Article
Agriculture, Dairy & Animal Science
Aritra Roy Choudhury, Ji-Young Park, Do Young Kim, Jeongyun Choi, Satabdi Acharya, Jung-Ho Park
Summary: This study evaluates the gut bacterial diversity of rainbow trout exposed to oxy-tetracycline and predicts the metabolic functioning of the bacterial community. The results show that antibiotic treatment leads to changes in gut bacterial community composition and affects certain metabolic processes.
Article
Microbiology
Amruta Rajarajan, Justyna Wolinska, Jean-Claude Walser, Minea Mader, Piet Spaak
Summary: Host-associated bacterial communities play a crucial role in host fitness and disease resistance. This study investigates the tripartite interaction between a host, parasite, and host-associated bacterial communities in water fleas. The results reveal significant changes in the gut bacterial communities with the presence of parasite infection, including decreased alpha diversity and increased beta diversity. Specific bacterial taxa associated with infected hosts also appear. This study highlights the link between host-microbiota-infection and raises questions about the role of host-associated microbiota in natural disease epidemics.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Biology
Tian Zeng, Hong-Ai Su, Ya-Lan Liu, Jian-Fang Li, Ding-Xin Jiang, Yong-Yue Lu, Yi-Xiang Qi
Summary: This study found that serotonin plays an important role in regulating gut homeostasis and provides new insights into the gut-microbe interactions in metazoans.
Article
Biotechnology & Applied Microbiology
Stephanie P. Gill, Deric R. Learman, Mandy L. Annis, Daelyn A. Woolnough
Summary: This study investigated the effects of agricultural contaminants on the gut microbiota and physiology of freshwater mussels and their host fish. The results showed that the gut microbiota of the mussels were significantly affected by the contaminants, with an increase in potentially pathogenic bacteria. The study also revealed a core microbiota within both the mussels and the fish. In terms of physiology, the contaminated mussels exhibited decreased movement and marsupial gill display.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Patrick J. Hu
Summary: The study in C. elegans model showed that a conserved insulin-like signaling pathway plays an important role in shaping the phylogenetic composition of the gut microbiome.
Article
Environmental Sciences
Iresha Sumudumali, Chandramali Kumari Jayawardana, Sarath Malavipathirana, Sunethra Kanthi Gunatilake, Nimal Udayakumara
Summary: This study investigated the direct and indirect effects of the fungicide chlorothalonil on aquatic plankton community structure. The highest concentration levels of chlorothalonil exposure had a significant impact on certain phytoplankton and zooplankton taxa. Phytoplankton taxa Amphora sp. and Staurastrum sp., and zooplankton taxa Moina sp. and copepod Nauplius were highly sensitive to chlorothalonil exposure. However, the presence of chlorothalonil also led to an increase in the abundance of phytoplankton taxa Mougeotia sp. and did not significantly reduce the individuals of zooplankton taxa Aeolosoma sp.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Tianying Lyu, Jinyong Zhu, Xianming Yang, Wen Yang, Zhongming Zheng
Summary: This study tracked the dynamics of the gut microbiota in a freshwater gastropod to explore its response to cyanobacterial blooms. The results showed that exposure to cyanobacterial blooms led to decreased alpha diversity of the gut microbiota. Microcystins and water temperature were the primary factors influencing the gut microbial community. Additionally, differences in 14 metabolic pathways were observed between the two periods.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Parasitology
Ephantus J. Muturi, Teresia M. Njoroge, Christopher Dunlap, Carla E. Caceres
Summary: Mixed blood meals have a synergistic effect on operational taxonomic unit richness and Shannon diversity index in mosquito gut microbiota. Host species identity and mixed blood-feeding are key determinants of microbial community composition. Microenvironmental conditions play an important role in structuring mosquito gut microbial communities.
PARASITES & VECTORS
(2021)
Article
Ecology
Yunga Wu, Cao Hao, Zhijing Xie, Yufeng Zhang, Pingting Guan, Donghui Wu, Stefan Scheu
Summary: Distance-decay of similarity is observed in both environmental and geographic distance for soil and earthworm gut bacteria. The foregut of earthworms is most affected by environmental changes. These findings suggest that the gut passage of earthworms contributes to the similarity of soil microbial communities.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2023)
Article
Microbiology
Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss
Summary: Clostridioides difficile colonization can lead to a range of infection severities, from mild diarrhea to life-threatening conditions. While factors such as patient age, blood cell count, and C. difficile characteristics have been associated with disease severity, the role of specific gut bacteria in influencing severity is unclear. This study demonstrates that different gut bacterial communities can contribute to variations in Clostridioides difficile infection outcomes. Certain bacterial groups were associated with more severe outcomes, while others were associated with milder outcomes. Incorporating gut bacterial community data into severity models may aid in identifying at-risk patients and improving interventions.
