Article
Biology
Xinxu Zhang, Zongbao Liu, Wei Xu, Jie Pan, Yuhan Huang, Mingwei Cai, Zhuhua Luo, Meng Li
Summary: Metagenomic exploration of the ocean's Yap Trench led to the discovery of three new monophyletic bacterial lineages named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. The genomes of these new lineages suggest a versatile lifestyle and a preference for oxygen-limited or particle-attached environments. Evolutionary analysis indicated the importance of gene gain and loss events, as well as horizontal gene transfer, in shaping the genomic and metabolic features of these new phyla.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Plant Sciences
Samuel G. S. Hibdige, Pauline Raimondeau, Pascal-Antoine Christin, Luke T. Dunning
Summary: Research on 17 diverse grass species found LGT to be a widespread phenomenon, with the amount and success of transfers depending on species growth habits and phylogenetic relatedness.
Article
Biology
Lukas Malfertheiner, Clara Martinez-Perez, Zihao Zhao, Gerhard J. Herndl, Federico Baltar
Summary: SAR324 is a diverse group of bacteria found in various environments, with metabolic flexibility that helps explain its importance in global biogeochemical cycles.
Article
Microbiology
Francesca Fanelli, Marco Montemurro, Daniele Chieffi, Gyu-Sung Cho, Charles M. A. P. Franz, Anna Dell'Aquila, Carlo Giuseppe Rizzello, Vincenzina Fusco
Summary: This study sequenced and analyzed the genomes of several strains belonging to the Weissella genus and investigated their ability to metabolize carbohydrates. The findings led to a reassessment of the Weissella species groups and provided insights into the diversity and potential applications of these strains in fermentation processes and biotechnology.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Qingmei Li, Yingli Zhou, Rui Lu, Pengfei Zheng, Yong Wang
Summary: In this study, the phylogeny and metabolic potential of KSB1, a candidate phylum composed of uncultured bacteria, were comprehensively analyzed. The results revealed the classification and metabolic capabilities of KSB1, providing insights into their ecological roles and anaerobic heterotrophic lifestyle.
Article
Microbiology
Alexander L. Jaffe, Alex D. Thomas, Christine He, Ray Keren, Luis E. Valentin-Alvarado, Patrick Munk, Keith Bouma-Gregson, Ibrahim F. Farag, Yuki Amano, Rohan Sachdeva, Patrick T. West, Jillian F. Ban
Summary: The study found that the transitions of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.
Article
Biotechnology & Applied Microbiology
C. Sangavai, P. Chellapandi
Summary: Acetoanaerobium sticklandii DSM519 is a non-pathogenic anaerobe capable of producing high levels of ammonia using amino acids as carbon and energy sources. Comparative genomic analysis reveals that CST shares genomic context with other hyper-ammonia producing, purinolytic, and proteolytic bacteria, suggesting a slow evolution rate and common ancestry for certain genetic elements. Genomic and metabolic analysis predicts unique metabolic subsystems for amino acid catabolism and hydrogen production in CST.
Article
Oncology
Enrico Moiso, Paolo Provero
Summary: This study systematically investigates the associations between metabolic alterations and other tumor features using a comprehensive collection of data. The results provide a guide for formulating specific mechanistic hypotheses and contribute to our understanding of the role of metabolic alterations in cancer and the development of precision therapeutic strategies.
Review
Clinical Neurology
Andrew T. Nelson, Davide Trotti
Summary: ALS is a devastating neurodegenerative disease that affects motor neurons, causing muscle atrophy, paralysis, and death. Despite progress in research, there are currently no effective treatments available. Alterations to bioenergetic and metabolic homeostasis have been identified as potential therapeutic targets for ALS.
