20 results on '"Lebrun, Laura"'
Search Results
2. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
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Martínez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura A., Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît J., Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric C., Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., and Wilmes, Paul
- Published
- 2021
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3. Mutation of SOCS2 induces structural and functional changes in mammary development.
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Ivanova, Elitsa, Hue-Beauvais, Cathy, Castille, Johan, Laubier, Johann, Le Guillou, Sandrine, Aujean, Etienne, Lecardonnel, Jerome, Lebrun, Laura, Jaffrezic, Florence, Rousseau-Ralliard, Delphine, Péchoux, Christine, Letheule, Martine, Foucras, Gilles, Charlier, Madia, and Le Provost, Fabienne
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SUPPRESSORS of cytokine signaling ,MAMMARY glands ,SUPPRESSOR mutation ,GENE expression ,MILK yield ,SHEEP breeds - Abstract
Lactation is an essential process for mammals. In sheep, the R96C mutation in suppressor of cytokine signaling 2 (SOCS2) protein is associated with greater milk production and increased mastitis sensitivity. To shed light on the involvement of R96C mutation in mammary gland development and lactation, we developed a mouse model carrying this mutation (SOCS2KI/KI). Mammary glands from virgin adult SOCS2KI/KI mice presented a branching defect and less epithelial tissue, which were not compensated for in later stages of mammary development. Mammary epithelial cell (MEC) subpopulations were modified, with mutated mice having three times as many basal cells, accompanied by a decrease in luminal cells. The SOCS2KI/KI mammary gland remained functional; however, MECs contained more lipid droplets versus fat globules, and milk lipid composition was modified. Moreover, the gene expression dynamic from virgin to pregnancy state resulted in the identification of about 3000 differentially expressed genes specific to SOCS2KI/KI or controlmice. Our results show that SOCS2 is important for mammary gland development and milk production. In the long term, this finding raises the possibility of ensuring adequate milk production without compromising animal health and welfare. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
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Herold, Malte, Martínez Arbas, Susana, Narayanasamy, Shaman, Sheik, Abdul R., Kleine-Borgmann, Luise A. K., Lebrun, Laura A., Kunath, Benoît J., Roume, Hugo, Bessarab, Irina, Williams, Rohan B. H., Gillece, John D., Schupp, James M., Keim, Paul S., Jäger, Christian, Hoopmann, Michael R., Moritz, Robert L., Ye, Yuzhen, Li, Sujun, Tang, Haixu, Heintz-Buschart, Anna, May, Patrick, Muller, Emilie E. L., Laczny, Cedric C., and Wilmes, Paul
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- 2020
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5. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses
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Kunath, Benoît, Hickl, Oskar, Teixeira Queiros, Pedro, Martin-Gallausiaux, Camille, Lebrun, Laura, Halder, Rashi, Laczny, Cedric Christian, Schmidt, Thomas Sebastian, Hayward, Matthew, Becher, Dorte, Heintz-Buschart, Anna, de Beaufort, Carine, Bork, Peer, May, Patrick, Wilmes, Paul, Fonds National de la Recherche - FnR [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]
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Meta-Omics ,Microbiologie [F11] [Sciences du vivant] ,Type 1 Diabetes ,Microbiology [F11] [Life sciences] ,Microbiome - Abstract
Background: Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain‑resolved, integrated meta‑genomic, transcriptomic, and proteomic analyses of paired saliva and stool samples collected from 35 individuals from eight families with multiple cases of type 1 diabetes mellitus (T1DM). Results: We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain‑variants from the oral cavity to the gut at the individual omic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract. Conclusions: Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of “mouth‑to‑gut” transfer of Streptococcus salivarius. Our results indicate that the observed oral‑cavity‑driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi‑omic analyses, we resolve strain‑variant “mouth‑to‑gut” transfer in a disease context.
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- 2022
6. Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics
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Chaib De Mares, Maryam, Jiménez, Diego Javier, Palladino, Giorgia, Gutleben, Johanna, Lebrun, Laura A., Muller, Emilie E. L., Wilmes, Paul, Sipkema, Detmer, and van Elsas, Jan Dirk
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- 2018
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7. Bioremediation of 27 Micropollutants by Symbiotic Microorganisms of Wetland Macrophytes.
