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Dive into the research topics where Lucas Auer is active.

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Featured researches published by Lucas Auer.


Bioresource Technology | 2015

Efficient anaerobic transformation of raw wheat straw by a robust cow rumen-derived microbial consortium.

Adèle Lazuka; Lucas Auer; Sophie Bozonnet; D. P. Morgavi; Michael J. O'Donohue; Guillermina Hernandez-Raquet

A rumen-derived microbial consortium was enriched on raw wheat straw as sole carbon source in a sequential batch-reactor (SBR) process under strict mesophilic anaerobic conditions. After five cycles of enrichment the procedure enabled to select a stable and efficient lignocellulolytic microbial consortium, mainly constituted by members of Firmicutes and Bacteroidetes phyla. The enriched community, designed rumen-wheat straw-derived consortium (RWS) efficiently hydrolyzed lignocellulosic biomass, degrading 55.5% w/w of raw wheat straw over 15days at 35°C and accumulating carboxylates as main products. Cellulolytic and hemicellulolytic activities, mainly detected on the cell bound fraction, were produced in the earlier steps of degradation, their production being correlated with the maximal lignocellulose degradation rates. Overall, these results demonstrate the potential of RWS to convert unpretreated lignocellulosic substrates into useful chemicals.


BMC Genomics | 2016

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems.

Anne Abot; Grégory Arnal; Lucas Auer; Adèle Lazuka; Delphine Labourdette; Sophie Lamarre; Lidwine Trouilh; Elisabeth Laville; Vincent Lombard; Gabrielle Potocki-Véronèse; Bernard Henrissat; Michael J. O’Donohue; Guillermina Hernandez-Raquet; Claire Dumon; Véronique Anton Leberre

BackgroundMicroorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans.ResultsThis DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota.ConclusionsThe CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.


Molecular Ecology Resources | 2017

Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description

Lucas Auer; Mahendra Mariadassou; Michael J. O'Donohue; Christophe Klopp; Guillermina Hernandez-Raquet

Next‐generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α‐ and β‐diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α‐ and β‐community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates.


Frontiers in Microbiology | 2018

Screening of Phytophagous and Xylophagous Insects Guts Microbiota Abilities to Degrade Lignocellulose in Bioreactor

Amandine Gales; Lucile Chatellard; Maider Abadie; Anaïs Bonnafous; Lucas Auer; Hélène Carrère; Jean-Jacques Godon; Guillermina Hernandez-Raquet; Claire Dumas

Microbial consortia producing specific enzymatic cocktails are present in the gut of phytophagous and xylophagous insects; they are known to be the most efficient ecosystems to degrade lignocellulose. Here, the ability of these consortia to degrade ex vivo lignocellulosic biomass in anaerobic bioreactors was characterized in term of bioprocess performances, enzymatic activities and bacterial community structure. In a preliminary screening, guts of Ergates faber (beetle), Potosia cuprea (chafer), Gromphadorrhina portentosa (cockroach), Locusta migratoria (locust), and Gryllus bimaculatus (cricket) were inoculated in anaerobic batch reactors, in presence of grounded wheat straw at neutral pH. A short duration fermentation of less than 8 days was observed and was related to a drop of pH from 7 to below 4.5, leading to an interruption of gas and metabolites production. Consistently, a maximum of 180 mgeq.COD of metabolites accumulated in the medium, which was related to a low degradation of the lignocellulosic biomass, with a maximum of 5 and 2.2% observed for chafer and locust gut consortia. The initial cell-bound and extracellular enzyme activities, i.e., xylanase and β-endoglucanase, were similar to values observed in the literature. Wheat straw fermentation in bioreactors leads to an increase of cell-bounded enzyme activities, with an increase of 145% for cockroach xylanase activity. Bacterial community structures were insect dependent and mainly composed of Clostridia, Bacteroidia and Gammaproteobacteria. Improvement of lignocellulose biodegradation was operated in successive batch mode at pH 8 using the most interesting consortia, i.e., locust, cockroaches and chafer gut consortia. In these conditions, lignocellulose degradation increased significantly: 8.4, 10.5, and 21.0% of the initial COD were degraded for chafer, cockroaches and locusts, respectively in 15 days. Consistently, xylanase activity tripled for the three consortia, attesting the improvement of the process. Bacteroidia was the major bacterial class represented in the bacterial community for all consortia, followed by Clostridia and Gammaproteobacteria classes. This work demonstrates the possibility to maintain apart of insect gut biological activity ex vivo and shows that lignocellulose biodegradation can be improved by using a biomimetic approach. These results bring new insights for the optimization of lignocellulose degradation in bioreactors.


