180 results on '"Lebrun, Laura"'
Search Results
2. Glutamylation imbalance leads to photoreceptor degeneration
- Author
-
Mercey, Olivier, primary, Gadadhar, Sudarshan, additional, Magiera, Maria M., additional, Lebrun, Laura, additional, Kostic, Corinne, additional, Moulin, Alexandre, additional, Arsenijevic, Yvan, additional, Janke, Carsten, additional, Guichard, Paul, additional, and Hamel, Virginie, additional
- Published
- 2024
- Full Text
- View/download PDF
3. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
- Author
-
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
- Full Text
- View/download PDF
4. Forecasting the dynamics of a complex microbial community using integrated meta-omics
- Author
-
Delogu, Francesco, primary, Kunath, Benoit J., additional, Queirós, Pedro M., additional, Halder, Rashi, additional, Lebrun, Laura A., additional, Pope, Phillip B., additional, May, Patrick, additional, Widder, Stefanie, additional, Muller, Emilie E. L., additional, and Wilmes, Paul, additional
- Published
- 2023
- Full Text
- View/download PDF
5. Mutation of SOCS2 induces structural and functional changes in mammary development.
- Author
-
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
- Subjects
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]
- Published
- 2024
- Full Text
- View/download PDF
6. Artefactual source of 2-hydroxypyridine
- Author
-
Wilmes, Paul, primary, Trezzi, Jean-Pierre, additional, Aho, Velma, additional, Jäger, Christian, additional, Schade, Sebastian, additional, Janzen, Annette, additional, Hickl, Oskar, additional, Kunath, Benoit, additional, Thomas, Mélanie, additional, Schmit, Kristopher, additional, Garcia, Pierre, additional, Sciortino, Alessia, additional, Martin-Gallausiaux, Camille, additional, Halder, Rashi, additional, Huarte, Oihane Uriarte, additional, Heurtaux, Tony, additional, Heins-Marroquin, Ursula, additional, Gomez-Giro, Gemma, additional, Weidenbach, Katrin, additional, Delacour, Léa, additional, Laczny, Cédric, additional, Novikova, Polina, additional, Ramiro-Garcia, Javier, additional, Singh, Randolph, additional, Andújar, Begoña Talavera, additional, Lebrun, Laura, additional, Daujeumont, Annegrait, additional, Habier, Janine, additional, Dong, Xiangyi, additional, Gavotto, Floriane, additional, Heintz-Buschart, Anna, additional, Schneider, Jochen, additional, Jehmlich, Nico, additional, von Bergen, Martin, additional, Schymanski, Emma, additional, Schmitz, Ruth, additional, Schwamborn, Jens, additional, Glaab, Enrico, additional, Linster, Carole, additional, Kitami, Toshimori, additional, Buttini, Manuel, additional, May, Patrick, additional, Trenkwalder, Claudia, additional, Oertel, Wolfgang, additional, and Mollenhauer, Brit, additional
- Published
- 2023
- Full Text
- View/download PDF
7. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
- Author
-
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
- Published
- 2020
- Full Text
- View/download PDF
8. Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions
- Author
-
Shah, Pranjul, primary, Muller, Emilie E. L., additional, Lebrun, Laura A., additional, Wampach, Linda, additional, and Wilmes, Paul, additional
- Published
- 2018
- Full Text
- View/download PDF
9. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses
- Author
-
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]
- Subjects
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.
- Published
- 2022
10. Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics
- Author
-
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
- Published
- 2018
- Full Text
- View/download PDF
11. An archaeal compound as a driver of Parkinson’s disease pathogenesis
- Author
-
Wilmes, Paul, primary, Trezzi, Jean-Pierre, additional, Aho, Velma, additional, Jäger, Christian, additional, Schade, Sebastian, additional, Janzen, Annette, additional, Hickl, Oskar, additional, Kunath, Benoit, additional, Thomas, Mélanie, additional, Schmit, Kristopher, additional, Garcia, Pierre, additional, Sciortino, Alessia, additional, Martin-Gallausiaux, Camille, additional, Halder, Rashi, additional, Huarte, Oihane Uriarte, additional, Heurtaux, Tony, additional, Heins-Marroquin, Ursula, additional, Gomez-Giro, Gemma, additional, Weidenbach, Katrin, additional, Delacour, Léa, additional, Laczny, Cédric, additional, Novikova, Polina, additional, Ramiro-Garcia, Javier, additional, Singh, Randolph, additional, Andújar, Begoña Talavera, additional, Lebrun, Laura, additional, Daujeumont, Annegrait, additional, Habier, Janine, additional, Dong, Xiangyi, additional, Gavotto, Floriane, additional, Heintz-Buschart, Anna, additional, Schneider, Jochen, additional, Jehmlich, Nico, additional, von Bergen, Martin, additional, Schymanski, Emma, additional, Schmitz, Ruth, additional, Schwamborn, Jens, additional, Glaab, Enrico, additional, Linster, Carole, additional, Kitami, Toshimori, additional, Buttini, Manuel, additional, May, Patrick, additional, Trenkwalder, Claudia, additional, Oertel, Wolfgang, additional, and Mollenhauer, Brit, additional
- Published
- 2022
- Full Text
- View/download PDF
12. Forecasting of a complex microbial community using meta-omics
- Author
-
