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Dr Florence Abram

Ph.D., MSc, MSc

 
researcher
 

Biography

I am an Associate Professor in Microbiology and the Director of the Functional Environmental Microbiology research group, which was established in 2010. The group research activities centres around the application of novel technologies, including omics and machine learning, to investigate the response of microorganisms and microbiomes to changing environmental conditions. Current research includes work on: i) using deep machine learning to improve de novo protein identification; ii) impact of metal on anaerobic digestion; iii) metagenomics of anaerobic microbiomes for farm-based anaerobic digestion; iv) mining soil metagenomes for antibiotic resistance genes; v) assessing the impact of soil management on microbiome functioning and soil health; vi) ensuring microbial safety of organic waste spread on land; vii) microbial responses to forever chemicals and viii) multi-omics investigation into Streptococcus pyogenes pathogenicity.  To date I have supervised/co-supervised 20 PhD students (14 of whom have graduated) and 1 research MSc (graduated). I have also mentored 3 postdoctoral researchers. Passed students have secured employment in academia and in industry, with most of whom I retain collaborative links.

Research Interests

My research interests are as follows:
  • Microbial Ecology
  • Systems Biology
  • Application of Machine Learning to Microbiology
  • Application of Proteomics and  Metaproteomics to investigate microbial behaviour
  • Persistence of invasive species in the environment such as Escherichia coli in soils
  • Trade-off between stress resistance and nutrition in microorganisms

