Annual Congress 2019 The Danish Microbiological Society - 11 NOVEMBER 2019 COPENHAGEN DENMARK - dms.dk
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Programme & Abstracts
The Danish Microbiological Society
Annual Congress 2019
11 NOVEMBER 2019
EIGTVEDS PAKHUS
COPENHAGEN · DENMARK
www.dmselskab.dk
Index Programme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Flash poster presentations . . . . . . . . . . . . . . . . . . . . . . 7 About DMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Speakers’ abstracts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Industry symposia . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Poster sessions and Poster Index . . . . . . . . . . . . . . . 35
Programme
09.00 Registration, poster mounting and coffee 12:35- Bruker Symposium:
13:00 ISO 16140-6 validation of Maldi Biotyper (see p. 31) ROOM II, second floor
ROOM II Second floor ROOM III Second floor
13:10- Nordic Biosite Symposium:
10.00 Welcome and opening address by Welcome and opening address by 13:35 Standardizing microbiomics - removing bias in collection,
DMS President DMS Vice-president purification and analyses (see p. 31) ROOM II, second floor
Carsten Suhr Jacobsen Trine Rolighed Thomsen
PARALLEL SESSIONS
10.15 [O01] Citizen science in systematic and [O02] Vaccine hesitancy – a major threat
applied microbiology for global health ROOM II Second floor ROOM III Second floor ROOM IV Second floor
Speaker: Preben Nielsen, Novozymes Speaker: Kåre Mølbak, Statens Serum Institut
Big data and deep learning Novel antimicrobial The challenge of slow
10.45 Coffee and exhibition First & second floor meets microbiology therapies growing bacteria
Chair: Mads Albertsen, Chair: Ole Højberg, Aarhus Chair: Peter Stougaard,
PARALLEL SESSIONS Aalborg University University Aarhus University
ROOM II Second floor ROOM III Second floor ROOM IV Second floor DMS co-chair: Trine DMS co-chair: Rikke Louise DMS co-chair: Kasper
Thomsen, Teknologisk Meyer, Aarhus University Nørskov Kragh, University of
Biodiversity and Vaccines Microbial food web in soil Institut Copenhagen
biogeography Chair: Anders Miki Bojesen, Chair: Tim Urich, Universität
Chair: Per Halkjær Nielsen, University of Copenhagen Greifswald 13.45 Chair introduction Chair introduction Chair introduction
Aalborg University DMS co-chair: Mette DMS co-chair: Carsten Suhr 13.50 [O12] Microbes inside and [O15] ICARS - The [O18] Microbiological and
DMS co-chair: Trine Burmølle, University of Jacobsen, Aarhus University out International Center for pathogenesis features
Thomsen, Teknologisk Copenhagen Daniel Mc Donald, University Antimicrobial Resistance distinguishing Lyme
Institut of California San Diego, USA Solutions disease and relapsing fever
11.00 Chair introduction Chair introduction Chair introduction Robert Skov, Statens Serum spirochetes
Institut Sven Bergström, Umeå
11.05 [O03] Microflora Danica [O06] Preventing disease [O09] Predatory bacteria University
meets Earth Microbiome and antimicrobial use in in soil: key-stone taxa of
Project animals by vaccination microbial foodwebs? 14.15 [O13] Binning microbial [O16] Fecal transplants [O19] Tuberculosis
Per Halkjær Nielsen, Anders Miki Bojesen, Tim Urich, Universität genomes using deep – the ultimative probiotic – diagnosis from a
Aalborg University & Daniel University of Copenhagen Greifswald, Germany learning for pigs? laboratory point of view
McDonald, University of Simon Rasmussen, Nuria Canibe, Aarhus Dorte Bek Folkvardsen,
California, San Diego, USA University of Copenhagen University Statens Serum Institut
11.30 [O04] Project SoilTracker [O07] Using viruses to fight [O10] Significance of micro- 14.30 [O14] Trash to treasure: [O17] Local drug delivery to [O20] Slow-growth and
- solving crimes with soil- viruses – perspectives for predator diversity in the exploring the wastewater target biofilm infections no-growth in natural
microbiodiversity future vaccines rhizosphere system with high quality Rikke Meyer, Aarhus environment
Tobias Guldberg Frøslev, Allan Randrup Thomsen, Flemming Ekelund, MAGs from large-scale University Hans Røy, Aarhus University
Centre for GeoGenetics, University of Copenhagen University of Copenhagen Nanopore data
University of Copenhagen Caitlin Singleton, Aalborg
University
11.45 [O05] Atmospheric [O08] Adjuvants: From [O11] Patterns of
microorganisms in the immunologist’s dirty little microbiome predator 14.45 Flash poster presentations Flash poster presentations Flash poster presentations
Arctic secret to vaccinologist’s communities at a global (see page 7) (see page 7) (see page 7)
Tina Santl-Temkiv, Aarhus requisite for success scale 15.00 Coffee and exhibition First & second floor
University Dennis Christensen, Statens Stefan Geisen,
Serum Institut Department of Terrestrial 15.15 POSTER SESSION (UNEVEN NUMBERS)
Ecology, Netherlands SALON B, ground floor & first floor
Institute of Ecology, NIOO-
KNAW 15:15- Leymus Genomics Symposum:
15:40 Long-read single molecule on Illumina instruments for a ground-breaking new level
12.00 Flash poster presentations Flash poster presentations Flash poster presentations of bacteria identification (see p. 33) ROOM II, second floor
(see page 7) (see page 7) (see page 7)
15:50- Clinical Microbiomics Symposium:
12.15 Lunch Salon C, ground floor 16:15 Nothing in biology makes sense except in the light of evolution (see p. 33) ROOM II, Second floor
12.15 Exhibition First & second floor 16.15 Pasteur travel grant ceremony ROOM III, Second floor
12.35 GENERAL ASSEMBLY Det Danske Pasteur Selskab ROOM IV, second floor 16.30 [O21] Keynote by Kevin Foster ROOM III, Second floor
Cooperation and competition in bacteria: from model systems to the microbiome
12.45 POSTER SESSION (EVEN NUMBERS) SALON B, ground floor & first floor
17.30 Reception with fermented beverage SALON C, ground floor
