Biology subjects

Foucault, P.

Publications and source records attributed to Foucault, P..

5 recordsLinked to original sources

bioRxiv2024

A summer in the Greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lakes within a relatively restricted area. Here, a four-month time-series was carried out during summertime to monitor planktonic microbial communities of nine lakes located within a [~]70 km radius around Paris (Ile-de-France, France) of comparable morphologies, yet distinct trophic statuses (mesotrophic to hypereutrophic). The contribution of the trophic status and intra-summer variations were investigated on prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). Sampled lakes harbored highly distinct and diverse prokaryotic communities. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. The trophic status appears as the main driver of both community structure and functional potential. When focusing on function involved in biogeochemical cycles, responses to phosphorus limitation (mostly polyphosphate-related processes) were highlighted between trophic statuses. Hypereutrophic lakes communities displayed the highest contrast and heterogeneity over time, suggesting a regime shift compared to lakes of lower trophic status. This study explores the influence of eutrophication on lakes microbiome ecology, by comparing for the first time the planktonic microbial communities and their functional potential of lakes of distinct trophic status in close vicinity over a summer season.

microbiology↗

bioRxiv2023

New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

Untargeted metabolomics is a non-a priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if the metabolite annotation remains lacunar due to database gaps, the global metabolomic fingerprint allows for trend analyses of dose-response curves for hundreds of cellular metabolites. The combination of untargeted metabolomic features and benchmark-dose (BMD) calculations then makes it possible to determine concentration range inducing defense responses (CRIDeR) and concentration range inducing damage responses (CRIDaR). To develop this approach in a context of time-dependent microbial community changes, mature river biofilms were exposed for 1 month to four cobalt (Co) concentrations (background concentration, 1 x 10-7, 5 x 10-7 and 1 x 10- 6 M) in an open system of artificial streams. The meta-metabolomic response of biofilms was compared against a multitude of biological parameters (including bioaccumulation, biomass, chlorophyll a content, composition and structure of prokaryotic and eukaryotic communities) monitored at set exposure times (from 1 hour to 28 days). Cobalt exposure induced extremely rapid responses of the meta-metabolome, with time range inducing defense responses (TRIDeR) of around ten seconds, and time range inducing damage responses (TRIDaR) of several hours. Even in biofilms whose structure had been altered by Co bioaccumulation (reduced biomass, chlorophyll a contents and changes in the composition and diversity of prokaryotic and eukaryotic communities), CRIDeRs with similar initiation thresholds (1.41 {+/-} 0.77 x 10-10 M Co2+ added in the exposure medium) were set up at the meta-metabolome level at every time point. In contrast, the CRIDaR initiation thresholds increased by 10 times in long-term Co exposed biofilms. The present study demonstrates that defense and damage responses of biofilm meta-metabolome exposed to Co are rapidly and sustainably impacted, even within tolerant and resistant microbial communities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/567369v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e7a87eorg.highwire.dtl.DTLVardef@e712b7org.highwire.dtl.DTLVardef@7de128org.highwire.dtl.DTLVardef@493053_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIProkaryotic community structures were impacted after 1 h of exposure to Co C_LIO_LIBiofilm meta-metabolome was impacted after 36 s of exposure to Co C_LIO_LIBiofilm meta-metabolome response was faster than changes in biofilm communities C_LIO_LIShort- and long-term exposed biofilms have similar CRIDeR initiation thresholds C_LIO_LILong-term exposed biofilms have higher CRIDaR initiation thresholds C_LI

molecular biology↗

bioRxiv2023

Multi-omics analyses from a single sample: Prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types

Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Non-targeted metabolomics are a suitable tool to bridge this gap, yet extractions protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA sequencing after direct DNA extraction, or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on non-axenic cultures of cyanobacteria, lake water column, biofilm, gut of wild and lab-reared fish, indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.

microbiology↗

bioRxiv2023

Gut microbiota and maternal immune transfer at birth influence pre-allergic clinical outcome.

The gut microbiota of 2-3 month-old infants is associated with later pre-allergic signs, while the microbiota at the time of allergic manifestation is not. We hypothesized that the infant gut microbiota and immune system are primed shortly after birth, and that this is influenced by maternal transfer of humoral immunity. We investigated the association between allergic outcomes and composition and humoral immunity to gut microbiota at birth, 2 months, and 2 years-of-age. Meconium microbiota clustered into three groups dominated by Escherichia, Enterococcus, and mixed genera, respectively. The Escherichia cluster was associated with protection against later allergic manifestations. We moreover studied the proportion and specificity of humoral immunity to gut microbiota. Humoral immunity to gut microbiota at birth was associated with future allergies. Future studies should evaluate whether interventions to alter gut microbiota and humoral immunity in early-life protects against allergy.

immunology↗

bioRxiv2022

Gut microbiota and holobiont metabolome composition of the Medaka fish (Oryzias latipes) are affected by a short exposure to the cyanobacterium Microcystis aeruginosa

Blooms of toxic cyanobacteria are a common stress encountered by aquatic fauna. Evidence indicates that long-lasting blooms affect fauna-associated microbiota. Because of their multiple roles, host-associated microbes are nowadays considered relevant to ecotoxicology, yet the respective timing of microbiota versus functional changes in holobionts response needs to be clarified. The response of gut microbiota and holobionts metabolome to exposure to a dense culture of Microcystis aeruginosa was investigated as a microcosm-simulated bloom in the model fish species Oryzias latipes (medaka). Both gut microbiota and gut metabolome displayed significant composition changes after only 2 days of exposure. A dominant symbiont, member of the Firmicutes, plummeted whereas various genera of Proteobacteria and Actinobacteriota increased in relative abundance. Changes in microbiota composition occurred earlier and faster compared to metabolome composition, suggesting that the microbiota drives the holobionts response. Liver and muscle metabolome were much less affected than guts, supporting that gut and associated microbiota are in the front row upon exposure. This study highlights that even short cyanobacterial blooms, that are increasingly frequent, trigger changes in microbiota composition and holobiont metabolome. It emphasizes the relevance of multi-omics approaches to explore organisms response to an ecotoxicological stress. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/499308v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@112a904org.highwire.dtl.DTLVardef@16589forg.highwire.dtl.DTLVardef@1146629org.highwire.dtl.DTLVardef@3f25e4_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- A 2-day exposure to a simulated M. aeruginosa bloom is enough to sharply decrease the Firmicute/Proteobacteria ratio in the gut of Oryzias latipes fish. - The exposure induced changes in metabolome composition after 2 days in the gut and 4 days in the liver. - The gut bacterial microbiota response occurred faster than metabolomes; we hypothesize that changes in gut microbiota may drive the gut metabolome compositional changes.

microbiology↗