Article
Multidisciplinary Sciences
Laura Vega, Giovanny Herrera, Marina Munoz, Manuel A. Patarroyo, Jenny G. Maloney, Monica Santin, Juan David Ramirez
Summary: This study investigated the co-occurrence of Blastocystis and Clostridioides difficile infections in patients, revealing a higher abundance of beneficial bacteria in B+/C+ patients. No statistical differences were observed in eukaryotic communities between the study groups. This provides preliminary descriptive information on potential microbiota profiling in this rare scenario.
Article
Microbiology
Jennifer J. Dawkins, Jessica R. Allegretti, Travis E. Gibson, Emma McClure, Mary Delaney, Lynn Bry, Georg K. Gerber
Summary: This study conducted a longitudinal analysis of the gut microbiome and metabolome changes in patients with primary Clostridioides difficile infection (CDI). The results showed that metabolomic data can accurately predict the recurrence of CDI, providing important insights for the development of diagnostic tests and treatments.
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
Multidisciplinary Sciences
Giovanny Herrera, Laura Vega, Manuel Alfonso Patarroyo, Juan David Ramirez, Marina Munoz
Summary: The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Different microbiota compositions were found in CDI positive groups, with intrahospital-acquired diarrhea playing a significant role in modulating bacterial, archaea, and eukaryotic populations in the intestines. Interactions between bacteria and eukaryotes in the intestinal ecosystem were also highlighted as important for understanding CDI pathophysiology.
SCIENTIFIC REPORTS
(2021)
Review
Gastroenterology & Hepatology
Giovanny Herrera, Daniel Paredes-Sabja, Manuel Alfonso Patarroyo, Juan David Ramirez, Marina Munoz
Summary: Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, with altered intestinal microbiota composition. Microbial species from different domains are associated with CDI, and understanding the relationships among microorganisms may lead to new predictive factors for infection and improved treatment options, reducing morbidity and mortality.
Article
Immunology
Si Yu, Xiaomeng Ge, Hui Xu, Bei Tan, Bowen Tian, Yujie Shi, Yimin Dai, Yue Li, Songnian Hu, Jiaming Qian
Summary: This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. The results showed that IBD patients with CDI had decreased bacterial alpha diversity and significant differences in bacterial and fungal beta diversity compared to healthy individuals and IBD patients without CDI. Specific bacterial and fungal taxa were overrepresented in IBD patients with CDI. These findings provide insights into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Susan Hromada, Yili Qian, Tyler B. Jacobson, Ryan L. Clark, Lauren Watson, Nasia Safdar, Daniel Amador-Noguez, Ophelia S. Venturelli
Summary: This study explores the principles of gut microbiome colonization resistance to the pathogen Clostridioides difficile, demonstrating a strong negative interaction between C. difficile and other species, inhibition mechanisms such as environment acidification and resource competition were identified. Increasing the initial density of C. difficile can increase its abundance in the community, but the maximum achievable abundance is determined by the community context.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Review
Microbiology
Iulia-Magdalena Vasilescu, Mariana-Carmen Chifiriuc, Gratiela Gradisteanu Pircalabioru, Roxana Filip, Alexandra Bolocan, Veronica Lazar, Lia-Mara Ditu, Coralia Bleotu
Summary: This review focuses on the gut microbiota profiles in individuals colonized or infected with Clostridioides difficile. The study found that CDI patients have decreased gut microbiota diversity and resilience, with an abundance of Proteobacteria and lower levels of butyrogenic and lactic acid-bacteria. In infants, colonization with specific bacteria and immunological factors may explain the lack of clinical symptoms. Gut dysbiosis can be improved through administration of biotics or non-toxigenic C. difficile preparations and fecal microbiota transplantation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Sang Hoon Lee, Han-Ki Park, Chang Don Kang, Dae Hee Choi, Sung Chul Park, Jin Myung Park, Seung-Joo Nam, Gi Bong Chae, Kyoung Yul Lee, Hyunseok Cho, Sung Joon Lee
Summary: The study suggests that vitamin D supplementation may increase the abundance of beneficial bacteria and could potentially be used in the treatment of Clostridioides difficile infections (CDI).