19.00 Optional congress dinner Spiseloppen, Christiania
4 5
novozymes.com
Flash poster presentations
PARALLEL SESSIONS, MORNING
ROOM II Second floor ROOM III Second floor ROOM IV Second floor
Biodiversity & biogeography Vaccines Microbial food web in soil
12.00 [P021] Metagenomics [P077] Campylobacter phages [P049] Two novel
profiling uncovers diversity, mimic the host defense bacteriophage genera
ecological success and strategy by using phase discovered in a groundwater
habitat preference of variation to create new reservoir indicate large
comammox nitrospira phenotypes with modified predator-prey diversity in
Barth Smets, Technical receptor binding proteins subsurface environments
University of Denmark Martine Sørensen, Ole Hylling,
University of Copenhagen Aarhus University
12.05 [P013] Smoke on the water: [P101] One size does not [P050] Biological drivers
Drafting the genome fit all; the gap between of bacterial communities
of the pigmented algea standardized in vitro in the arctic water inflow
mesotaenium berggrenii biofilm-infected wound region revealed through
that darkens the greenland models and in vivo clinical manipulations of microbial
ice sheet settings food web interactions
Athanasios Zervas, Ida Clement Thaarup, Oliver Müller,
Aarhus University University of Copenhagen University of Bergen
12.10 [P075] MIDAS 4: A [P097] Effect of A-hemolysin [P071] Multi-kingdom
comprehensive reference producing e. coli in two microbial communities in
Novozymes is
database of microbes in different mice strains/ earthworms
wastewater treatment breads in a dss model to Rumakanta Sapkota,
systems across the globe study ibd Aarhus University
the world leader
Morten Simonsen Dueholm, Hengameh Chloe
Aalborg University Mirsepasi-Lauridsen,
Statens Serum Institut
in biological PARALLEL SESSIONS, AFTERNOON
solutions
Big data and deep learning Novel antimicrobial The challenge of slow
meets microbiology therapies growing bacteria
14.45 [P036] Increasing the [P004] Antibacterial [P089] Domain analysis
Together with customers, partners and the global phylogenetic resolution cue from ecological of the cell wall proteinase,
of pseudomonas in soil neighbor increases lactocepin, of lactococcus
community, we improve industrial performance while microbiomes by rpod- holomycin production in lactis
preserving the planet’s resources and helping to build specific primers photobacterium galatheae Ida Nynne Laforce,
Jonas Greve Lauritsen, Yannick Buijs, Technical National Food Institute
better lives. As the world’s largest provider of enzyme DTU Bioengineering University of Denmark
and microbial technologies, our bioinnovation enables 14.50 [P037] Big production [P008] Combination of [P084] Deep purple: The
higher agricultural yields, low-temperature washing, without the use of cannabidiol and bacitracin biological darkening of the
energy-efficient production, renewable fuel and many antibiotics - impact on against resistant bacteria greenland ice sheet
the pig resistome and Claes S. Wassmann, Laura Halbach,
other benefits that we rely on today and in the future. microbiome University of Southern Aarhus University
We call it Rethink Tomorrow Katrine Wegener Tams, Denmark
DTU Bioengenerring
14.55 [P043] Uncovering the [P002] Potential of a [P083] The oxygen
hidden diversity of asgard bacteriophage cocktail consumption rate of cable
archaea to treat rainbow trout bacteria
Jakob Brandt, fry syndrome (RTFS): Stefano Scilipoti,
Aalborg University Comparison of delivery Aarhus University
methods
Valentina Laura Donati,
Technical University of
Denmark
6 7
About DMS
The Danish Microbiological Society (DMS) Scientific Committee
is a professional association in the fields of
human and veterinary medical microbiology, Thomas Bjarnsholt
general microbiology, food microbiology, (Congress Chairman and Treasurer),
BIOCHEMICAL JOURNAL
environmental microbiology and biotech- Department of Immunology and
nology. DMS has existed since 1958, and is Microbiology, University of Copenhagen
dedicated to the advancement of microbi-
ology, both applied and basic, and promotes Carsten Suhr Jacobsen
microbiological information to the public. (President of Danish Microbiological Society),
These aims are achieved by organizing Department of Environmental Sciences,
Molecular mechanisms in biology annual congresses, workshops and symposia Aarhus University
- and by taking part in the current microbio-
THE NEXT HOME FOR YOUR PAPER
logical debate. Trine Rolighed Thomsen
(Vice-President of the Danish Microbiological
Furthermore, DMS collaborates with the Society), Danish Technological Institute and
Danish Pasteur Society on the award of travel Aalborg University
grants to students and researchers in micro-
biology, immunology and related science. Mette Burmølle
(Secretary), Department of Biology,
Being a member of DMS, you are part of the University of Copenhagen
advancement of microbiology in Denmark.
Additionally, as a member of DMS, you are Marie Allesen-Holm
entitled to discounts at FEMS meetings Novo Nordisk
(Federation of European Microbiological
Societies) and for FEMS journals. Lars Bogø Jensen
National Food Institute,
Technical University of Denmark
Contact
The Danish Microbiological Kasper Nørskov Kragh
Society Secretariat Department of Immunology and
c/o CAP Partner Microbiology, University of Copenhagen
Nordre Fasanvej 113
SUBMIT YOUR BEST DK 2000 Frederiksberg
info@dmselskab.dk
Rikke Louise Meyer
Interdisciplinary Nanoscience Center
RESEARCH AT (iNANO) and Department of Bioscience,
Aarhus University
biochemj.msubmit.net Michael Thomas-Poulsen
Department of Biology,
University of Copenhagen
Katrine Uhrbrand
FORCE Technology
Ole Højberg
Aarhus University
Department of Animal Science
The DMS 2019 Congress is supported by the American Society for Microbiology (ASM).
