Article
Multidisciplinary Sciences
Michael Sieber, Arne Traulsen, Hinrich Schulenburg, Angela E. Douglas
Summary: The prevalence of specific microbes in a host population can increase even when they do not provide specific benefits to the host, especially when there is overlap in their lifecycles and they share dispersal routes. This suggests that host enrichment alone is not a reliable indicator of beneficial host-microbe interactions, but increased time spent associated with a host can lead to new selection conditions, potentially favoring microbial adaptations towards a host-associated lifestyle and laying the foundation for the evolution of mutually beneficial coevolved symbioses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Zohreh Riahi Rad, Zahra Riahi Rad, Hossein Goudarzi, Mehdi Goudarzi, Mohammad Mahmoudi, Javad Yasbolaghi Sharahi, Ali Hashemi
Summary: miRNAs play a critical role in gene expression regulation, affecting biological or pathological processes by targeting specific mRNAs. Bacterial pathogens suppress host miRNA expression for their own benefit, while miRNAs have been extensively studied in the interaction between host and bacterial pathogens.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Ecology
Jacob A. Rasmussen, Pia Kiilerich, Abdullah S. Madhun, Rune Waagbo, Erik-Jan R. Lock, Lise Madsen, M. Thomas P. Gilbert, Karsten Kristiansen, Morten T. Limborg
Summary: Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform our understanding of adaptive phenotypic traits. This study reveals a strong co-evolution between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations, indicating an interplay between the host and its resident bacteria.
Article
Microbiology
Qiuyu Ma, Yonghong Cui, Xu Chu, Guoqiang Li, Meijiao Yang, Rong Wang, Guanghong Liang, Songqing Wu, Mulualem Tigabu, Feiping Zhang, Xia Hu
Summary: The gut microbiota of insects play a crucial role in influencing the host's health and behavior, which can be influenced by the host's environment and diet. This study found significant differences in morphological traits and gut microbiota diversity of Lymantria xylina fed on different diets, indicating vertical inheritance without changes during development. The results help understand the impact of microbial symbiosis on L. xylina and offer new possibilities for controlling these bacteria.
Article
Medicine, Research & Experimental
Yaoxian Xiang, Chan Zhang, Jing Wang, Yurong Cheng, Li Wang, Yingying Tong, Dong Yan
Summary: This study used Mendelian randomization (MR) analysis to identify a causal relationship between gut microbiota and colorectal cancer (CRC), and revealed a possible correlation between genes and pathogenic microbiota in CRC patients. These findings suggest that studying the gut microbiome and its further multi-omics analysis is crucial for the prevention and treatment of CRC.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Dentistry, Oral Surgery & Medicine
S. F. Yang, C. W. Lin, C. Y. Chuang, Y. C. Lee, W. H. Chung, H. C. Lai, L. C. Chang, S. C. Su
Summary: This study conducted a microbiome genome-wide association study in patients with oral squamous cell carcinoma and noncancer individuals, identifying associations between specific genetic loci and oral microbiota composition. These loci were found to be enriched for genes involved in the regulation of oncogenic and angiogenic responses, highlighting a genetic influence on the structure of oral microbial communities.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Guan-Hong Wang, Jessica Dittmer, Brecia Douglas, Long Huang, Robert M. Brucker
Summary: Researchers exposed parasitoid wasps to the herbicide atrazine for multiple generations and found that atrazine exposure led to adaptive changes in the microbiome and host genome, as well as alterations in gene expression and immune response. Microbiome transplant experiments showed that the evolved microbiome of the atrazine-exposed population decreased survival rates of adult wasps from the control population, indicating xenobiotic-induced selection mediated host-microbiome coadaptation, leading to a new host genome-microbiome equilibrium.
Article
Multidisciplinary Sciences
Suguru Nishijima, Naoyoshi Nagata, Yuya Kiguchi, Yasushi Kojima, Tohru Miyoshi-Akiyama, Moto Kimura, Mitsuru Ohsugi, Kohjiro Ueki, Shinichi Oka, Masashi Mizokami, Takao Itoi, Takashi Kawai, Naomi Uemura, Masahira Hattori
Summary: This study investigates the indigenous bacteriophage communities in the human gut and their relationship with the bacterial communities and anti-viral defense mechanisms. The distribution of host bacteria is found to be a key factor in determining the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defense mechanisms of the bacteriome. Various factors, including age, sex, lifestyle, diet, disease, and medication, significantly affect the virome structure.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Henan Zhang, Junrui Wu, Na Li, Rina Wu, Wei Chen
Summary: Inflammatory bowel disease (IBD) is associated with complex complications that may lead to tumors. An imbalance in the host gut microbiota often accompanies intestinal inflammation. This review examines the relationship between gut barrier disruption, unbalanced microbial translocation, and their impact on various organs and tumor initiation.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2023)
Review
Engineering, Multidisciplinary
Jiachao Zhang, Rob Knight
Summary: Next-generation sequencing technology has revolutionized our ability to study the taxonomic composition and functions of host-associated microbiota and microbiomes. In the next decade, there will be an increase in human microbiome research projects, particularly those focusing on genomic mutations within the microbiome. This review discusses the coevolution of microbes within a microbiome, the relationship between microbial genomic mutations and metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Furthermore, it explores advancements in methods and algorithms for annotating and analyzing microbial genomic mutations.