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Jian Wan, Yujie Zhang, Wenfang He, Zuhong Tian, Junchao Lin, Zhenzhen Liu, Yani Li, Min Chen, Shuang Han, Jie Liang, Yongquan Shi, Xuan Wang, Lei Zhou, Ying Cao, Jiayun Liu, Kaichun Wu
Summary: Patients with ulcerative colitis (UC) are at a higher risk of developing Clostridioides difficile infection (CDI), but the gut microbial structure and metabolites in UC and CDI patients have been poorly studied. This study identifies significant differences in gut microbiota and metabolites between UC and CDI patients compared to those with UC alone.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexander B. Smith, Matthew L. Jenior, Orlaith Keenan, Jessica L. Hart, Jonathan Specker, Arwa Abbas, Paula C. Rangel, Chao Di, Jamal Green, Katelyn A. Bustin, Jennifer A. Gaddy, Maribeth R. Nicholson, Clare Laut, Brendan J. Kelly, Megan L. Matthews, Daniel R. Evans, Daria Van Tyne, Emma E. Furth, Jason A. Papin, Frederic D. Bushman, Jessi Erlichman, Robert N. Baldassano, Michael A. Silverman, Gary M. Dunny, Boone M. Prentice, Eric P. Skaar, Joseph P. Zackular
Summary: Enterococci can shape the metabolic environment in the gut and enhance the fitness and pathogenesis of Clostridioides difficile through nutrient restriction and cross-feeding. This microbial interaction plays a role in the susceptibility to and the severity of C. difficile infection.
Review
Medicine, General & Internal
Teena Chopra, Gail Hecht, Glenn Tillotson
Summary: Clostridioides difficile infection poses challenges due to its recurrent nature, and current antibiotic management does not address the underlying issue of dysbiosis. Restoring the microbiome through therapies like live biotherapeutics can lead to positive clinical outcomes. Several such therapies are currently being investigated.
FRONTIERS IN MEDICINE
(2023)
Review
Microbiology
Elisa Martinez, Bernard Taminiau, Cristina Rodriguez, Georges Daube
Summary: This review investigates the relationship between gut microbiota and Clostridioides difficile infection and colonization. Factors such as antibiotics, proton pump inhibitors, hospitalization, and age increase the risk of C. difficile infection. Colonized individuals show altered gut microbiota while CDI patients have reduced abundances of certain bacteria.
Article
Gastroenterology & Hepatology
Shanlin Ke, Nira R. Pollock, Xu-Wen Wang, Xinhua Chen, Kaitlyn Daugherty, Qianyun Lin, Hua Xu, Kevin W. Garey, Anne J. Gonzales-Luna, Ciaran P. Kelly, Yang-Yu Liu
Summary: The study highlights the sensitivity of interactions between gut microbiota and host immune markers to the status of C. difficile colonization and infection. Utilizing both types of data can improve the distinction between CDI and other groups. Symbolic classification using selected features resulted in simple mathematical formulas that explicitly quantify the interactions between the gut microbiome and host immune markers.
Article
Public, Environmental & Occupational Health
Ashley Bartlett, Anna Montgomery, Kimberly Hammer, Siddharth Singhal, Tze Shien Lo
Summary: This study examines the impact of a policy change on C. difficile testing and treatment initiation time. The results show that allowing bedside nurses to order tests significantly decreases the time to receive results. This change may reduce the risk of infections among patients and lessen the economic burden on hospitals.