Read more about ASM at www.asm.org
portlandpress.com/biochemj @PPPublishing PortlandPressPublishing
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Speakers’ abstracts
[O01] CITIZEN SCIENCE IN SYSTE- [O02] VACCINE HESITANCY - A MAJOR [O03] MICROFLORA DANICA MEETS
MATIC AND APPLIED MICROBIOLOGY THREAT FOR GLOBAL HEALTH EARTH MICROBIOME PROJECT
Preben Nielsen1 Kåre Mølbak1 Per Halkjær Nielsen1, Mads Albertsen2,
Daniel A. McDonald3
1
Novozymes, Microbe Technology, Lyngby, 1
Statens Serum Institute, Department of Infec-
Denmark tious Disease Epidemiology, Department of 1
Aalborg University, Aalborg University, Dep. of
Infectious Disease Epidemiology, Copenhagen, Chemistry and Bioscience, Aalborg, Denmark
Denmark 2
Aalborg University, Center for Microbial
Communities, Dept. Chemistry and Bioscience,
Aalborg, Denmark
“Masseeksperimentet 2018” was an extensive In 2019, WHO identified vaccine hesitancy as Research has not been able to confirm the as- 3
University of California, San Diego, United States
Citizen science project conducted by school one of the ten threats to global health. Thus, sociation between HPV vaccine and adverse
children from all over Denmark. We wanted to vaccine hesitancy ranks among major health events including autonomic dysfunctions.
nurse the interest in biology and biotechnolo- threats including ebola and other high-threat Nonetheless, the concerns seems to linger on How many microbial species exist on the
gy, show that “good” microbes are surrounding pathogens, pandemic influenza, dengue and as vaccination uptake is not yet back to the lev- planet, and how do environments shape their
us, and that by relatively simple tools we can antimicrobial drug resistance. el we saw before the crisis. communities? How are they distributed across
show the presence of Lactic Acid Bacteria. natural and cultivated habitats on a local and
Vaccine hesitancy is the reluctance or re- Suboptimal vaccine coverage should not au- global scale? These are some of the questions
In 3 weeks, 25,000 pupils collected samples fusal to vaccinate despite the availability tomatically be framed as vaccine hesitancy. the two projects, “Microflora Danica” and
and tested for presence of lactic acid bacteria of vaccines, and threatens to reverse pro- Research shows that vaccine hesitancy is not “Earth Microbiome Project” are trying to an-
by a simple fermentation experiment. More gress made in tackling vaccine-preventa- the major cause for being non-vaccinated in swer. Novel DNA-based sequencing technolo-
than 11,000 positive samples were found and ble diseases. Vaccination is one of the most Denmark. While nearly all infants receive the gies now allow a robust and high-throughput
submitted to the project. From a subset of cost-effective ways of avoiding disease – it first vaccine at 3 months of age, some parents identification of microorganisms in any habi-
5,000 samples, 12,000 bacterial strains were currently prevents 2-3 million deaths a year, (in the busy every-day life) simply forget about tat. Here, we present the plans and first results
identified to species level, of which 4000 and a further 1.5 million could be avoided if vaccines when children grow older. We envis- for Microflora Danica, or “the Microbiome of
unique isolates were cultivated, preserved in a global coverage of vaccinations improved. age that a new national and “smart” reminder Denmark”, where over the next 3 years we will
strain collection and characterized by shut gun service will serve as a tool to further increase establish a reference database over “all” mi-
WGS. Based on comparative WGS a subset of Measles, for example, has seen a 30% increase vaccination coverage in Denmark. crobes in Denmark cross various habitats. In
the strains could be affiliated to at least 10 novel in cases globally. The reasons for this rise are conjunction with the Earth Microbiome Pro-
species. The data were presented to the pupils complex, and not all of these cases are due to ject and The Microsetta Initiative, we applied
in a FAST-ANI tree linking up to a map of Den- vaccine hesitancy. However, some countries the same DNA-based sequencing technique
mark showing sample locations and metadata that were close to eliminating the disease have to a collection of over 500 samples from a di-
(see bacteriadanica.dk). seen a resurgence. Weak health care and con- verse set of geographically distributed envi-
sequences of conflicts may play an important ronments. These samples include host and
role - but in many settings, vaccine hesitancy is non-host associated collections, including
part of the challenge. multiple distinct human populations, and pro-
vide a glimpse of deep bacterial RNA operon
The reasons why people choose not to vacci- diversity at a global scale. We show a recapitu-
nate are complex. Lack of awareness of vac- lation short read based observations of the 16S
cine-preventable diseases, inconvenience in gene for the same samples, provide substan-
accessing vaccines, belief in advantages of tial increase in taxon specificity, and describe
natural infections, and lack of confidence to the distribution operon elements with respect
experts and authorities are key reasons un- to environmental variables. These data pro-
derlying hesitancy. In spite of research that vide a critical expansion to these open-access
confirm the safety of the MMR vaccine, myths resources pairing with other rich data gener-
about association between MMR vaccine and ation presently underway for the same Earth
autism continues to play a role in the public Microbiome Project sample set.
discourse. In Denmark, concerns about the
safety of HPV vaccines caused a temporary
set-back for the HPV vaccination programme.
This concern was based on case stories that
were disseminated by sensationalist media
coverage and social media platforms.