Peer Reviewed Journals

  Year Publication
(2023) 'Critical evaluation of the use of artificial data for machine learning based de novo peptide identification'
Kevin McDonnell, Enda Howley, Florence Abram (2023) 'Critical evaluation of the use of artificial data for machine learning based de novo peptide identification'. Computational and Structural Biotechnology Journal, [Details]
(2023) 'Assessing the impact of interfering organic matter on soil metaproteomic workflow'
Matthias Waibel, Kevin McDonnell, Maria Tuohy, Sally Shirran, Sylvia Synowsky, Barry Thornton, Eric Paterson, Fiona Brennan, Florence Abram (2023) 'Assessing the impact of interfering organic matter on soil metaproteomic workflow'. European Journal Of Soil Science, [Details]
(2012) 'Exploring mixed microbial community functioning: recent advances in metaproteomics'
Siggins, A; Gunnigle, E; Abram, F (2012) 'Exploring mixed microbial community functioning: recent advances in metaproteomics'. Fems Microbiology Ecology, 80 (2):265-280 [DOI] [Details]
(2023) 'Impacts of metal stress on extracellular microbial products, and potential for selective metal recovery'
Parvin Hasani Zadeh, Fernando G Fermoso, Gavin Collins, Antonio Serrano, Simon Mills, Florence Abram (2023) 'Impacts of metal stress on extracellular microbial products, and potential for selective metal recovery'. Ecotoxicology And Environmental Safety, [Details]
(2022) 'Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding'
Kevin McDonnell, Florence Abram, Enda Howley (2022) 'Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding'. Journal Of Proteome Research, [Details]
(2022) 'The Survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in Sandy and Clay Loam Textured Soils When Applied in Bovine Slurry or Unpasteurised Digestate and the Run-Off Rate for a Test Bacterium, Listeria innocua, When Applied to Grass in Slurry and Digestate'
Lauren Russell, Paul Whyte, Annetta Zintl, Stephen V Gordon, Bryan Markey, Theo de Waal, Stephen Nolan, Vincent O'Flaherty, Florence Abram, Karl Richards, Owen Fenton, Declan Bolton (2022) 'The Survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in Sandy and Clay Loam Textured Soils When Applied in Bovine Slurry or Unpasteurised Digestate and the Run-Off Rate for a Test Bacterium, Listeria innocua, When Applied to Grass in Slurry and Digestate'. Frontiers In Sustainable Food Systems, [Details]
(2022) 'Development of an enhanced chain elongation process for caproic acid production from waste-derived lactic acid and butyric acid'
Corine orline Nzeteu, Fabiana Coelho, Anna Christine Trego, Florence Abram, Javier Ramiro-Garcia, Lara Paulo, Vincent O'Flaherty (2022) 'Development of an enhanced chain elongation process for caproic acid production from waste-derived lactic acid and butyric acid'. Journal Of Cleaner Production, [Details]
(2022) 'The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms'
Kevin McDonnell, Enda Howley, Florence Abram (2022) 'The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms'. Computational and Structural Biotechnology Journal, [Details]
(2021) 'Resource recovery from the anaerobic digestion of food waste is underpinned by cross-kingdom microbial activities'
C Nzeteu, A Joyce, C Thorn, K McDonnell, S Shirran, V O'Flaherty, F Abram (2021) 'Resource recovery from the anaerobic digestion of food waste is underpinned by cross-kingdom microbial activities'. Bioresource technology report, [Details]
(2021) 'Survival of Escherichia coli and Listeria innocua on Lettuce after Irrigation with Contaminated Water in a Temperate Climate'
Bernardino Machado-Moreira, Karl Richards, Florence Abram, Fiona Brennan, Michael Gaffney, Catherine M Burgess (2021) 'Survival of Escherichia coli and Listeria innocua on Lettuce after Irrigation with Contaminated Water in a Temperate Climate'. Foods (Basel, Switzerland), [Details]
(2021) 'Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation'
Trego AC, McAteer PG, Nzeteu C, Mahony T, Abram F, Ijaz UZ & O¿Flaherty V (2021) 'Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation'. Frontiers In Microbiology, [Details]
(2021) 'Simultaneous adsorption and biodegradation of trichloroethylene occurs in a biochar packed column treating contaminated landfill leachate'
