Article
Microbiology
Mary Hannah Swaney, Shelby Sandstrom, Lindsay R. Kalan
Summary: The skin microbiome plays a crucial role in maintaining skin health, and cobamide sharing may mediate dynamics within skin microbial communities.
Article
Oncology
Ricardo Costeira, Laila Evangelista, Rory Wilson, Xinyu Yan, Fabian Hellbach, Lucy Sinke, Colette Christiansen, Sergio Villicana, Olatz Masachs, Pei-Chien Tsai, Massimo Mangino, Cristina Menni, Sarah Berry, Marian Beekman, Diana van Heemst, P. Eline Slagboom, Bastiaan Heijmans, Karsten Suhre, Gabi Kastenmueller, Christian Gieger, Annette Peters, Kerrin Small, Jakob Linseisen, Melanie Waldenberger, Jordana Bell
Summary: This study investigates blood metabolomic biomarkers of folate and vitamins B6 and B12 and carries out epigenome-wide analyses across three European cohorts. The results show that intake of B vitamins is associated with specific metabolites and differentially methylated positions in the epigenome.
CLINICAL EPIGENETICS
(2023)
Article
Multidisciplinary Sciences
Huang Lin, Merete Eggesbo, Shyamal Das Peddada
Summary: SECOM is a tool for analyzing linear and nonlinear relationships in microbiome data, and it demonstrates superior performance in human skin and infant gut microbiome data. The SECOM method proposed in the paper is able to explore previously undescribed interactions among microbiomes.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Sydney B. Wizenberg, Laura R. Newburn, Rodney T. Richardson, Mateus Pepinelli, Ida M. Conflitti, Mashaba Moubony, Daniel Borges, M. Marta Guarna, Ernesto Guzman-Novoa, Leonard J. Foster, Amro Zayed
Summary: Honey bees, traditionally known as pollinators of flowering plants, may also play a role in dispersing non-flowering plant taxa. The study sheds light on the broad impact of honey bees on plant-pollinator interactions and suggests their potential role as vectors of gene flow.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Miaoxiao Wang, Xiaonan Liu, Yong Nie, Xiao-Lei Wu
Summary: Microbes release public goods to benefit the population, leading to metabolic cross-feeding. Through simulations, it was found that genotypes could evolve from autonomous ancestors to develop three types of interdependent patterns influenced by function cost and redundancy. Additionally, random evolutionary events and the positioning of genotype emergence play important roles in governing community assembly.
Review
Biotechnology & Applied Microbiology
Yanyan Wang, Linxia Liu, Zhaoxia Jin, Dawei Zhang
Summary: Vitamins are essential for maintaining normal metabolism and health, with wide applications in various industries. Using microbial cell factories for vitamin production is both environmentally friendly and economically sustainable, covering water-soluble and fat-soluble vitamins.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Manon A. Morin, Anneliese J. Morrison, Michael J. Harms, Rachel J. Dutton
Summary: Non-pairwise interactions, or higher-order interactions (HOIs), have been identified as significant drivers of emergent features in microbial communities. This study investigated the re-organization of microbial interactions between pairwise cultures and larger communities in a simple microbiome. The results showed a deep reorganization of interaction-associated mutants and the emergence of multiple HOIs. Furthermore, quantitative genetics analysis revealed that 82% of conserved interactions followed an additive pattern.
SCIENTIFIC REPORTS
(2022)
Review
Food Science & Technology
Palni Kundra, Carole Rachmuhl, Christophe Lacroix, Annelies Geirnaert
Summary: In patients with inflammatory bowel diseases (IBD), low dietary micronutrient intake and deficiencies are common, which may also affect the functioning of the gut microbiota. There is a need for further research to understand the mechanisms of micronutrient-microbiome-host interactions and their role in alleviating inflammation in IBD.