12 13
Speakers’ abstracts
[O04] PROJECT SOILTRACKER - [O05] ATMOSPHERIC MICROORGAN- [O06] PREVENTING DISEASE AND
SOLVING CRIMES WITH SOIL MICRO- ISMS IN THE ARCTIC ANTIMICROBIAL USE IN ANIMALS
BIODIVERSITY BY VACCINATION
Tina Šantl-Temkiv1, IPG Marshall2, C Mi-
Tobias Guldberg Frøslev1 gnani3, M Alsved4, D Beddows5, M Lever2, P Anders Miki Bojesen1
Starnawski2, J Löndahl4, U Gosewinkel6, R
1
Terrestrial Ecology, University of Copenhagen, Lange6, A Massling6, H Wex7, K Finster8 1
University of Copenhagen, Department of
Denmark Veterinary Disease Biology, Frederiksberg C,
1
Aarhus University, Stellar Astrophysics Centre, Denmark
Department of Physics and Astronomy,
Dept. of Bioscience, Aarhus, Denmark
2
Aarhus University, Centre for Geomicrobiology, particles, (iii) community composition of total Bacteria are common causes of disease in ani-
Aarhus, Denmark and active bacterial communities using next mals kept for food production. For more than a
3
University of Basel, Department of Environmen- generation sequencing of 16S rRNA molecules 100 years prevention of disease by vaccination
DNA extracted from environmental samples tal Sciences, Basel, Switzerland and genes. Selected results of these studies will has been an option employed to increase animal
(eDNA) – especially soil – is beginning to find 4
Lund University, Faculty of Engineering, Lund, be presented that reveal latitudinal and sea- welfare and production yield. With the advent of
use in forensic case work. It has been estab- Sweden sonal trends in the concentrations of airborne antimicrobials prevention of bacterial infections
lished that using eDNA metabarcoding to de- 5
School of Geography, Earth and Environmental bacteria, their predominant terrestrial and ma- by vaccination was significantly less popular
rive “biologigal fingerprints” of soils can be Sciences, University of Birmingham, Birmingham, rine sources and their airborne activity, in par- yet with the rise of antimicrobial resistance re-
used for matching of soil samples. the same United Kingdom ticular in relation to their climatic relevance. newed interest has been placed in research and
kind of data is beginning to be used in prov- 6
Aarhus University, Department of Environmental development of vaccines targeting bacteria.
enance prediction of unknown samples. As Science, Roskilde, Denmark Key words: airborne bacteria – atmospheric
part of the SoilTracker project we evaluated the 7
Leibniz Institute for Tropospheric Research, dispersal – Arctic atmosphere – bacterial ac- Two major challenges to veterinary vaccine
performance of different molecular marker for Leipzig, Germany tivity –biogenic ice nucleating particles development include a considerable antigen-
provenancing soil traces of unknown origin. 8
Aarhus University, Department of Bioscience, ic variation within individual bacterial species
We tested the performance of eDNA metabar- Microbiology Section, Aarhus University, References and a requirement of a very low production
coding of different genetic markers to predict Stellar Astrophysics Centre, Department of Phys- 1. Šantl-Temkiv, T. et al. Bioaerosol Field Meas- cost in order to allow an economically viable
the origin of unknown soil samples, and also to ics and Astronomy, Aarhus, Denmark urements: Challenges and Perspectives in product. Regarding antigenic variation many
predict habitat characteristics (forest, meadow, Outdoor Studies. Aerosol Sci. Technol. (2019). do animal pathogens contain from a few to sever-
agriculture, etc..) of the sample origin. Over- i:10.1080/02786826.2019.1676395 al hundred serotypes, each of which in princi-
all, we achieved good predictions of environ- Arctic is affected by several climatic feedback 2. Šantl-Temkiv, T. et al. A high volume im- ple would require an individual vaccine to en-
mental gradients and habitat classes to derive processes, caused by changes in albedo, sea- pinger for the study of concentration, viabili- sure protection against disease. For this reason
a relatively accurate description of the “crime ice extent, ice-sheet melt, and glacial retreats, ty, activity, and ice nucleation activity of air- the practical implementation of vaccination at
scene”. Thus, we conclude, that there is a large which have an impact on the Arctic radiation borne microorganisms. Environ. Sci. Technol. farm level has been focused on the most prev-
potential for the use of metabarcoding prove- budget. Microorganisms dispersing through 51, 11224–11234 (2017). alent serotypes knowing that other types could
nancing of soil trace samples. the atmosphere can affect some of these pro- 3. Šantl-Temkiv, T., Gosewinkel, U., Starnawski, represent a risk. Current vaccine research is
cesses, either by their role in cloud formation P., Lever, M. & Finster, K. Aeolian dispersal of therefore highly aware of the need for broad
or by changing the albedo, and consequently bacteria in southwest Greenland: their sources, scope vaccines that cover broader than just
the melt processes of icy surfaces. In addition, abundance, diversity and physiological states. one or a few serotypes. As profit margins in the
melting of terrestrial ice opens up new envi- Fems Micriobiology Ecol. 94, 1–10 (2018). animal production generally are very small any
ronments for microbial colonization and suc- 4. Šantl-Temkiv, T. et al. Biogenic Sources of intervention like vaccination need to be cheap
cession. For all these reasons, the Arctic is of Ice Nucleation Particles at the High Arctic Site to be justified economically. This not only ap-
special interest for aeromicrobiology1. We per- Villum Research Station. Environ. Sci. Technol. plies to the cost of the actual vaccines but also
formed several field campaigns at different lo- 53, 10580–10590 (2019). the cost of administering the vaccine. Having
cations in the Arctic, i.e. Nuuk Basic Research to inject a vaccine into each and every animal
Station, Villum Research Station and during a is not an option e.g. in a poultry flock of 50.000
cruise in Baffin Bay to investigate bacterial di- individuals. Technological advances allowing
versity, sources and environmental impacts of mass administration of vaccines while secur-
airborne microbial communities. We collected ing proper stimulation of a protective immune
air samples with high-volume impingers2 and response is thus a very important requirement.
on filters, precipitation samples and potential
local terrestrial and marine source samples3,4. Finally, the trend of moving production animals
Samples were investigated for (i) bacterial con- back to their natural habitat as happens in free-
centrations using cell counts and qPCR target- range or organic production systems re-intro-
ing 16S rRNA genes, (ii) concentration of total duce a much broader spectrum of disease caus-
and proteinaceous ice-nucleation ing microorganism including bacteria, demands
a considerably more elaborate prevention effort.