Article
Microbiology
Siyue Zhao, Caiwu Li, Tao Zhu, Lei Jin, Wenwen Deng, Ke Zhao, Yongguo He, Guo Li, Yaowu Xiong, Ti Li, Bei Li, Yan Huang, Hemin Zhang, Likou Zou
Summary: The study revealed that giant pandas with anorexia have lower gut microbiota richness and significant differences in microbial structure compared to healthy ones. The increased abundance of phylum Firmicutes and unidentified genus Clostridiales, along with decreased Weissella and Streptococcus, may play a role in causing anorexia symptoms. Streptococcus could potentially be used as probiotics to control the growth of Clostridium associated with anorexia.
CURRENT MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kazuki Nagashima, Aishan Zhao, Katayoon Atabakhsh, Minwoo Bae, Jamie E. Blum, Allison Weakley, Sunit Jain, Xiandong Meng, Alice G. Cheng, Min Wang, Steven Higginbottom, Alex Dimas, Pallavi Murugkar, Elizabeth S. Sattely, James J. Moon, Emily P. Balskus, Michael A. Fischbach
Summary: Certain bacterial strains from the microbiome induce a potent T cell response, and many T cells in the gut repertoire recognize multiple bacterial strains. 13 T cell clones show a one-to-many TCR-to-strain relationship, recognizing 18 Firmicutes strains.
Article
Ecology
Meiqi Ma, Xiaotong Chen, Siqun Li, Jing Luo, Runhua Han, Letian Xu
Summary: Insect gut bacteria have a significant impact on the biology of the host, which can either benefit or harm the insect's fitness. This study investigated the gut bacterial community of the walnut leaf beetle throughout its life cycle using high-throughput sequencing. The results showed higher diversity in the gut bacterial community of larvae compared to adults, with young larvae having the most diverse and abundant community. The gut microbiota of adults formed distinct clusters, independent of the larvae. The dominant phyla were Proteobacteria and Firmicutes, with Enterobacter, Rosenbergiella, Erwinia, Pseudomonas, and Lactococcus as the main genera. Functional prediction revealed enrichment in metabolic pathways, specifically carbohydrate and amino acid metabolism. This study enhances our understanding of the gut microbiota of the walnut leaf beetle and its potential interactions with the host insect, aiding the development of microbial-based pest management strategies.
Article
Allergy
Christine L. M. Joseph, Alexandra R. Sitarik, Haejin Kim, Gary Huffnagle, Kei Fujimura, Germaine Jia Min Yong, Albert M. Levin, Edward Zoratti, Susan Lynch, Dennis R. Ownby, Nicholas W. Lukacs, Brent Davidson, Charles Barone, Christine Cole Johnson
Summary: This study found that variations in infant gut bacterial composition were associated with the risk of IgE-FA at age 3-5, including lack of bacterial diversity and deficiencies in specific operational taxonomic units. The results support dysbiosis as a factor in the pathogenesis of IgE-FA.
PEDIATRIC ALLERGY AND IMMUNOLOGY
(2022)
Article
Ecology
Anna S. Weiss, Anna G. Burrichter, Abilash Chakravarthy Durai Raj, Alexandra von Strempel, Chen Meng, Karin Kleigrewe, Philipp C. Muench, Luis Roessler, Claudia Huber, Wolfgang Eisenreich, Lara M. Jochum, Stephanie Goeing, Kirsten Jung, Chiara Lincetto, Johannes Huebner, Georgios Marinos, Johannes Zimmermann, Christoph Kaleta, Alvaro Sanchez, Baerbel Stecher
Summary: This study focuses on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community in gut microbiome research. By conducting experiments, it was found that the OMM12 interaction network is influenced by exploitative and interference competition, with Enterococcus faecalis KB1 identified as an important driver of community composition.