MOLECULAR NUTRITION & FOOD RESEARCH
(2021)
Article
Materials Science, Biomaterials
Mattia Saggioro, Stefania D'Agostino, Anna Gallo, Sara Crotti, Sara D'Aronco, Diana Corallo, Giulia Veltri, Gabriele Martinez, Antonella Grigoletto, Anna Maria Tolomeo, Giovanni Tafuro, Marco Agostini, Sanja Aveic, Valentina Serafin, Alessandra Semenzato, Gianfranco Pasut, Michela Pozzobon
Summary: Hydrogels offer important advantages for 3D cell culture, and a biocompatible hyaluronic acid-polyethylene glycol hydrogel was developed to study the migratory behavior of alveolar rhabdomyosarcoma cells. Proteomic analysis revealed the composition of the extracellular matrix, and the optimal hydrogel for ARMS cell growth was selected based on various factors. The study validated the role of the fibronectin receptor ITGA5 in ARMS cell migration and investigated key pathways using a reverse phase protein array to understand potential hallmarks of cancer cell resistance and dissemination.
BIOMATERIALS SCIENCE
(2021)
Article
Biodiversity Conservation
Yuqi Zhou, Baoyu Sun, Baohua Xie, Kai Feng, Zhaojing Zhang, Zheng Zhang, Shuzhen Li, Xiongfeng Du, Qi Zhang, Songsong Gu, Wen Song, Linlin Wang, Jianyang Xia, Guangxuan Han, Ye Deng
Summary: Global warming can significantly alter the diversity and structure of microbial communities in soil ecosystems, impacting key species within the networks. The interactions among microbial groups are influenced by environmental stress and soil nutrients, highlighting the complex feedback mechanisms at play in response to warming conditions.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Chemistry, Analytical
R. Benedetti, F. Bajardi, S. Capozziello, V Carafa, M. Conte, M. R. Del Sorbo, A. Nebbioso, M. Singh, H. G. Stunnenberg, M. Valadan, L. Altucci, C. Altucci
Summary: A novel technique using ultrashort ultraviolet laser pulses to crosslink cells was demonstrated, along with a fast method to pre-screen suitable irradiation conditions. This method was applied to living human cells transfected with a vector coding for Estrogen Receptor alpha (ER alpha) to detect interactions with cell DNA. Additionally, a novel approach using Chern-Simons super-gravity methods to analyze DNA and RNA sequences, focusing on mutations within the KRAS human gene, was presented.
ANALYTICAL LETTERS
(2021)
Article
Microbiology
Alan R. Pacheco, Charlie Pauvert, Dileep Kishore, Daniel Segre
Summary: This article proposes guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). It discusses the potential for new insights that can be gained through the integration of microbial interaction data and envisions potential trajectories for the deployment of FAIR microbial interaction data within the community.
Review
Microbiology
Dallas L. Mould, Deborah A. Hogan
Summary: Microbial interactions play a crucial role in microbial physiology, with quorum sensing and metabolite exchange being key elements. Loss-of-function mutations in quorum-sensing components are common across different species, and quorum sensing is modulated by small molecules and environmental conditions. Recent evidence suggests that strain heterogeneity can impact microbial interactions and act as selective pressures on the emergence of common mutations in quorum sensing genes.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yan-Bin Wang, Ce Li, Jin-Yang Yan, Tian-Yu Wang, Ya-Lin Yao, Fei-Rong Ren, Jun-Bo Luan
Summary: This study demonstrates the critical role of autophagy in regulating the metabolic interactions between whitefly and two intracellular symbionts. The symbionts evade autophagy in whitefly bacteriocytes by activating the TOR pathway through providing essential nutrients. The findings also provide insights into the cellular basis of bacteriocyte evolution and symbiosis persistence in the whitefly.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Engineering, Chemical
Attia Iram, Ali Ozcan, Irfan Turhan, Ali Demirci
Summary: Humankind has been utilizing food fermentations unknowingly since the creation of bread and cheese. Microbial fermentation has been extensively used for production of commodity chemicals and natural food ingredients. This review summarizes the prominent food ingredients and novel fermentation food products currently being produced via microbial fermentation, along with strategies to enhance such processes and the potential of economical feedstocks for value-added products.
Article
Biochemistry & Molecular Biology
Olga M. Sokolovskaya, Tanja Plessl, Henry Bailey, Sabrina Mackinnon, Matthias R. Baumgartner, Wyatt W. Yue, D. Sean Froese, Michiko E. Taga
Summary: This study examined the impact of various cobamide cofactors on the function of MMUT and found differences in how they support the enzyme, as well as variations in the catalytic rescue of disease-associated MMUT variants. The findings challenge the sole focus on cobalamin in human physiology, suggesting that diverse cobamides can play a role in supporting human enzyme function.
