Dr Emily Hoedt

Dr Emily Hoedt

Postdoctoral Researcher

School of Medicine and Public Health

Career Summary

Biography

Dr Emily Hoedt is a microbiologist with expertise in microbiome/metagenome analysis and interpretation. Her research experience includes microbiome studies within gastroenterology, probiotic development and microbial/food bioreactors. She was awarded a BBioTech Hons I and PhD in Microbiology Biotechnology by the University of Queensland, Australia in 2017. Her PhD studies focused on the functional and comparative study of heterotrophic methanogens from different gastrointestinal environments. The project received funding through an Australian Postgraduate Award in addition to an industry top-up scholarship from Meat and Livestock Australia. 

In June 2018 Dr Hoedt relocated to Ireland to pursue an Academic-Industry collaborative project conducted at APC Microbiome Ireland. Her role as the lead Postdoctoral Researcher required her to plan, manage and liaise with the Industry partner for the successful completion of the project. This work encompassed the molecular interrogation (in silico and in vitro) of bifidobacterial strains as well as assessing potential host and microbiota (mouse model) benefits during gastrointestinal distress (antibiotic and/or pathogen) in order to determine the commercial viability of the bifidobacterial strains as a probiotic product. During her career Dr Hoedt developed a refined set of skills for the computational analysis of isolate microbial genomes as well as complex 16S/metagenomic datasets.

Dr Hoedt has published on various microbiological driven studies, examples include the isolation and characterisation of novel microorganisms, pan-genomic analysis of microbial isolate and shotgun recovered genomes, and microbiome shifts in response to different dietary fibre types in bioreactors. She has collaborated on a wide variety of projects outside her appointed roles in order to provide computational support and as such is listed as a contributing author on associated publications in leading microbiological and molecular biology research journals.

Dr Hoedt now works The University of Newcastle, Australia as a member of the Centre of Research (CRE) in Digestive Health team, here she oversees all aspects of microbiome research conducted by the CRE.



Qualifications

  • Doctor of Philosophy, University of Queensland
  • Bachelor of Biotechnology, University of Queensland

Keywords

  • 16S rRNA amplicon sequencing
  • Metagenomic shotgun sequencing
  • Microbial genomics
  • Microbial isolation
  • Microbiome
  • Pan-genomics
  • methanogens

Languages

  • English (Mother)

Fields of Research

Code Description Percentage
310409 Microbial taxonomy 40
310704 Microbial genetics 30
320203 Clinical microbiology 30

Professional Experience

UON Appointment

Title Organisation / Department
Postdoctoral Researcher University of Newcastle
School of Medicine and Public Health
Australia

Academic appointment

Dates Title Organisation / Department
25/6/2018 - 11/9/2020 Postdoctoral Researcher University College Cork
Ireland
1/5/2017 - 22/6/2018 Postdoctoral Researcher The University of Queensland
Medicine
Australia

Awards

Award

Year Award
2016 CSIRO Agriculture and Food Directors Award; Next Generation category
CSIRO - Commonwealth Scientific and Industrial Research Organisation
2016 Travel award to Theo Murphy Australian Frontiers of Science symposium
Theo Murphy Australian Frontiers of Science
2012 Australian Postgraduate Award
Australian Federal Government
2012 Meat and Livestock Australia Postgraduate award
Meat and Livestock Australia (MLA)

Distinction

Year Award
2011 Dean’s Commendation for High Achievement
The University of Queensland

Prize

Year Award
2013 QAAFI Animal Science Olympics
Elanco Innovation
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Chapter (1 outputs)

Year Citation Altmetrics Link
2021 Hoedt EC, Bongers RS, Bottacini F, Knol J, MacSharry J, van Sinderen D, 'Bifidobacterium Transformation', Methods in Molecular Biology 13-19 (2021) [B1]

The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective p... [more]

The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective properties onto strains as well as allowing the user to introduce or knock out/in selected genes for phenotypic characterization purposes. We have generalized on the plasmid chosen for transformation and antibiotic selection marker, but the protocol is versatile in this respect and we are able to achieve transformation efficiencies up to 107¿transformants/µg of DNA.

