Northwest Microbiology Group
10th Annual Conference 2014
Monday 8thSeptember 2014
MediaCityUK
PROGRAMME
08:30
REGISTRATION
09:30
Welcome and Housekeeping
9.45 - 11:00
Microbial Pathogens
Laura Bricio Moreno
African Streptococcus pneumoniae Serotype-1 in nasopharyngeal carriage
and invasive disease in murine models of infection
Emily Davies
Long-term coevolution of Pseudomonas aeruginosa and temperate
bacteriophages in artificial sputum
David Williams
Population structure of P. aeruginosa during chronic infections of the
airways of cystic fibrosis patients inferred by whole genome sequencing
Jessica Hall
Exploring the spatial and temporal variations in Borreliaburgdorferi in
Ixodesricinus in north west England
Claire Scantlebury
Tackling Epizootic Lymphangitis in Horses; new approaches to aid detection
of Histoplasmacapsulatumvarfarciminosum direct from equine clinical samples
11-11:45
COFFEE BREAK
11:45-1:00
Host-pathogen Interactions
Jane King
Heterogeneous expression of capsule by uropathogenicEscherichia coli a fitness strategy?
Yvette Merga
A sticky business: Adherent, Invasive E. coli in Crohn’s Disease
Carsten Kröger
An Infection-Relevant Transcriptomic Compendium for Salmonella enterica
serovarTyphimurium
Shabarinath
Srikumar
Chloe James
Chair: Prof Richard Birtles
Chair: Dr Nicky High
The primary transcriptome of Salmonella Typhimurium within macrophages
identifies a genus specific sRNA that controls acid resistance and virulence
Deborah Cantu
The Campylobacter jejuniglpTpseudogene encodes a functional protein
required for the utilisation of 3-phosphoglycerate
Suzanna Gore
Augmented passive immunotherapy for the treatment of severe bacterial
infections.
1:00-2:15
LUNCH
2:15 - 3:30:
Microbial Community Analysis
Chair: Prof Alan McCarthy
Tracy Perkins
The role of estuarine sediments as a reservoir for pathogenic microorganisms
Ashley Houlden
Brain Injury induces specific changes in the caecalmircoflora of mice
Ryan Joynson
Metagenomic analysis of the gut microbiome of the common black slug
Arionater in search of novel lignocellulose degrading enzymes
Anshul Gupta
Metagenomic and metatranscriptomic analysis of cellulose degradation in
Landfill
Emma Ransom-Jones
Characterising the oak microbiome; towards an understanding of Acute
Oak Decline
3:30 - 4:30
TEA BREAK and SCIENCE CAKES
4:30 - 5:15
Steve DiggleKeynote speech: “Cooperation and conflict in bacterial populations”
5:15 - 5:30
Prizes and close
5:30 - 6:30
WINE RECEPTION
ABSTRACTS FOR ORAL PRESENTATIONS
Session 1: Microbial Pathogens
African Streptococcus pneumoniae Serotype-1 in nasopharyngeal carriage
and invasive disease in murine models of infection
Laura Bricio-Moreno
University of Liverpool
Streptococcus pneumoniae is a common inhabitant of the nasopharynx of healthy individuals but
can also cause serious diseases such as pneumonia, meningitis and septicaemia in children, the elderly
and the immuno-compromised. Pneumococcal serotype-1 is one of the main causes of invasive
pneumococcal disease in sub-Saharan Africa, but unlike other serotypes, it is rarely found in carriage. The
first aim of this study is to understand whether African serotype-1 isolates carry in the nasopharynx and if
they do so how they interact with host immunity during carriage, whilst the second aim is to understand
how African serotype-1 isolates progress into invasive pneumococcal disease. Serotpye-1 exhibits
geographically distinct clonal populations. For that reason we have used isolates from Malawi and the
Gambia, as well as different sequence types to analyse the overall in vivo dynamics of serotype-1
Long-term coevolution of Pseudomonas aeruginosa and temperate
bacteriophages in artificial sputum
E. V. Davies1,2, C. E. James3, M. A. Brockhurst4, S. Haldenby2, S. Paterson2& C. Winstanley1.
Institute of Infection and Global Health, University of Liverpool; 2Institute of Integrative Biology, University of
Liverpool; 3School of Environment and Life Sciences, University of Salford; 4Department of Biology, University of
York.
1
Pseudomonas aeruginosa is capable of causing chronic lung infections in individuals affected
with Cystic Fibrosis (CF), that once established are almost impossible to eradicate. Over time, P.
aeruginosa adapts to the unique CF lung environment and undergoes extensive diversification, yet the
factors driving this remain incompletely understood. The Liverpool Epidemic Strain (LES) is a
particularly virulent and transmissible strain that is notable for the presence of multiple prophages, of
which several have been implicated in the in vivo competitiveness of the strain. Bacteriophages are known
to drive bacterial diversification, but the role they play in the evolution of P. aeruginosa populations is
unclear. We took an experimental evolution approach by constructing a model of chronic CF infection,
coevolving the well-characterised reference strain PAO1 with three LES phages in Artificial Sputum
Media (ASM) for 240 bacterial generations. Multiple isolates were selected from each endpoint
population and subjected to phenotypic characterisation and pooled for sequencing, allowing for a
comparison of intrapopulation diversity and evolution in the presence or absence of phages. We identified
genetic changes common to chronic CF isolates, as well as evidence of phage-driven adaptation to the
artificial sputum environment.
