Publications

Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects

Published in The ISME Journal, 2023

In this paper, we reported the bacterial symbiosis of scale insects with Burkholderia bacteria that have tiny genomes.

Recommended citation: Anna Michalik, Eugen Bauer, Teresa Szklarzewicz, and Martin Kaltenpoth. "Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects." The ISME Journal. 17(12), 2221-2231. https://academic.oup.com/ismej/article/17/12/2221/7506642

Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles

Published in The ISME Journal, 2023

In this paper, the dual bacterial symbiosis of xylophagous beetles and its function was reported.

Recommended citation: Julian Kiefer, Eugen Bauer, Genta Okude, Takema Fukatsu, Martin Kaltenpoth, and Tobias Engl. "Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles." The ISME Journal. 17(7), 1029-1039. https://academic.oup.com/ismej/article/17/7/1029/7505789

Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis

Published in Communications biology, 2021

In this paper, the influence of glyphosate on mutualistic bacteria of grain pest beetles was investigated.

Recommended citation: Julian Kiefer, Suvdanselengee Batsukh, Eugen Bauer, Bin Hirota, Benjamin Weiss, Jurgen Wierz, Takema Fukatsu, Martin Kaltenpoth, and Tobias Engl. "Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis." Communications biology. 4(1), 554. https://www.nature.com/articles/s42003-021-02057-6

Bacterial symbionts support larval sap feeding and adult folivory in (semi-) aquatic reed beetles

Published in Nature Communications, 2020

In this paper, the dual symbiont function of amino acid provisioning and pectinase activity is analyzed in reed beetles.

Recommended citation: Frank Reis, Roy Kirsch, Yannick Pauchet, Eugen Bauer, Lisa Carolin Bilz, Kayoko Fukumori, Takema Fukatsu, Gregor Kölsch, and Martin Kaltenpoth. (2020). "Bacterial symbionts support larval sap feeding and adult folivory in (semi-) aquatic reed beetles." Nature Communications. 11(1), 1-15. https://www.nature.com/articles/s41467-020-16687-7

Minimal fermentative metabolism fuels extracellular symbiont in a leaf beetle

Published in The ISME Journal, 2020

In this paper, the minimal metabolism of an extracellular symbiont is described in relation to the transcriptomic response of the host.

Recommended citation: Eugen Bauer, Martin Kaltenpoth, Hassan Salem. (2020). "Minimal fermentative metabolism fuels extracellular symbiont in a leaf beetle." The ISME Journal. 14(3). https://www.nature.com/articles/s41396-019-0562-1

Global network of computational biology communities: ISCB’s Regional Student Groups breaking barriers

Published in F1000Research, 2019

Recommended citation: Sayane Shome, R Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman (2019). "Global network of computational biology communities: ISCBs Regional Student Groups breaking barriers" F1000Research. 8. https://f1000research.com/articles/8-1574/v1

From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohns disease

Published in NPG Systems Biology and Applications, 2018

In this paper, BacArena was applied to study dietary effects on the gut microbiota of Crohns disease patients.

Recommended citation: Eugen Bauer, Ines Thiele. (2018). "From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohns disease." NPG Systems Biology and Applications. 4(1). https://www.nature.com/articles/s41540-018-0063-2

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

Published in mSystems, 2018

In this review, different methods in community modeling and their impact on the human microbiota are discussed.

Recommended citation: Eugen Bauer, Ines Thiele. (2018). "From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota" mSystems. 3(3). https://msystems.asm.org/content/3/3/e00209-17

Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont

Published in Cell, 2017

In this paper, we discovered an extracellular pectinolytic symbiont with a drastically reduced genome.

Recommended citation: Hassan Salem, Eugen Bauer, Roy Kirsch, Aileen Berasategui, Michael Cripps, Benjamin Weiss, Ryuichi Koga, Kayoko Fukumori, Heiko Vogel, Takema Fukatsu, Martin Kaltenpoth. (2017). "Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont" Cell. 171(7). https://www.ncbi.nlm.nih.gov/pubmed/29153832

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Published in PLoS Computational Biology, 2017

In this paper, we describe a new method to study the metabolic interactions in microbial communities.