AMERICAN JOURNAL OF INFECTION CONTROL
(2023)
Article
Biotechnology & Applied Microbiology
Carl Simon Strittmatter, Anja Poehlein, Axel Himmelbach, Rolf Daniel, Alexander Steinbuchel
Summary: The number of genes encoding beta-oxidation enzymes in Cupriavidus necator H16 is high, but only two operons, A0459-A0464 and A1526-A1531, were expressed during growth with long-chain-length fatty acids (LCFAs). The deletion of these operons had a negative effect on growth with longer chain fatty acids. RNA-Seq analysis revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Ines Friedrich, Alisa Kuritsyn, Robert Hertel, Rolf Daniel
Summary: The present study describes a novel species within the genus Luteibacter (EIF3(T)). The strain was analyzed genomically, morphologically and physiologically and identified as a new species of Luteibacter. In silico analysis indicated the presence of two putative prophages. The bacterial strain exhibits an elliptical morphotype with multiple flagella at one end and is resistant to certain antibiotics.
Article
Multidisciplinary Sciences
Delphine Clara Zemp, Nathaly Guerrero-Ramirez, Fabian Brambach, Kevin Darras, Ingo Grass, Anton Potapov, Alexander Roell, Isabelle Arimond, Johannes Ballauff, Hermann Behling, Dirk Berkelmann, Siria Biagioni, Damayanti Buchori, Dylan Craven, Rolf Daniel, Oliver Gailing, Florian Ellsaesser, Riko Fardiansah, Nina Hennings, Bambang Irawan, Watit Khokthong, Valentyna Krashevska, Alena Krause, Johanna Kueckes, Kevin Li, Hendrik Lorenz, Mark Maraun, Miryam Sarah Merk, Carina C. M. Moura, Yeni A. Mulyani, Gustavo B. Paterno, Herni Dwinta Pebrianti, Andrea Polle, Di Ajeng Prameswari, Lena Sachsenmaier, Stefan Scheu, Dominik Schneider, Fitta Setiajiati, Christina Ani Setyaningsih, Leti Sundawati, Teja Tscharntke, Meike Wollni, Dirk Hoelscher, Holger Kreft
Summary: There are still knowledge gaps in how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes in the United Nations Decade on Ecosystem Restoration. This study presents findings from a 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, showing higher indicators of biodiversity and ecosystem functioning in tree islands compared to conventionally managed oil palm. Enriching oil palm-dominated landscapes with tree islands is a promising ecological restoration strategy that does not decrease oil palm yield.
Article
Environmental Sciences
Jimyung Moon, Anja Schubert, Anja Poehlein, Rolf Daniel, Volker Mueller
Summary: To inactivate the Wood-Ljungdahl pathway in Acetobacterium woodii, two subunits of the methylene-tetrahydrofolate reductase were genetically deleted. The mutant was unable to grow on C1 compounds, lactate, ethanol, or butanediol, but could grow on fructose with lower rates and yields compared to the wild-type. Growth on fructose was restored by the addition of an external electron sink, such as glycine betaine + CO2 or caffeate. Transcriptome analyses revealed enzymes potentially involved in mixed acid fermentation (MAF) from fructose in A. woodii.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Ines Friedrich, Hannes Neubauer, Alisa Kuritsyn, Bernhard Bodenberger, Faina Tskhay, Sara Hartmann, Anja Poehlein, Mechthild Boemeke, Michael Hoppert, Dominik Schneider, Robert Hertel, Rolf Daniel
Summary: By investigating host-associated metaviromes, we found that the classical isolation technique may miss the diversity of non-plaque forming phages. Through direct plaque-based isolation using new hosts, we discovered a higher phage diversity in Brevundimonas and Serratia. This study demonstrates the potential of combining metavirome analysis with traditional isolation techniques to reveal further phage diversity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Green & Sustainable Science & Technology
Najeeb Al-Amin Iddris, Greta Formaglio, Carola Paul, Volker von Gross, Guantao Chen, Andres Angulo-Rubiano, Dirk Berkelmann, Fabian Brambach, Kevin F. A. Darras, Valentyna Krashevska, Anton Potapov, Arne Wenzel, Bambang Irawan, Muhammad Damris, Rolf Daniel, Ingo Grass, Holger Kreft, Stefan Scheu, Teja Tscharntke, Aiyen Tjoa, Edzo Veldkamp, Marife D. Corre
Summary: This full factorial experiment conducted in an Indonesian state-owned industrial oil palm plantation evaluated the effects of reduced management practices on ecosystem functions and biodiversity. The results showed that mechanical weeding exhibited higher multifunctionality and increased plant species diversity compared to herbicide treatment. Furthermore, reduced fertilization and mechanical weeding increased profit and gross margin while achieving similar yields.