Population structure of Pseudomonasaeruginosa during chronic
infections of the airways of cystic fibrosis patients inferred by whole genome
sequencing
David Williams1, Benjamin Evans1,2, Sam Haldenby1, Martin J. Walshaw3, Michael A. Brockhurst4, Craig
Winstanley5, Steve Paterson1
1
Institute of Integrative Biology, University of Liverpool, 2Department of Life Sciences, Anglia Ruskin University,
3
Liverpool Heart and Chest Hospital NHS Foundation Trust, 4 Department of Biology, University of York, 5Institute
of Infection and Global Health, University of Liverpool
Pseudomonas aeruginosa are the predominant cause of recalcitrant infections of the mucus-rich
airways of individuals with cystic fibrosis. These infections are characterised by acute and chronic stages
leading to high rates of morbidity and mortality but little is known about population-level diversity and its
potential contribution to clinical outcomes. We examined the diversity within sets of 40 Liverpool
Epidemic Strain P. aeruginosa isolate genome sequences, mostly pooled, from numerous sputum samples
to infer population structure and evolutionary processes within infections.
A prevalence of genetically distinct but co-existing P. aeruginosa lineages among sputum
samples from nine CF patients is evident from population-level comparisons of genome sequences.
Reconstruction of the genealogy of these well-defined sub-populations reveals distinct origins and a
complex history of transmissions affecting the sampled patients.
Previous reports have demonstrated the transmissability of P. aeruginosa among CF patients and
the ability of the pathogens to displace each other during the course of a chronic infection. The coexistence of genetically distinct populations within individual patients revealed by our population-level
analysis is consistent with newly acquired P. aeruginosa infections persisting with previously contracted
infections within the airway of a patient.
Exploring the spatial and temporal variations in
BorreliaburgdorferiinIxodesricinus in north west England
Jessica Hall
University of Salford
Borreliaburgdorferisensulato (s.l.) group of spirochetes are the causative agents of the ticktransmitted zoonosis Lyme borreliosis, of which an estimated 3000 cases occur annually in the UK.
Ixodesricinus is the principal vector of B. burgdorferis.l. in the United Kingdom, and this tick species is
widely distributed across the country. The main aim of this project was to investigate the temporal and
spatial dynamics of B. burgdorferi populations in Ixodesricinusin Cumbria. Questing Ixodesricinus ticks
were collected at 3 sites in southern Cumbria every four weeks and tested for the presence of B.
burgdorferigenospecies using realtime PCR and reverse line blot analysis. The prevalence of B.
burgdorferi infections in ticks at each site ranged from 0.0% to 14.03%. Four genospecies, B. afzelii, B.
burgdorferisensustricto, B. garinii and B. valaisiana, were detected across the region although the
contribution that each genospecies made to the borrelial population at each site varied markedly. To
assess the public health impact a questionnaire was sent to GP’s in the areas to quantify the cases of LB
around the survey site in the last three years the data showed that 59 cases of LB had been diagnosed, 84
cases of LB were suspected and over 295 ticks had been removed from patients. B. burgdorferis.l. appears
to be a threat to public health in the southern Cumbria area.
Tackling Epizootic Lymphangitis in horses;
new approaches for a neglected disease with major welfare and social impact.
C.E. Scantleburya, G.L. Pinchbeckb, R.M. Christleyb, A.P. Stringerc, N. Aklilud, T. Ashined, P. Loughnanea, L.
Gordona, A.J. McCarthya.
a
Institute of Integrative Biology, University of Liverpool,b Institute of infection and global health, University of
Liverpool, Leahurst,c SPANA UK, London,d SPANA Ethiopia, College of Veterinary Medicine and Agriculture,
Addis Ababa University,
Epizootic Lymphangitis (EZL) caused by Histoplasmacapsulatum var. farciminosum (HCF), is
endemic within Ethiopia. Despite its high prevalence, EZL is under-researched and disease control
strategies are limited. This project aimed to develop rapid methods for diagnosing EZL to facilitate future
studies.
Blood samples and pus aspirates were obtained from 29 horses with suspected EZL from several regions
of Ethiopia. DNA extracts were prepared using a commercial kit. Blood was also collected from 20 horses
with no EZL lesions. Aliquots of blood and heat-treated pus were inoculated onto Whatman FTA cards. A
nested PCR targeting the ITS region was used to identify HCF.
Twenty-six of 29 horses with suspected EZL were confirmed by DNA sequencing of amplimers. To date,
9 blood samples have also been confirmed positive. Bioinfomatic analysis will explore diversity among
the samples and examine correlations with clinical data. The performance of the PCR between clinically
suspected and unaffected horses will also be reported.
These findings demonstrate the use of PCR to diagnose HCF directly from equine samples. Whatman
FTA technology was successfully adapted for use with equine pus and allowed downstream molecular
analyses. The identification of HCF in blood warrants further investigation of the organism’s
pathogenicity in horses.
Session 2: Host-pathogen Interactions
Heterogeneous expression of capsule by uropathogenicEscherichia coli - a
fitness strategy?