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Brunhoferova, Hana, Venditti, Silvia, Laczny, Cédric C., Lebrun, Laura, and Hansen, Joachim
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Background: Micropollutants in bodies of water represent many challenges. We addressed these challenges by the application of constructed wetlands, which represent advanced treatment technology for the removal of micropollutants from water. However, which mechanisms specifically contribute to the removal efficiency often remains unclear. Methods: Here, we focus on the removal of 27 micropollutants by bioremediation. For this, macrophytes Phragmites australis, Iris pseudacorus and Lythrum salicaria were taken from established wetlands, and a special experimental set-up was designed. In order to better understand the impact of the rhizosphere microbiome, we determined the microbial composition using 16S rRNA gene sequencing and investigated the role of identified genera in the micropollutant removal of micropollutants. Moreover, we studied the colonization of macrophyte roots by arbuscular mycorrhizal fungi, which are known for their symbiotic relationship with plants. This symbiosis could result in increased removal of present micropollutants. Results: We found Iris pseudacorus to be the most successful bioremediative system, as it removed 22 compounds, including persistent ones, with more than 80% efficiency. The most abundant genera that contributed to the removal of micropollutants were Pseudomonas, Flavobacterium, Variovorax, Methylotenera, Reyranella, Amaricoccus and Hydrogenophaga. Iris pseudacorus exhibited the highest colonization rate (56%). Conclusions: Our experiments demonstrate the positive impact of rhizosphere microorganisms on the removal of micropollutants. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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8. The Bric-à-Brac BTB/POZ transcription factors are necessary in niche cells for germline stem cells establishment and homeostasis through control of BMP/DPP signaling in the Drosophila melanogaster ovary.
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Miscopein Saler, Laurine, Hauser, Virginie, Bartoletti, Mathieu, Mallart, Charlotte, Malartre, Marianne, Lebrun, Laura, Pret, Anne-Marie, Théodore, Laurent, Chalvet, Fabienne, and Netter, Sophie
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STEM cell niches ,STEM cells ,DROSOPHILA melanogaster ,TRANSCRIPTION factors ,BONE morphogenetic proteins - Abstract
Many studies have focused on the mechanisms of stem cell maintenance via their interaction with a particular niche or microenvironment in adult tissues, but how formation of a functional niche is initiated, including how stem cells within a niche are established, is less well understood. Adult Drosophila melanogaster ovary Germline Stem Cell (GSC) niches are comprised of somatic cells forming a stack called a Terminal Filament (TF) and associated Cap and Escort Cells (CCs and ECs, respectively), which are in direct contact with GSCs. In the adult ovary, the transcription factor Engrailed is specifically expressed in niche cells where it directly controls expression of the decapentaplegic (dpp) gene encoding a member of the Bone Morphogenetic Protein (BMP) family of secreted signaling molecules, which are key factors for GSC maintenance. In larval ovaries, in response to BMP signaling from newly formed niches, adjacent primordial germ cells become GSCs. The bric-à-brac paralogs (bab1 and bab2) encode BTB/POZ domain-containing transcription factors that are expressed in developing niches of larval ovaries. We show here that their functions are necessary specifically within precursor cells for TF formation during these stages. We also identify a new function for Bab1 and Bab2 within developing niches for GSC establishment in the larval ovary and for robust GSC maintenance in the adult. Moreover, we show that the presence of Bab proteins in niche cells is necessary for activation of transgenes reporting dpp expression as of larval stages in otherwise correctly specified Cap Cells, independently of Engrailed and its paralog Invected (En/Inv). Moreover, strong reduction of engrailed/invected expression during larval stages does not impair TF formation and only partially reduces GSC numbers. In the adult ovary, Bab proteins are also required for dpp reporter expression in CCs. Finally, when bab2 was overexpressed at this stage in somatic cells outside of the niche, there were no detectable levels of ectopic En/Inv, but ectopic expression of a dpp transgene was found in these cells and BMP signaling activation was induced in adjacent germ cells, which produced GSC-like tumors. Together, these results indicate that Bab transcription factors are positive regulators of BMP signaling in niche cells for establishment and homeostasis of GSCs in the Drosophila ovary. Author summary: A stem cell is able to divide and produce two daughter cells, one of which retains stem cell status, the second, in contrast, becoming specialized for functions in the corresponding organ. Harnessing the potential of stem cells therefore represents opportunities for cell therapy upon organ damage. Maintenance of stem cells requires their interaction with specific cellular microenvironments called niches. Very little is known about how stem cell microenvironments are established during development and in pathological settings such as during cancer