Siggins, A;Thorn, C;Healy, MG;Abram, F (2021) 'Simultaneous adsorption and biodegradation of trichloroethylene occurs in a biochar packed column treating contaminated landfill leachate'. Journal Of Hazardous Materials, 403 [DOI] [Details]
(2021) 'Application of plasma activated water for decontamination of alfalfa and mung bean seeds'
Machado-Moreira B;Tiwari BK;Richards KG;Abram F;Burgess CM; (2021) 'Application of plasma activated water for decontamination of alfalfa and mung bean seeds'. Food Microbiology, 96 [DOI] [Details]
(2020) 'Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater'
McAteer PG;Christine Trego A;Thorn C;Mahony T;Abram F;O'Flaherty V; (2020) 'Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater'. Bioresource Technology, 307 [DOI] [Details]
(2020) 'Chordomics: a visualization tool for linking function to phylogeny in microbiomes'
McDonnell K, Waters N, Howley E, & Abram F (2020) 'Chordomics: a visualization tool for linking function to phylogeny in microbiomes'. Bioinformatics, [Details]
(2020) 'A Small Study of Bacterial Contamination of Anaerobic Digestion Materials and Survival in Different Feed Stocks'
Russell L;Whyte P;Zintl A;Gordon S;Markey B;de Waal T;Cummins E;Nolan S;O'Flaherty V;Abram F;Richards K;Fenton O;Bolton D; (2020) 'A Small Study of Bacterial Contamination of Anaerobic Digestion Materials and Survival in Different Feed Stocks'. Bioengineering (Basel, Switzerland), 7 (3) [DOI] [Details]
(2020) 'Landspreading with co-digested cattle slurry, with or without pasteurisation, as a mitigation strategy against pathogen, nutrient and metal contamination associated with untreated slurry'
Nolan, S,Thorn, CE,Ashekuzzaman, SM,Kavanagh, I,Nag, R,Bolton, D,Cummins, E,O'Flaherty, V,Abram, F,Richards, K,Fenton, O (2020) 'Landspreading with co-digested cattle slurry, with or without pasteurisation, as a mitigation strategy against pathogen, nutrient and metal contamination associated with untreated slurry'. Science Of The Total Environment, 744 [DOI] [Details]
(2020) 'Pyrolysed waste materials show potential for remediation of trichloroethylene-contaminated water'
Siggins, A;Abram, F;Healy, MG (2020) 'Pyrolysed waste materials show potential for remediation of trichloroethylene-contaminated water'. Journal Of Hazardous Materials, 390 [DOI] [Details]
(2020) 'Soil prokaryotic community resilience, fungal colonisation and increased cross-domain co-occurrence in response to a plant-growth enhancing organic amendment'
Paula, FS;Tatti, E;Thorn, C;Abram, F;Wilson, J;O'Flaherty, V (2020) 'Soil prokaryotic community resilience, fungal colonisation and increased cross-domain co-occurrence in response to a plant-growth enhancing organic amendment'. Soil Biology & Biochemistry, 149 [DOI] [Details]
(2020) 'Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool'
Waters NR, Abram F, Brennan F, Holmes A, & Pritchard L (2020) 'Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool'. Access Microbiology, [DOI] [Details]
(2020) 'Impact of beef extract used for sample concentration on the detection of Escherichia coli DNA in water samples via qPCR'
Machado-Moreira, B;Monteiro, S;Santos, R;Martinez-Murcia, A;Rajkovic, A;Smigic, N;Richards, KG;Abram, F;Burgess, CM (2020) 'Impact of beef extract used for sample concentration on the detection of Escherichia coli DNA in water samples via qPCR'. Journal Of Microbiological Methods, 168 [DOI] [Details]
(2019) 'The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei'
Paula, FS,Chin, JP,Schnurer, A,Muller, B,Manesiotis, P,Waters, N,Macintosh, KA,Quinn, JP,Connolly, J,Abram, F,McGrath, JW,O'Flaherty, V (2019) 'The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei'. Scientific Reports, 9 [DOI] [Details]
(2019) 'Microbial Contamination of Fresh Produce: What, Where, and How?'
Machado-Moreira B;Richards K;Brennan F;Abram F;Burgess CM; (2019) 'Microbial Contamination of Fresh Produce: What, Where, and How?'. Comprehensive Reviews In Food Science And Food Safety, 18 (6) [DOI] [Details]
(2019) 'Deciphering adaptation through mobile element pangenome composition'
Waters N, Holmes A, Abram F, L Pritchard L, & Brennan F (2019) 'Deciphering adaptation through mobile element pangenome composition'. Access Microbiology, [DOI] [Details]
(2019) 'Chordomics: a visualization tool for linking function to phylogeny in microbiomes'
McDonnell, K;Waters, NR;Howley, E;Abram, F (2019) 'Chordomics: a visualization tool for linking function to phylogeny in microbiomes'. Bioinformatics, 36 :1309-1310 [DOI] [Details]
