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QUADRAT DTP: Increasing culture biodiversity and eco-evolutionary understanding of novel bacterial isolates using culturonmics and computational tools


School of Biological Sciences

About the Project

Microbiomes are defined as the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions (Marchesi et al, 2015). Soil and gastrointestinal tracts contain some of the most complex microbiomes in nature, as they are composed of bacteria, archaea, ciliates, fungi and viruses (Huws et al., 2018). The function of these microbes defines host and soil health coupled with other factors such as their environmental impact e.g. greenhouse gas emissions (GHG). Indeed, the rumen microbiome defines ruminant livestock production and environmental impact (nitrogen and methane emissions).

Although they have been intensively studied for many years and their importance is well recognised, relatively few of these microorganisms have been isolated, cultured and genome sequenced (Soldenet al., 2016; Seshadri et al., 2018;). Issues regarding cultivability for whole community biodiversity studies led to the onset of sequencing technologies, which bypass the cultivability issue and allow the whole community to be accessed. Nonetheless, our ability to understand the ecology of these microbes and enable development of innovative technologies to reduce environmental impact requires improvements in biodiversity within our microbial culture collections as ’omic technologies are often correlative and lack causal proof which in vitro studies can provide.

Before the explosion in sequencing technologies in recent times, culture was the main tool to assess diversity and investigate microbial ecology. The art of culturing has consequently been somewhat lost, but in recent years an insurgence of innovation encompassing so called ’culturomic’ technologies have emerged. These innovations include the dilution to extinction technique, facilitating exclusion of fastidious competitive bacteria, allowing slow growing bacteria to grow, and later be isolated on solid media. These novel technologies have vastly enhanced the cultured biodiversity of microbes available in culture from human gastrointestinal tract, and aquatic and soil environments, and importantly allowed ecological hypothesis to move from correlations to causality.

The development of computational techniques to isolate metagenomically-assembled genomes (MAGs) from metagenomic sequences has also helped identify missing genomes from culture collections (Stewart et al., 2018; Sheridan et al., 2020, in press). These MAGs can also be used to develop bespoke culture media based on the metabolic requirements of those microbes. Consequently, the main aim of the PhD studentship is to use innovative technologies to enhance the cow rumen/faecal and soil microbial biodiversity within culture collections. These ecosystems have been chosen due to their connectivity i.e. cow faecal microbes are often also found in abundance in soils, particularly those grazed by ruminants, and consequently the cross-disciplinary expertise required to culture ‘novel’ microbes from both environments will be similar. Following the use of novel culturomics technologies developed by the groups in Queen’s University Belfast and the University of Aberdeen, resultant isolated microbes will then be taxonomically identified using 16S rDNA sequencing and if deemed novel they will then be genome sequenced to understand their functional capacity (aligning to NERC themes Biodiversity, Systematics, Taxonomy). A detailed study of the genomes will then be pursued and isolates will then be investigated in terms of ecological function (cellulolytic, proteolytic, amylolytic, etc.) and their evolution (aligning to NERC themes Microbial Ecology and Evolutionary Ecology). Consequently, this PhD will provide the candidate with an array of skills from classical microbiology through to bioinformatics, much sought after skills for career development.

More project details are available here: https://www.quadrat.ac.uk/projects/increasing-culture-biodiversity-and-eco-evolutionary-understanding-of-novel-bacterial-isolates-using-culturonmics-and-computational-tools/

How to apply: https://www.quadrat.ac.uk/how-to-apply/

Note that applications should NOT be submitted directly to Queen’s.

Funding Notes

QUADRAT studentships are open to UK and international candidates (EU and non-EU). Funding will cover UK tuition fees/stipend/research & training support grant only.

Before applying please check full funding and eligibility information: View Website

References

Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Front Microbiol. 2018 Sep 25;9:2161. doi: 10.3389/fmicb.2018.02161. PMID: 30319557; PMCID: PMC6167468.

Sabino YNV, Santana MF, Oyama LB, Santos FG, Moreira AJS, Huws SA, Mantovani HC. Characterization of antibiotic resistance genes in the species of the rumen microbiota. Nat Commun. 2019 Nov 20;10(1):5252. doi: 10.1038/s41467-019-13118-0. PMID: 31748524; PMCID: PMC6868206.

Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Thames Consortium, Williams TA, Gubry-Rangin C. (In Press) Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Comms.

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