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

Abstract

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