Jane King
University of Manchester
UropathogenicEscherichia coli (UPEC) are the predominant cause of urinary tract infections. The
K1 polysaccharide capsule on the surface of UPEC strain UTI89 is a key virulence factor and evidence
suggests its expression may be regulated both spatially and temporally during UTI. We sought to follow
capsule gene expression during UTI from extracellular growth in urine to intracellular growth in bladder
epithelial cells using a green fluorescent protein (gfp) fusion to the capsule gene promoter. We found
there is an average down regulation of capsule expression in urine compared to growth in rich media
(LB), but when examined at the single cell level, in both media, the capsule genes appear to be expressed
in a non-uniform manner. Using anti-K1 antibody we show this heterogeneity in gene expression is
reflected on the cell surface where phenotypic diversity of capsule is observed. In fact around 4% of
UTI89 routinely appear un-encapsulated in urine (1% in LB) and we present evidence that these capsule
minus bacteria are the initial colonizers both in a biofilm model and to bladder epithelial cells. We
propose that this physiological diversity in capsule ensures that at least some of the bacterial cells have
the appropriate phenotype under a given environment hence increasing the strain’s fitness during UTI.
A Sticky Business: Adherent, Invasive E. coli in Crohn’s Disease
Yvette Merga
Department of Gastroenterology, Institute of Translational Medicine, University of Liverpool
Crohn’s disease (CD) is a painful and debilitating inflammatory disease of the gastrointestinal
tract, affecting ~1 in 650 people in the UK. Thought to be caused by a combination of environmental,
immunological and host genetic factors, CD is characterised by granulomatous lesions in the gut mucosa
and dysbiosis (imbalance of the gut microbiota); specifically a reduction in Firmicutes and overabundance of Proteobacteria, particularly increased numbers of adherent, invasive E. coli (AIEC).
Whilstlacking key virulence genes characteristic of diarrhoeagenicE. coli, isolates from CD patients
promote inflammation, invade the epithelium and possess the ability to survive and replicate within
mucosal macrophages. Isolates also form granulomas in vitro characteristic of early Crohn’s lesions.
The portal of entry across the gut mucosa is through specialised microfold (M)-cells of the follicleassociated epithelium overlying Peyer’s patches in the ileum and lymphoid follicles in the colon. The
interaction of AIEC with M cells is dependent on possession of long polar fimbriae (Lpf). However,
receptors for AIEC Lpf remain a mystery. I aim to identify Crohn’s AIEC Lpf interactions with M cells
using extracted intestinal glycolipids/proteins, bacterial overlay assays and mass spectrometry. Blockade
of bacterial entry via M-cells represents an important potential target for Crohn's therapies.
An Infection-Relevant Transcriptomic Compendium for Salmonella
entericaserovarTyphimurium
Carsten Kröger1,4, Aoife Colgan1, Shabarinath Srikumar1, Kristian Händler1, Sathesh K. Sivasankaran1, Disa L.
Hammarlöf4, Rocío Canals4, Joe E. Grissom2, Tyrrell Conway2, Karsten Hokamp3 and Jay C. D. Hinton1,4
1
Moyne Institute of Preventive Medicine, Trinity College Dublin, 2Department of Microbiology and Plant Biology,
University of Oklahoma, USA, 3Smurfit Institute of Genetics, Trinity College Dublin,
4
Institute of Integrative Biology, University of Liverpool UK.
The advent RNA-sequencing allows bacterial transcription to be studied at the level of the
individual nucleotide in the context of the millions of nucleotides that comprise the genome. Because
bacterial gene expression is remarkably sensitive to environmental conditions, we combined information
from bacteria exposed to multiple environmental factors to gain a complete picture of the transcriptome.
We devised a suite of 22 infection-relevant growth conditions that stimulate characteristic expression
profiles of the Salmonella entericaserovarTyphimuriumvirulence. Overall, the suite of conditions induced
the transcription of 86% of S.Typhimurium genes [1].
The differential RNA-seqtranscriptomic approach has recently facilitated the large-scale
identification of bacterial small RNAs and promoters [2,3]. We present a new simplified approach for
global promoter and small RNA identification that identified the majority of bacterial promoters and
sRNAs in just two RNA-seq experiments. This global approach revealed that transcription of the majority
of the 3825 S. Typhimurium promoters is environmentally-responsive and the expression patterns of 280
sRNAs which we analysed in the context of their chromosome localisation and Hfq-association. The
levels of environmentally-controlled expression of every coding gene and sRNA of S. Typhimurium are
now available as an online resource for the research community.
[1] Krögeret al. (2013) Cell Host Microbe. 14:683-95
[2] Sharma et al. (2010) Nature. 464:250-5
[3] Krögeret al. (2012) PNAS. 109:E1277-86
The primary transcriptome of Salmonella Typhimurium within macrophages
identifies STnc1850, a genus specific sRNA that controls acid resistance and
virulence
Shabarinath Srikumar1,2, Carsten Kröger1,2, Magali Hébrard1, Aoife Colgan1, Michael Beckett1, Laura Luque1, Lu
Wang3, Sathesh K Sivasankaran1, Katie Breen1, Daoguo Zhou3, Andrew D. S. Cameron4, Karsten Hokamp1, Jay C.