Article
Nutrition & Dietetics
Congmei Xiao, Jia-ting Wang, Chang Su, Zelei Miao, Jun Tang, Yifei Ouyang, Yan Yan, Zengliang Jiang, Yuanqing Fu, Menglei Shuai, Wanglong Gou, Fengzhe Xu, Evan Y-W Yu, Yuhui Liang, Xinxiu Liang, Yunyi Tian, Jiali Wang, Feifei Huang, Bing Zhang, Huijun Wang, Yu-ming Chen, Ju-Sheng Zheng
Summary: This study investigates the relationship between dietary diversity and the gut environment as well as host metabolism using a multiomics approach. The results suggest that high dietary diversity is associated with a diverse gut microbiota and specific gut microbial features and metabolites. These findings provide potential hypotheses for further research in preventing metabolic diseases.
AMERICAN JOURNAL OF CLINICAL NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Giorgos Skoufos, Filippos S. Kardaras, Athanasios Alexiou, Ioannis Kavakiotis, Anastasia Lambropoulou, Vasiliki Kotsira, Spyros Tastsoglou, Artemis G. Hatzigeorgiou
Summary: Peryton is a database of experimentally supported microbe-disease associations, curated manually from biomedical articles. It offers various functionalities for users to query multiple microorganisms and diseases simultaneously, with advanced filtering options and interactive visualizations available for refined results and enhanced user experience.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
Francesco Di Pierro
Summary: The enterotype is an early classification of bacterial consortia in the human gut microbiota, with different models describing clusters or continuous gradients. These models have highlighted correlations between specific enterotypes and characteristics, such as predisposition towards certain pathologies. Analysis of water content in stool has allowed further sub-division of enterotypes, indicating potential clinical applications in preventive medicine.
Article
Microbiology
Pil Soo Kim, Na-Ri Shin, Jae-Bong Lee, Min-Soo Kim, Tae Woong Whon, Dong-Wook Hyun, Ji-Hyun Yun, Mi-Ja Jung, Joon Yong Kim, Jin-Woo Bae
Summary: This study comprehensively characterized gut bacterial communities in fish, revealing that the dominant phyla were Proteobacteria and Firmicutes. The gut microbiota in fish was more strongly influenced by host habitat than by host taxonomy or trophic level.
Article
Biochemistry & Molecular Biology
Edda Russo, Leandro Di Gloria, Matteo Cerboneschi, Serena Smeazzetto, Gian Paolo Baruzzi, Francesca Romano, Matteo Ramazzotti, Amedeo Amedei
Summary: In this study, the variation in facial skin microbiome architecture through aging and its functional association with host genetic factors were investigated in a cohort of healthy women. The facial skin microbiota showed different composition in different age groups and between normal and dry skins. Functional variations associated with collagen biosynthesis and oxidative stress damage repair were observed in middle-aged women.
Article
Ecology
Stefano Giaimo, Arne Traulsen
Summary: A common measure of generation time is the average distance between recruitment events along a genetic lineage. When the environment fluctuates, the calculation of generation time must take into account the elasticities of the stochastic growth rate to fecundities. Additionally, generation time in fluctuating environments may deviate from the average environment.
AMERICAN NATURALIST
(2023)
Article
Multidisciplinary Sciences
Maria Alejandra Ramirez, Matteo Smerlak, Arne Traulsen, Juergen Jost
Summary: Social dilemmas involve conflicts between collective welfare and individual gain. The Traveler's Dilemma, a well-studied example, highlights the conflict between human behavior and game theoretic reasoning. Players are motivated to undercut their opponent, leading to a mutual undercutting until the lowest possible payoff is reached. However, if players were satisfied with a high payoff, both individuals and the collective would benefit. Our analysis reveals that escaping local maximization and transitioning to a global game is necessary to achieve the cooperative equilibrium. Diversity, represented by suboptimal strategies, plays a crucial role in facilitating the transition towards cooperation.
SCIENTIFIC REPORTS
(2023)
Article
Ecology
Michael Raatz, Arne Traulsen
Summary: When cancers or bacterial infections occur, a small group of cells need to escape regulation, evolve and adapt to their environment. The shape of the fitness landscape determines the adaptation trajectory of birth and death rates. Treatment strategies targeting both birth and death rates are most effective but increase evolvability. By mapping physiological adaptation pathways and molecular drug mechanisms to traits and treatments with clear eco-evolutionary consequences, we can better understand the dynamics of cancer and bacterial infections.