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], University of Luxembourg: High Performance Computing - ULHPC [research center], The project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research. This work was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 863664). The work of P.M. was funded by the ‘Plan Technologies de la Santé du Gouvernement du Grand-Duché de Luxembourg’ through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. S.W. was supported by the Austrian Science Fund (FWF) Elise Richter V585- B31. P.B.P is grateful for support from The Research Council of Norway (FRIPRO program: 250479) and The Novo Nordisk Foundation (Project no. 0054575). [sponsor], Delogu, Francesco, Kunath, Benoît, Queirós, P. M., Halder, Rashi, Lebrun, Laura, Pope, P. B., May, Patrick, Widder, S., Muller, E. E. L., Wilmes, Paul, 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], University of Luxembourg: High Performance Computing - ULHPC [research center], The project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research. This work was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 863664). The work of P.M. was funded by the ‘Plan Technologies de la Santé du Gouvernement du Grand-Duché de Luxembourg’ through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. S.W. was supported by the Austrian Science Fund (FWF) Elise Richter V585- B31. P.B.P is grateful for support from The Research Council of Norway (FRIPRO program: 250479) and The Novo Nordisk Foundation (Project no. 0054575). [sponsor], Delogu, Francesco, Kunath, Benoît, Queirós, P. M., Halder, Rashi, Lebrun, Laura, Pope, P. B., May, Patrick, Widder, S., Muller, E. E. L., and Wilmes, Paul
- Abstract
Microbial communities are complex assemblages whose dynamics are shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in the future. In this context, communities in biological wastewater treatment plants (BWWTPs) represent excellent model systems, because forecasting them is required to ultimately control and operate the plants in a sustainable manner. Here, we forecast the microbial community from the water-air interface of the anaerobic tank of a BWWTP via longitudinal meta-omics (metagenomics, metatranscriptomics and metaproteomics) data covering 14 months at weekly intervals. We extracted all the available time-dependent information, summarised it in 17 temporal signals (explaining 91.1 of the temporal variance) and linked them over time to rebuild the sequence of ecological phenomena behind the community dynamics. We forecasted the signals over the following five years and tested the predictions with 21 extra samples. We were able to correctly forecast five signals accounting for 22.5 of the time-dependent information in the system and generate mechanistic predictions on the ecological events in the community (e.g. a predation cycle involving bacteria, viruses and amoebas). Through the forecasting of the 17 signals and the environmental variables readings we reconstructed the gene abundance and expression for the following 5 years, showing a nearly perfect trend prediction (coefficient of determination >= 0.97) for the first 2 years. The study demonstrates the maturity of microbial ecology to forecast composition and gene expression of open microbial ecosystems using year-spanning interactions between community cycles and environmental parameters.
- Published
- 2022
13. Bioremediation of 27 Micropollutants by Symbiotic Microorganisms of Wetland Macrophytes
- Author
-
Brunhoferova, Hana, Venditti, Silvia, Laczny, Cedric Christian, Lebrun, Laura, Hansen, Joachim, Brunhoferova, Hana, Venditti, Silvia, Laczny, Cedric Christian, Lebrun, Laura, and Hansen, Joachim
- Abstract
Background: Micropollutants in bodies of water represent many challenges. We addressedthese challenges by the application of constructed wetlands, which represent advanced treatmenttechnology for the removal of micropollutants from water. However, which mechanisms specificallycontribute to the removal efficiency often remains unclear. Methods: Here, we focus on the removalof 27 micropollutants by bioremediation. For this, macrophytesPhragmites australis,Iris pseudacorusandLythrum salicariawere taken from established wetlands, and a special experimental set-up wasdesigned. In order to better understand the impact of the rhizosphere microbiome, we determinedthe microbial composition using 16S rRNA gene sequencing and investigated the role of identifiedgenera in the micropollutant removal of micropollutants. Moreover, we studied the colonizationof macrophyte roots by arbuscular mycorrhizal fungi, which are known for their symbiotic rela-tionship with plants. This symbiosis could result in increased removal of present micropollutants.Results: We foundIris pseudacorusto be the most successful bioremediative system, as it removed22 compounds, including persistent ones, with more than 80% efficiency. The most abundant generathat contributed to the removal of micropollutants werePseudomonas, Flavobacterium, Variovorax,Methylotenera, Reyranella, AmaricoccusandHydrogenophaga.Iris pseudacorusexhibited the highest colo-nization rate (56%). Conclusions: Our experiments demonstrate the positive impact of rhizospheremicroorganisms on the removal of micropollutants.
- Published
- 2022
- Full Text
- View/download PDF
14. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses
- Author
-
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], Fonds National de la Recherche - FnR [sponsor], 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, 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], Fonds National de la Recherche - FnR [sponsor], 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, and Wilmes, Paul
- 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.