(2019) 'A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures'
Thorn, CE,Bergesch, C,Joyce, A,Sambrano, G,McDonnell, K,Brennan, F,Heyer, R,Benndorf, D,Abram, F (2019) 'A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures'. Molecular Ecology Resources, 19 :439-455 [DOI] [Details]
(2018) 'Toward Assessing Farm-Based Anaerobic Digestate Public Health Risks: Comparative Investigation With Slurry, Effect of Pasteurization Treatments, and Use of Miniature Bioreactors as Proxies for Pathogen Spiking Trials'
Nolan, S;Waters, NR;Brennan, F;Auer, A;Fenton, O;Richards, K;Bolton, DJ;Pritchard, L;O'Flaherty, V;Abram, F (2018) 'Toward Assessing Farm-Based Anaerobic Digestate Public Health Risks: Comparative Investigation With Slurry, Effect of Pasteurization Treatments, and Use of Miniature Bioreactors as Proxies for Pathogen Spiking Trials'. Frontiers In Sustainable Food Systems, 2 [DOI] [Details]
(2018) 'Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass'
Joyce, A,Ijaz, UZ,Nzeteu, C,Vaughan, A,Shirran, SL,Botting, CH,Quince, C,O'Flaherty, V,Abram, F (2018) 'Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass'. Frontiers In Microbiology, 9 [DOI] [ARAN Link] [Details]
(2018) 'Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system'
Nzeteu, CO,Trego, AC,Abram, F,O'Flaherty, V (2018) 'Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system'. Biotechnology For Biofuels, 11 [DOI] [ARAN Link] [Details]
(2018) 'Absence of Curli in Soil-Persistent Escherichia coli Is Mediated by a C-di-GMP Signaling Defect and Suggests Evidence of Biofilm-Independent Niche Specialization'
Somorin, YM,Vollmerhausen, T,Waters, N,Pritchard, L,Abram, F,Brennan, F,O'Byrne, C (2018) 'Absence of Curli in Soil-Persistent Escherichia coli Is Mediated by a C-di-GMP Signaling Defect and Suggests Evidence of Biofilm-Independent Niche Specialization'. Frontiers In Microbiology, 9 [DOI] [Details]
(2018) 'riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions'
Waters NR, Abram F, Brennan F, Holmes A, Pritchard L (2018) 'riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions'. Nucleic Acids Research, [Details]
(2017) 'Roles for RpoS in survival of Escherichia coli during protozoan predation and in reduced moisture conditions highlight its importance in soil environments'
Somorin, Y,Bouchard, G,Gallagher, J,Abram, F,Brennan, F,O'Byrne, C (2017) 'Roles for RpoS in survival of Escherichia coli during protozoan predation and in reduced moisture conditions highlight its importance in soil environments'. Fems Microbiology Letters, 364 [DOI] [Details]
(2017) 'Agricultural anaerobic digestion power plants in Ireland and Germany: policy and practice'
Auer, A,Burgt, NHV,Abram, F,Barry, G,Fenton, O,Markey, BK,Nolan, S,Richards, K,Bolton, D,De Waal, T,Gordon, SV,O'Flaherty, V,Whyte, P,Zintl, A (2017) 'Agricultural anaerobic digestion power plants in Ireland and Germany: policy and practice'. Journal Of The Science Of Food And Agriculture, 97 :719-723 [DOI] [ARAN Link] [Details]
(2017) 'Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment'
Paula, FS,Tatti, E,Abram, F,Wilson, J,O'Flaherty, V (2017) 'Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment'. Journal Of Environmental Management, 196 :476-486 [DOI] [Details]
(2016) 'The General Stress Response Is Conserved in Long-Term Soil-Persistent Strains of Escherichia coli'
Somorin, Y,Abram, F,Brennan, F,O'Byrne, C (2016) 'The General Stress Response Is Conserved in Long-Term Soil-Persistent Strains of Escherichia coli'. Applied And Environmental Microbiology, 82 :4628-4640 [DOI] [Details]
(2016) 'Comparative Proteomics Implicates a Role for Multiple Secretion Systems in Electrode-Respiring Geobacter sulfurreducens Biofilms'
Kavanagh, P,Botting, CH,Jana, PS,Leech, D,Abram, F (2016) 'Comparative Proteomics Implicates a Role for Multiple Secretion Systems in Electrode-Respiring Geobacter sulfurreducens Biofilms'. Journal Of Proteome Research, 15 :4135-4145 [DOI] [Details]
(2015) 'Systems-based approaches to unravel multi-species microbial community functioning'
Florence Abram (2015) 'Systems-based approaches to unravel multi-species microbial community functioning'. Computational and Structural Biotechnology Journal, 13 :24-32 [ARAN Link] [Details]
(2015) 'Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion'