DOI 10.1007/978-1-0716-1274-3_2

Journal article (12 outputs)

Year Citation Altmetrics Link
2021 Hoedt EC, Shanahan ER, Keely S, Shah A, Burns GL, Holtmann GJ, et al., 'Draft Genome Sequence of Streptococcus salivarius AGIRA0003, Isolated from Functional Gastrointestinal Disorder Duodenal Tissue.', Microbiol Resour Announc, 10 e0075821 (2021)
DOI 10.1128/MRA.00758-21
2021 Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, et al., 'Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve', Frontiers in Microbiology, 12 (2021) [C1]

Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems.... [more]

Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an a-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.

DOI 10.3389/fmicb.2021.636822
2021 Teh JJ, Berendsen EM, Hoedt EC, Kang S, Zhang J, Zhang F, et al., 'Novel strain-level resolution of Crohn s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing', ISME Journal, (2021)

The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn¿s disease pathophysiology but remains largely uncharacterised beyond its taxonomic compositi... [more]

The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn¿s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn¿s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn¿s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.

DOI 10.1038/s41396-021-00991-1
2021 Burns GL, Hoedt EC, Keely S, 'Spore-forming probiotics for functional dyspepsia.', Lancet Gastroenterol Hepatol, 6 772-773 (2021)
DOI 10.1016/S2468-1253(21)00260-0
Co-authors Simon Keely, G Burns
2021 Zhang J, Hoedt EC, Liu Q, Berendsen E, Teh JJ, Hamilton A, et al., 'Elucidation of Proteus mirabilis as a Key Bacterium in Crohn's Disease Inflammation', GASTROENTEROLOGY, 160 317-+ (2021)
DOI 10.1053/j.gastro.2020.09.036
Citations Scopus - 1Web of Science - 1
2020 Bui AT, Williams BA, Hoedt EC, Morrison M, Mikkelsen D, Gidley MJ, 'High amylose wheat starch structures display unique fermentability characteristics, microbial community shifts and enzyme degradation profiles', FOOD & FUNCTION, 11 5635-5646 (2020)
DOI 10.1039/d0fo00198h
Citations Scopus - 11Web of Science - 9
2020 Feng G, Mikkelsen D, Hoedt EC, Williams BA, Flanagan BM, Morrison M, Gidley MJ, 'In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry', FOOD & FUNCTION, 11 7892-7904 (2020)
DOI 10.1039/d0fo01103g
Citations Scopus - 4Web of Science - 4
2018 Cuiv PO, Giri R, Hoedt EC, McGuckin MA, Begun J, Morrison M, '&ITEnterococcus faecalis&IT AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells', FRONTIERS IN IMMUNOLOGY, 9 (2018)
DOI 10.3389/fimmu.2018.00790
Citations Scopus - 6Web of Science - 3
2018 Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, et al., 'Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size', ISME JOURNAL, 12 2942-2953 (2018)
DOI 10.1038/s41396-018-0225-7
Citations Scopus - 3Web of Science - 3
2016 Hoedt EC, Cuiv PO, Evans PN, Smith WJM, McSweeney CS, Denman SE, Morrison M, 'Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids', ISME JOURNAL, 10 2376-2388 (2016)
DOI 10.1038/ismej.2016.41
Citations Scopus - 14Web of Science - 14
2016 Hoedt EC, Cuiv PO, Morrison M, 'Methane matters: from blue-tinged moos, to boozy roos, and the health of humans too', ANIMAL FRONTIERS, 6 15-21 (2016)
DOI 10.2527/af.2016-0029
Citations Scopus - 1Web of Science - 1
Cuív PÓ, Giria R, Hoedt EC, McGuckin MA, Begun J, Morrison M, 'Enterococcus faecalisAHG0090 is a genetically tractable bacterium and produces a secreted peptidic bioactive that suppresses NF-kB activation in human gut epithelial cells
DOI 10.1101/275719
Show 9 more journal articles