metastasis. The Drosophila adult ovary is probably the best characterized niche-stem cell system. It has been shown that niche cells secrete signaling proteins of the Bone Morphogenetic Protein (BMP) family, which by binding to receptors present at the membrane of adjacent Germline Stem Cells (GSCs), instruct these cells to maintain stem cell status. The analysis of ovaries mutant for the two bric-à-brac (bab) genes, showed that they are necessary within precursor cells for correct formation of GSC niches and for activation of the BMP pathway leading to the establishment of the first GSCs in the developing ovary. We have also found that Bab proteins contribute to GSC maintenance in the adult along with other transcription factors, Engrailed/Invected. Importantly, overproduction of one of the Bab proteins leads to the production of GSC tumors in the adult ovary underlining a role for this protein in GSC homeostasis. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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9. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
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Jarosz, Yohan, Herold, Malte, Kaysen, Anne, Pinel, Nicolas, Roume, Hugo, Heintz-Buschart, Anna, Muller, Emilie, May, Patrick, Satagopam, Venkata, Laczny, Cédric, Narayanasamy, Shaman, Lebrun, Laura, Hoopmann, Michael, Schupp, James, Gillece, John, Hicks, Nathan, Engelthaler, David, Sauter, Thomas, Keim, Paul, Moritz, Robert, Wilmes, Paul, ALYOTECH TS&I, ALYOTECH, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany, Université du Luxembourg (Uni.lu), Center for Microbial Genetics and Genomics, Northern Arizona University [Flagstaff], Section des Sciences de la Terre, and University of Geneva [Switzerland]
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[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,0303 health sciences ,030306 microbiology ,Community structure ,[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN] ,Computational biology ,15. Life on land ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Article ,6. Clean water ,Transcriptome ,03 medical and health sciences ,Metagenomics ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Metaproteomics ,Identification (biology) ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Keystone species ,Gene ,Function (biology) ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Biotechnology - Abstract
Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT. A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively. Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella. Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as ‘keystone genes’ as they are likely to be encoded by keystone species. The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future. Charting metabolic activity in diverse microbial communities could help scientists control the behavior of these communities, new research shows. Paul Wilmes and colleagues at the University of Luxembourg, alongside scientists from the United States, set out to characterize the biological function of bacterial communities—normally a daunting task due to the sheer number of species involved. To accomplish this, Wilmes and colleagues took a community-wide approach, collecting genomic, transcriptomic and proteomic data from lipid-accumulating microbial consortia in a wastewater treatment tank and assembling functional maps reflecting overall biochemical processes. The scientists were then able to identify ‘keystone’ genes that play a critical role in the community—for example, genes involved in fatty acid biosynthesis were particularly prominent. Such findings could guide strategies for manipulating microbial communities for optimized disease control or biofuel production in future.
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- 2015
10. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
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Roume, Hugo, Buschart, Anna, Muller, Emilie, May, Patrick, Satagopam, Venkata, Laczny, Cedric Christian, Narayanasamy, Shaman, Lebrun, Laura, Hoopmann, Michael, Schupp, James, Gillece, John, Hicks, Nathan, Engelthaler, David, Sauter, Thomas, Keim, Paul, Moritz, Robert, Wilmes, Paul, Fonds National de la Recherche - FnR [sponsor], National Science Foundation [sponsor], National Institute of General Medical Sciences [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Institute for Systems Biology (ISB) [research center], The Translational Genomic Research Institute-North (Tgen) [research center], University of Luxembourg: High Performance Computing - ULHPC [research center], and University of Luxembourg: Life Science Research Unit [research center]
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Environmental sciences & ecology [F08] [Life sciences] ,Sciences de l'environnement & écologie [F08] [Sciences du vivant] ,Microbiologie [F11] [Sciences du vivant] ,Microbiology [F11] [Life sciences] ,Genetics & genetic processes [F10] [Life sciences] ,Génétique & processus génétiques [F10] [Sciences du vivant] - Abstract
BACKGROUND: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT. METHODS: A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively. RESULTS: Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella. Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as ‘keystone genes’ as they are likely to be encoded by keystone species. CONCLUSION: The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future.