- Published
- 2022
15. Bioremediation of 27 Micropollutants by Symbiotic Microorganisms of Wetland Macrophytes
- Author
-
Brunhoferova, Hana, primary, Venditti, Silvia, additional, Laczny, Cédric C., additional, Lebrun, Laura, additional, and Hansen, Joachim, additional
- Published
- 2022
- Full Text
- View/download PDF
16. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
- Author
-
Martinez Arbas, Susana(*), Narayanasamy, Shaman(*), Herold, Malte, Lebrun, Laura, Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît, Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric Christian, 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., Wilmes, Paul, Martinez Arbas, Susana(*), Narayanasamy, Shaman(*), Herold, Malte, Lebrun, Laura, Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît, Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric Christian, 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
- Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
- Published
- 2020
17. 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
- Author
-
Miscopein Saler, Laurine, primary, Hauser, Virginie, additional, Bartoletti, Mathieu, additional, Mallart, Charlotte, additional, Malartre, Marianne, additional, Lebrun, Laura, additional, Pret, Anne-Marie, additional, Théodore, Laurent, additional, Chalvet, Fabienne, additional, and Netter, Sophie, additional
- Published
- 2020
- Full Text
- View/download PDF
18. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
- Author
-
Martínez Arbas, Susana, primary, Narayanasamy, Shaman, additional, Herold, Malte, additional, Lebrun, Laura A., additional, Hoopmann, Michael R., additional, Li, Sujun, additional, Lam, Tony J., additional, Kunath, Benoît J., additional, Hicks, Nathan D., additional, Liu, Cindy M., additional, Price, Lance B., additional, Laczny, Cedric C., additional, Gillece, John D., additional, Schupp, James M., additional, Keim, Paul S., additional, Moritz, Robert L., additional, Faust, Karoline, additional, Tang, Haixu, additional, Ye, Yuzhen, additional, Skupin, Alexander, additional, May, Patrick, additional, Muller, Emilie E. L., additional, and Wilmes, Paul, additional
- Published
- 2020
- Full Text
- View/download PDF
19. Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants (Nature Microbiology, (2019), 4, 7, (1183-1195), 10.1038/s41564-019-0426-5)
- Author
-
Wu, Linwei, Ning, Daliang, Zhang, Bing, Li, Yong, Zhang, Ping, Shan, Xiaoyu, Zhang, Qiuting, Brown, Mathew Robert, Li, Zhenxin, Van Nostrand, Joy D., Ling, Fangqiong, Xiao, Naijia, Zhang, Ya, Vierheilig, Julia, Wells, George F., Yang, Yunfeng, Deng, Ye, Tu, Qichao, Wang, Aijie, Acevedo, Dany, Agullo-Barcelo, Miriam, Alvarez, Pedro J.J., Alvarez-Cohen, Lisa, Andersen, Gary L., de Araujo, Juliana Calabria, Boehnke, Kevin F., Bond, Philip, Bott, Charles B., Bovio, Patricia, Brewster, Rebecca K., Bux, Faizal, Cabezas, Angela, Cabrol, Léa, Chen, Si, Criddle, Craig S., Etchebehere, Claudia, Ford, Amanda, Frigon, Dominic, Sanabria, Janeth, Griffin, James S., Gu, April Z., Habagil, Moshe, Hale, Lauren, Hardeman, Steven D., Harmon, Marc, Horn, Harald, Hu, Zhiqiang, Jauffur, Shameem, Johnson, David R., Keller, Jurg, Keucken, Alexander, Kumari, Sheena, Leal, Cintia Dutra, Lebrun, Laura A., Lee, Jangho, Lee, Minjoo, Lee, Zarraz M.P., Li, Mengyan, Li, Xu, Liu, Yu, Luthy, Richard G., Mendonça-Hagler, Leda C., de Menezes, Francisca Gleire Rodriguez, Meyers, Arthur J., Mohebbi, Amin, Nielsen, Per H., Oehmen, Adrian, Palmer, Andrew, Parameswaran, Prathap, Park, Joonhong, Patsch, Deborah, Reginatto, Valeria, de los Reyes, Francis L., Rittmann, Bruce E., Noyola, Adalberto, Rossetti, Simona, Sidhu, Jatinder, Sloan, William T., Smith, Kylie, de Sousa, Oscarina Viana, Stahl, David A., Stephens, Kyle, Tian, Renmao, Tiedje, James M., Tooker, Nicholas B., De los Cobos Vasconcelos, Daniel, Wagner, Michael, Wakelin, Steve, Wang, Bei, and Weaver, Joseph E.