D. Hinton1, 2 #
1
2
Moyne Institute of Preventive Medicine, Ireland. University of Liverpool, UK. 3Purdue University, West Lafayette,
USA.4University of Regina, Saskatchewan, Canada.
Salmonella enterica is the best-studied bacterial pathogen, but crucial details about the genetic
programs it uses to persist in macrophage have remained obscure due to the difficulty of studying
intracellular pathogens. Here we report the first use of deep sequencing of cDNA (RNA-seq) to
interrogate the transcriptional architecture and gene activity of Salmonella in macrophage, thus providing
unprecedented insight into the strategies used by the pathogen to survive in the very immune cells that
seek to destroy it.Analysis of the gene expression of 282 S. Typhimurium small RNAs showed that, a
novel Salmonella specific sRNA, STnc1850, is required for macrophage survival and mouse infection; by
modulating acid resistance and persister formation. We identified 31 S. Typhimurium genes that are
strongly induced inside macrophage but are expressed at low levels in diverse in vitro conditions. We also
characterized 3583 transcriptional start sites that are active within macrophages and 11 of these are
excellent candidates for the delivery of heterologous antigens from Salmonella vaccine strains.
The Campylobacter jejuniglpTpseudogene encodes a functional
proteinrequired for the utilisation of 3-phosphoglycerate
Deborah Cantu
University of Manchester
Campylobacter jejuni is the most common bacterial cause of gastrointestinal illness worldwide.
Despite of its importance, the exact nutritional and metabolic requirements for this pathogen remain
poorly understood. The current knowledge of C. jejuni metabolism indicates that it lacks enzymes and
transporters needed to metabolize glucose and galactose via the glycolytic pathway thought it may utilize
other energy sources such as 3-phosphoglycerate which requires only the lower part of the glycolytic
pathway. Recently the C. jejuni adhesin PEB3 was shown to bind 3-phosphoglycerate (3PG) and this
protein was necessary for 3-PG dependent growth promotion. The exact role of PEB3 in utilisation of 3PG was not defined. Intriguingly the peb3 gene is located adjacent to a glpT gene that encodes a putative
phosphoglycerate transporter however, at least in strain NCTC 11168, this is designated as a pseudogene.
In this study we investigated the role of peb3 and glpT and identified two independent phenotypes, the
ability to utilise 3PG for growth and sensitivity to fosfomycin, that require glpT but not peb3. Our
findings therefore show that the NCTC 11168 glpTpseudogene despite containing two frameshift
mutations has the capacity to encode a functional protein.
Augmented passive immunotherapy for the treatment of severe bacterial
infections.
S. Gore1, B. Morton2, D. Neill1, M. Bangert1, 2, G. Rajam3, E. Ades3, S. Gordon2, A. Kadioglu1.
Institute of Infection and Global Health, University of Liverpool; 2Respiratory Infection Group, Liverpool School of
Tropical Medicine; 3Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
1
Background: Antibacterial resistance is increasing and novel therapeutic strategies are urgently
needed for the treatment of severe bacterial infections. One strategy that has shown much promise is P4
peptide therapy. P4 peptide increases expression of Fcγ receptors on phagocytes leading to a significant
increase in opsonophagocytosis of the pathogen when combined with pathogen specific antibody. In
animal models of pneumococcal pneumonia, treatment with P4 peptide therapy resulted in increased
survival and prevented progression to sepsis.This project goes on to look at the efficacy of P4 treatment
against Gram-negative infections and ex vivo assessment of P4 efficacy in a cohort of ICU patient.
Methods: P4 peptide efficacy was assessed through murine models of acute infection and
opsonophagocytosis killing assays with neutrophils isolated from patients admitted to ICU with
community-acquired pneumonia.
Results: In murine models co-administration of the P4 peptide with antibiotics increased 24 hour survival
from 10% to 60% and increased 7 day survival from 20% to 70% when compared with antibiotic
treatment alone for E.coli and K. pneumoniae respectively. Ex vivo treatment of neutrophils from
community-acquired pneumonia patients with P4 peptide resulted in 65% of patients displaying an
increase in phagocytosis with 50% of those patients showing an increase in phagocytosis of more than 2
fold.
Conclusion: P4 peptide therapy significantly increased both survival in murine models and phagocytic
killing in patients with severe community-acquired pneumonia. This novel adjunct therapy specifically
boosts the host innate immune response to infection, enhancing bacterial killing and has potential as a
future treatment.
Session 3: Microbial Community Analysis
The role of estuarine sediments as a reservoir for pathogenic microorganisms
Tracy Perkins
University of Bangor
Using both culturable and molecular methods to determine the abundance and spatial variation of
microbial pathogens in relation to sediment composition within an estuarine environment.
Microbial pathogens present in faecal matter can contaminate estuarine environments via a
number of point and diffuse sources. Once in the water column attachment of bacteria to suspended
particles can facilitate their settling into sediments, which can enhance their survival. Estuarine sediments
represent a significant reservoir for pathogenic bacteria and resuspension under certain hydrodynamic
conditions can transport microbial contaminants throughout the estuary and to any surrounding beaches
and/or shellfish harvesting waters, therefore posing a risk to human health. This study determined the
abundance of culturableE. coli, total coliforms, enterococci, Salmonella, Campylobacter and Vibrio spp.
