Biology subjects

Walker, A. W.

Publications and source records attributed to Walker, A. W..

5 recordsLinked to original sources

bioRxiv2026

Assessment of inter-individual variation in metabolism of flavonoids from bilberry and grape seed extracts using an in vitro digestion and faecal fermentation model

The gut microbiota plays an essential role in the conversion of anthocyanins and (epi-)catechins into smaller phenolic acids, which are then absorbed into the blood stream. The phenolic composition of a commercial bilberry extract and grape seed extract was assessed, as well as a formulation extract containing a combination of both extracts. The extracts were subjected to an in vitro salivary, gastric and intestinal digestion environment, based on the INFOGEST Model. The solid fraction end-product of the combined extract from the in vitro digestion was further fermented with faecal samples from six healthy donors, for 72 hours, to assess phenolic acid metabolism, short-chain fatty acid formation and changes in microbial composition. During the in vitro digestion, flavonoid content in all three extract samples (bilberry, grape seed and the formulation extracts) decreased significantly. In the process of anthocyanin and flavonoid digestion, smaller phenolic acid compounds such as benzoic acid, cinnamic acid and mandelic acid increased in bilberry, grape seed and formulation extract samples. All faecal donors harboured unique microbiota compositions, however all faecal microbiota were able to fully convert catechin/epicatechin, the most prominent flavonoids in the formulation extract sample, into smaller phenolic metabolites (phenylacetic, phenylpropionic and benzoic acids) within 24 hours. Using 16S rRNA gene amplicon sequencing, Anaerobutyricum and Enterocloster spp. were correlated with catechin/epicatechin metabolism in the fermentation procedure, however, in single bacterial strain fermentation experiments with the formulation extract or catechin standard, these bacteria were not capable of metabolising flavonoids. HighlightsO_LIFaecal microbiota converted (epi-)catechin to phenolic metabolites within 24 h. C_LIO_LI(Epi-)catechin correlated negatively with Anaerobutyricum and Enterocloster spp. C_LIO_LIFaecal bacterial cultures did not show (epi-)catechin metabolism capacity. C_LI

microbiology↗

bioRxiv2022

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome

Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observe that adding cultured reference genomes from the rumen to the reference database greatly improves classification rate and accuracy. We also demonstrate that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.

genomics↗

bioRxiv2021

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans

The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via mechanisms such as competition for nutrients and by production of antimicrobial compounds. Here, we investigated the antagonist activity of human gut bacteria towards Candida albicans, an opportunistic fungal pathogen that can cause severe infections and mortality in susceptible patients. Co-culture batch incubations of C. albicans in the presence of faecal microbiota from six different healthy individuals revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene sequence profiling of these faecal co-culture bacterial communities showed that the Bifidobacteriaceae family, and Bifidobacterium adolescentis in particular, were most correlated with antagonistic activity against C. albicans. Follow up mechanistic studies confirmed that culture supernatants of Bifidobacterium species, particularly B. adolescentis, inhibited C. albicans in vitro under both aerobic and anaerobic conditions. Production of the fermentation acids acetate and lactate, together with the concomitant decrease in pH, were strong drivers of the inhibitory activity. Bifidobacteria may therefore represent attractive targets for the development of probiotics and prebiotic interventions tailored to enhance inhibitory activity against C. albicans in vivo.

microbiology↗

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↗

bioRxiv2018

The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics

Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialised stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enzymes responsible. Here we present a comprehensive analysis of over 6.5 terabytes of Illumina and Nanopore sequence data, including assembly of 4941 metagenome-assembled genomes, and several single-contig, whole-chromosome assemblies of novel rumen bacteria. We also present the largest dataset of predicted proteins from the rumen, and provide rich annotation against public datasets. Together these data will form an essential part of future studies of rumen microbiome structure and function.

microbiology↗