References of "Lebrun, Laura 50002185"
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See detailA multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community
Martinez Arbas, Susana UL; Narayanasamy, Shaman; Herold, Malte et al

Poster (2018, September 11)

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See detailIntegrated time-resolved multi-omics for understanding microbial niche ecology
Herold, Malte UL; Narayanasamy, Shaman UL; Martinez Arbas, Susana UL et al

Poster (2018, August)

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 ... [more ▼]

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. [less ▲]

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See detailExpressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.
Chaib De Mares, Maryam; Jimenez, Diego Javier; Palladino, Giorgia et al

in Scientific reports (2018), 8(1), 11795

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 ... [more ▼]

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. [less ▲]

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See detailSequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.
Shah, Pranjul UL; Muller, Emilie UL; Lebrun, Laura UL et al

in Microbial Proteomics (2018)

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 ... [more ▼]

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. [less ▲]

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See detailFirst draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Muller, Emilie UL; Narayanasamy, Shaman UL; Zeimes, Myriam et al

in Standards in Genomic Sciences (2017), 12(64),

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome ... [more ▼]

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-β-hydroxyalkanoate within wastewater. [less ▲]

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See detailIdentification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
Laczny, Cedric C.; Muller, Emilie UL; Heintz-Buschart, Anna UL et al

in Frontiers in Microbiology (2016), 7(884),

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 ... [more ▼]

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. [less ▲]

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See detailIntegrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
Heintz-Buschart, Anna UL; May, Patrick UL; Laczny, Cedric C. et al

in Nature microbiology (2016), 2

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 ... [more ▼]

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. [less ▲]

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See detailErratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.
Heintz-Buschart, Anna UL; May, Patrick UL; Laczny, Cedric C. et al

in Nature microbiology (2016), 2

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See detailComparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
Roume, Hugo UL; Buschart, Anna UL; Muller, Emilie UL et al

in Biofilms and Microbiomes (2015), 1(15007),

BACKGROUND: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships ... [more ▼]

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. [less ▲]

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See detailMethod optimization for fecal sample collection and fecal DNA extraction.
Mathay, Conny; Hamot, Gael; Henry, Estelle et al

in Biopreservation and biobanking (2015), 13(2), 79-93

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 ... [more ▼]

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. [less ▲]

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See detailIn situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella
Sheik, Abdul UL; Muller, Emilie UL; Audinot, Jean-Nicolas et al

in ISME Journal (The) (2015)

Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium ... [more ▼]

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. [less ▲]

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See detailCommunity-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie UL; Pinel, Nicolas; Laczny, Cedric Christian UL et al

in Nature Communications (2014)

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 ... [more ▼]

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. [less ▲]

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See detailIn situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella
Sheik, Abdul UL; Muller, Emilie UL; Audinot, Jean-Nicolas et al

Poster (2014, October 16)

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See detailBet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella?
Sheik, Abdul UL; Muller, Emilie UL; Audinot, Jean-Nicolas et al

Scientific Conference (2014, September 29)

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See detailDynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans
Kaysen, Anne UL; Heintz-Buschart, Anna UL; Lebrun, Laura UL et al

Poster (2014, April)

The human gastrointestinal tract is colonized by communities of endogenous microbes, commonly referred to as the microbiome. Here, the microbiota are in close contact with the host intestinal mucosa and ... [more ▼]

The human gastrointestinal tract is colonized by communities of endogenous microbes, commonly referred to as the microbiome. Here, the microbiota are in close contact with the host intestinal mucosa and its innate and adaptive immune systems. The fact that certain stimuli induce an inflammatory response whereas others induce tolerance suggests, that the host immune system interacts with the microbiota and vice versa in different ways. However, the exact details of theses interactions remain largely unknown. It is known that cancer treatment can result in severe adverse effects like mucositis and in combination with allogeneic stem cell transplantation (Tx), in graft-versus host disease (GvHD). However, there is at present only sparse information available on the effects of chemotherapy on the intestinal microbiota and resulting changes in microbiome-immune system interactions. Almost no data exists on the effect of allogeneic stem cell Tx on the composition of the gastrointestinal microbiota. In this project, we are studying the complex interactions between the host and the intestinal microbiota after chemotherapy with or without allogeneic Tx and the occurrence of severe adverse side effects such as mucositis and GvHD. Using a systems biology approach including metagenomics and RNAseq, fecal samples and blood plasma samples from patients undergoing these treatments for malignancies will be analysed to identify the composition of the gastrointestinal microbiome and bacterial small RNAs. The main research hypothesis is that there are quantitative and qualitative changes in the gastrointestinal microbiome following chemotherapy and allogeneic Tx which are linked to the immune status of the patients and possible treatment side-effects, in particular mucositis and GvHD. We aim to provide knowledge on how the host's intestinal mucosa and immune system influence the gastrointestinal microbiome and on the role and involvement of the gastrointestinal microbiota in development in mucositis and GvHD. Importantly, this could help in the formulation of measures to prevent mucositis and GvHD development. [less ▲]

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