(used as proxies for pathogen abundance and described as pathogen indicator bacteria (PIB)) in relation to
sediment composition (e.g. particle grain size and organic matter content) in the Conwy estuary.
Significant positive correlations were found between all cultured bacterial groups and sediments that
contained higher silt and clay and organic matter content, revealing spatial “hotspots” of contamination.
The average abundance of E. coli, coliform and Vibrio spp. (colony forming units (CFU)/100g) in
sediments was 281, 433 and 58-fold greater than in the overlying water column (CFU/100ml)
respectively. To ascertain if PIB are suitable proxies for the behavior of actual pathogenic bacteria within
sediments, the enumeration and detection of specific bacterial pathogen groups and their virulence factors
were determined by the use of both end-point and quantitative PCR techniques. Estuarine environments
can provide a wealth of ecosystem services such as food and recreation, the identification of pathogenic
bacterial hotspots within estuarine sediments has implications for water quality and subsequently human
health. The results of this investigation suggest that the composition of estuarine sediments and the
geomorphology can be used as a predictor to model potential hotspots of pathogen contamination. In
addition, the data has important implications for the modelling and prediction of human health risk in
relation to sediment transport and resuspension.
Brain Injury induces specific changes in the caecalmircoflora of mice
Ashley Houlden,Marie Goldrick, David Brough, SzilveszterVizi, BernadettMartinecz , Adam Denes, Ian Roberts
University of Manchester
Intestinal microbiota have a critical impact on health with changes associated with a diverse range
of human diseases. Recent research suggests that an altered intestinal microbiota can also profoundly
affect brain function. However, whether altering brain function directly affects the microbiota is not
known. In this study we tested the hypothesis that a loss of brain function, caused by experimental stroke,
induced changes in the intestinal microbiota. We report that in mice, experimental stroke altered the
composition of the microbiota in the large intestine with specific changes seen in Peptococcaceae and
Prevotellaceace families. Correlations with the scale of the change in these organisms, the extent of injury
were also evident. In addition, we show that brain injury increases the level of noradrenaline in the caecal
tissue as a consequence of release from host sympathetic nerves in the caecum. Although the changes in
the levels of Peptococcaceae and Prevotellaceace in the caecum were directly correlated with the level of
noradrenaline, the effect of noradrenaline on these genera was likely to be indirect. It is likely that
coordinated changes in intestinal microbiota after stroke may shape an organism's recovery, or their
behaviour post injury.
Metagenomic analysis of the gut microbiome of the common black slug
Arionater in search of novel lignocellulose degrading enzymes
R.E. Joynson1, E. Osemwekha1, D.M. Wood2, N. Ferry1
University of Salford, UK; 2 University of Durham, UK
1
There is increasing pressure on the global community to lower CO2 emissions, mainly through
adopting more sustainable energy sources. Bioethanol derived from lignocellulose is considered to be one
of the most promising direct liquid fossil fuel replacements. Cellulose is the most abundant organic
compound on the planet, making up approximately 33% of all plant matter making it a logical and
sustainable feedstock for bioethanol production. However, lack of adequate carbohydrate active enzymes
(CAZymes) has hindered the necessary feedstock transition. Many organisms have overcome the
difficulties of lignocellulose breakdown, some having adopted it as their sole source of carbon.
Using Illumina sequencing technology we carried out a metagenomic study of the gut microbiome of the
gastropod Arionater, a plant eating pest species, focusing on identification of novel CAZymes. Firstly gut
cellulolytic activity was confirmed using zymography and microbial growth plate assays. Gut microbial
metagenomic DNA was then extracted, sequenced and de novo assembly of the resultant 26,046,645
250bp pair-end reads (totalling 5.8 Gbp) was carried out. Following assembly 108,691 open reading
frames were predicted and annotated against the NCBI non-redundant protein database and the PfamA
database.
Functional analysis revealed more than 3000 gylcoside hydrolase (GH) domains and
carbohydrate binding modules (CBM). Of these ~46% are thought to be involved in the breakdown of
plant cell wall components with the greatest number targeting hemicellulose and oligosaccharides. 322 of
these genes belonged to GH groups targeting long chain hemicellulose and 366 to groups which target the
resultant partially digested hemicellulose oligosaccharides. Multiple genes were also identified that target
cellulose and pectin suggesting full utilisation of each carbohydrate component of lignocellulose by
Arionater. This research demonstrates the untapped potential of organisms in groups such as the
gastropods as treasure troves of novel lignocellulose degrading enzymes for the biofuel industry.