NATURE SUSTAINABILITY
(2023)
Article
Microbiology
Dominik Schneider, Aygun Ganbarzade, Sina Post, Daniela Zuehlke, Tjorven Hinzke, Jacqueline Hollensteiner, Anja Poehlein, Katharina Riedel, Rolf Daniel
Summary: The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was found in a hospital wastewater sample in Greifswald, Germany. Its genome consists of one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome contains 5,322 coding sequences, shows high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Environmental Sciences
Vannesa Montoya-Sanchez, Holger Kreft, Isabelle Arimond, Johannes Ballauff, Dirk Berkelmann, Fabian Brambach, Rolf Daniel, Ingo Grass, Jes Hines, Dirk Hoelscher, Bambang Irawan, Alena Krause, Andrea Polle, Anton Potapov, Lena Sachsenmaier, Stefan Scheu, Leti Sundawati, Teja Tscharntke, Delphine Clara Zemp, Nathaly Guerrero-Ramirez
Summary: Increasing landscape heterogeneity through establishing tree islands in oil-palm plantations can enhance multi-taxa diversity, particularly due to the increased presence of soil fauna and habitat diversity. Soil fauna, bacteria, and fungi have a stronger association with the overall community than aboveground taxa, emphasizing the importance of considering soil biota in strategies to enhance multi-taxa diversity.
COMMUNICATIONS EARTH & ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Tim Boeer, Frank R. Bengelsdorf, Mechthild Boemeke, Rolf Daniel, Anja Poehlein
Summary: This study reports the complete genome sequences of acetogenic strains from the genus Terrisporobacter, along with functional annotation and pathway reconstruction analysis. The study also identifies species-specific nutrient requirements and constructs a model for acetogenesis in Terrisporobacter.
Article
Microbiology
Simone Anza, Dominik Schneider, Rolf Daniel, Michael Heistermann, Somboon Sangmaneedet, Julia Ostner, Oliver Schuelke
Summary: Maternal glucocorticoids (GCs) can have detrimental effects on offspring development, particularly during early gestation. This study found that high maternal GC levels during early gestation were associated with reduced bacterial richness in the offspring's gut microbiota. The effect of maternal GCs on the gut microbiota worsened with offspring age and was 10 times stronger than the effect of exposure during late prenatal or postnatal periods.
Article
Microbiology
Miriam Antonia Schueler, Rolf Daniel, Anja Poehlein
Summary: This study presents the complete genome of a non-toxigenic Clostridioides difficile strain isolated from horse feces. The genome consists of one chromosome and one plasmid, and encodes 3,798 putative genes. The strain represents a sub-cluster in the cryptic clade C-III.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Ecology
Benjamin Zeldes, Anja Poehlein, Surbhi Jain, Christoph Baum, Rolf Daniel, Volker Mueller, Mirko Basen
Summary: DNA uptake is a common mechanism in microorganisms for rapid adaptation to new environments. This study found that a thermophilic bacterium, Thermoanaerobacter kivui, adapted to high concentrations of carbon monoxide through a horizontal gene transfer event with another thermophile, Thermoanaerobacter sp. strain X514, within the laboratory. This transfer also led to the deletion of a native operon for thiamine biosynthesis, explaining why the adapted strain required added vitamins for growth.
ISME COMMUNICATIONS
(2023)
Article
Microbiology
Jacqueline Hollensteiner, Dominik Schneider, Anja Poehlein, Axel Himmelbach, Rolf Daniel
Summary: This study reports 10 particle-associated metagenome-assembled genomes (MAGs) from the mesopelagic zone of Pacific Ocean seawaters. Functional annotation suggests that these genomes are involved in central particulate organic carbon conversion, nitrogen cycling, and phosphorus cycling.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
