Program

Program

25th – 28th  October 2023 | Alicante, Spain

UNIVERSIDAD MIGUEL HERNÁNDEZ

Edificio Severo Ochoa / Severo Ochoa Building

Wednesday, October 25, 2023 
15.30-19.15 | Registration
16.30 | Francisco Rodriguez-Valera (University Miguel Hernández, San Juan de Alicante, Spain)
Why the Local-Pangenome? Welcoming address
 
17.15-19.15 | Session 1. Defining the Pangenome | Chair: Eduardo Rocha
17.15-17.45. Kostas Konstantinidis (Georgia Institute of Technology, USA)
Comparative omics reveals an ANI-gap within species to define strains and the mechanism that underlies the species and subspecies gaps
17.45-18.15. Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences, USA).
Microbiome-wide rate and phylogenetic range of lateral gene transfer in marine prokaryoplankton
18.15-18.45. Matthew Kellom (JGI, USA)
Metagenome-assembled genomes, isolate genomes, and pangenomics in large-scale data
18.45-19.15. Martin Polz (Vienna, Austria)
Defining the role of the pangenome within a population genomic framework
 
20.00. Welcome. Informal gathering with drinks and food – Castillo de Santa Bárbara (BUS)
 
Thursday, October 26, 2023
09.00-11.00. Session 2. Genomics of the Pangenome | Chair: Tal Dagan
9.00-9.30. Federico Rosconi (Biology Department, Boston College, USA)
Bacterial pangenomes shape essentiality and gene-phenotype associations
9.30-10.00. Aitor Blanco-Míguez (University of Trento, Italy)
A large-scale pangenome-based  framework for improved meta-omics profiling
10.00-10.30. Eduardo Rocha (Institute Pasteur, Paris, France)
The contribution of interactions between mobile elements to the bacterial pangenome
10.30-11.00. Yusuke Okazaki (Kyoto University, Japan)
Single-cell genomics uncovers microbial genomic microdiversity and virus-host interactions that had eluded high-resolution metagenomics
 
11.00-11.30 | Coffee Break
 
11.30-13.30. Session 3. Evolution of the pangenome | Chair: Martin Polz
11.30-12.00. Moritz Buck
Pangenome traits across Bacteria and Archaea: from genome sizes to functions
12.00-12.30. Alex Mira (FISABIO, Valencia, Spain)
Do Darwinian evolutionary principles apply to prokaryotes?
12.30-13.00. Tal Dagan (University of Kiel, Germany)
Pangenomes as documents of the species evolutionary history
13.00-13.30. Carolina A. Martinez-Gutierrez (University of North Carolina, Greensboro, USA)
Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria and Archaea 
 
13.30-14.30 | Lunch Break
 
14.30-16.30 Session 4. Ecology and the pangenome | Chair: Kostas Konstantinidis
14.30-15.00. Mattias Hotzinger (Swedish University of Agricultural Sciences, Uppsala, Sweden)
The bipartite flexible genome of a freshwater bacterial species – Strain individuality and additive phyisological functions
15.00-15.30. Joshua Hamm (NIOZ Texel, The Netherlands)
Strain-level variation alters host-symbiont interaction dynamics in the Halorubrum lacusprofundi – Candidatus Nanohaloarchaeum antarcticus system
15.30-16.00. Jose Haro-Moreno (University Miguel Hernandez, San Juan de Alicante, Spain)

O-antigen diversity in the Order Pelagibacterales 
16.00-16.30. Pedro J. Cabello-Yeves (University of Warwick, UK)
Why do alpha-cyanobacteria with form 1A RuBisCO dominate aquatic habitats worldwide?
 

16.30-17.00 | Coffe Break
 
17.00-19.30. Flash talks I (5 min) | Chair: Joshua Hamm

Order

Author

Tittle

1

Puente Sánchez, Fernando

Turning metagenomics into metapangenomics: the next frontier in microbial ecology

2

Brouns, Roos Chiara Antoinette

Predicting the environment of microbial communities from community and pangenome data

3

Valiente Mullor, Carlos

Closing the pangenome: openness analysis of >40.000 bacterial genomes reveals the limits of Heaps law

4

von Meijenfeldt, Bastiaan

A large pangenome allows for a broad niche range

5

García-González, Neris

Improving core genome gene alignments for large-scale evolutionary and transmission studies