Article
Ecology
Rocco Tiberti, Francesco Buscaglia, Cristiana Callieri, Michela Rogora, Gabriele Tartari, Ruben Sommaruga
Article
Marine & Freshwater Biology
Javier Alcocer, Clara N. Delgado, Ruben Sommaruga
JOURNAL OF PLANKTON RESEARCH
(2020)
Article
Ecology
Nadine Werner, Maria Orfanoudaki, Anja Hartmann, Markus Ganzera, Ruben Sommaruga
Summary: Cyanobacteria, one of the oldest organisms on Earth, have developed adaptations to avoid the damaging effects of solar UV radiation, including the synthesis of sunscreen substances like mycosporine-like amino acids (MAAs). This study investigated the temporal dynamics of MAAs in a benthic algal community dominated by cyanobacteria in a clear alpine lake. Results showed that benthic cyanobacteria exhibited less pronounced temporal changes in MAAs concentration in response to changes in solar UV exposure compared to phytoplankton.
FRESHWATER BIOLOGY
(2021)
Article
Microbiology
Christopher M. Bellas, Ruben Sommaruga
Summary: Analysis of metaviromes from an alpine lake revealed abundant Polinton-like virus genome sequences, leading to the identification of 82 new Polinton-like viruses and the discovery of five major new groups of eukaryotic viruses linked to diverse eukaryotic hosts. The study suggests that Polintons in unicellular eukaryotes are viruses, supported by the presence of viral major capsid proteins in eukaryotic host transcriptomes. The findings highlight the diverse assemblage of globally distributed viruses associated with a wide range of unicellular eukaryotic hosts, and provide a foundation for continued discovery and analysis of these viral groups.
Article
Microbiology
Karel Kopejtka, Juergen Tomasch, Yonghui Zeng, Vadim Selyanin, Marko Dachev, Kasia Piwosz, Martin Tichy, David Bina, Zdenko Gardian, Boyke Bunk, Henner Brinkmann, Robert Geffers, Ruben Sommaruga, Michal Koblizek
Correction
Microbiology
Christopher M. Bellas, Ruben Sommaruga
Summary: An amendment to this paper has been published and is accessible through the original article.
Article
Microbiology
Karel Kopejtka, Yonghui Zeng, David Kaftan, Vadim Selyanin, Zdenko Gardian, Juergen Tomasch, Ruben Sommaruga, Michal Koblizek
Summary: Strain AAP5 is an aerobic bacterium producing bacteriochlorophyll a, belonging to the genus Sphingomonas with a close phylogenetic relationship to Sphingomonas glacialis. It has a genomic DNA G + C content of 65.9% and shared 76.2% orthologous gene clusters with Sphingomonas paucimobilis, supporting their classification into the same genus.
Article
Multidisciplinary Sciences
Stephen F. Jane, Gretchen J. A. Hansen, Benjamin M. Kraemer, Peter R. Leavitt, Joshua L. Mincer, Rebecca L. North, Rachel M. Pilla, Jonathan T. Stetler, Craig E. Williamson, R. Iestyn Woolway, Lauri Arvola, Sudeep Chandra, Curtis L. DeGasperi, Laura Diemer, Julita Dunalska, Oxana Erina, Giovanna Flaim, Hans-Peter Grossart, K. David Hambright, Catherine Hein, Josef Hejzlar, Lorraine L. Janus, Jean-Philippe Jenny, John R. Jones, Lesley B. Knoll, Barbara Leoni, Eleanor Mackay, Shin-Ichiro S. Matsuzaki, Chris McBride, Dorthe C. Muller-Navarra, Andrew M. Paterson, Don Pierson, Michela Rogora, James A. Rusak, Steven Sadro, Emilie Saulnier-Talbot, Martin Schmid, Ruben Sommaruga, Wim Thiery, Piet Verburg, Kathleen C. Weathers, Gesa A. Weyhenmeyer, Kiyoko Yokota, Kevin C. Rose
Summary: The concentration of dissolved oxygen in aquatic systems plays a crucial role in regulating biodiversity, nutrient biogeochemistry, greenhouse gas emissions, and drinking water quality. Climate change and human activities have led to declines in dissolved oxygen in lakes, impacting the physical and chemical environment, as well as essential ecosystem services.