14 15
Speakers’ abstracts
[O07] USING VIRUSES TO FIGHT [O08] ADJUVANTS: FROM IMMU- [O09] PREDATORY BACTERIA IN SOIL: [O10] SIGNIFICANCE OF
VIRUSES – PERSPECTIVES FOR NOLOGIST’S DIRTY LITTLE SECRET KEY-STONE TAXA OF MICROBIAL MICROPREDATOR DIVERSITY IN THE
FUTURE VACCINES TO VACCINOLOGIST’S REQUISITE FOODWEBS? RHIZOSPHERE
FOR SUCCESS
Allan Randrup Thomsen1 Tim Urich1 Flemming Ekelund1
Dennis Christensen 1
1
University of Copenhagen, Department of University of Copenhagen, Denmark
1
Immunology and Microbiology, Copenhagen, Statens Serum Institute, Copenhagen S,
1
Denmark Denmark
Most current vaccines work through the in- Novel vaccine strategies include the so-called While food web models of aboveground eco-
duction of humoral immune responses result- subunit vaccines, which encompass only the systems normally operate with well-defined
ing in the production of protective antibodies. part of the pathogen to which immune rec- species with well-defined characteristics; and
However, protection against a number of im- ognition results in protection. The high pu- include terms such as generalists and special-
portant human infections like HIV and hepati- rity of these vaccines make adverse events ists, belowground models assemble organ-
tis C also require the generation of cell-mediat- less likely, but it also makes the vaccines less isms in broad trophic groups; e.g. bacteria,
ed immunity; even in the case a viral infection immunogenic and therefore potentially less protozoa, nematodes. The vast taxon richness
like flu, a cell-mediated immune response is effective. Vaccine adjuvants that increase and belowground is most likely a major reason
likely to improve protection. We therefore need modulate the immunogenicity of the vaccine for this difference. Still, we would probably
vaccines, which are capable of inducing potent are therefore added to solve this problem. Be- achieve a much better understanding of the
and long-standing T-cell mediated immuni- sides aluminum salts, which have been used dynamics and functioning of the belowground
ty. While live attenuated vaccines will do that, in vaccines for 90 years, a number of novel network if we acknowledged that bacteria,
newer split vaccines are generally not efficient vaccine adjuvants include delivery systems protozoa, nematodes etc. cannot satisfactorily
in raising efficient cell-mediated immunity. like liposomes and emulsions have been in- be described in this simplistic way and that, for
Returning to our original roots, the next gener- cluded in licensed vaccines over the last 30 example, the generalist vs. specialist concept
ation of vaccines are therefor likely to involve years. However trial-and-error has been the also is relevant when describing underground
various vector based, but replication impaired explorative approach of choice, for the de- systems. I will present a few examples that sup-
vaccines that mimic the antigen presentation sign of novel vaccine adjuvants due to major port this point of view and argue that future re-
associated with live bacteria or viruses. Exam- gaps in the knowledge about immunological search that follow this road will be fruitful. In
ples of this line of thinking will be presented. activation processes. Increasing insight into particular, I suggest to search for bacterial spe-
immunological mechanisms and how to ma- cialist and generalist predators from soil, using
nipulate them has replaced empirical with ra- largely inedible and largely edible bacteria as
tional design of adjuvants, leading to vaccine bait, and to test whether presence of certain
adjuvants with increased and customized im- specialist predators may provide more diverse
munogenicity profiles without compromising and functionally superior bacterial communi-
vaccine safety. I will present an overview of ties.
where vaccine adjuvant research is today.