Gunnigle, E,Nielsen, JL,Fuszard, M,Botting, CH,Sheahan, J,O'Flaherty, V,Abram, F (2015) 'Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion'. Fems Microbiology Ecology, 91 [DOI] [Details]
(2015) 'Low-temperature anaerobic digestion is associated with differential methanogenic protein expression'
Gunnigle, E,Siggins, A,Botting, CH,Fuszard, M,O'Flaherty, V,Abram, F (2015) 'Low-temperature anaerobic digestion is associated with differential methanogenic protein expression'. Fems Microbiology Letters, 362 [DOI] [ARAN Link] [Details]
(2014) 'Adhesive Proteins of Stalked and Acorn Barnacles Display Homology with Low Sequence Similarities'
Jonker, JL,Abram, F,Pires, E,Coelho, AV,Grunwald, I,Power, AM (2014) 'Adhesive Proteins of Stalked and Acorn Barnacles Display Homology with Low Sequence Similarities'. Plos One, 9 (10) [DOI] [Details]
(2013) 'Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistent Escherichia coli'
Brennan, FP,Grant, J,Botting, CH,O'Flaherty, V,Richards, KG,Abram, F (2013) 'Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistent Escherichia coli'. Fems Microbiology Ecology, 84 :75-85 [DOI] [Details]
(2013) 'A Functional Approach To Uncover the Low-Temperature Adaptation Strategies of the Archaeon Methanosarcina barkeri'
Gunnigle, E;McCay, P;Fuszard, M;Botting, CH;Abram, F;O'Flaherty, V (2013) 'A Functional Approach To Uncover the Low-Temperature Adaptation Strategies of the Archaeon Methanosarcina barkeri'. Applied And Environmental Microbiology, 79 :4210-4219 [DOI] [Details]
(2012) 'Exploring mixed microbial community functioning: recent advances in metaproteomics'
Siggins, A., Gunnigle, E., and Abram, F (2012) 'Exploring mixed microbial community functioning: recent advances in metaproteomics'. Fems Microbiology Ecology, [Details]
(2012) 'Impact of Trichloroethylene Exposure on the Microbial Diversity and Protein Expression in Anaerobic Granular Biomass at 37 degrees C and 15 degrees C'
Siggins, A;Enright, AM;Abram, F;Botting, C;O'Flaherty, V (2012) 'Impact of Trichloroethylene Exposure on the Microbial Diversity and Protein Expression in Anaerobic Granular Biomass at 37 degrees C and 15 degrees C'. Archaea-An International Microbiological Journal, [DOI] [ARAN Link] [Details]
(2011) 'A metaproteomic approach gives functional insights into anaerobic digestion'
Abram, F,Enright, AM,O'Reilly, J,Botting, CH,Collins, G,O'Flaherty, V (2011) 'A metaproteomic approach gives functional insights into anaerobic digestion'. Journal Of Applied Microbiology, 110 :1550-1560 [DOI] [Details]
(2010) 'Characterization of Environmentally Persistent Escherichia coli Isolates Leached from an Irish Soil'
Brennan, FP,Abram, F,Chinalia, FA,Richards, KG,O'Flaherty, V (2010) 'Characterization of Environmentally Persistent Escherichia coli Isolates Leached from an Irish Soil'. Applied And Environmental Microbiology, 76 :2175-2180 [DOI] [Details]
(2009) 'Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms'
Abram, F,Gunnigle, E,O'Flaherty, V (2009) 'Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms'. Electrophoresis, 30 :4149-4151 [DOI] [Details]
(2008) 'Proteomic analyses of a Listeria monocytogenes mutant lacking sigma(B) identify new components of the sigma(B) regulon and highlight a role for sigma(B) in the utilization of glycerol'
Abram, F,Wan-Lin, S,Wiedmann, M,Boor, KJ,Coote, P,Botting, C,Karatzas, KAG,O'Byrne, CP (2008) 'Proteomic analyses of a Listeria monocytogenes mutant lacking sigma(B) identify new components of the sigma(B) regulon and highlight a role for sigma(B) in the utilization of glycerol'. Applied And Environmental Microbiology, 74 :594-604 [DOI] [Details]
(2008) 'Identification of Components of the Sigma B Regulon in Listeria monocytogenes That Contribute to Acid and Salt Tolerance'
Abram, F;Starr, E;Karatzas, KAG;Matlawska-Wasowska, K;Boyd, A;Wiedmann, M;Boor, KJ;Connally, D;O'Byrne, CP (2008) 'Identification of Components of the Sigma B Regulon in Listeria monocytogenes That Contribute to Acid and Salt Tolerance'. Applied And Environmental Microbiology, 74 :6848-6858 [DOI] [Details]
(2003) 'Modelling and optimization of inactivation of Lactobacillus plantarum by pulsed electric field treatment'
Abram, F., Smelt, J.P.P.M., Bos, R., and Wouters P.C. (2003) 'Modelling and optimization of inactivation of Lactobacillus plantarum by pulsed electric field treatment'. Journal Of Applied Microbiology, [Details]