- Published
- 2015
11. First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.
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Muller, Emilie E. L., Narayanasamy, Shaman, Zeimes, Myriam, Laczny, Cédric C., Lebrun, Laura A., Herold, Malte, Hicks, Nathan D., Gillece, John D., Schupp, James M., Keim, Paul, and Wilmes, Paul
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NUCLEOTIDE sequencing ,ZOOGLOEA ,GRAM-negative bacteria ,GENOMICS ,LIPID metabolism ,SEWAGE disposal plants - Abstract
The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-ß-hydroxyalkanoate within wastewater. [ABSTRACT FROM AUTHOR]
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- 2017
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12. Method Optimization for Fecal Sample Collection and Fecal DNA Extraction.
- Author
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Mathay, Conny, Hamot, Gael, Henry, Estelle, Georges, Laura, Bellora, Camille, Lebrun, Laura, de Witt, Brian, Ammerlaan, Wim, Buschart, Anna, Wilmes, Paul, and Betsou, Fay
- Abstract
Background: This is the third in a series of publications presenting formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks. We report here optimization of a stool processing protocol validated for fitness-for-purpose in terms of downstream DNA-based analyses. Methods: Stool collection was initially optimized in terms of sample input quantity and supernatant volume using canine stool. Three DNA extraction methods (PerkinElmer MSM I
® , Norgen Biotek All-In-One® , MoBio PowerMag® ) and six collection container types were evaluated with human stool in terms of DNA quantity and quality, DNA yield, and its reproducibility by spectrophotometry, spectrofluorometry, and quantitative PCR, DNA purity, SPUD assay, and 16S rRNA gene sequence-based taxonomic signatures. Results: The optimal MSM I protocol involves a 0.2 g stool sample and 1000 μL supernatant. The MSM I extraction was superior in terms of DNA quantity and quality when compared to the other two methods tested. Optimal results were obtained with plain Sarstedt tubes (without stabilizer, requiring immediate freezing and storage at −20°C or −80°C) and Genotek tubes (with stabilizer and RT storage) in terms of DNA yields (total, human, bacterial, and double-stranded) according to spectrophotometry and spectrofluorometry, with low yield variability and good DNA purity. No inhibitors were identified at 25 ng/μL. The protocol was reproducible in terms of DNA yield among different stool aliquots. Conclusions: We validated a stool collection method suitable for downstream DNA metagenomic analysis. DNA extraction with the MSM I method using Genotek tubes was considered optimal, with simple logistics in terms of collection and shipment and offers the possibility of automation. Laboratories and biobanks should ensure protocol conditions are systematically recorded in the scope of accreditation. [ABSTRACT FROM AUTHOR]- Published
- 2015
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13. Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia.
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Hugerth, Luisa W., Muller, Emilie E. L., Hu, Yue O. O., Lebrun, Laura A. M., Roume, Hugo, Lundin, Daniel, Wilmes, Paul, and Andersson, Anders F.
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RIBOSOMAL RNA ,PRIMERS (Coating) ,EUKARYOTES ,NUCLEOTIDE sequence ,PHYLOGENY ,PROTOZOOLOGY - Abstract
High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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14. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.
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Muller, Emilie E. L., Pinel, Nicolás, Laczny, Cédric C., Hoopmann, Michael R., Narayanasamy, Shaman, Lebrun, Laura A., Roume, Hugo, Lin, Jake, May, Patrick, Hicks, Nathan D., Heintz-Buschart, Anna, Wampach, Linda, Liu, Cindy M., Price, Lance B., Gillece, John D., Guignard, Cédric, Schupp, James M., Vlassis, Nikos, Baliga, Nitin S., and Moritz, Robert L.
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- 2014
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15. Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.