Article
Biochemistry & Molecular Biology
Henry Goehlich, Olivia Roth, Michael Sieber, Cynthia M. Chibani, Anja Poehlein, Jelena Rajkov, Heiko Liesegang, Carolin C. Wendling
Summary: Infections by filamentous phages can influence bacterial fitness, with the production of viral particles being energetically costly. Bacteria can evolve resistance if the costs outweigh the benefits, shortening phage epidemics. The impact of abiotic conditions on host resistance evolution is still unknown.
Article
Biology
Arne Traulsen, Nikoleta E. Glynatsi
Summary: Evolutionary game theory is an interdisciplinary subject that extends beyond biology, attracting mathematicians, social scientists, and computer scientists. The field has the potential for convergence or continued cross-fertilization between different disciplines, as insights are discovered and applied in various fields. The popularity of evolutionary game theory lies in its explanatory power and intuitive models.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Arne Traulsen, Simon A. Levin, Chadi M. Saad-Roy
Summary: Individual and societal reactions to a pandemic can create social dilemmas. The extent of regulations to reduce transmission is small in most countries, resulting in interventions driven by individual decision-making. We propose a framework to quantify this situation based on protection, infection risk, and intervention costs, and discuss the tension between individual and societal benefits.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L. Staubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Hafliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma Slack
Summary: This study used genetically barcoded Bacteroides thetaiotaomicron strains to quantify population bottlenecks during colonization of the mouse gut. The results showed an inverse relationship between microbiota complexity and the colonization probability of wildtype B. theta clones. The polysaccharide capsule of B. theta is important for resistance against attacks, and the acapsular strain loses in competitive colonization.
Article
Biology
Yuanyuan Ma, Jinru He, Michael Sieber, Jakob von Frieling, Iris Bruchhaus, John F. F. Baines, Ulf Bickmeyer, Thomas Roeder
Summary: The close relationship between animals and their associated microbiota is beneficial for both partners. The flatworm Macrostomum lignano was used as a model to study the host-microbiota interaction in detail. The study found that different developmental stages of the flatworm have specific microbiota and that the microbiota plays a physiological role in the host's fitness, particularly under conditions of limited food supply. The microbiota of M. lignano exhibits a circadian rhythm and influences the behavior of specific bacterial taxa, while the presence of the worm affects the composition of bacterial communities in the environment. Overall, this study provides insights into host-microbe interactions in marine invertebrates using the Macrostomum-microbiota system.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Nancy Obeng, Anna Czerwinski, Daniel Schuetz, Jan Michels, Jan Leipert, Florence Bansept, Maria J. Garcia Garcia, Thekla Schultheiss, Melinda Kemlein, Janina Fuss, Andreas Tholey, Arne Traulsen, Holger Sondermann, Hinrich Schulenburg
Summary: This study identified microbial traits that mediate adaptation to hosts by experimentally evolving a free-living bacterium in the presence of a nematode host. The researchers found that the evolution of beneficial host-specialist bacteria was associated with increased biofilm formation, which was caused by mutations that upregulate the bacterial second messenger, cyclic diguanylate (c-di-GMP). Further experiments confirmed that upregulation of c-di-GMP consistently increased host association in different Pseudomonas strains and species.
NATURE MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sedigheh Yagoobi, Nikhil Sharma, Arne Traulsen
Summary: The structure of a population greatly impacts its evolutionary dynamics, with individuals interacting more often with those nearby. Evolutionary graph theory is commonly used to model population structure, where nodes represent reproducing individuals and links connect them to their neighbors. By replacing single individuals with subpopulations at nodes, a graph-structured metapopulation is formed. The dynamics between local subpopulations are determined by update mechanisms.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Multidisciplinary Sciences
Felix Geoffroy, Arne Traulsen, Hildegard Uecker
Summary: When vaccine supply is limited, careful consideration should be given to the allocation of available doses. Stretching the interval between first and second doses allows for faster vaccination of more individuals with the first dose, but there is concern that intermediate levels of immunity in partially vaccinated individuals may promote the evolution of vaccine escape mutants. Therefore, there is a trade-off between reducing the burden and the risk of vaccine escape evolution.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Ecology
Roman Zapien-Campos, Florence Bansept, Michael Sieber, Arne Traulsen
Summary: This study uses a mathematical model to investigate the effect of microbial inheritance from parents to offspring. The results show that even without selection, the inheritance of microbes can have a significant impact on hosts with shorter lifespans or limited colonization, particularly in terms of acquiring rare microbes.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Roman Zapien-Campos, Michael Sieber, Arne Traulsen
Summary: Theoretical models are useful for understanding the drivers of community dynamics. In the case of neutral models, the predictions may not be robust to type-specific rates. Large immigration and biodiversity can lead to the occurrence-abundance pattern regardless of neutral or non-neutral rates.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