- Subjects
microbiome ,activated sludge ,wastewater treatment plants ,bacterial communities - Abstract
In the version of this Article originally published, the name of the author 'Mathew Robert Brown' was incorrectly written as 'Mathew Brown' in the main author list and as 'Matthew Brown' in the Global Water Microbiome Consortium list. In addition, in the Global Water Microbiome Consortium list, the names of the authors 'Kevin F. Boehnke', 'Janeth Sanabria' and 'Adalberto Noyola' were incorrectly written as 'Kevin Boehnke', 'Janeth Sanabria Gómez' and 'Adalberto Noyola Robles', respectively. The names have now been corrected and the author initials in the author contributions section updated accordingly.
- Published
- 2019
20. Global diversity and biogeography of bacterial communities in wastewater treatment plants
- Author
-
Wu, Linwei, Ning, Daliang, Zhang, Bing, Li, Yong, Zhang, Ping, Shan, Xiaoyu, Zhang, Qiuting, Brown, Mathew, Li, Zhenxin, Van Nostrand, Joy D., Ling, Fangqiong, Xiao, Naijia, Zhang, Ya, Vierheilig, Julia, Wells, George F., Yang, Yunfeng, Deng, Ye, Tu, Qichao, Wang, Aijie, Zhang, Tong, He, Zhili, Keller, Jurg, Nielsen, Per H., Alvarez, Pedro J.J., Criddle, Craig S., Wagner, Michael, Tiedje, James M., He, Qiang, Curtis, Thomas P., Stahl, David A., Alvarez-Cohen, Lisa, Rittmann, Bruce E., Wen, Xianghua, Zhou, Jizhong, Acevedo, Dany, Agullo-Barcelo, Miriam, Andersen, Gary L., de Araujo, Juliana Calabria, Boehnke, Kevin, Bond, Philip, Bott, Charles B., Bovio, Patricia, Brewster, Rebecca K., Bux, Faizal, Cabezas, Angela, Cabrol, Léa, Chen, Si, Etchebehere, Claudia, Ford, Amanda, Frigon, Dominic, Gómez, Janeth Sanabria, Griffin, James S., Gu, April Z., Habagil, Moshe, Hale, Lauren, Hardeman, Steven D., Harmon, Marc, Horn, Harald, Hu, Zhiqiang, Jauffur, Shameem, Johnson, David R., Keucken, Alexander, Kumari, Sheena, Leal, Cintia Dutra, Lebrun, Laura A., Lee, Jangho, Lee, Minjoo, Lee, Zarraz M.P., Li, Mengyan, Li, Xu, Liu, Yu, Luthy, Richard G., Mendonça-Hagler, Leda C., de Menezes, Francisca Gleire Rodriguez, Meyers, Arthur J., Mohebbi, Amin, Oehmen, Adrian, Palmer, Andrew, Parameswaran, Prathap, Park, Joonhong, Patsch, Deborah, Reginatto, Valeria, de los Reyes, Francis L., Noyola, Adalberto, Rossetti, Simona, Sidhu, Jatinder, Sloan, William T., Smith, Kylie, de Sousa, Oscarina Viana, Stephens, Kyle, Tian, Renmao, Tooker, Nicholas B., De los Cobos Vasconcelos, Daniel, Wakelin, Steve, Wang, Bei, Weaver, Joseph E., West, Stephanie, Wilmes, Paul, Woo, Sung Geun, Wu, Jer Horng, University of Oklahoma (OU), Tsinghua University [Beijing] (THU), College of Resource and Environment Southwest University, Newcastle University [Newcastle], Northeastern Normal University, Washington University in Saint Louis (WUSTL), University of Vienna [Vienna], Northwestern University [Evanston], Shandong University, Chinese Academy of Sciences [Beijing] (CAS), The University of Hong Kong (HKU), Sun Yat-Sen University [Guangzhou] (SYSU), University of Queensland [Brisbane], Aalborg University [Denmark] (AAU), Rice University [Houston], Stanford University, Michigan State University System, The University of Tennessee [Knoxville], University of Washington [Seattle], University of California [Berkeley] (UC Berkeley), University of California (UC), Arizona State University [Tempe] (ASU), University of California [Berkeley], and University of California
- Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Biodiversity ,microbiome ,Applied Microbiology and Biotechnology ,Global Water Microbiome Consortium ,Wastewater treatment plants ,RNA, Ribosomal, 16S ,activated sludge ,0303 health sciences ,Geography ,Sewage ,Ecology ,[SDE.IE]Environmental Sciences/Environmental Engineering ,Microbiota ,Bacterial ,6. Clean water ,Wastewater ,Medical Microbiology ,Sewage treatment ,Infection ,Sequence Analysis ,Microbiology (medical) ,DNA, Bacterial ,16S ,[SDE.MCG]Environmental Sciences/Global Changes ,Immunology ,BACTÉRIAS ,Theoretical ecology ,Microbiology ,Water Purification ,03 medical and health sciences ,Microbial ecology ,Genetics ,14. Life underwater ,030304 developmental biology ,Ribosomal ,Bacteria ,030306 microbiology ,Species diversity ,Cell Biology ,DNA ,Sequence Analysis, DNA ,bacterial communities ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Activated sludge ,13. Climate action ,Biological dispersal ,RNA ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
International audience; Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.