Biotechnology for Biofuels | 2018

Anaerobic lignocellulolytic microbial consortium derived from termite gut: enrichment, lignocellulose degradation and community dynamics

Adèle Lazuka; Lucas Auer; Michael J. O’Donohue; Guillermina Hernandez-Raquet

BackgroundLignocellulose is the most abundant renewable carbon resource that can be used for biofuels and commodity chemicals production. The ability of complex microbial communities present in natural environments that are specialized in biomass deconstruction can be exploited to develop lignocellulose bioconversion processes. Termites are among the most abundant insects on earth and play an important role in lignocellulose decomposition. Although their digestive microbiome is recognized as a potential reservoir of microorganisms producing lignocellulolytic enzymes, the potential to enrich and maintain the lignocellulolytic activity of microbial consortia derived from termite gut useful for lignocellulose biorefinery has not been assessed. Here, we assessed the possibility of enriching a microbial consortium from termite gut and maintaining its lignocellulose degradation ability in controlled anaerobic bioreactors.ResultsWe enriched a termite gut-derived consortium able to transform lignocellulose into carboxylates under anaerobic conditions. To assess the impact of substrate natural microbiome on the enrichment and the maintenance of termite gut microbiome, the enrichment process was performed using both sterilized and non-sterilized straw. The enrichment process was carried out in bioreactors operating under industrially relevant aseptic conditions. Two termite gut-derived microbial consortia were obtained from Nasutitermes ephratae by sequential batch culture on raw wheat straw as the sole carbon source. Analysis of substrate loss, carboxylate production and microbial diversity showed that regardless of the substrate sterility, the diversity of communities selected by the enrichment process strongly changed compared to that observed in the termite gut. Nevertheless, the community obtained on sterile straw displayed higher lignocellulose degradation capacity; it showed a high xylanase activity and an initial preference for hemicellulose.ConclusionsThis study demonstrates that it is possible to enrich and maintain a microbial consortium derived from termite gut microbiome in controlled anaerobic bioreactors, producing useful carboxylates from raw biomass. Our results suggest that the microbial community is shaped both by the substrate and the conditions that prevail during enrichment. However, when aseptic conditions are applied, it is also affected by the biotic pressure exerted by microorganisms naturally present in the substrate and in the surrounding environment. Besides the efficient lignocellulolytic consortium enriched in this study, our results revealed high levels of xylanase activity that can now be further explored for enzyme identification and overexpression for biorefinery purposes.


Cement and Concrete Research | 2015

An innovative approach to reproduce the biodeterioration of industrial cementitious products in a sewer environment. Part I: Test design

Matthieu Peyre Lavigne; Alexandra Bertron; Lucas Auer; Guillermina Hernandez-Raquet; Jean-Noël Foussard; Gilles Escadeillas; Arnaud Cockx; Etienne Paul


Cement and Concrete Research | 2016

Innovative approach to simulating the biodeterioration of industrial cementitious products in sewer environment. Part II: Validation on CAC and BFSC linings

Matthieu Peyre Lavigne; Alexandra Bertron; Catherine Botanch; Lucas Auer; Guillermina Hernandez-Raquet; Arnaud Cockx; Jean-Noël Foussard; Gilles Escadeillas; Etienne Paul


F1000Research | 2016

FROGS: Find Rapidly OTU with Galaxy Solution

Frédéric Escudié; Lucas Auer; Maria Bernard; Laurent Cauquil; Katia Vidal; Sarah Maman; Mahendra Mariadassou; Guillermina Hernandez-Raquet; Géraldine Pascal


JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques | 2015

How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities?

Lucas Auer; Laurent Cauquil; Stephane Chaillou; Céline Delbès; Eric Dugat-Bony; Hélène Falentin; Guillermina Hernandez Raquet; Mahendra Mariadassou; Aurélie Nicolas; Géraldine Pascal; Etienne Rifa; Sophie Schbath; Anne-Laure Abraham; Sébastien Terrat


International Conference on Anaerobic Digestion. AD Technology and Microbial Ecology for Sustainable Development (ADTech2015) | 2015

Taming lignocellulosic degradation activity of consortia from phytophagous insects guts in batch reactors: microbial diversity and enzymatic activities kinetics

Amandine Gales; Jean-Jacques Godon; Maider Abadie; Adèle Lazuka; Lucas Auer; Claire Dumas; Guillermina Hernandez Raquet

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Amandine Gales

Institut national de la recherche agronomique

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Claire Dumas

Institut national de la recherche agronomique

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Jean-Jacques Godon

Institut national de la recherche agronomique

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Mahendra Mariadassou

Institut national de la recherche agronomique

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Michael J. O'Donohue

Institut national de la recherche agronomique

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