Metagenomic and metatranscriptomic analysis of cellulose degradation in
landfill
Anshul Gupta
University of Liverpool
Anaerobic microbial communities that degrade cellulose are structurally and metabolically
complex, and studies addressing the abundance and relative activity of their constituent microbial groups
have mainly focussed on the herbivore gut. As a consequence, relatively unexplored anoxic environments
such as landfill sites can be viewed as a potential reservoir of novel cellulolytic agents. For example,
previous studies conducted in our lab have detected cellulose-degrading relatives of the bacterial genus
Fibrobacter and the fungal genus Neocallimastigales in landfill leachate, species of which were
previously thought to be obligate gut inhabitants. High-throughput sequencing of metagenomes and
metatranscriptomes enables the analysis of these diverse microbial communities that are rich in
uncultivable species, whilst overcoming the bias associated with the use of amplicon clone libraries to
determine diversity and relative abundances. Gene mining for novel polysaccharide hydrolases, including
cellulases, is also a core objective of this research. We are currently investigating the metatranscriptome
and metagenome of cellulose biofilms recovered from landfill leachate microcosms. A fosmid DNA
library has also been generated from parallel samples and is screened for cellulase-encoding genes using
primers designed from the metatranscriptomic data alongside conventional expression screens.
Proteobacteria, Firmicutes and Euryarchaeota are the predominant phyla in the landfill cellulose
metatranscriptome, where >1,700 predicted ORFs matched glycosyl hydrolases involved in
polysaccharide degradation. Apart from improving our understanding of cellulose degradation in anoxic
environments, novel cellulases have commercial significance in biomass processing including production
of second-generation biofuels.
Characterising the oak microbiome; towards an understanding of Acute Oak
Decline
Emma Ransom-Jones1, Sandra Denman2 and James E. McDonald1
School of Biological Sciences, Bangor University, Deiniol Road, Bangor,
2
Forest Research,Alice Holt Lodge, Gravel Hill Road, Farnham, GU10 4LH, UK
1
Acute Oak Decline (AOD) affects native oaks in the UK and is identified by the presence of
visible stem bleeds that overlie areas of necrotic tissue. Larvae of the buprestid beetle Agrilusbiguttatus
and two putative bacterial pathogens (Gibbsiellaquercinecans and Brenneriagoodwinii) are consistently
associated with necrotic tissue in AOD-affected trees; however, their role in this syndrome is poorly
understood. Microbiome studies are therefore necessary to gain a greater understanding of the structure
and function of microbial communities associated with healthy and AOD-affected trees. However, these
studies have been hindered by the dominance of oak nucleic acids in metagenomic DNA extracts. Here,
we optimised the extraction and enrichment of microbial DNA from oak tissue samples in order to
generate metagenome profiles of the microbiome associated with both healthy and AOD-affected oak
trees at various stages of the syndrome. CpG-methylated oak DNA was removed from total DNA extracts
using an NEB microbiome DNA enrichment kit, with qPCR demonstrating a 1020 fold enrichment of
microbial DNA. In addition, we sequenced the total metatranscriptome (rRNA and mRNA) of the
microbiome associated with necrotic lesions on AOD affected trees. These data provide important
insights into the role of the oak microbiome in AOD.
POSTERS
1 AshwagShami
Compartive genomics of animal E. faecium
2 EmanAlshehri
Comparative and functional genomic analysis of Toxoplasma gondii
3 Christina Bronowski
Campylobacter Population Diversity in the Farm Environment
4 Reham Yahya
Phenotypic characterisation of European sequence types of Streptococcus
pneumoniae Serotype-1
5 Ian Goodhead
Comparative genomics and transcriptomics of Sodalisglossinidius, a secondary
endosymbiont of the tsetse fly
6 Matthew Moore
Clinical Exploitation of Pseudomonas International Genomics Consortium Data.
7 Gemma Wattret
Exploring genetic diversity of the PorA gene in Campylobacter jejuni and
Campylobacter coli from poultry in Kenya
8 Laura Campbell
T. spiralis infection induces microbiome changes at various mucosal sites
9 White Emily
A metagenomic approach to understanding parasite interactions withthe
gut microbiome
10 Nicholas Ellaby
The Dove Project: Analysis of Faecal Volatile Organic Compounds & 16S rRNA
contentin Preterm Infants WhoDevelop Necrotising Enterocolitis inthe UK.
11 Katie Muddiman
Copper homeostasis in the food-borne pathogen Salmonella Typhimurium
12 RoobinideviRagupathy
Characterisation of the roles of SstR and SstA in the food-borne pathogen
Salmonella Typhimurium
13 Helen Jesse
Two Zinc Uptake Systems Contribute to the Full Virulence of Listeria
monocytogenes during Growth In Vitro and In Vivo
14 Paz Aranega-Bou
The role of microbial communities in the water survival of Campylobacter
jejuni
15 Amy Wedley
Campylobacter on the dairy farm.
16 Elli Wright
Survival of Campylobacter in the Poultry Farm Environment
17 Sian Owen
RNA-seq resolves the activity of temperate bacteriophages within the genome
of an invasive Salmonella Typhimurium isolate
18 Hasan AalOwaif
Regulation of Capsular Polysaccharide Expression of E. coli
19 Stuart McEwen
Phage-mediated dissemination of Shiga toxin genes via conserved host
protein, BamA
20 Bradley Meehan
Investigating bacteria-induced Wnt signalling as a mechanism for
malignant development in the colon.
21 Nor AiniLubisMhd Zain
Understanding the importance of nrgAB uptake system of L. monocytogenes
in different environments.
