B4
Recognition and Communication

Microbial interactions within the metaorganism: mechanisms of bacterial niche specialization and warfare in symbiosis

Metaorganisms are built on interactions between eukaryotic and prokaryotic organisms. Although these interactions are evident, many aspects concerning the contribution of host-microbe and microbe-microbe interactions to the origins of symbiosis and metaorganism function remain understudied. Project B4 was added to the CRC in the second funding phase with a focus on the evolution of niche specialization and interactions among host-associated bacteria in multiple CRC metaorganisms.

The study of microbial interactions within the host habitat, and how those are affected by – or have an effect on – the host environment, provides a unique opportunity to understand symbiosis. Our research focus is on the evolution of stable persistence within the host habitat and the mechanisms involved in ecological interactions within the host-associated microbial community.

In the ongoing funding phase, subproject B4.1 (PI Dagan) reconstructed the evolution of symbiosis plasmids in Pantoea, revealing the role of extrachromosomal genetic elements during adaptation to a plant-associated lifestyle. Further, subproject B4.2 (PI Unterweger) phenotypically characterized a novel bacterial species whose relative abundance is associated with individual mouse genetics and identified positive and negative bacteria-bacteria interactions among mouse-associated Bacteroides. Both subprojects joined forces to study the role of the type VI secretion system (T6SS) in competition among plant-associated Pantoea (B4.1) and mobile genetic elements that encode T6SS genes in mouse-associated Bacteroides (B4.2).

In the third funding phase, we plan to extend our project to microbe-host interactions in collaboration with Nancy Obeng, whose research is focused on the evolution of horizontally transmitted symbionts and their interaction with the host. Her current research shows that the bacterial second messenger c-di-GMP mediates host adaptation of pseudomonads to the nematode Caenorhabditis elegans.

The overall objective of this project in the third funding phase is to investigate the mechanisms of bacterial niche specialization with a focus on mechanisms of interaction with the host and mechanisms of competitive interaction within the host-associated microbiome. Specifically, we aim to:

(i) Determine the diverse currencies at the origin of symbiosis and study the evolution of symbiosis plasmids (B4.1, PI Dagan).

(ii) Study the regulation of T6SS within the host environment in the context of competitive interactions within the microbiome and communication with the host (B4.2, PI Unterweger).

(iii) Investigate the role of c-di-GMP in shaping microbe-host interactions and bacterial success across metaorganisms (B4.3, PI Obeng).

Connecting both within B4 and beyond, this project will coordinate two cross-model-system studies of the CRC that will investigate

(i) the importance of microbe-microbe interactions as drivers of microbiome community composition and

(ii) the role of c-di-GMP as a central symbiosis switch. Focusing on mechanisms of bacterial niche specialization and bacterial interactions, our studies make use of material from across the CRC and are expected to reveal specific mechanisms and general principles that can be used to better understand – and manipulate – community composition within the metaorganism.

B4
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2023
A2
B2
B4

Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice

Hanna Fokt, Shauni Doms, Malte C. Rühlemann, Maxime Godfroid, Ruth A. Schmitz, Britt M. Hermes, John F. Baines (2023) Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice BioRxiv

 

2023
B4

Phylogenomic Testing of Root Hypotheses

Fernando D. K. Tria, Giddy Landan, Devani Romero Picazo, Tal Dagan (2023) Phylogenomic Testing of Root Hypotheses
2023
A3
B4

T6SS-mediated competitive exclusion among Pantoea agglomerans associated with plants

Kai Ripcke, Devani Romero Picazo, Shreya Vichare, Daniel Unterweger, Tal Dagan, Nils Fredrik Huelter (2023)
2023
A1
A2
B2
B4
Z2
Z3

Closely related Bacteroides of the murine intestinal microbiota affect each other’s growth positively or negatively

Hanna Fokt, Gabija Sakalyte, Rahul Unni, Mohammad Abukhalaf, Liam Cassidy, Georgios Marinos, Maxime Godfroid, Birhanu M Kinfu, Ruth A Schmitz, Christoph Kaleta, Andreas Tholey, John F Baines, Tal Dagan, Daniel Unterweger (2023) BioRxiv
2022
A2
B4
Z2

Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice.

Hanna Fokt, Rahul Unni, Urska Repnik, Ruth A. Schmitz, Marc Bramkamp, John F. Baines, Daniel Unterweger. Archives of Microbiology 204:546.
doi: 10.1007/s00203-022-03148-6

2022
A3
B4

Denitrification in foraminifera has ancient origin and is complemented by associated bacteria.

Woehle C, Roy A-S, Glock N, Michels J, Wein T, Weissenbach J, Romero D, Hiebenthal C, Gorb SN, Schönfeld J, Dagan T (2022) PNAS. 119(25):e2200198119 doi: 1073/pnas.2200198119

2022
B4

Presence and absence of type VI secretion systems in bacteria.

Unni R, Pintor KL, Diepold A, Unterweger D (2022) Microbiology. 168:001151 doi: 10.1099/mic.0.001151

2022
B4

Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

Romero Picazo D, Werner A, Dagan T, Kupczok A, Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance, Genome Biology and Evolution, Volume 14, Issue 7, July 2022, evac098, https://doi.org/10.1093/gbe/evac098

2021
B4

Segregational drift constrains the evolutionary rate of prokaryotic plasmids

Garoña A, Hülter NF, Romero Picazo D, Dagan T (2021)  Biol. Evol. 38(12):5610–5624 doi:10.1093/molbev/msab283

2021
A3
B4

Colonization dynamics of Pantoea agglomerans in the wheat root habitat

Soluch R, Hülter NF, Romero Picazo D, Özkurt E, H Stukenbrock E, Dagan T (2021) Environ Microbiol. 23(4):2260-2273. doi: 10.1111/1462-2920.15430.

2019
B4

Currency, Exchange, and Inheritance in the Evolution of Symbiosis

Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TBH, Martin WF, Dagan T (2019) Trends in Microbiology doi: 10.1016/j.tim.2019.05.010

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