- Author
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Shah P, Muller EEL, Lebrun LA, Wampach L, and Wilmes P
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- Animals, Mice, Organ Specificity, Workflow, DNA isolation & purification, Gastrointestinal Microbiome, Host Microbial Interactions, Metabolomics methods, Proteins metabolism, RNA isolation & purification
- Abstract
The gastrointestinal microbiome plays a central role in health and disease. Imbalances in the microbiome, also referred to as dysbiosis, have recently been associated with a number of human idiopathic diseases ranging from metabolic to neurodegenerative. However, to causally link specific microorganisms or dysbiotic communities with tissue-specific and/or systemic disease-associated phenotypes, systematic in vivo studies are fundamental. Gnotobiotic mouse models have proven to be particularly useful for the elucidation of microbiota-associated characteristics as they provide a means to conduct targeted perturbations followed by analyses of induced localized and systemic effects. Here, we describe a methodology in the framework of systems biology which allows the comprehensive isolation of high quality biomolecular fractions (DNA, RNA, proteins and metabolites) from limited and/or heterogeneous sample material derived from murine brain, liver, and colon tissues, as well as from intestinal contents (fecal pellets and fecal masses). The obtained biomolecular fractions are compatible with current high-throughput genomic, transcriptomic, proteomic, and metabolomic analyses. The resulting data fulfills the premise of systematic measurements and allows the detailed study of tissue-specific and/or systemic effects of host-microbiota interactions in relation to health and disease.
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- 2018
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16. Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
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Heintz-Buschart A, May P, Laczny CC, Lebrun LA, Bellora C, Krishna A, Wampach L, Schneider JG, Hogan A, Beaufort C, and Wilmes P
- Published
- 2016
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17. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
- Author
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Heintz-Buschart A, May P, Laczny CC, Lebrun LA, Bellora C, Krishna A, Wampach L, Schneider JG, Hogan A, de Beaufort C, and Wilmes P
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- Gene Expression Profiling, Humans, Metagenomics, Proteome analysis, Diabetes Mellitus, Type 1 microbiology, Gastrointestinal Microbiome, Gastrointestinal Tract microbiology, Microbiota
- Abstract
The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM). Analysis of intra- and inter-individual variation demonstrates that family membership has a pronounced effect on the structural and functional composition of the gastrointestinal microbiome. In the context of T1DM, consistent taxonomic differences were absent across families, but certain human exocrine pancreatic proteins were found at lower levels. The associated microbial functional signatures were linked to metabolic traits in distinct taxa. The methodologies and results provide a foundation for future large-scale integrated multi-omic analyses of the gastrointestinal microbiome in the context of host-microbe interactions in human health and disease.
- Published
- 2016
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18. Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.
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Laczny CC, Muller EE, Heintz-Buschart A, Herold M, Lebrun LA, Hogan A, May P, de Beaufort C, and Wilmes P
- Abstract
Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBIN post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBIN de novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes.
- Published
- 2016
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19. In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella.
- Author
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Sheik AR, Muller EE, Audinot JN, Lebrun LA, Grysan P, Guignard C, and Wilmes P
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- Carbon Isotopes chemistry, Chromatography, Liquid, Glycerol chemistry, Microscopy, Atomic Force, Oleic Acid chemistry, Phenotype, Phosphates chemistry, Tandem Mass Spectrometry, Temperature, Triolein chemistry, Water Purification methods, Actinobacteria genetics, Sewage microbiology, Wastewater microbiology
- Abstract
Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium Candidatus Microthrix parvicella (Ca. M. parvicella) has been found to fine-tune its gene expression for optimized substrate assimilation. Here we investigated in situ substrate assimilation by single cells of Ca. M. parvicella using nano-scale secondary-ion mass spectrometry (nanoSIMS). NanoSIMS imaging highlighted phenotypic heterogeneity among Ca. M. parvicella cells of the same filament, whereby (13)C-oleic acid and (13)C-glycerol-3-phosphate assimilation occurred in ≈21-55% of cells, despite non-assimilating cells being intact and alive. In response to alternating aerobic-anoxic regimes, (13)C-oleic acid assimilation occurred among subpopulations of Ca. M. parvicella cells (≈3-28% of cells). Furthermore, Ca. M. parvicella cells exhibited two temperature optima for (13)C-oleic acid assimilation and associated growth rates. These results suggest that phenotypic heterogeneity among Ca. M. parvicella cells allows the population to adapt rapidly to fluctuating environmental conditions facilitating its widespread occurrence in biological wastewater treatment plants.
- Published
- 2016
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20. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.
- Author
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Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC, Narayanasamy S, Lebrun LA, Hoopmann MR, Schupp JM, Gillece JD, Hicks ND, Engelthaler DM, Sauter T, Keim PS, Moritz RL, and Wilmes P
- Abstract
Background: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT., Methods: A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively., Results: Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella . Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as 'keystone genes' as they are likely to be encoded by keystone species., Conclusion: The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future., Competing Interests: The authors declare no conflict of interest.
- Published
- 2015
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