Article
Environmental Sciences
Benjamin M. Kraemer, Rachel M. Pilla, R. Iestyn Woolway, Orlane Anneville, Syuhei Ban, William Colom-Montero, Shawn P. Devlin, Martin T. Dokulil, Evelyn E. Gaiser, K. David Hambright, Dag O. Hessen, Scott N. Higgins, Klaus D. Johnk, Wendel Keller, Lesley B. Knoll, Peter R. Leavitt, Fabio Lepori, Martin S. Luger, Stephen C. Maberly, Dorthe C. Mueller-Navarra, Andrew M. Paterson, Donald C. Pierson, David C. Richardson, Michela Rogora, James A. Rusak, Steven Sadro, Nico Salmaso, Martin Schmid, Eugene A. Silow, Ruben Sommaruga, Julio A. A. Stelzer, Dietmar Straile, Wim Thiery, Maxim A. Timofeyev, Piet Verburg, Gesa A. Weyhenmeyer, Rita Adrian
Summary: Long-term temperature changes in lakes lead to thermal habitat changes, exacerbated by seasonal and depth-related constraints. Tropical lakes show higher thermal non-overlap compared to lakes at other latitudes, and lakes with high biodiversity and endemism exhibit higher thermal habitat changes.
NATURE CLIMATE CHANGE
(2021)
Article
Ecology
Rebecca Oester, Ryan Greenway, Marvin Moosmann, Ruben Sommaruga, Barbara Tartarotti, Jakob Brodersen, Blake Matthews
Summary: This study investigated the effect of Arctic charr and threespine stickleback on the photoprotective phenotype of the copepod Leptodiaptomus minutus in lake ecosystems in southern Greenland. The results showed that lakes with stickleback had the lowest average content of astaxanthin and mycosporine-like amino acids (MAAs), and these compounds were not affected by the presence of charr. Furthermore, there was a higher variance in astaxanthin among copepods in the presence of stickleback, and the content of astaxanthin was negatively correlated with increasing stickleback density.
ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Barbara Tartarotti, Ruben Sommaruga, Nadine Saul
Summary: This study investigates the phenotypic and molecular responses of copepods to different environmental conditions and UV radiation in alpine lakes. The researchers found variations in photoprotective compounds and antioxidant capacities between copepod populations from different lakes, as well as seasonal changes in copepod gene expression. The expression patterns of heat shock protein genes were influenced by phenotypic traits, particularly the hsp70 gene. These findings suggest that copepods have adaptive responses to environmental stressors, which may be crucial for their survival in alpine lakes.
FRESHWATER BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Karel Kopejtka, Jurgen Tomasch, David Kaftan, Alastair T. Gardiner, David Bina, Zdenko Gardian, Christopher Bellas, Astrid Droge, Robert Geffers, Ruben Sommaruga, Michal Koblizek
Summary: Bacterium Sphingomonas glacialis AAP5 isolated from an alpine lake has the ability to use both bacteriochlorophyll-based photosystems and proton-pumping rhodopsins to harvest light energy, depending on temperature and light conditions. This allows the bacteria to adapt to changing environmental conditions and optimize their light-harvesting machinery accordingly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Marine & Freshwater Biology
Erik Jeppesen, Thomas A. Davidson, Mariana Meerhoff, Luc De Meester, Ivan Gonzalez-Bergonzoni, Nicolas Vidal, Hartmut Arndt, Klaus Juergens, Ruben Sommaruga, Korhan Ozkan, Torben L. Lauridsen, Sh Tserenpil
Summary: With the retreat of glaciers, new ponds and lakes are formed, which become more productive as vegetation develops. Our study in West Greenland found that older lakes had higher nutrient concentrations and organic matter content, as well as higher biomass and richness of certain aquatic organisms. The food web in the older lakes was more complex, with a longer food chain and higher taxonomic diversity, suggesting a succession process following glacial retreat.
Article
Multidisciplinary Sciences
Christopher Bellas, Thomas Hackl, Marie-Sophie Plakolb, Anna Koslova, Matthias G. Fischer, Ruben Sommaruga
Summary: Eukaryotic genomes contain endogenous viral elements (EVEs) derived from RNA and ssDNA viruses, which are considered genomic fossils. However, the study of EVEs has focused mostly on animals and plants, neglecting protists. This study reveals that protist genomes contain diverse dsDNA viruses, including virophages and Polinton-like viruses, which were hidden due to their repetitive nature. The study suggests that many protist EVEs are intact, actively colonizing hosts across the eukaryotic tree, and may be functional viruses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Agricultural Economics & Policy
Ruben Sommaruga, Honor May Eldridge
Summary: The avocado market is rapidly expanding globally, but production is facing significant water conflicts and environmental issues. Urgent action is needed to address these issues, with support from key stakeholders and consumer participation in ethical consumption and environmental conservation.