- Published
- 2018
21. Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease
- Author
-
Trezzi, Jean-Pierre, Ramiro Garcia, Javier, Laczny, Cedric Christian, Daujeumont, Annegrät, Halder, Rashi, Lebrun, Laura, Heintz, Anna, Oertel, Wolfgang, Mollenhauer, Brit, Wilmes, Paul, Trezzi, Jean-Pierre, Ramiro Garcia, Javier, Laczny, Cedric Christian, Daujeumont, Annegrät, Halder, Rashi, Lebrun, Laura, Heintz, Anna, Oertel, Wolfgang, Mollenhauer, Brit, and Wilmes, Paul
- Published
- 2018
22. Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.
- Author
-
Fonds National de la Recherche - FnR [sponsor], Chaib De Mares, Maryam, Jimenez, Diego Javier, Palladino, Giorgia, Gutleben, Johanna, Lebrun, Laura, Muller, Emilie, Wilmes, Paul, Sipkema, Detmer, van Elsas, Jan Dirk, Fonds National de la Recherche - FnR [sponsor], Chaib De Mares, Maryam, Jimenez, Diego Javier, Palladino, Giorgia, Gutleben, Johanna, Lebrun, Laura, Muller, Emilie, Wilmes, Paul, Sipkema, Detmer, and van Elsas, Jan Dirk
- Abstract
Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont "Candidatus Synechococcus spongiarium", suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.
- Published
- 2018
23. Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.
- Author
-
Fonds National de la Recherche - FnR [sponsor], Shah, Pranjul, Muller, Emilie, Lebrun, Laura, Wampach, Linda, Wilmes, Paul, Fonds National de la Recherche - FnR [sponsor], Shah, Pranjul, Muller, Emilie, Lebrun, Laura, Wampach, Linda, and Wilmes, Paul
- 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.
- Published
- 2018
24. Integrated time-resolved multi-omics for understanding microbial niche ecology
- Author
-
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Fonds National de la Recherche - FnR [sponsor], Herold, Malte, Narayanasamy, Shaman, Martinez Arbas, Susana, Muller, Emilie, Kleine-Borgmann, Anna Luise, Lebrun, Laura, Roume, Hugo, Sheik, Abdul, Bessarab, Irina, Williams, Rohan, Gillece, John, Schupp, Jim, Keim, Paul, Jäger, Christian, Hoopmann, Michael, Li, Sujun, Tang, Haixu, Heintz, Anna, May, Patrick, Laczny, Cedric Christian, Wilmes, Paul, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Fonds National de la Recherche - FnR [sponsor], Herold, Malte, Narayanasamy, Shaman, Martinez Arbas, Susana, Muller, Emilie, Kleine-Borgmann, Anna Luise, Lebrun, Laura, Roume, Hugo, Sheik, Abdul, Bessarab, Irina, Williams, Rohan, Gillece, John, Schupp, Jim, Keim, Paul, Jäger, Christian, Hoopmann, Michael, Li, Sujun, Tang, Haixu, Heintz, Anna, May, Patrick, Laczny, Cedric Christian, and Wilmes, Paul
- Abstract
Microbial communities are strongly shaped by the niche breadths of their constituent populations. However, a detailed understanding of microbial niche ecology is typically lacking. Integrated multi-omic analyses of host- or environment-derived samples offer the prospect of resolving fundamental and realised niches in situ. In turn, this is considered a prerequisite for niche engineering in order to drive an individual population or a community towards a specific phenotype, e.g., improvement of a biotechnological process. Here, we sampled floating islets on the surface of an activated sludge tank in a time-series spanning 51 time-points over 14 months. Multi-omics datasets (metagenomics, metatranscriptomics, metaproteomics, and (meta-)metabolomics) were generated for all time-points. Leveraging nucleotide sequencing data, we analyzed the community structure and reconstructed genomes for specific populations of interest. Moreover, based on their metabolic potential, three major groups emerged, serving as proxies for their respective fundamental niches . Time-resolved linkage of the proteomic and transcriptomic data to the reconstructed genomes revealed a fine-grained picture of niche realization. In particular, environmental factors (temperature, metabolites, oxygen) were significantly associated with gene expression of individual populations. Furthermore, we subjected the community to controlled oxygen conditions (stable or dynamic) in a bioreactor experiment and measured the transcriptomic response. Our results suggest short-term adaptations of populations of interest with respect to lipid metabolism, among other pathways. In conclusion, our work demonstrates how longitudinal multi-omic datasets can be integrated in order to further our understanding of microbial niche ecology within a biotechnological process with potential applications beyond waste water treatment.