22 HeshamMalak
The role of the pneumococcal toxin pneumolysin during nasopharyngeal
colonisation
23 Laura Jacques
Investigating the role of Streptococcus pneumoniaeserotype 1 polysaccharide
capsule in carriage and invasive disease
24 Marie Yang
Elucidation of the pathogenesis of pneumococcal meningitis in a nasopharynxto-meninges translocation mouse model
25 Ashraf Elgallali
Characterisation of lipoproteins in Staphylococcus aureus.
26 Sari Alhoufie
Observation of the global transcriptional alteration in Staphylococcus aureus
during stringent response by next generation sequencing(RNA-seq).
27 MunirahAldayel
Staphylococcus aureus survival mechanism of skin antimicrobial
28 Lauren Perrin
Investigating the role of the European badger (Melesmeles) in
the ecology of Lyme Disease in the UK
29 Hannah Simpson
Do soluble plantain fibres inhibit Clostridium difficile (bacterium, spores, toxin)
interactions with intestinal epithelial cells?
30 Lizeth Lacharme-Lora
The effects of B lymphocyte depletion on Campylobacter colonisation in the chicken
31 Nike Adeyemi
Potato Extract: A potential treatment for H. pyloriinfection
32 Danielle Weaver
Investigating the use of N-linked glycans as targets for antibody-based detection of
Campylobacter
33 Anjeet Jhutty
Development of molecular biological methods for detecting bacterial
contamination
34 Stewart Barker
Rifampicin-loaded sol-gel coatings for orthopaedic prosthetics
DELEGATES
UNIVERSITY OF BANGOR
MacDonald
James
Perkins
Tracy
Ransom-Jones
Emma
UNIVERSITY OF
BOLTON
Jonathan
Thomas
j.mcdonald@bangor.ac.uk
tracy.perkins@bangor.ac.uk
e.ransom-jones@bangor.ac.uk
j.thomas@bolton.ac.uk
UNIVERSITY OF CENTRAL LANCASHIRE
Phillips-Jones
Mary
McShane
Laura
MPhillips-Jones@uclan.ac.uk
LMcShane1@uclan.ac.uk
UNIVERSITY OF LANCASTER
Dillon
Rod
Dowd
Sarah
Gatherer
Derek
r.dillon@lancaster.ac.uk
s.dowd@lancaster.ac.uk
d.gatherer@lancaster.ac.uk
UNIVERSITY OF LIVERPOOL
Ahmed
Muhammad
Aldayel
Munirah
Allison
Heather
Alshehri
Eman
Bricio Moreno
Laura
Bronowski
Christina
Campbell
Barry
Canals Alvarez
Rocio
Chaloner
Gemma
Coates
Rosanna
Cowley
Gwen
Darby
Alistair
Davies
Emily
Dillon
Vivian
Ellaby
Nicholas
Fothergill
Jo
Gill
Christina
Goodhead
Ian
Goodman
Sean
Gordon
Lauren
Gore
Suzanna
Gupta
Anshul
Hall
Amanda
mahmed@liverpool.ac.uk
muni1234@liv.ac.uk
hallison@liv.ac.uk
E.A.Alshehri@liverpool.ac.uk
lbricio@liv.ac.uk
C.Bronowski@liverpool.ac.uk
bjcampbl@liv.ac.uk
R.Canals-Alvarez@liverpool.ac.uk
g.chaloner@liv.ac.uk
Rosanna.Coates@liv.ac.uk
G.Cowley@liv.ac.uk
Alistair.Darby@liv.ac.uk
md0u738c@liv.ac.uk
V.M.Dillon@Liverpool.ac.uk
nfellaby@gmail.com
j.fothergill@liv.ac.uk
Cgill@liv.ac.uk
Ian.Goodhead@liverpool.ac.uk
seanyg@liverpool.ac.uk
laurengordon18@yahoo.com
sgore@liv.ac.uk
bs0u81a2@liverpool.ac.uk
mandyh@liv.ac.uk
Hinton
Jaques
Jhutty
Kadioglu
Kröger
Lacharme-Lora
Lewanczyk
Loughnane
Mahalhal
Malak
McCarthy
McEwen
Meehan
Merga
Mohaisen
Moore
Neill
Nubgan
Ormandy
Owen
Parsons
Pinchbeck
Pongchaikul
Pybus
Scantlebury
Shami
Simpson
Srikumar
Veses Garcia
Wedley
Williams
Williams
Winstanley
Wright
Yahya
Yang
Jay
Laura
Anjeet
Aras
Carsten
Lizeth
Milena
Paul
Awad
Hesham
Alan
Stuart
Bradley
Yvette
Mohammed
Matthew
Daniel
Amer
Emma
Sian
Bryony
Gina
Pisut
Simon
Claire
Ashwag
Hannah
Shabarinath
Marta
Amy
David
Nicola
Craig
Elli
Reham
Marie
Jay.Hinton@liverpool.ac.uk
ljacques@liv.ac.uk
a.jhutty@liverpool.ac.uk