Book Chapters

  Year Publication
(2021) 'Evolutionary trade-offs between growth and survival: The delicate balance between reproductive success and longevity in bacteria'
Abram F, T Arcari, D Guerreiro & CP O'Byrne (2021) 'Evolutionary trade-offs between growth and survival: The delicate balance between reproductive success and longevity in bacteria' In: Advances in Microbial Physiology. Amsterdam: Elsevier. [Details]
(2014) 'APPLICATION OF METAPROTEOMICS TO THE EXPLORATION OF MICROBIAL N-CYCLING COMMUNITIES'
Smith C and Abram F (2014) 'APPLICATION OF METAPROTEOMICS TO THE EXPLORATION OF MICROBIAL N-CYCLING COMMUNITIES' In: Metagenomics of the Nitrogen Cycle. uk: Horizon Scientific Press and Caister Academic Press. [Details]
(2013) 'Ecology of Environmental Biofilms'
Gavin Collins, Florence Abram, Therese Mahony, Vincent O’Flaherty, William T. Sloan and Christopher Quince (2013) 'Ecology of Environmental Biofilms' In: Biofilms in Bioengineering. New York, USA: Nova Science Publishers, Inc. [Details]
(2009) 'Ireland's Rural Environment: Research Highlights from Johnstown Castle'
Brennan, F.,O'Flaherty, V. ,Abram, F.,Chinalia, F.A.,Richards, K.,Lalor, S.,O' hUallacháin, D (2009) 'Ireland's Rural Environment: Research Highlights from Johnstown Castle' In: E.coli in Soils: Visitors or Residents?. :40-41 Wexford: Teagasc, Johnstown castle. [Details]
(2009) 'Johnstown Castle Environment Research Centre: Research Report 2008'
Brennan, F.P. ,Chinalia, F.A.,Abram, F.,O’Flaherty, V.,Richards, K (2009) 'Johnstown Castle Environment Research Centre: Research Report 2008' In: Physiological and Molecular Characterisation of Environmentally Persistent E. coli Strains in a Temperate Gley Soil. :51-52 Wexford: Teagasc. [Details]

Editorial

  Year Publication
(2019) Editorial: Using Genomics, Metagenomics and Other Omics to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications.
Marco, DE,Abram, F (2019) Editorial: Using Genomics, Metagenomics and Other Omics to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications. Editorial [DOI] [Details]

Reviews

  Year Publication
(2019) Microbial Contamination of Fresh Produce: What, Where, and How?.
Machado-Moreira, B;Richards, K;Brennan, F;Abram, F;Burgess, CM (2019) Microbial Contamination of Fresh Produce: What, Where, and How?. HOBOKEN: WILEY Reviews [DOI] [Details]
(2015) Systems-based approaches to unravel multi-species microbial community functioning.
Abram, F (2015) Systems-based approaches to unravel multi-species microbial community functioning. Reviews [DOI] [Details]
(2012) Exploring mixed microbial community functioning: recent advances in metaproteomics.
Siggins, A;Gunnigle, E;Abram, F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. OXFORD: OXFORD UNIV PRESS Reviews [DOI] [Details]

Committees

  Committee Function From / To
Microbiology Society - Irish Division Chair Elect 01-JAN-24 /
School of Biological and Chemical Sciences Athena Swan Self Assessment Team Chair 01-SEP-22 /
School of Biological and Chemical Sciences Executive Committee member 01-SEP-22 /
School of Natural Sciences Equality Diversity and Inclusion Chair 01-NOV-18 / 01-SEP-22
College of Science and Engineering EDI committee SNS EDI committee chair 04-JAN-21 /
School of Natural Sciences Athena Swan Self Assessment Team Chair 03-JUN-19 / 01-SEP-22
Academic Council Elected Member 01-JUN-18 / 30-JUN-21
School of Natural Sciences Executive committee EDI committee chair 01-NOV-18 / 01-SEP-22
Microbiology Society Irish Division Committee Member 01-JAN-18 / 31-DEC-23

Employment

  Employer Position From / To
University of Galway Lecturer in Microbiology 01-AUG-13 /
University of Galway Associate Professor 01-OCT-21 /
University of Galway University Fellow (Teaching & Research) in Microbiology 01-AUG-10 / 31-JUL-13
University of Galway Postdoctoral Researcher in Microbiology 01-SEP-07 / 31-JUL-10
Unilog IT Services, Paris, France Computer Programmer 01-SEP-01 / 28-FEB-03
Unilever Research Vlaardingen, The Netherlands Research Microbiologist 03-JAN-00 / 31-AUG-01

Education

  Year Institution Qualification Subject
2013 University of Galway Postgraduate Diploma Academic Practice
2007 University of Galway PhD Microbiology
2000 Wageningen University Msc Biotechnology
1999 Ecole Nationale Superieure d'Agronomie et des Industries Alimentaires Msc Food Technology and Bioprocess Technology

Teaching Interests

I teach Environmental Microbiology, Systems Biology and Biotechnology at the undergraduate and postgraduate level. I hold a Postgraduate Diploma in Academic Practice.