6

Rubio Portillo, Esther

What we can expect from pangenome analysis using MAGs

7

Walter Costa, Maria Beatriz

Predicting Salinity Preferences from Bacterial Genomes with Machine Learning

TIME FOR QUESTIONS  (10 min)

8

Enav, Hagay

SynTracker differentiates evolution via mutation or recombination on a per-species basis in complex microbiomes

9

Jean, Mainguy

PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes

10

Arnoux, Jérôme

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

11

Maistrenko, Oleksandr

Population genomics of Archaea

12

feriel, bouderka

Evolution of the Patescibacteria symbiotic lifestyle

13

Palacín Lizarbe, Carlos

Nitrate-reducing microbes in winter in sediments of large boreal lakes affected by browning and mining

14

Richy, Etienne

Exploring Microbial Processes and Genomic Islands in Deadwood Decomposition: Integrating Metagenomics and Metatranscriptomics

TIME FOR QUESTIONS  (10 min)

15

Pardeshi, Lakhansing Arun

Pangenomics to understand the emergence of a new Pectobacterium brasiliense pathovar

16

García-Fraile, Paula

Comparative enomics of the Pseudomonas pangenome reveals host- and environment-specific evolution

17

Suárez-Moo, Pablo

Analysis of the pangenome in Thaumarchaeota from the western Mediterranean sea in seasons with mixed and stratified water column

18

Albers, Justine

A global pangenome of marine nitrite-oxidizing bacteria highlights differences in nutrient acquisition strategies

19

Knudsen, Anne Kalinka Sand

Uncovering Methane Sink Potential and Habitat Preferences of Methanotrophs in Denmark

20

Vestergaard, Sofie Zacho

Genomic diversity of Zoogloea: Exploring secrets of biopolymer production in the world of activated sludge

21

Liébana Gracía, Raquel

Exopolysaccharide biosynthesis genes clusters in Alteromonas: a role in carbon remineralization and environmental adaptation

22

Zaragoza, Asier

A novel machine learning prediction tool for extracellular proteins doubles current size of the marine secretome

TIME FOR QUESTIONS   (10 min)
 
 
Friday October 27, 2023
09.00-11.00. Session. 5. Ecology II | Chair: Ramunas Stapanauskas
9.00-9.30. Rachel Whitaker (University of Illinois, Urbana-Champaign, USA)
Contributions of multiscale symbiosis to the dynamics of pangenome
9.30-10.00. Jose de la Torre (San Francisco State University, USA)
Population-level genome dynamics of archaea in hot spring microbial communities 
10.00-10.30. Felipe Coutinho (CSIC-ICM, Barcelona, Spain)
A deep dive into the genomic diversity of marine Archaea and Bacteria
10.30-11.00. Zaki Saati-Santamaría (Czech Academy of Sciences, Prague, Czech Republic)
Analysis of the prokaryotic genome evolution within a 5.5 million years trapped chemolithotrophic cave 
 
11.00-11.30 | Coffee Break
 
11.30-13.30. Sesion 6. Dynamics of the pangenome | Chair: Jose Penadés
11.30-12.00. Miguel Rodriguez Rojas (University of Innsbruck, Austria)
Quantifying genetic variation at the edge of metagenomic resolution to characterize in situ population dynamics
12.00-12.30. Fiona J. Whelan (University of Nottingham, UK) 
Gene-gene associations and the role of selection in microbial pangenomes
12.30-13.00. Franz Baumdicker (University of Tübingen, Germany)
Common misconceptions when disentangling the processes that shape pangenomes
13.00-13.30. Mario Rodríguez Mestre (INIA-CSIC, Madrid, Spain)
Regions of Genome Plasticity: A Comparative Analysis of Mobility and Retention Patterns in Bacterial and Archaeal Pangenomes 
 
13:30-14:30 | Lunch Break
 
14.30-16.30. Session 7. Pangenomes of animal/plant denizens | Chair: Rafal Mostowy
14.30-15.00. Aiswarya Prasad (University of Lausanne, Switzerland)
Variation and specialization of structure and function of gut microbial community across host species 
15.00-15.30. Jaime Iranzo (University Politecnica Madrid, Spain)
High-order metabolic interdependencies dominate the human gut microbiome 
15.30-16.00. Anne Kupczok (Wageningen University, The Netherlands)
Large-scale investigation of orphan genes in the human gut microbiome elucidates their evolutionary origins
16.00-16.30. Sheila Roitman (Max Planck Institute for Biology, Tuebingen, Germany)
Expanding the plant holobiont
 
