Biology subjects

Bernier-Latmani, R.

Publications and source records attributed to Bernier-Latmani, R..

10 recordsLinked to original sources

bioRxiv2025

Decoupling bile acid 7α-dehydroxylation from colonization resistance to Clostridioides difficile

Secondary bile acids, generated through microbial transformation of primary bile acids secreted in bile, play a role in shaping intestinal microbial communities, modulating host immunity, and regulating energy metabolism. In vitro studies have shown that the balance between primary and secondary bile acids strongly affects spore germination, growth, and cellular physiology of Clostridioides difficile, a major nosocomial gut pathogen. In vivo correlations between microbiome composition, bile acid metabolome, and colonization resistance have led to the hypothesis that 7-dehydroxylating bacteria such as Clostridium scindens protect against C. difficile infection by producing secondary bile acids like deoxycholic acid. However, due to the genetic intractability of known 7-dehydroxylating species, direct experimental validation of this causal relationship has been challenging. In this study, we leveraged the first available 7-dehydroxylation-deficient baiH mutant to test the direct role of 7-dehydroxylated bile acid production in C. difficile colonization resistance in vivo. We colonized gnotobiotic mice with isogenic wild-type or baiH strains of the recently described 7-dehydroxylating species Faecalicatena contorta, including wild-type C. scindens-colonized mice as a positive control. Wild-type F. contorta accumulated 7-dehydroxylated bile acids at levels equivalent to C. scindens, in a strictly baiH-dependent manner. However, despite equivalent bile acid profiles, wild-type F. contorta failed to replicate the C. difficile-restrictive phenotype observed with C. scindens. These findings demonstrate that commensal clostridial 7-dehydroxylation alone is not sufficient for enhancing colonization resistance to C. difficile. Our results highlight the existence of additional, potentially bile acid-independent mechanisms by which certain commensals mediate protection, with important implications for microbiota-based therapies. Importance7-dehydroxylated secondary bile acids, including deoxycholic acid and lithocholic acid, produced by commensal clostridia are widely assumed to inhibit the important nosocomial pathogen Clostridioides difficile, yet their precise role in colonization resistance remains unresolved. Using a defined mouse microbiota and an isogenic Faecalicatena contorta strain pair differing in a single 7-dehydroxylation gene (baiH), we show that restoration of secondary bile acid production is not sufficient to delay C. difficile colonization in vivo. This contrasts with the protective effect of Clostridium scindens, which generates a similar bile acid profile. Our findings uncouple bile acid metabolism from protection and suggest that additional, strain-specific functions - such as nutrient competition or antimicrobial production - play a critical role. Understanding these mechanisms is essential for the rational design of next-generation microbiota-based therapies to prevent or treat recurrent C. difficile infection.

microbiology↗

bioRxiv2025

High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules

Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most microbial taxa remain uncultured, hindering research and biotechnological applications. Isolating environmental anaerobes using traditional methods is particularly cumbersome and low throughput. Here, we present a novel, high-throughput approach for the cultivation and isolation of anaerobes, which involves trapping and growing single microbes within selectively permeable hydrogel capsules followed by fluorescence-activated cell sorting to distribute compartmentalized isolates into liquid medium for further growth. We show that diverse anaerobes can grow within capsules and that slower-growing ones (e.g. methanogens) can be enriched with this platform. We also applied this approach to isolate anaerobes from soil, including strains of the sulfate-reducing bacteria Desulfovibrio desulfuricans and Nitratidesulfovibrio vulgaris. Overall, this work introduces a robust, high-throughput alternative to traditional techniques for isolating environmental anaerobes and expands the emerging set of microfluidics-based tools for the cultivation of novel taxa.

microbiology↗

bioRxiv2025

Modulation of intestinal bile acids influences colonic mucosal responses

BackgroundElevated levels of secondary bile acids produced by the gut microbiome, in particular deoxycholic acid (DCA), influence epithelial cell proliferation and accelerate the development of colorectal cancer (CRC) under adverse dietary conditions, such as long-term, high fat intake. However, their effects on the intestinal epithelium have not been studied in detail. AimTo determine gut epithelial responses to bile acid modulation in vivo and in situ. MethodsWe performed targeted colonization of gnotobiotic mice followed by single-cell RNA sequencing (scRNA-Seq) of colonic epithelial cells combined with immunostaining of human biopsies from: (i) an observational patient cohort with hyperproliferative polyps or cancer; (ii) an interventional study with bile acid-scavenging drugs. ResultsColonization of mice with a synthetic bacterial community together with the 7-dehydroxylating species Extibacter muris resulted in DCA production. ScRNA-Seq of colonic epithelial cells revealed increased cell density of bile acid-sensitive enterocytes but fewer stem cells, goblet cells, and transit amplifying cells in mice exposed to DCA. This was associated with increased expression of pyruvate dehydrogenase kinase (Pdk4) and decreased expression of mucin (Muc2). PDK expression was also increased in human hyperplastic polyps and adenomas, whilst MUC2 expression was reduced in adenomas and carcinomas compared to normal mucosa. In addition, human exposure to bile acid sequestrants was associated with enhanced epithelial proliferation. ConclusionThis study provides insight into intestinal epithelial cell responses to bile acids and their potential clinical relevance.