16 17
Speakers’ abstracts
[O11] PATTERNS OF MICROBIOME [O12] MICROBES INSIDE AND OUT [O13] BINNING MICROBIAL GE-
PREDATOR COMMUNITIES AT A NOMES USING DEEP LEARNING
GLOBAL SCALE Daniel McDonald1, Justin Shaffer2, Gail Ack-
ermann2, Yan He3, Hongwei Zhou3, Junjun Jakob Nybo Nissen1, Joachim Johansen2,
Stefan Geisen1 Wang4, Gabriela Sheets5, Jordan Bisanz6, Rosa Lundbye Allesøe2, Casper Kaae Sønder-
Alexandra Obregon-Tito7, Gregor Reid8, Maria by3,
1
Netherlands Institute of Ecology (Nioo-Knaw), Gloria Dominguez-Bello9, Emily Vogtmann10, Jose Juan Almagro Armenteros4, Christopher
Wageningen, Netherlands Rashmi Sinha10, Global Microbiome Con- Heje Grønbech3, Henrik Bjørn Nielsen5,
servancy consortium11, Mathilde Poyet12, Thomas Nordahl Petersen6, Ole Winther7,
Mathieu Groussin12, Eric Alm12, Edgar Diaz13, Simon Rasmussen8
Rob Knight14
The microbiome has a key role in host perfor- Populations differ in host genetics, diet, life- 1
Department of Health Technology, Technical
mance and in environmental functioning. We 1
Uc San Diego, San Diego, United States style and environment. Within that back- University of Denmark, Novo Nordisk Foundation
are increasingly understanding the processes 2
Department of Pediatrics, University of Califor- ground, unattributed factors drive variation in Center for Protein Research, Faculty of Health
that structure microbiomes with profound ef- nia, San Diego, California, United States the gut microbiome. Here, we bring together and Medical Sciences, University of Copenhagen,
forts in the last years being conducted in soils. 3
Microbiome Medicine Center, Division of Lab- data from The Microsetta Initiative and the Denmark
Most studies focused on bacteria and fungi, oratory Medicine, Zhujiang Hospital, Southern Global Microbiome Conservancy, projects 2
Novo Nordisk Foundation Center for Protein
the primary drivers of many processes in soils. Medical University, Guangzhou, China which spans multiple populations, and inte- Research, Faculty of Health and Medical Sciences,
Yet, we lack an understanding of larger mi- 4
Ministry of Agriculture Feed Industry Centre, grate these data in a meta-analysis with other University of Copenhagen, Copenhagen, Denmark
crobiome components, while often ignoring College of Animal Science and Technology population datasets that used the Earth Micro- 3
Bioinformatics Centre, Department of Biology,
(trophic) interactions that likely contribute in China biome Project protocols. The combined anal- University of Copenhagen, Copenhagen, Denmark
structuring soil microbiomes. Here I will show Agricultural University, Beijing, China ysis spans over 30,000 human samples. Spe- 4
Department of Health Technology, Technical
the recent advances that help in filling these 5
Department of Anthropology, Emory College of cifically, 16S rRNA V4 amplicon data from The University of Denmark, Kongens Lyngby, Denmark
knowledge gaps. I will highlight work on pro- Arts and Sciences, Atlanta, Georgia, United States Microsetta Initiative and other studies using 5
Center for Genomic Medicine, Copenhagen
tists and nematodes, both representing the key 6
Hooper Foundation, University of California, San common molecular protocols were integrated University Hospital, Copenhagen, Denmark
predators of bacteria and fungi and as such Francisco, United States using Qiita. These data recapitulate and extend 6
National Food Institute, Technical University of
likely are important in structuring the microbi- 7
Department of Anthropology, University of Yatsunenko et al. (2012, Nature), showing that Denmark, Kongens Lyngby, Denmark
ome. After giving an overview on these groups Oklahoma, Oklahoma, United States European, Australian, and North American 7
Bioinformatics Centre, Department of Biolo-
of organisms, I will show their functional im- 8
Centre for Human Microbiome and Probiot- populations are more similar to one other than gy, University of Copenhagen, Department of
portance and global efforts that aim at deci- ic Research, Lawson Health Research Insti- each is to South American or sub-Saharan Applied Mathematics and Computer Science,
phering their community structures in soils. tute, Department of Biochemistry and Applied African populations. Unexpectedly, individu- Technical University of Denmark, Center for
Together I will show that this work will help in Mathematics, The University of Western Ontario, als from Bangladesh, the Philippines and Iran Genomic Medicine, Copenhagen University
furthering our knowledge on the global distri- London, Canada exhibit an intermediate relationship between Hospital, Denmark
bution and functioning of soil biodiversity. 9
Department of Anthropology and of Bioche- Western and non-Western groupings. These 8
Nnf Center for Protein Research, University of
mistry and Microbiology, Rutgers University, data were then integrated with the Earth Mi- Copenhagen, København N, Denmark
New Brunswick, Nj, United States crobiome Project, highlighting the microbial
10
Metabolic Epidemiology Branch, Division of connection between humans and the envi-
Cancer Epidemiology and Genetics, National ronment. Defining how populations relate is a Despite recent advances in metagenomic
Cancer Institute, Bethesda, Maryland, United critical step in translating microbiome results. binning, reconstruction of microbial species
States This backdrop carries medical implications, as from metagenomics data remains a challeng-
11
Center for Microbiome Informatics and Thera- it is presently unknown whether such massive ing task. Here we use recent advances in deep
peutics, Department of Biological Engineering, differences in microbial community composi- learning to develop an algorithm that uses
Massachusetts Institute of Technology, Cam- tion among populations have the potential to deep variational autoencoders to encode se-
bridge, Massachusetts, United States modulate microbiome therapies. quence co-abundance and k-mer distribution
12
Center for Microbiome Informatics and Ther- information prior to clustering. We show that
apeutics, Department of Biological Engineering, our variational autoencoder is able to inte-
Massachusetts Institute of Technology, The grate these two distinct data types without any
Broad Institute of Mit and Harvard, Cambridge, prior knowledge of the datasets. Our method
Massachusetts, United States outperforms existing state-of-the-art binners
13
Department of Pediatrics, University of Califor- on contig datasets, reconstructing 127-167%
nia, San Diego, La Jolla, California, United States as many precise and complete genomes. Ad-
14
Department of Pediatrics, University of ditionally, we developed a multi-sample and
California, Department of Computer Science & splitting strategy, that enables assembly of 23-
Engineering, Center for Microbiome Innovation, 89% more strains compared to commonly used
University of California San Diego, La Jolla, single binning strategies. Furthermore, our
California, United States method enables direct high-resolution taxo-
nomic profiling across samples.
18 19Speakers’ abstracts
[O14] TRASH TO TREASURE: EXPLOR- [O15] ICARS-THE INTERNATIONAL [O16] FECAL TRANSPLANTS – THE
ING THE WASTEWATER SYSTEM CENTER FOR ANTIMICROBIAL ULTIMATIVE PROBIOTIC FOR PIGS?