Conference (11 outputs)

Year Citation Altmetrics Link
2020 Giri R, Hoedt EC, Khushi S, Salim A, Capon R, Morrison M, et al., 'INVESTIGATING THE ROLE OF BIOACTIVES PRODUCED BY GUT BACTERIA TO MODULATE IMMUNE RESPONSE IN IBD', GASTROENTEROLOGY, Austin, TX (2020)
2019 Zhang J, Berendsen E, Hoedt EC, Liu Q, Xu Z, Zhang F, et al., 'PROTEUS IS A KEY CANDIDATE IN THE PATHOGENESIS OF CROHN'S DISEASE: MUCOSA, STOOL GENOMICS AND FUNCTIONAL ANALYSIS: THE ENIGMA STUDY', GASTROENTEROLOGY, San Diego, CA (2019)
Citations Web of Science - 2
2019 Loayza JJJ, Berendsen E, Teh J-J, Hoedt EC, Zhang J, Liu Q, et al., 'THE COMMON FOOD ADDITIVES SODIUM SULFITE AND POLYSORBATE 80 HAVE A PROFOUND INHIBATORY EFFECT ON THE COMMENSAL, ANTI-INFLAMMATORY BACTERIUM FAECALIBACTERIUM PRAUSNITZII. THE ENIGMA STUDY', GASTROENTEROLOGY, San Diego, CA (2019)
Citations Web of Science - 1
2019 Berendsen E, Hoedt EC, Teh J-J, Zhang J, Zhang F, Liu Q, et al., 'UREASE-POSITIVE PROTEOBACTERIA IN CROHN'S DISEASE IDENTIFIED BY NOVEL EX-VIVO MUCOSAL MICROBE CULTURE COMBINED WITH METGENOMIC SEQUENCING (MC-MGS). THE ENIGMA STUDY', GASTROENTEROLOGY, San Diego, CA (2019)
2019 Berendsen E, Hoedt EC, Teh J-J, Zhang J, Zhang F, Liu Q, et al., 'CHARACTERIZATION OF CROHN'S DISEASE MUCOSA-ASSOCIATED MICROBIOTA BY A NOVEL COMBINATION OF MICROBE CULTURE AND METAGENOMIC SEQUENCING (MC-MGS). THE ENIGMA STUDY', GASTROENTEROLOGY, San Diego, CA (2019)
2019 Loayza JJJ, Berendsen EM, Teh J-J, Hoedt EC, Zhang J, Liu Q, et al., 'The common food additives sodium sulfite and polysorbate 80 have a profound inhibitory effect on the commensal, anti-inflammatory bacterium Faecalibacterium prausnitzii: the ENIGMA study', JOURNAL OF CROHNS & COLITIS (2019)
2019 Berendsen EM, Hoedt EC, Teh J-J, Zhang J, Zhang F, Liu Q, et al., 'Urease-positive proteobacteria in Crohn's disease identified by novel ex vivo mucosal microbe culture combined with metagenomic sequencing (MC-MGS): the ENIGMA study', JOURNAL OF CROHNS & COLITIS (2019)
DOI 10.1093/ecco-jcc/jjy222.973
2019 Berendsen EM, Hoedt EC, Teh J-J, Zhang J, Zhang F, Liu Q, et al., 'Characterisation of Crohn's disease mucosa-associated microbiota by a novel combination of microbe culture and metagenomic sequencing (MC-MGS): the ENIGMA study', JOURNAL OF CROHNS & COLITIS (2019)
DOI 10.1093/ecco-jcc/jjy222.976
2019 Zhang J, Berendsen E, Hoedt E, Liu Q, Zhang F, Xu Z, et al., 'Proteus is a key candidate in the pathogenesis of Crohn's disease: mucosa, stool genomics and functional analysis: the ENIGMA study', JOURNAL OF CROHNS & COLITIS (2019)
DOI 10.1093/ecco-jcc/jjy222.958
Citations Web of Science - 1
2018 Murtaza N, McNamara L, Hoedt EC, Muir J, Gibson PR, Morrison M, 'DIETS WITH DIFFERENT PREBIOTIC CONTENT ALTER THE GUT PROKARYOTE AND FUNGAL MICROBIOTA', GASTROENTEROLOGY, Washington, DC (2018)
2016 Burman S, Hoedt EC, Pottenger S, Mohd-Najman N-S, Cuiv PO, Morrison M, 'An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease?', DIGESTIVE DISEASES (2016)
DOI 10.1159/000443759
Citations Scopus - 8Web of Science - 8
Show 8 more conferences
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Grants and Funding