16.30-17.00 | Coffe Break
 
17.00-19.15 Flash talks II | Chair: Alex Mira
 

 FLASH TALKS. Friday, 27th october

 

23

Mascarós Núñez, Patricia

Staphylococcus aureus: Antibiotic Resistance and Virulence – A Comparative Approach

24

Díaz Méndez, José Francisco

Exploring Staphylococcus aureus: Pangenome, Phylogeny and Comparative Analysis of Mobile Genetic Elements among Clonal Complexes

25

Sabnis, Akshay

Low plasmid mobility benefits cheaters and prevents eradication in nature

26

Rodriguez Mestre, Mario

Unraveling the role of plasmids in disseminating prokaryotic immune systems across different ecosystems

27

Figueroa Chavez, Wendy

Lateral transduction is the main route of horizontal gene transfer in immunocompetent bacteria

28

Robinson, Christopher

Longitudinal tracking of the ecology and evolution of mobile genes in the honey bee microbiome

29

Priest, Taylor

Circularised mobile genetic elements and their eco-evolutionary patterns at ecosystem and global scales

TIME FOR QUESTIONS   (10 min)

30

Romero Picazo, Devani

The evolution of domesticated plasmids coincides with species divergence in the plant-associated genus Pantoea

31

Mehrshad, Maliheh

Phage co-infection; a mystifying shuffling trick for the pangenome deck

32

Gonzalez-Serrano, Rafael

Homologous host recognition modules in distant families of Alteromonas phages

33

Ashkenazy, Haim

The evolution of Arabidopsis thaliana-associated Pseudomonas

34

Lomeli Ortega, Carlos Omar

Modulation of shrimp microbiota using phage therapy during a controlled infection

35

Guridi Fernández, Pablo

Exploring DNA transfer and integration in human cells upon infection with intracellular bacterial pathogens

36

Sánchez-Nieto, Esperanza

Prokaryotic reverse transcriptases. Retroelements converted into specialized defense systems

TIME FOR QUESTIONS  (10 min)

37

Nadal Molero, Francisco

MITES as a tool to Associate Virus to Microbial Host

38

Koszucki, Janusz

Using genome-wide associations studies to identify putative genetic determinants of phage host-range in Klebsiella

39

Rosselli, Riccardo

Exploring the potential of CRISPR-Cas module transfers between bacteria lineages to overcome Anti-CRISPR inhibition

40

Smug, Bogna

How phages play with LEGO: studying protein-level mosaicism in phages and its evolutionary implications

41

Pinilla Redondo, Rafael

Phages suppress CRISPR-Cas immunity via RNA-based anti-CRISPRs

42

López Beltrán, Adrián

Virus-Host Ecological Interactions in the Gut Microbiome Through the Analysis of CRISPR Arrays

43

Pimenoff, Ville

Ecology of oncogenic human papillomaviruses after the eradication of vaccine-targeted types

44

Martinez-Martinez, Daniel

Navigating the E. coli Pangenome to Identify Metformin Drivers

TIME FOR QUESTIONS  (10 min)

 
20.30. Joint organized dinner. Finca Santa Luzia (Av. de Alicante, 38, BAJO, 03550 Sant Joan d’Alacant, Alicante)
 
 
Saturday, October 28, 2023
09.00-11.00. Session 8. Phages and pangenome | Chair: Manuel Martínez García
9.00-9.30. Jose Penades (Imperial College London, UK)
Redefining mobility in bacterial genetics and its impact on infectious disease
9.30-10.00. Rafal Mostowy (Jagiellonian University, Kraków, Poland)
Using a pan-genome approach to better understand how phages interact and coevolve with bacterial hosts
10.00-10.30. Chris Bellas (University of Innsbruck, Austria)
Bacteriophage pangenomes from metagenomes
10.30-11.00. Maite Muniesa (University of Barcelona)
Unveiling the expansive pangeome of Crassvirales: Novel CrAss-like phage isolates reveal genetic heterogeneity and worldwide distribution
 
11:00-11:30 | Coffee Break
 
11:30-12:30 | Closing keynote lecture 
Eugene Koonin (National Center for Biotechnology Information, Bethesda, USA)
The Virosphere: Megataxonomy and Global Ecology