E; Lobry, C; Delgenes, JP; Godon, JJ
ENVIRONMENTAL MICROBIOLOGY 8 4 720 731 10.1111/j.1462-2920.2005.00950.x APR 2006 2006
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 simulation inputs. Diversity results in experimental patterns 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. 77 78 1462-2912 WOS:000235892000015