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Louis, P.

Publications and source records attributed to Louis, P..

3 recordsLinked to original sources
bioRxiv2022

Process-based modelling of microbial community dynamics in the human colon

The human colon contains a dynamic microbial community whose composition has important implications for human health. In this work we build a process-based model of the colonic microbial ecosystem and compare with general empirical observations and the results of in-vivo experiments. Based our previous work (Kettle et al., 2015), the microbial model consists of 10 microbial functional groups, 4 substrates and 10 metabolites; to this we add the interaction with a human host to give simulations of the in-situ colonic microbial ecosystem. This model incorporates absorption of short chain fatty acids (SCFA) and water by the host through the gut wall, variations in incoming dietary substrates (in the form of "meals" whose composition varies in time), bowel movements, feedback on microbial growth from changes in pH resulting from SCFA production, and multiple compartments to represent the proximal, transverse and distal colon. We verify our model against a number of observed criteria, e.g. total SCFA concentrations, SCFA ratios, mass of bowel movements, pH and water absorption over the transit time; and then run simulations investigating the effect of colonic transit time, and the composition and amount of indigestible carbohydrate in the host diet, which we compare with in-vivo studies. Gut microbiota are highly complex and poory understood yet our work shows that it is nevertheless possible to develop predictive models of the key components of the dynamics of this ecological system. The code is available as an R package (microPopGut) to aid future research. Author SummaryKettle wrote the model code and led the writing of the manuscript. Louis and Flint both contributed to writing the manuscript and all aspects of microbiolgy. All authors contributed critically to the drafts and gave final approval for publication.

microbiology↗
bioRxiv2021

ETV2 regulates PARP-1 binding protein to induce ER stress-mediated cell death in tuberin-deficient cells

Lymphangioleiomyomatosis (LAM) is a rare progressive disease, characterized by mutations in the tuberous sclerosis complex genes (Tsc1 or Tsc2), and hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1). The effectiveness of mTORC1 inhibitors is limited by their lack of cytotoxic effects. Here, we report that E26 transformation specific (ETS) Variant Transcription Factor 2 (ETV2) is a critical regulator of Tsc2-deficient cell survival. Nuclear localization of ETV2 in Tsc2-deficient cells is mTORC1-independent and is enhanced by spleen tyrosine kinase (Syk) inhibition. In the nucleus, ETV2 transcriptionally regulates poly(ADP-ribose) polymerase 1 binding protein (PARPBP), a coregulator of transcription, mRNA and protein expression. Silencing of ETV2 or PARPBP in Tsc2-deficient cells induced ER-stress and increased cell death in vitro and in vivo. We also found ETV2 expression in human cells with loss of heterozygosity for TSC2 lending support to the translational relevance of our findings. In conclusion, we report a novel signaling axis unique to Syk-inhibition is mTORC1-independent and promotes a cytocidal response in Tsc2-deficient cells, and therefore, maybe a potential alternative therapeutic target in LAM.

cell biology↗
bioRxiv2021

Distribution, organization and expression of genes concerned with anaerobic lactate-utilization in human intestinal bacteria

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analysis was performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar, or hexose plus lactate. In A. soehngenii L2-7, six genes of the lct cluster including NAD-independent D-lactate dehydrogenase (i-LDH) were co-ordinately upregulated during growth on equimolar D and L-lactate (DL-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. An i-LDH homolog in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of DL-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate utilization genes by fructose in the non-glucose utilizer C. catus. This implies that bacteria such as C. catus might be more important in curtailing lactate accumulation in the gut. Impact statementLactate can be produced as a fermentation by-product by many gut bacteria but has the potential to perturb intestinal microbial communities by lowering luminal pH, and its accumulation has been linked to a range of deleterious health outcomes. Fortunately, in healthy individuals, lactate tends not to accumulate as it is consumed by cross-feeding lactate-utilizing bacteria, which can convert it into the beneficial short chain fatty acids butyrate and propionate. Lactate-utilizing gut bacteria are therefore promising candidates for potential development as novel probiotics. However, lactate-utilizers are taxonomically diverse, and the genes that underpin utilization of lactate by these specialized gut bacteria are not fully understood. In this study we used transcriptomics to compare gene expression profiles of Anaerobutyricum soehngenii and Coprococcus catus, two prominent lactate-utilizing species in the human gut, during growth on lactate alone, sugar alone, or sugar plus lactate. The results revealed strong upregulation of key, but distinct, gene clusters that appear to be responsible for lactate utilization by these, and other, gut bacterial species. Our results therefore increase mechanistic understanding of different lactate utilization pathways used by gut bacteria, which may help to inform selection of optimal lactate-utilizing species for development as novel therapeutics against colonic microbiota perturbations. Data summaryNovel draft genomes generated for this study have been made available from GenBank (https://www.ncbi.nlm.nih.gov/bioproject/) under BioProject number PRJNA701799. RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-10136. Further details of additional existing genomic data that were analyzed in this project are given in Table 1 and Table S2. O_TBL View this table: org.highwire.dtl.DTLVardef@13fd07borg.highwire.dtl.DTLVardef@90796dorg.highwire.dtl.DTLVardef@1140a60org.highwire.dtl.DTLVardef@b53597org.highwire.dtl.DTLVardef@d16268_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONNew and existing strains used for in vitro cultivation studies in this work, and their corresponding genomes. "N/A" indicates no genome available for this strain, which was used for in vitro work only. The full list of strains used for genomic-based analyses is shown in Table S2. C_TABLECAPTION C_TBL

microbiology↗