physiology↗

bioRxiv2024

Impact of redox fluctuations on the spatial distribution of the microbial community in a forest soil: A lysimeter experiment

Climate change is expected to affect precipitation intensity and soil temperature and indirectly impact the release of leached dissolved organic carbon (LDOC) from leaf litter during the early stages of its decomposition, which could affect the health and function of forest soil ecosystem. Here, we experimentally investigate the spatially-explicit impact of LDOC on the forest soil microbiome and the associated biogeochemical processes. Homogenized soil columns were subjected to realistic artificial precipitation for 3 months with the initial level of LDOC adjusted by the number of times the leaf litter was flushed in preparation for the experiment. Hydrological and geochemical parameters (redox potential, pH, dissolved oxygen, soil moisture, matric potential, chemical speciation) were measured continuously as a function of time and depth. The same initial microbial community developed into distinct communities under different LDOC and above and below the water table. The LDOC from leaf litter increased the availability of carbon (C) and nitrogen (N) in porewater four-fold and two-fold respectively in the first two weeks. This resulted in the expansion of the anoxic zone above the water table and a decrease in the soil microbial metabolic potential for cellulolysis and N2 fixation in unsaturated soil along with an increase of soil microbial metabolic potential for fermentation at all depths. Finally, increased LDOC decreased the stability, phylogenetic diversity, and complexity of the soil microbiome, limiting its functional diversity. Thus, management of leaf litter should receive more attention due to its indirect role in the impact of climate change on the soil microbiome. HighlightsO_LIDecreased microbiome diversity and stability due to enhanced leaf litter leaching C_LIO_LIExpansion of the anoxic zone into the unsaturated zone due to increased organic carbon supply C_LIO_LIDecreased soil microbiome metabolic potential for cellulolysis and N2 fixation in unsaturated soil C_LIO_LIDepth-dependent response of microbial community to increased organic carbon availability C_LIO_LIImplications for soil response to climate change C_LI

microbiology↗

bioRxiv2023

Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer

Western diet is an important risk factor for the development of sporadic colorectal cancer (CRC). Dietary fat stimulates bile acid (BA) production by the host and their conversion to secondary BAs by 7-dehydroxylating (7DH+) bacteria, but causal proof of their tumor-promoting effects in vivo is lacking. To address this, we performed feeding studies in a genetically engineered pig model of CRC combined with multi-omics analyses and gnotobiotic mouse studies. Western diet worsened the disease phenotype in APC1311/+ pigs. This was accompanied by microbiota changes, increased levels of the secondary bile acid deoxycholic acid (DCA), and higher colonic epithelial cell proliferation. The latter was counteracted by using the BA-scavenging drug colestyramine. Metagenomic analysis across multiple cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in stool of CRC subjects (n = 1,034). Using two gnotobiotic mouse models of CRC, we demonstrate that colonization with 7DH+ bacteria (C. scindens or Extibacter muris) increased colonic tumor loads. This work provides clear evidence for the causal role of microbiome-derived DCA production in CRC under detrimental dietary conditions, opening avenues for future preventive strategies.

microbiology↗

bioRxiv2023

The Effect of Growth Substrate Availability on Anaerobic Arsenic Methylation by Paraclostridium bifermentans strain EML