Editorial Material
Biochemistry & Molecular Biology
Zachary F. Hallberg, Michiko E. Taga
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Microbiology
Kenny C. Mok, Olga M. Sokolovskaya, Alexa M. Nicolas, Zachary F. Hallberg, Adam Deutschbauer, Hans K. Carlson, Michiko E. Taga
Article
Microbiology
Alexa M. Nicolas, Alexander L. Jaffe, Erin E. Nuccio, Michiko E. Taga, Mary K. Firestone, Jillian F. Banfield
Summary: This study focused on Candidate Phyla Radiation (CPR) bacteria and DPANN archaea in soil, which are often overlooked. By concentrating small particles from soil, the researchers were able to identify these organisms as part of the rare soil biosphere with unique metabolic platforms. Some of these predicted symbionts have acquired aerobic capacity through lateral transfer, enabling them to adapt to oxic soil environments.
Article
Biotechnology & Applied Microbiology
Freddy Bunbury, Carlos Rivas, Victoria Calatrava, Amanda N. Shelton, Arthur Grossman, Devaki Bhaya
Summary: Phototactic strategies may be adaptable and finely tuned to the light and local environment. Differences in phototactic responses and photoreceptor genes were observed between Synechococcus isolates from thermal springs in Yellowstone National Park. These findings highlight the diversity of phototactic strategies even among closely related cyanobacteria and provide insights into the importance of phototaxis in microbial biofilm communities.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Sebastian Gude, Gordon J. Pherribo, Michiko E. Taga
Summary: Salvaging, a process of recycling and reusing, is a potentially important mechanism for microbial populations to acquire and provision metabolites, enabling efficient resource utilization and stable metabolite provisioning.
Article
Biochemistry & Molecular Biology
Zachary F. Hallberg, Erica C. Seth, Kersh Thevasundaram, Michiko E. Taga
Summary: Vitamin B-12 plays an essential role in human health and also affects microbial metabolism and community function. Cobalamin, a type of cobamide cofactor, is produced by certain prokaryotes and is considered a shared nutrient in microbial communities. Different microbes have metabolic specificity for specific cobamides, and the availability of cobamides in the environment is important for cobamide-dependent microbes.
Article
Microbiology
Kristopher J. Kennedy, Florian J. Widner, Olga M. Sokolovskaya, Lina Innocent, Rebecca R. Procknow, Kenny C. Mok, Michiko E. Taga
Summary: In bacteria, riboswitches are gene regulatory RNAs that directly bind and detect metabolites, controlling many essential metabolic processes. Cobalamin riboswitches are an exception as they can respond to multiple variants of cobalamin (vitamin B-12), known as corrinoids. This study found that cobalamin riboswitches vary in their specificity for corrinoids, with some being broadly responsive and others being more selective. Analyses and models suggest that cobalamin riboswitches indirectly differentiate among corrinoids by sensing differences in their structural conformation. These findings provide insights into how bacteria can sense and respond to the chemical diversity of essential metabolites.
Article
Ecology
Gordon J. Pherribo, Michiko E. Taga
Summary: Microbial communities often contain auxotrophs, organisms that cannot synthesize certain metabolites necessary for growth. This study investigates the mechanisms by which these metabolites are released from producer cells to be utilized by auxotrophs. The researchers found that cell lysis by bacteriophages could be a dominant mechanism of metabolite provisioning in microbial communities. These findings suggest that the collective lysis of different hosts by multiple phages contributes to the availability of intracellular metabolites for auxotrophs.
Article
Microbiology
Myka A. Green, Zoila I. Alvarez-Aponte, Valentine V. Trotter, Michiko E. Taga
Summary: The draft genome sequence of Pedococcus sp. strain 5OH_020, a soil bacterium isolated on a natural cobalamin analog, consists of 4.4 Mbp with 4,108 protein-coding genes. The genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests it is a novel species within the genus Pedococcus.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Multidisciplinary Sciences
Alexa M. Nicolas, Ella T. Sieradzki, Jennifer Pett-Ridge, Jillian F. Banfield, Michiko E. Taga, Mary K. Firestone, Steven J. Blazewicz
Summary: This study investigates the response of viruses and microbes in soil to wet-up. The results show that wet-up leads to a decrease in viral richness but an increase in viral biomass, and viral lysis plays an important role in microbial death following wet-up.
NATURE COMMUNICATIONS
(2023)