I have supervised/co-supervised to date 1 MSc per research (graduated) and 20 PhD students, including 15 to completion, 2 in final year (Marco Prevedello, and Niranjana Rose Edwin), one in third year (Raffaello Mattiussi), one in second year (Sean Conway)  and one in first year (Sailusha Kuntamukkula).


.

Recent Postgraduate Students

  Graduation Name Degree Primary Supervisor
2023 Kevin McDonnell PhD
2022 Sorcha Kelly PhD
2021 Matthias Waibel PhD Y
2021 Bernardino Moreira PhD Y
2021 Stephen Nolan PhD Y
2020 Nicholas Waters PhD
2018 Paul McAteer PhD
2018 Camilla Thorn PhD Y
2018 Gustavo Sambrano PhD
2017 Yinka Somorin PhD
2017 Nicola Byrne Msc Y
2016 Aoife Joyce PhD Y
2016 Corine Nzeteu PhD
2013 Eoin Gunnigle PhD Y

Current Postgraduate Students (Research)

  Student Degree Type Type
Gaurav Chugh Doctorate - Structured PhD (Science) Supervisor
Sean Conway Doctorate - Structured PhD (Science) Supervisor
Parvin Hasani Zadeh Doctorate - Structured PhD (Science) Supervisor
Niranjana Edwin Doctorate - Structured PhD (Science) Supervisor
Marco Prevedello Doctorate - Structured PhD (Science) Supervisor
Raffaello Mattiussi Doctorate - Structured PhD (Science) Supervisor

Modules Taught

  Term/Year Module Title Module Code Subject / Desc
1st year Biology BO101 Microbiomes
2nd year Microbes and the Environment MI204 Microbes and Disease
3rd year Environmental Microbiology MI322 Molecular Microbiology & Nutrient cycling
3rd year Microbial Metabolic and Molecular. Systems MI326 Horizontal Gene Transfer
4th year Microbial Ecosystems Services & Systems Biology MI4102 Systems Biology
4th year The Meaning of Life: Bioinformatics MI439 Machine Learning in Microbiology
MSc Frontiers in Biotechnology BG5101 Scientific calculations & Research Integrity
MSc Advanced Industrial Processes MI5103 Bioprocess Technology

Internal Collaborators

  Name Description of Collaboration
Prof Vincent O'Flaherty
Environmental biotechnology
Prof Piet Lens
Modelling of agriculture-based anaerobic digestion
Dr Gavin Collins
Environmental Microbiology and Microbiomes
Dr Enda Howley
Machine learning
Prof Mark Healy
Bioremediation
Prof Conor O'Byrne
Soil Escherichia coli
Prof Olivier Thomas
Metabolomics
Prof Donal Leech
Microbial Fuel Cells

External Collaborators

  Name Organisation / Institute Country Description of Collaboration
Prof Christopher Quince Earlham Institute UNITED KINGDOM
Bioinformatics
Dr Umer Ijaz University of Glasgow UNITED KINGDOM
Bioinformatics
Dr Leighton Pritchard University of Strathclyde UNITED KINGDOM
Bioinformatics, statistics, modelling
Dr Johannes Werner University of Tübingen GERMANY
Bioinformatics
Dr Dirk Benndorf Max Planck Institute, Magdeburg GERMANY
Metaproteomics
Dr Catherine Botting University of St Andrews UNITED KINGDOM
Proteomics, metaproteomics
Dr Cyril Jousse Universite Clermont Auvergne FRANCE
Cloud microbiology
Prof John mcGrath Queen's University Belfast UNITED KINGDOM
Microbial polyphosphate metabolism
Dr Eric Paterson James Hutton Institute, Aberdeen UNITED KINGDOM
Soil microbiology
Dr Fiona Brennan Teagasc Johnstown Castle IRELAND
Soil microbiology
Dr Orla O'Sullivan Teagasc Food Research Centre IRELAND
Soil metagenomics
Dr Kaye Burgess Teagasc Ashtown IRELAND
Food pathogens
Dr Karl Richards Teagasc Johnstown Castle IRELAND
Agriculture-based anaerobic digestion
Dr Owen Fenton Teagasc Johnstown Castle IRELAND
Agriculture-based anaerobic digestion