- Published
- 2018
25. Critical transitions in microbial communities: mobile genetic elements as drivers of the microbial community dynamics within activated sludge of wastewater treatment
- Author
-
Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Lam, Tony, Laczny, Cedric Christian, Ye, Yuzhen, Keim, Paul S., Muller, Emilie E.L., May, Patrick, Wilmes, Paul, Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Lam, Tony, Laczny, Cedric Christian, Ye, Yuzhen, Keim, Paul S., Muller, Emilie E.L., May, Patrick, and Wilmes, Paul
- Published
- 2018
26. A multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community
- Author
-
Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Laczny, Cedric Christian, Keim, Paul S., Muller, Emilie E.L., May, Patrick, Wilmes, Paul, Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Laczny, Cedric Christian, Keim, Paul S., Muller, Emilie E.L., May, Patrick, and Wilmes, Paul
- Published
- 2018
27. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
-
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]
- Subjects
[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.
- Published
- 2015
28. First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
- Author
-
Muller, Emilie E. L., primary, Narayanasamy, Shaman, additional, Zeimes, Myriam, additional, Laczny, Cédric C., additional, Lebrun, Laura A., additional, Herold, Malte, additional, Hicks, Nathan D., additional, Gillece, John D., additional, Schupp, James M., additional, Keim, Paul, additional, and Wilmes, Paul, additional
- Published
- 2017
- Full Text
- View/download PDF
29. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
-
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]
- Subjects
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
30. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
- Author
-
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], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Heintz-Buschart, Anna, May, Patrick, Laczny, Cedric C., Lebrun, Laura, Bellora, Camille, Krishna, Abhimanyu, Wampach, Linda, Schneider, Jochen, Hogan, Angela, de Beaufort, Carine, Wilmes, Paul, 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], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Heintz-Buschart, Anna, May, Patrick, Laczny, Cedric C., Lebrun, Laura, Bellora, Camille, Krishna, Abhimanyu, Wampach, Linda, Schneider, Jochen, Hogan, Angela, de Beaufort, Carine, and Wilmes, Paul
- 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
31. Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
- Author
-
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], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Laczny, Cedric Christian, Muller, Emilie, Heintz, Anna, Herold, Malte, Lebrun, Laura, Hogan, Angela, May, Patrick, de Beaufort, Carine, Wilmes, Paul, 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], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Laczny, Cedric Christian, Muller, Emilie, Heintz, Anna, Herold, Malte, Lebrun, Laura, Hogan, Angela, May, Patrick, de Beaufort, Carine, and Wilmes, Paul
- 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 VIZBINpost hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBINde 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
32. Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
- Author
-
University of Luxembourg: High Performance Computing - ULHPC [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Fonds National de la Recherche - FnR [sponsor], Heintz, Anna, May, Patrick, Laczny, Cedric C., Lebrun, Laura, Bellora, Camille, Krishna, Abhimanyu, Wampach, Linda, Schneider, Jochen, Hogan, Angela, Beaufort, Carine De, Wilmes, Paul, University of Luxembourg: High Performance Computing - ULHPC [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Fonds National de la Recherche - FnR [sponsor], Heintz, Anna, May, Patrick, Laczny, Cedric C., Lebrun, Laura, Bellora, Camille, Krishna, Abhimanyu, Wampach, Linda, Schneider, Jochen, Hogan, Angela, Beaufort, Carine De, and Wilmes, Paul
- Published
- 2016
33. Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
- Author
-
Heintz-Buschart, Anna, primary, May, Patrick, additional, Laczny, Cédric C., additional, Lebrun, Laura A., additional, Bellora, Camille, additional, Krishna, Abhimanyu, additional, Wampach, Linda, additional, Schneider, Jochen G., additional, Hogan, Angela, additional, Beaufort, Carine de, additional, and Wilmes, Paul, additional
- Published
- 2016
- Full Text
- View/download PDF
34. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
- Author
-
Heintz-Buschart, Anna, primary, May, Patrick, additional, Laczny, Cédric C., additional, Lebrun, Laura A., additional, Bellora, Camille, additional, Krishna, Abhimanyu, additional, Wampach, Linda, additional, Schneider, Jochen G., additional, Hogan, Angela, additional, de Beaufort, Carine, additional, and Wilmes, Paul, additional
- Published
- 2016
- Full Text
- View/download PDF
35. Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
- Author
-
Laczny, Cedric C., primary, Muller, Emilie E. L., additional, Heintz-Buschart, Anna, additional, Herold, Malte, additional, Lebrun, Laura A., additional, Hogan, Angela, additional, May, Patrick, additional, de Beaufort, Carine, additional, and Wilmes, Paul, additional
- Published
- 2016
- Full Text
- View/download PDF
36. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
-
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], University of Luxembourg: Life Science Research Unit [research center], Fonds National de la Recherche - FnR [sponsor], National Science Foundation [sponsor], National Institute of General Medical Sciences [sponsor], 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, 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], University of Luxembourg: Life Science Research Unit [research center], Fonds National de la Recherche - FnR [sponsor], National Science Foundation [sponsor], National Institute of General Medical Sciences [sponsor], 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, and Wilmes, Paul
- 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
37. In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella
- Author
-
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, Guignard, Cédric, Wilmes, Paul, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, Guignard, Cédric, and Wilmes, Paul
- 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 13C-oleic acid and 13C-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, 13C-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 13C-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