Microbial arsenic methylation is established as a detoxification process under aerobic conditions (converting arsenite to monomethylated arsenate) but proposed to be a microbial warfare strategy under anoxic conditions due to the toxicity of its main product monomethylarsonous acid (MMAs(III)). Here, we leveraged a paddy soil-derived anaerobic arsenic methylator, Paraclostridium bifermentans strain EML, to gain insights into this process. Strain EML was inoculated into a series of media involving systematic dilutions of Reinforced Clostridial Broth (RCB) with 25 M arsenite to assess the impact of growth substrate concentration on arsenic methylation. Growth curves evidenced the sensitivity of strain EML to arsenite, and As speciation analysis revealed the production of MMAs(III). Concentrations of MMAs(III) and arsenic methylation gene (arsM) transcription were found to be positively correlated with the RCB dilution, suggesting that substrate limitation enhances arsM gene expression and associated anaerobic arsenic methylation. We propose that growth substrate competition between microorganisms may also lead to an increase in anaerobic As methylation. This hypothesis was further evaluated in an anaerobic co-couture mode of strain EML with either wild-type Escherichia coli K-12 MG1655 (WT) or E. coli expressing the MMAs(III)-resistance gene (arsP), (ArsP E. coli). We found increased MMAs(III) production in the presence of E. coli than its absence and growth inhibition of WT E. coli to a greater extent than ArsP E. coli, presumably due to MMAs(III) produced by strain EML. Taken together, our findings point to an ecological role for anaerobic arsenic methylation, highlighting the role of microbe-microbe competition/interaction in this process. IMPORTANCEAnaerobic arsenic methylation is enhanced in rice paddy soils under flooding conditions than that under drying conditions, leading to increased methylated arsenic accumulation in rice grains. Unlike the known detoxification role for aerobic arsenic methylation, the ecological role of anaerobic arsenic methylation remains elusive and is proposed to be an antibiotic-producing process involving in microbial warfare. In this study, we interrogated a rice paddy soil-derived anaerobic arsenic-methylating bacterium (Paraclostridium bifermentans strain EML) to investigate the effect of growth substrate limitation on arsenic methylation by strain EML in the context of the microbial warfare hypothesis. We provide direct evidence for the role of growth substrate competition in anaerobic arsenic methylation by strain EML. Furthermore, we evidence a feedback loop, by which a bacterium resistant to MMAs(III) enhances its production, presumably through enhanced arsM expression resulting from substrate limitation. Our work uncovers complex interactions between an anaerobic arsenic methylator and potential competitors.

microbiology↗

bioRxiv2022

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

Bile acids (BAs) are steroid-derived molecules with important roles in digestion, the maintenance of host metabolism and immunomodulation. Primary BAs are synthesised by the host, while secondary BAs are produced by the gut microbiome through transformation of the former. Regulation of microbial production of secondary BAs is not well understood, particularly the production of 7-dehydroxylated BAs, which are the most potent agonists for host BA receptors. The 7-dehydroxylation of cholic acid (CA) is well established and is linked to the expression of a bile acid-inducible (bai) operon responsible for this process. However, little to no 7-dehydroxylation has been reported for other host-derived BAs (e.g., chenodeoxycholic acid, CDCA or ursodeoxycholic acid, UDCA). Here, we demonstrate that the 7-dehydroxylation of CDCA and UDCA by Clostridium scindens is induced by CA suggesting that CA-dependent transcriptional regulation of 7-dehydroxylation is generalisable to CDCA and UDCA. In contrast, the murine isolate Extibacter muris did not respond to CA exposure in vitro, suggesting that bai genes are regulated differently in this strain. However, it could 7-dehydroxylate in vivo and its in vitro activity was promoted by the addition of cecal content. The accessory gene baiJ was only upregulated in the Clostridium scindens ATCC 35704 strain, implying mechanistic differences amongst isolates. Interestingly, the human-derived C. scindens strains were also capable of 7-dehydroxylating murine bile acids (muricholic acids) to a limited extent. This study shows novel 7-dehydroxylation activity in vitro as a result of CA-driven induction and suggests distinct bai gene induction mechanisms across bacterial species.

microbiology↗

bioRxiv2022

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

microbiology↗

bioRxiv2021

Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface

Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance ([≤]1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface. Significance StatementThe deep terrestrial subsurface remains an environment in which there is limited understanding of the extant microbial metabolisms, despite its reported large contribution to the overall biomass on Earth. It is much less well studied than deep marine sediments. We show that microorganisms in the subsurface are active, and that methane and sulfur provide fuel in the oligotrophic and anoxic subsurface. We also uncover taxonomically and metabolically diverse ultra-small organisms that interact with larger host cells through surface attachment (episymbiosis). Methane and sulfur are commonly reported in terrestrial crystalline bedrock environments worldwide and the latter cover a significant proportion of the Earths surface. Thus, methane- and sulfur-dependent microbial metabolisms have the potential to be widespread in the terrestrial deep biosphere.

microbiology↗

bioRxiv2020

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Extremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution "multi-omics" enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the "tragedy of common goods". Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name "halt and catch fire" for this way of life.

microbiology↗