Publications by authors named "Christopher C Cheng"

4 Publications

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sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., five novel species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of adapted to the gastrointestinal tract of specific vertebrate hosts.

Int J Syst Evol Microbiol 2021 Feb;71(2)

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada.

Ten strains, BG-AF3-A, pH52_RY, WF-MT5-A, BG-MG3-A, Lr3000, RRLNB_1_1, STM3_1, STM2_1, WF-MO7-1 and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as . However, average nucleotide identity and digital DNA-DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names sp. nov. (type strain BG-AF3-A=DSM 110574=LMG 31633), sp. nov. (type strain WF-MT5-A=DSM 110569=LMG 31629), sp. nov. (type strain Lr3000=DSM 110573=LMG 31632), sp. nov. (type strain STM3_1=DSM 110572=LMG 31631) and sp. nov. (type strain WF-MO7-1=DSM 110576=LMG 31630). Core genome phylogeny and experimental evidence of host adaptation of strains of further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of : subsp. subsp. nov. (type strain AP3=DSM 110703=LMG 31724), subsp. subsp. nov. (type strain 3c6=DSM 110571=LMG 31635), subsp. subsp. nov. (type strain lpuph1=DSM 110570=LMG 31634), subsp. subsp. nov. (type strain F 275=DSM 20016=ATCC 23272), subsp. subsp. nov. (type strain 1063=ATCC 53608=LMG 31752) and subsp. subsp. nov. (type strain 100-23=DSM 17509=CIP 109821).
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http://dx.doi.org/10.1099/ijsem.0.004644DOI Listing
February 2021

A Phylogenetic View on the Role of Glycerol for Growth Enhancement and Reuterin Formation in .

Front Microbiol 2020 21;11:601422. Epub 2020 Dec 21.

Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.

Lineages within the species have specialized to various hosts and their genomes reflect these adaptations. The gene cluster is conserved in most human and poultry isolates but is infrequent in rodent and porcine isolates. This gene cluster confers the transformation of glycerol into 3-hydroxy-propionaldehyde (reuterin), which can either be secreted and function as precursor of the antimicrobial compound acrolein or serve as an electron acceptor that enhances the organisms' growth rate. However, it remains unclear which of these two functions is more relevant for evolution and ecology. Here we characterized the effect of glycerol on growth rate and reuterin formation in strains across different phylogenetic lineages during growth on ecologically relevant carbohydrates. We further evaluated the innate reuterin resistance among these strains to infer a possible role of reuterin in the evolution of strains. Results revealed that the poultry/human lineage VI strain, DSM 17938 shows more growth enhancement through glycerol and greater capacity for reuterin production on glucose and maltose as compared to human lineage II strains. Interestingly, reuterin production in lineage II strains was significantly elevated on raffinose and lactose, reaching levels similar to DSM 17938. On all carbohydrates tested, reuterin production occurred during the exponential growth phase and became undetectable during the stationary growth phase. The amount of reuterin produced was sufficient to inhibit , suggesting that it could be ecologically relevant, but the resistance towards reuterin among strains was highly variable and, for the most part, unrelated to the strain's capacity for reuterin production. Overall, the findings suggest differences in the substrate-specific regulation of the cluster in lineages that might be reflective of their ecological niches, e.g., chicken foregut versus human infant and adult large intestine. Such information can inform future studies on the ecology of and guide the development of synbiotic applications to improve the therapeutic use of this species.
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http://dx.doi.org/10.3389/fmicb.2020.601422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779471PMC
December 2020

Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts.

Appl Environ Microbiol 2020 05 19;86(11). Epub 2020 May 19.

Department of Biological Sciences, University of Alberta, Edmonton, Canada

Cross-feeding based on the metabolite 1,2-propanediol has been proposed to have an important role in the establishment of trophic interactions among gut symbionts, but its ecological importance has not been empirically established. Here, we show that growth of (syn. ) ATCC PTA 6475 is enhanced through 1,2-propanediol produced by UCC2003 and MG1655 from the metabolization of fucose and rhamnose, respectively. Work with isogenic mutants showed that the trophic interaction is dependent on the operon in , which encodes the ability to use 1,2-propanediol, and the l-fucose permease () gene in , which is required for 1,2-propanediol formation from fucose. Experiments in gnotobiotic mice revealed that, although the operon bestows a fitness burden on ATCC PTA 6475 in the mouse digestive tract, the ecological performance of the strain was enhanced in the presence of UCC2003 and the mucus-degrading species The use of the respective and mutants of and in the mouse experiments indicated that the trophic interaction was specifically based on 1,2-propanediol. Overall, our work established the ecological importance of cross-feeding relationships based on 1,2-propanediol for the fitness of a bacterial symbiont in the vertebrate gut. Through experiments in gnotobiotic mice that employed isogenic mutants of bacterial strains that produce () and utilize () 1,2-propanediol, this study provides mechanistic insight into the ecological ramifications of a trophic interaction between gut symbionts. The findings improve our understanding on how cross-feeding influences the competitive fitness of in the vertebrate gut and revealed a putative selective force that shaped the evolution of the species. The findings are relevant since they provide a basis to design rational microbial-based strategies to modulate gut ecosystems, which could employ mixtures of bacterial strains that establish trophic interactions or a personalized approach based on the ability of a resident microbiota to provide resources for the incoming microbe.
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http://dx.doi.org/10.1128/AEM.00190-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237793PMC
May 2020

Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production.

Cell Host Microbe 2020 Mar 30;27(3):389-404.e6. Epub 2020 Jan 30.

Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada; APC Microbiome Ireland, School of Microbiology, Department of Medicine, and APC Microbiome Institute, University College Cork - National University of Ireland, Cork T12 YT20, Ireland. Electronic address:

Dietary fibers (DFs) impact the gut microbiome in ways often considered beneficial. However, it is unknown if precise and predictable manipulations of the gut microbiota, and especially its metabolic activity, can be achieved through DFs with discrete chemical structures. Using a dose-response trial with three type-IV resistant starches (RS4s) in healthy humans, we found that crystalline and phosphate cross-linked starch structures induce divergent and highly specific effects on microbiome composition that are linked to directed shifts in the output of either propionate or butyrate. The dominant RS4-induced effects were remarkably consistent within treatment groups, dose-dependent plateauing at 35 g/day, and can be explained by substrate-specific binding and utilization of the RS4s by bacterial taxa with different pathways for starch metabolism. Overall, these findings support the potential of using discrete DF structures to achieve targeted manipulations of the gut microbiome and its metabolic functions relevant to health.
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http://dx.doi.org/10.1016/j.chom.2020.01.006DOI Listing
March 2020