- 2015
38. Integrated omics analyses of the human gut microbiome in a multiplex family study of type 1 diabetes mellitus.
- Author
-
Buschart, Anna, May, Patrick, Laczny, Cedric Christian, Lebrun, Laura, Wampach, Linda, Hogan, Angela, Schneider, Jochen, de Beaufort, Carine, Wilmes, Paul, Buschart, Anna, May, Patrick, Laczny, Cedric Christian, Lebrun, Laura, Wampach, Linda, Hogan, Angela, Schneider, Jochen, de Beaufort, Carine, and Wilmes, Paul
- Published
- 2015
39. Changes in the human gastrointestinal microbiome during cancer treatments
- Author
-
Kaysen, Anne, Heintz, Anna, Lebrun, Laura, Graf, N, Simon, A, Bittenbring, J, Kreis, Stephanie, Schneider, Jochen, Wilmes, Paul, Kaysen, Anne, Heintz, Anna, Lebrun, Laura, Graf, N, Simon, A, Bittenbring, J, Kreis, Stephanie, Schneider, Jochen, and Wilmes, Paul
- Published
- 2015
40. Method optimization for fecal sample collection and fecal DNA extraction.
- Author
-
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Mathay, Conny, Hamot, Gael, Henry, Estelle, Georges, Laura, Bellora, Camille, Lebrun, Laura, de Witt, Brian, Ammerlaan, Wim, Buschart, Anna, Wilmes, Paul, Betsou, Fay, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], 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(R), Norgen Biotek All-In-One(R), MoBio PowerMag(R)) 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 muL 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 degrees C or -80 degrees 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/muL. 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.
- Published
- 2015
41. In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella
- Author
-
Sheik, Abdul R, primary, Muller, Emilie EL, additional, Audinot, Jean-Nicolas, additional, Lebrun, Laura A, additional, Grysan, Patrick, additional, Guignard, Cedric, additional, and Wilmes, Paul, additional
- Published
- 2015
- Full Text
- View/download PDF
42. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
- Author
-
Roume, Hugo, primary, Heintz-Buschart, Anna, additional, Muller, Emilie E L, additional, May, Patrick, additional, Satagopam, Venkata P, additional, Laczny, Cédric C, additional, Narayanasamy, Shaman, additional, Lebrun, Laura A, additional, Hoopmann, Michael R, additional, Schupp, James M, additional, Gillece, John D, additional, Hicks, Nathan D, additional, Engelthaler, David M, additional, Sauter, Thomas, additional, Keim, Paul S, additional, Moritz, Robert L, additional, and Wilmes, Paul, additional
- Published
- 2015
- Full Text
- View/download PDF
43. Method Optimization for Fecal Sample Collection and Fecal DNA Extraction
- Author
-
Mathay, Conny, primary, Hamot, Gael, additional, Henry, Estelle, additional, Georges, Laura, additional, Bellora, Camille, additional, Lebrun, Laura, additional, de Witt, Brian, additional, Ammerlaan, Wim, additional, Buschart, Anna, additional, Wilmes, Paul, additional, and Betsou, Fay, additional
- Published
- 2015
- Full Text
- View/download PDF
44. Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
- Author
-
Hugerth, Luisa W., Muller, Emilie E. L., Hu, Yue O. O., Lebrun, Laura A. M., Roume, Hugo, Lundin, Daniel, Wilmes, Paul, Andersson, Anders F., 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.
- 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., QC 20140604
- Published
- 2014
- Full Text
- View/download PDF
45. Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
- Author
-
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], The Swedish Research Councils VR [grant 2011-5689], FORMAS [grant 2009-1174] and EC BONUS project BLUEPRINT partially funded by FORMAS through grants to A.F.A, the Luxemburg National Research fund [grants ATTRACT/A09/03 and CORE/11/BM/1186762 to P.W., PHD-MARP-04 to H.R. and PRD-2011-1/SR to E.M.] and the Chinese Scholarship Council [sponsor], Hugerth, Luisa, Muller, Emilie, Hu, Yue, Lebrun, Laura, Roume, Hugo, Lundin, Daniel, Wilmes, Paul, Andersson, Anders, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], The Swedish Research Councils VR [grant 2011-5689], FORMAS [grant 2009-1174] and EC BONUS project BLUEPRINT partially funded by FORMAS through grants to A.F.A, the Luxemburg National Research fund [grants ATTRACT/A09/03 and CORE/11/BM/1186762 to P.W., PHD-MARP-04 to H.R. and PRD-2011-1/SR to E.M.] and the Chinese Scholarship Council [sponsor], Hugerth, Luisa, Muller, Emilie, Hu, Yue, Lebrun, Laura, Roume, Hugo, Lundin, Daniel, Wilmes, Paul, and Andersson, Anders
- 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.