a.kadioglu@liv.ac.uk
carsten.kroger@liv.ac.uk
lacharme@liverpool.ac.uk
M.Lewanczyk@liverpool.ac.uk
jpl@liv.ac.uk
mahalhal@liv.ac.uk
hm168@liverpool.ac.uk
aj55m@liverpool.ac.uk
s.mcewen@liv.ac.uk
bradley.meehan@live.co.uk
Y.Sloane@liverpool.ac.uk
hsmmohai@liv.ac.uk
moorem@liverpool.ac.uk
d.neill@liv.ac.uk
a.s.nubgan@Liv.ac.uk
e.e.ormandy@liverpool.ac.uk
sian.owen@liverpool.ac.uk
bparsons@liv.ac.uk
ginap@liv.ac.uk
P.Pongchaikul@liv.ac.uk
S.pybus@liv.ac.uk
claire.scantlebury@liv.ac.uk
ashwag@liverpool.ac.uk
h.simpson@liv.ac.uk
S.Srikumar@liverpool.ac.uk]
martavg@liverpool.ac.uk
a.l.wedley@liverpool.ac.uk
david.williams@liv.d-dub.org.uk
njwillms@liv.ac.uk
C.Winstanley@liv.ac.uk
ewright@liv.ac.uk
R.Yahya@liv.ac.uk
Marie.Yang@liv.ac.uk
LIVERPOOL JOHN MOORES UNIVERSITY
Hobbs
Glyn
Nakouti
Ismini
Smith
Emily
g.hobbs@ljmu.ac.uk
i.nakouti@ljmu.ac.uk
emily_grace_smith@hotmail.com
UNIVERSITY OF MANCHESTER
AalOwaif
Hasan
Adeyemi
Nike
hasan.aalowaif@postgrad.manchester.ac.uk
temitope.adeyemi@manchester.ac.uk
Al Ghuwainem
Campbell
Cantu
Cavet
Derrick
Frost
Goldrick
High
Houlden
Humphrey
Jesse
Jia
King
Linton
Lord
Masri
Mhd Zain
Muddiman
Ollier
Ragupathy
Roberts
Short
Weaver
White
Whittingham-Dowd
Ghannimah
Laura
Deborah
Jennifer
Jeremy
Helen
Marie
Nicky
Ashley
Bruce
Helen
Jia
Jane
Dennis
Elizabeth
ms.gangosef@hotmail.com
Laura.campbell-2@manchester.ac.uk
deborah.cantu@postgrad.manchester.ac.uk
Jennifer.S.Cavet@manchester.ac.uk
Jeremy.Derrick@manchester.ac.uk
helen.frost@manchester.ac.uk
marie.goldrick@manchester.ac.uk
nicky.high@manchester.ac.uk
ashley.houlden@manchester.ac.uk
bruce.humphrey@manchester.ac.uk
helen.jesse@manchester.ac.uk
Jia.jia@manchester.ac.uk
jane.king-2@manchester.ac.uk
James.D.Linton@manchester.ac.uk
Nader
Nor AiniLubis
Katie
Bill
Roobinidevi
Ian
Andrea
Danielle
Emily
Jayde
norainilubisbinti.mhdzain@manchester.ac.uk
katie.muddiman@manchester.ac.uk
Bill.Ollier@manchester.ac.uk
roobinidevi.ragupathy@manchester.ac.uk
i.s.roberts@manchester.ac.uk
andrea.short@manchester.ac.uk
danielle.weaver@postgrad.manchester.ac.uk
emily.white@manchester.ac.uk
jayde.whittingham-dowd@manchester.ac.uk
UIVERSITY OF NOTTINGHAM
Diggle
Steve
Steve.Diggle@nottingham.ac.uk
UNIVERSITY OF SALFORD
Alhoufie
Sari
Al-neama
Raed
Arenega-Bou
Paz
Birtles
Richard
Elgallali
Ashraf
Ferry
Natalie
Foster
Howard
Goulart
Vinicius
Goulart
Camilla Cristina
Hall
Jess
James
Chloe
Joynson
Ryan
Passos
Luiza
Perrin
Lauren
s.t.s.alhoufie@edu.salford.ac.uk
R.T.Al-neama@edu.salford.ac.uk
P.AranegaBou@edu.salford.ac.uk
r.j.birtles@salford.ac.uk
a.elgallali@edu.salford.ac.uk
N.Ferry@salford.ac.uk
H.A.Foster@salford.ac.uk
v.d.l.r.goulart@edu.salford.ac.uk
millacris@gmail.com
J.L.Hall1@edu.salford.ac.uk
c.james@salford.ac.uk
r.e.joynson1@edu.salford.ac.uk
luizafp@gmail.com
L.D.Perrin1@edu.salford.ac.uk
SALFORD ROYAL FOUNDATION TRUST
Chadwick
Paul
paul.chadwick@srft.nhs.uk
UNIVERSITY OF SHEFFIELD
Stewart
Barker
Stewartb1991@hotmail.co.uk
UNIVERSITY OF ST ANDREWS
Wyness
Adam
Adam.Wyness@hutton.ac.uk
GOVTODAY
Aslam
Kauser
kauser.aslam@googlemail.com
EXHIBITORS
Appleton Woods
Luke Housley
luke.housley@appletonwoods.co.uk
Bioline
Sarah Panton
spanton@bioline.com
Don Whitley Scientific
Stuart Moore
Stuart_Moore@dwscientific.co.uk
Triple Red
Joanne Sowden
sowdenj@triplered.com
Thanks to our sponsors:
NOTES
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