WITH HIGH QUALITY MAGS FROM RESISTANCE SOLUTIONS
LARGE-SCALE NANOPORE DATA Nuria Canibe1
Robert Leo Skov1
Caitlin Singleton1, Martin Andersen2, Aarhus University, Tjele, Denmark
1
Rasmus Kirkegaard2, Thomas Michaelsen2, SSI, Microbiology, Denmark
1
Søren Karst2, Morten Dueholm2, Per Nielsen2,
Mads Albertsen2
1
Aalborg University, Centre for Microbial
Finally, to demonstrate the scalability of our Communities, Department of Chemistry and Despite recent global efforts to mitigate the It is becoming increasingly evident that the gas-
method, we bin a human gut microbiome da- Bioscience, Aalborg University, Aalborg, impact of antimicrobial resistance (AMR), in- trointestinal microbiota has a significant impact
taset from 1,000 samples. By employing GPU Denmark formation and evidence on the effects of AMR on the overall health and performance of the pig.
acceleration for training and clustering we re- 2
Aalborg University on health and the economy have so far failed This has led to intensified studies on the compo-
construct 30% more near-complete bins com- to be translated into actions in many parts of sition of the gastrointestinal microbiota, factors
pared to state-of-the-art and even ensemble the world, especially in low and middle income affecting it, and the impact of the microbiota on
strategies. Our method Variational Autoencod- Improvements to wastewater resource re- countries (LMICs). The International Centre for health, growth performance, and more recently,
ers for Metagenomic Binning (VAMB) can be covery and treatment efficiency are essential Antimicrobial Resistance Solutions – ICARS – behavior of the host. Pig production research has
run on standard hardware and is freely avail- for fulfilling the UN sustainable development is a new partnership that aims to conduct pol- been heavily focused on assessing the effects of
able at https://github.com/RasmussenLab/ goals for both sustainable cities (goal 11) and icy relevant applied research at international, feed additives and dietary modifications to al-
vamb. responsible production and consumption national and local level to identify knowledge ter or take advantage of select characteristics of
(goal 12). Microbes are central to the processes and evidence-based solutions in close collab- gastrointestinal microbes to improve health and
underpinning wastewater treatment, however oration with countries and key stakeholders. feed conversion efficiency. Research on faecal
knowledge of this complex community is lim- ICARS will support LMICs to conduct applied microbiota transplantation (FMT) as a possible
ited to isolates, marker genes or incomplete research relevant to their local challenges tool to improve outcomes in pigs through ma-
genomes. To improve our capacity to charac- and therefore implementing aspects of their nipulation of the gastrointestinal microbiome is
terise this community at the genome level, we AMR National Action Plans (NAPs). It will aim very recent and limited data is available. Results
conducted large-scale long-read sequencing to bridge the gap between science and poli- on FMT in humans demonstrating the transfer
of 23 Danish full-scale wastewater treatment cy translating national action plans into evi- of phenotypic traits from donors to recipients
plant (WWTP) metagenomes using the Nano- dence based practices on the ground. Projects and the high efficacy of FMT to treat Clostridium
pore PromethION platform, producing >1 Tbp and activities will aim to build local capacity difficile infections in humans, together with data
(or 17 TB raw) of long-read data. These data and capability to sustain and scale up the ev- from pigs relating gut microbiota composition
enabled the recovery of 987 metagenome-as- idence-based solutions identified. Output will with growth performance has likely played an
sembled genomes (MAGs), including 36 cir- be made accessible and where appropriate in important role in the interest towards this strate-
cular genomes, after short-read data polishing open repositories. ICARS will work interna- gy in pig production.
(>0.9 Tbp Illumina). The recovered MAGs met tionally as a solution development partner-
stringent high-quality draft requirements of ship with projects and activities in various There are obvious inherent biosecurity and
>90% completeness,Speakers’ abstracts
[O17] LOCAL DRUG DELIVERY TO [O18] MICROBIOLOGICAL AND [O19] TUBERCULOSIS–DIAGNOSIS
TARGET BIOFILM INFECTIONS PATHOGENESIS FEATURES DISTIN- FROM A LABORATORY POINT OF
GUISHING LYME DISEASE AND VIEW
Rikke Louise Meyer1, Raoul Walter2, Sig- RELAPSING FEVER SPIROCHETES
ne Maria Nielsen2, Pernille Ommen2, Line Dorte B. Folkvardsen1
Hansen2, Sven Bergstrom1
Hieu Quang3, Jørgen Kjems2, Alexander Ze- 1
Statens Serum Institut, International Reference
likin4, Rikke Christiansen5 Molecular Biology, Umeå University, Umeå,
1
Laboratory of Mycobacteriology, Copenhagen S,
Sweden Denmark
1
Interdiciplinary Nanoscience Centre (Inano),
Faculty of Science and Technology, Aarhus The recent proposal of splitting the genus
University, Aarhus, Denmark Aptamer-targeted liposomes accumulated in Mycobacteria are a diverse group of actino-
Borrelia into two genera in the newly formed
2
Interdisciplinary Nanoscience Center (Inano), S. aureus biofilms, resulting in eradication of bacteria, comprising more than 100 species.
family of Borreliaceae, i.e. Borrelia and
Aarhus University, Aarhus, Denmark biofilms in vitro, while non-targeted lipos- The most well-known and well characterized,
Borreliella has motivated us to reflect upon
3
Aarhus University, Denmark omes were less effective. Although this result is Mycobacterium tuberculosis (Mtb), is the caus-
how these organisms has been characterized
4
Department of Chemistry, Aarhus University, promising, the burst release offers little control ative agent of tuberculosis (TB). Other species
and differentiated. Herein we therefore aim to
Aarhus C over dosage and exposure time. We therefore are Mycobacterium leprae, causing leprosy and
take a closer look on the biology and virulence
5
Interdisciplinary Nanoscience Center (Inano), proceeded with prodrug therapy. The embed- non-tuberculous mycobacteria (NTM) that
attributes of the two suggested genera, i.e.
