Biology subjects

Hutchison, J.

Publications and source records attributed to Hutchison, J..

3 recordsLinked to original sources

bioRxiv2023

A chromosome-scale assembly for dAnjou pear

Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis cv. dAnjou. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica Honeycrisp apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of dAnjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.

genomics↗

bioRxiv2018

Increased production of the extracellular polysaccharide Psl can give a growth advantage to Pseudomonas aeruginosa in low-iron conditions

In infections, biofilm formation is associated with a number of fitness advantages, such as resistance to antibiotics and to clearance by the immune system. Biofilm formation has also been linked to fitness advantages in environments other than in vivo infections; primarily, biofilms are thought to help constituent organisms evade predation and to promote intercellular signaling. The opportunistic human pathogen Pseudomonas aeruginosa forms biofilm infections in lungs, wounds, and on implants and medical devices. However, the tendency toward biofilm formation originated in this bacteriums native environment, primarily plants and soil. Such environments are polymicrobial and often resource-limited. Other researchers have recently shown that the P. aeruginosa extracellular polysaccharide Psl can bind iron. For the lab strain PA01, Psl is also the dominant adhesive and cohesive \"glue\" holding together multicellular aggregates and biofilms. Here, we perform quantitative time-lapse confocal microscopy and image analysis of early biofilm growth by PA01. We find that aggregates of P. aeruginosa have a growth advantage over single cells of P. aeruginosa in the presence of Staphylococcus aureus in low-iron environments. Our results suggest the growth advantage of aggregates is linked to their high Psl content and to the production of an active factor by S. aureus. We posit that the ability of Psl to promote iron acquisition may have been linked to the evolutionary development of the strong biofilm-forming tendencies of P. aeruginosa.

microbiology↗

bioRxiv2018

Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism

Bile acids are metabolic links between hosts and their gut microbiomes, yet little is known about the roles they play in microbe-to-microbe interactions. Here we present a study designed to investigate the effect that a common probiotic, Lactobacillus acidophilus, has on microbial interactions that lead to formation of secondary bile acids. A model microbial consortium was built from three human gut isolates, Clostridium scindens, Collinsella aerofaciens, and Blautia obeum, and cultured under different bile acid and probiotic treatments. A multi-omics platform that included mass spectrometry-based metabolomics and activity-based proteomic probes was used to produce two major results. The first, was that an uncommon secondary bile acid - ursocholate - was produced by a multi-species chemical synthesis pathway. This result highlights a new microbe-to-microbe interaction mediated by bile acids. The second finding was that the probiotic strain, L. acidophilus, quenched the observed interactions and effectively halted consortial synthesis of ursocholate. Little is known about the role that ursocholate plays in human health and development. However, we did discover that a decrease in ursocholate abundance corresponded with successful weight loss in patients after gastric bypass surgery versus those who did not lose weight after surgery. Hence, this study uncovered basic knowledge that may aid future designs of custom probiotic therapies to combat obesity.

microbiology↗