- Published
- 2014
46. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
- Author
-
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], University of Luxembourg: High Performance Computing - ULHPC [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Machine Learning (Vlassis Group) [research center], Muller, Emilie, Pinel, Nicolas, Laczny, Cedric Christian, Hoopmann, Michael, Narayanasamy, Shaman, Lebrun, Laura, Roume, Hugo, Lin, Jake, May, Patrick, Hicks, Nathan, Buschart, Anna, Wampach, Linda, Liu, Cindy, Price, Lance, Gillece, John, Guignard, Cédric, Schupp, James, Vlassis, Nikos, Baliga, Moritz, Robert, Keim, Paul, Wilmes, Paul, 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], University of Luxembourg: High Performance Computing - ULHPC [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Machine Learning (Vlassis Group) [research center], Muller, Emilie, Pinel, Nicolas, Laczny, Cedric Christian, Hoopmann, Michael, Narayanasamy, Shaman, Lebrun, Laura, Roume, Hugo, Lin, Jake, May, Patrick, Hicks, Nathan, Buschart, Anna, Wampach, Linda, Liu, Cindy, Price, Lance, Gillece, John, Guignard, Cédric, Schupp, James, Vlassis, Nikos, Baliga, Moritz, Robert, Keim, Paul, and Wilmes, Paul
- Abstract
Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.
- Published
- 2014
47. In situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella
- Author
-
Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, Wilmes, Paul, Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, and Wilmes, Paul
- Published
- 2014
48. The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample
- Author
-
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Muller, Emilie, Buschart, Anna, Roume, Hugo, Lebrun, Laura, Wilmes, Paul, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Muller, Emilie, Buschart, Anna, Roume, Hugo, Lebrun, Laura, and Wilmes, Paul
- Abstract
Integrated omics of microbial consortia, comprising systematized metagenomic, metatranscriptomic, metaproteomic and meta-metabolomic analyses, allows in-depth characterization of organismal and functional diversity in situ. To allow meaningful meta-omic data integration, truly systematic measurements of the typically heterogeneous sample biomass is required. Therefore, there is a need for analyzing biomolecular fractions obtained from single, undivided samples. Here, we share a methodological workflow for the reproducible isolation of concomitant polar and non-polar metabolites, RNA, DNA and proteins from samples obtained from a biological wastewater treatment plant. The methodological framework is applicable to other biological samples [1,2], is compatible with different kits for biomacromolecular isolation [1,2] with minimal tailoring, and represents an important first step in standardization for the emerging field of Molecular Eco-Systems Biology.
- Published
- 2014
49. Community integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
- Author
-
Muller, Emilie, Pinel, Nicolás, Laczny, Cedric Christian, Hoopmann, Michael, Lebrun, Laura, Roume, Hugo, May, Patrick, Hicks, Nathan, Liu, Cindy, Price, Lance, Gillece, John, Guignard, Cédric, Schupp, James, Vlassis, Nikos, Moritz, Robert, Baliga, Nitin, Keim, Paul, Wilmes, Paul, Muller, Emilie, Pinel, Nicolás, Laczny, Cedric Christian, Hoopmann, Michael, Lebrun, Laura, Roume, Hugo, May, Patrick, Hicks, Nathan, Liu, Cindy, Price, Lance, Gillece, John, Guignard, Cédric, Schupp, James, Vlassis, Nikos, Moritz, Robert, Baliga, Nitin, Keim, Paul, and Wilmes, Paul
- Abstract
Microbial communities are complex and dynamic systems that are influenced by stochastic-neutral processes but are mainly structured by resource availability and usage. High-resolution “meta-omics” offer exciting prospects to investigate microbial populations in their native environment. In particular, integrated meta-omics, by allowing simultaneous resolution of fundamental niches (genomics) and realised niches (transcriptomics, proteomics and metabolomics), can resolve microbial lifestyles (generalist versus specialist lifestyle strategies) in situ. We have recently developed the necessary wet- and dry-lab methodologies to carry out systematic molecular measurements of microbial consortia over space and time, and to integrate and analyse the resulting data at the population-level. We applied these methods to oleaginous mixed microbial communities located on the surface of anoxic biological wastewater treatment tanks to investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to community-level phenotypes and ecological success (i.e. population size). Coupled metabolomics and 16S rRNA gene-based deep sequencing demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of Candidatus Microthrix parvicella. By integrating population-level genomic reconstructions with transcriptomic and proteomic data, we found that the dominance of this microbial generalist population results from finely tuned resource usage and optimal foraging behaviour. Moreover, the fluctuating environmental conditions constrain the accumulation of variations, leading to a genetically homogeneous population likely due to fitness trade-offs. By integrating metagenomic, metatranscriptomic, metaproteomic and metabolomic information, we demonstrate that natural microbial population sizes and structures are intricately linked to resource usage and that differing microbial lifestyle strategies may explain the varying degrees of with
- Published
- 2014
50. Bet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella?
- Author
-
Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, Wilmes, Paul, Sheik, Abdul, Muller, Emilie, Audinot, Jean-Nicolas, Lebrun, Laura, Grysan, Patrick, and Wilmes, Paul
- Published
- 2014
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.