Aarhus University, Denmark ded enzyme continuously converted the prod- are common in the environment and some of
those causing Lyme borreliosis and relapsing
rug to moxifloxacin at the implant surface, them are opportunistic pathogens.
fever borreliosis, respectively.
which prevented biofilm formation, even un-
Antibiotic treatment of biofilm infections often der flow. It is not an easy group of bacteria to culture,
fail because the dose that can be administered In fact, both these genera has a lot in common ranging from a few days to positive culture for
safely is insufficient to eradicate the biofilm. We Targeted drug delivery and pro-drug therapy with similar infection biology features . They the NTM fast growers, to 56 days until a nega-
hypothesize that treatment will be more effec- enable local antibiotic therapy. Drug the ex- are both characterised as bacterial zoonoses, tive culture for the majority, to the almost-im-
tive if drugs are delivered or synthesized at the posure time and concentration is better con- transmitted by hematophagous arthropods possible-to-grow Mycobacterium leprea.
site of infection, leading to a high local con- trolled in prodrug therapy, and we believe that with almost identical microbiological appear- Tuberculosis is the number one cause of death
centration with minimal side effects. We aimed our encouraging results will pave the way for ance. Nevertheless, a closer look at their gen- related to an infectious disease, recently it has
at delivering a high local dose of antibiotics implementing more potent drugs that target otypic and phenotypic characteristics clearly surpassed HIV/AIDS.
through two different approaches: i) targeted persister cells in treatment of biofilm infec- reveals several differences that might moti-
delivery of encapsulated antibiotics, and ii) lo- tions. vate the suggested split. On the other hand, a The quest for the fastest way to diagnose TB
cal drug synthesis through prodrug therapy. change of this well-established classification in the lab is still ongoing, and a number of
within the genus Borrelia might impose an molecular tests to rapid detection in primary
Targeted drug delivery uses drug encapsulation, economical burden as well as a great confusion specimens have been developed. However,
accumulation in the biofilm, and a triggered in the society, including medical and scientific the sensitivity is still lower than for culture,
burst release. We encapsulated vancomycin and societies as well as the general population. which besides taking several weeks, requires
rifampicin in temperature-sensitive liposomes expensive equipment, specialized media, and
decorated with aptamers that bind Staphylococ- skilled personnel. A big portion of the analyzes
cus aureus. Accumulation, drug release, and kill applied to TB specimens, are still delayed until
efficiency was quantified on S. aureus biofilms. sufficient growth of an isolated culture is ob-
tained.
Prodrug therapy uses immobilized enzymes to
convert non-toxic prodrugs to the active drug. Mtb is an enigma -a slow growing, not very
We developed a novel method for synthesizing contagious, hard to culture bug, with huge
glucuronide prodrugs, opening the door for an- success worldwide.
timicrobial prodrug therapy. We immobilized
the catalyst (β-glucuronidase) in a layer-by-lay-
er coating on titanium implants. Glucuronide
prodrugs of moxifloxacin was administered in
solution, and the effect on S. aureus viability
and biofilm formation was quantified.
22 23Speakers’ abstracts Keynote abstract
[O20] SLOW-GROWTH AND [O21] COOPERATION AND COMPE-
NO-GROWTH IN NATURAL TITION IN BACTERIA: FROM MODEL
ENVIRONMENT SYSTEMS TO THE MICROBIOME
Hans Røy1 Kevin Foster1
1
Institute for Bioscience, Aarhus University, 1
University of Oxford, Oxford, United Kingdom
Aarhus C, Denmark
Research within the ocean drilling projects Microbes display a dizzying array of social
have demonstrated large populations of traits, from enzymes released to break down
prokaryotes that live deep below the seafloor nutrients and antibiotics, through slimey se-
under extreme energy limitation. These or- cretions that protect and disperse, to draconi-
ganisms are not merely the dying remains of an molecular machines that stab, rupture and
the once thriving surface community, but cells poison their competitors. But what determines
that live in a delicate balance with the flux of whether microbes cooperate or compete with
energy that can be harvested from slow degra- each other, and how does this affect their
dation of ancient organic material. The com- hosts? To answer these questions, we combine
munity composition is distinctively different theory and experiments with pathogenic bac-
from that of the energy rich and dynamic sed- teria and the mammalian microbiome. This
iment surface, but the transition between the has revealed that clonemate patches naturally
two occur only 10 cm below the seafloor. Close emerge in microbial communities, which fa-
examination of the ratio between community vours strong cooperation by kin selection. But
size and community respiration confirms that interactions between strains and species are
the energy available for the individual organ- often competitive. We find that bacteria are of-
isms this close to the seafloor is just as meager ten at war and are even capable of reciproca-
as for those that have been buried for millions tion, detecting incoming attacks and respond-
of years without resupply of organic substrates. ing collectively in devastating counterattacks.
This demonstrate a life strategy linked to cellu- Microbial interactions follow the same evolu-
lar metabolism far below what we know from tionary principles that were first understood
laboratory cultures, which is still distinct from through the study of animal behavior. Howev-
dormancy. This this type of organisms are not er, one fascinating property of microbes is that
restricted to exotic niches buried deeply below their entire ecosystem can lie within another
the seafloor. They can be studied with relative evolving organism – a host - that is trying to
ease in sedimentary environments where they control them and their interactions. The result
constitute a dominating fraction of the com- appears to be a complex coevolutionary dance
munity. In environments where they co-exist with the host and its immune system on one
with fast growing types, however, their activity side, and the whole microbiota on the other.
may easily escape detection.
24 25Submit your next paper at
www.manuscriptmanager.com/apmis
APMIS
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Formerly Acta Pathologica, Microbiologica et
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