Recommended citation: Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta. (2017). "BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities" PLoS Computational Biology. 13(5). https://www.ncbi.nlm.nih.gov/pubmed/28531184

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Published in Nature Biotechnology, 2016

In this paper, we describe a new resource of metabolic reconstructions of gut microbes.

Recommended citation: Stefania Magnusdottir, Almut Heinken, Laura Kutt, Dmitry A. Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jaeger, Joanna Baginska, Paul Wilmes, Ronan M. T. Fleming, Ines Thiele. (2016). "Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota" Nature Biotechnology. 35(1). https://www.ncbi.nlm.nih.gov/pubmed/27893703

Symbiont transmission entails the risk of parasite infection

Published in Biology letters, 2015

In this paper, we describe how a symbiont transmission route can be exploited by a parasite.

Recommended citation: Hassan Salem, Thomas O. Onchuru, Eugen Bauer, Martin Kaltenpoth. (2015). "Symbiont transmission entails the risk of parasite infection" Biology letters. 11(12). https://www.ncbi.nlm.nih.gov/pubmed/26673937

Do genome‐scale models need exact solvers or clearer standards?

Published in Molecular systems biology, 2015

Recommended citation: Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Drager, Imam Famili, Adam M Feist, Ronan M. T. Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novere, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele (2015). "Do genome‐scale models need exact solvers or clearer standards?" Molecular systems biology. 11(10). https://www.ncbi.nlm.nih.gov/pubmed/26467284

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Published in Microbiome, 2015

In this paper, we analyzed the metabolic differences of representative human gut microbes.

Recommended citation: Eugen Bauer, Cedric C. Laczny, Stefania Magnusdottir, Paul Wilmes, Ines Thiele (2015). "Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires" Microbiome. 3(1). https://www.ncbi.nlm.nih.gov/pubmed/26617277

Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae)

Published in FEMS Microbiology, 2014

In this paper, we analyzed the microbiota of wood-feeding cockroaches.

Recommended citation: Eugen Bauer, Niclas Lampert, Aram Mikaelyan, Tim Kohler, Kiyoto Maekawa, Andreas Brune (2014). "Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae)" FEMS Microbiology. 91(2). https://www.ncbi.nlm.nih.gov/pubmed/25764554

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts

Published in PLoS ONE, 2014

In this paper, we investigated the differential expression of immune related genes in response to symbiont elimination.

Recommended citation: Eugen Bauer, Hassan Salem, Manja Marz, Heiko Vogel, Martin Kaltenpoth (2014). "Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts" PLoS ONE. 9(12). https://www.ncbi.nlm.nih.gov/pubmed/25490201

Reglucosylation of the Benzoxazinoid DIMBOA with Inversion of Stereochemical Configuration is a Detoxification Strategy in Lepidopteran Herbivores

Published in Angewandte Chemie International Edition, 2014

Recommended citation: Felipe C. Wouters, Michael Reichelt, Gaetan Glauser, Eugen Bauer, Matthias Erb, Jonathan Gershenzon, Daniel G. Vassao (2014). "Reglucosylation of the Benzoxazinoid DIMBOA with Inversion of Stereochemical Configuration is a Detoxification Strategy in Lepidopteran Herbivores" Angewandte Chemie International Edition. 53(42). https://www.ncbi.nlm.nih.gov/pubmed/25196135

Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

Published in Proceedings of the Royal Society B: Biological Sciences, 2014

In this paper, we presented results for vitamin supplementing gut microbes

Recommended citation: Hassan Salem, Eugen Bauer, Anja S. Strauss, Heiko Vogel, Manja Marz, Martin Kaltenpoth (2014). "Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host" Proceedings of the Royal Society B: Biological Sciences. 281(1796). https://www.ncbi.nlm.nih.gov/pubmed/25339726