Summary

Number of grants 3
Total funding $2,060,060

Click on a grant title below to expand the full details for that specific grant.


20213 grants / $2,060,060

Wheat proteins, the duodenal microbiome and immune activation in the aetiopathogenesis of non-coeliac gluten sensitivity and functional dyspepsia$2,025,110

Funding body: NHMRC (National Health & Medical Research Council)

Funding body NHMRC (National Health & Medical Research Council)
Project Team Professor Simon Keely, Doctor Kerith Duncanson, Doctor Michael Potter, Mrs Natasha Koloski, Dr Emily Hoedt, Doctor Emily Hoedt, Miss Cheenie Nieva
Scheme Ideas Grants
Role Investigator
Funding Start 2021
Funding Finish 2023
GNo G2000682
Type Of Funding C1100 - Aust Competitive - NHMRC
Category 1100
UON Y

A web-based interface for diet-microbiome-disease models$30,000

Funding body: NHMRC Centre of Research Excellence in Digestive Health

Funding body NHMRC Centre of Research Excellence in Digestive Health
Project Team

Kerith Duncanson, Emily C. Hoedt

Scheme 2020 Pilot Grant
Role Investigator
Funding Start 2021
Funding Finish 2022
GNo
Type Of Funding C1100 - Aust Competitive - NHMRC
Category 1100
UON N

Pilot data collection for analysis of the microbiome and pregnancy outcomes in the Newcastle 1000 study.$4,950

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor Emily Hoedt, Doctor Grace Burns, Doctor Tegan Grace
Scheme Research Grant
Role Lead
Funding Start 2021
Funding Finish 2021
GNo G2100165
Type Of Funding C3300 – Aust Philanthropy
Category 3300
UON Y
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Research Supervision

Number of supervisions

Completed0
Current3

Current Supervision

Commenced Level of Study Research Title Program Supervisor Type
2021 PhD Immune Screening as a Predictor of Food Triggers for Relapse in Crohn’s Disease. PhD (Immunology & Microbiol), College of Health, Medicine and Wellbeing, The University of Newcastle Co-Supervisor
2021 PhD A Mouse Model of Ileocolic Resection and the Changes in Microbiome and Bile Acid Physiology PhD (Surgical Science), College of Health, Medicine and Wellbeing, The University of Newcastle Co-Supervisor
2020 PhD Microbiome and Immune-Phenotyping of Dietary Wheat Sensitivity PhD (Immunology & Microbiol), College of Health, Medicine and Wellbeing, The University of Newcastle Co-Supervisor
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Dr Emily Hoedt

Position

Postdoctoral Researcher
Nick Talley
School of Medicine and Public Health
College of Health, Medicine and Wellbeing

Contact Details

Email emily.hoedt@newcastle.edu.au
Phone (02) 4042 0384

Office

Room HMRI Building, Level 3 East Wing, Desk 167
Building HMRI
Location HMRI, New Lambton Heights, New South Wales

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