Article
Clinical Neurology
Kailin Xia, Simon Witzel, Christina Witzel, Veronika Klose, Dongsheng Fan, Albert C. Ludolph, Johannes Dorst
Summary: This study identified distinct metabolic profiles in presymptomatic ALS gene carriers, which might be associated with disease progression in the symptomatic phase.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Microbiology
Alicia Garcia-Roldan, Ana Duran-Viseras, Rafael R. de la Haba, Paulina Corral, Cristina Sanchez-Porro, Antonio Ventosa
Summary: The genus Natronomonas is classified within the family Haloarculaceae and includes six species of extremely halophilic and neutrophilic archaea. These species have been isolated from various saline environments and salt mines. A genomic study was conducted to determine the phylogenetic structure of Natronomonas and its taxonomic status. The results showed that the species of Natronomonas form a coherent cluster at the genus level. Additionally, a new species of Natronomonas, named Natronomonas aquatica sp. nov., was characterized and found to have a versatile nitrogen metabolism. Metagenomic analysis also revealed the widespread distribution of Natronomonas species in saline lakes, salterns, and saline soils.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Geriatrics & Gerontology
Kamar Ghaibour, Melanie Schuh, Sirine Souali-Crespo, Celine Chambon, Anouk Charlot, Joe Rizk, Daniela Rovito, Anna-Isavella Rerra, Qingshuang Cai, Nadia Messaddeq, Joffrey Zoll, Delphine Duteil, Daniel Metzger
Summary: Disrupting the androgen/androgen receptor axis impairs glycolytic activity and promotes the development of type 2 diabetes in male mice, but not in females. It also leads to oxidative stress and necrosis in muscle fibers.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Immunology
Bin Sun, Boguang Sun, Beibei Zhang, Li Sun
Summary: Water temperature elevation as a consequence of global warming increases the incidence of bacterial disease in fish farming. This study found that high temperature promotes the dissemination of Edwardsiella tarda, a bacterial pathogen, in flounder tissues. Comparative metabolomics revealed a decreased level of amino acids and TCA intermediates, such as succinate, during E. tarda infection at elevated temperature. Additionally, 38 potential metabolite markers associated with temperature and bacterial infection were identified. Two of these markers, L-methionine and UDP-glucose, effectively regulated cytokine expression and suppressed E. tarda infection in flounder leukocytes.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Microbiology
J. Diez, A. Lopez-Lozano, M. A. Dominguez-Martin, G. Gomez-Baena, M. C. Munoz-Marin, Y. Melero-Rubio, J. M. Garcia-Fernandez
Summary: Marine picocyanobacteria, such as Prochlorococcus and Synechococcus, have developed unique adaptive mechanisms in nitrogen metabolism to thrive in oligotrophic oceans, including strategies such as reducing GC and protein contents, utilizing truncated proteins, and perceiving nanomolar nitrate concentrations. These adaptations contrast with the knowledge obtained in freshwater cyanobacteria and are essential for the ecological success of these microorganisms.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Microbiology
Jia V. Li, Hutan Ashrafian, Magali Sarafian, Daniel Homola, Laura Rushton, Grace Barker, Paula Momo Cabrera, Matthew R. Lewis, Ara Darzi, Edward Lin, Nana Adwoa Gletsu-Miller, Stephen L. Atkin, Thozhukat Sathyapalan, Nigel J. Gooderham, Jeremy K. Nicholson, Julian R. Marchesi, Thanos Athanasiou, Elaine Holmes
Summary: Bariatric surgery, especially Roux-en-Y gastric bypass (RYGB), has a significant impact on the metabolism and gut microbiota of patients, leading to changes in metabolites and bacterial composition that are associated with successful weight loss and metabolic improvements. Further research is needed to understand the functional clinical outcomes of these metabolic changes.
Correction
Microbiology
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-Francois Brugere, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger
NATURE MICROBIOLOGY
(2022)
Article
Ecology
Alexander L. Jaffe, Masae Konno, Yuma Kawasaki, Chihiro Kataoka, Oded Beja, Hideki Kandori, Keiichi Inoue, Jillian F. Banfield
Summary: This study found that Saccharibacteria Type-1 rhodopsins function as outward proton pumps and can rapidly uptake the chromophore retinal. The co-occurring microorganisms with Saccharibacteria showed evidence of the ability to produce retinal from beta-carotene, suggesting a potential association between them.
Article
Microbiology
Diego Cantoni, Ashley Osborne, Najwa Taib, Gary Thompson, Ruben Martin-Escolano, Eleanna Kazana, Elizabeth Edrich, Ian R. Brown, Simonetta Gribaldo, Campbell W. Gourlay, Anastasios D. Tsaousis
Summary: This study investigates the evolution and function of alternative oxidase (AOX) in Naegleria species using a multidisciplinary approach. The research shows that AOX plays a crucial role in the biology of Naegleria species, as demonstrated by the effects of its inactivation on proliferation.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Solenne Ithurbide, Simonetta Gribaldo, Sonja-Verena Albers, Nika Pende
Summary: This review highlights recent findings on cell division processes in archaea, particularly focusing on the differences between halophiles and methanobacteria in their reliance on two FtsZ proteins and one FtsZ protein, respectively. The discussion also explores how these differences relate to the distinct cell envelopes of these two archaeal model systems.
TRENDS IN MICROBIOLOGY
(2022)
Article
Biology
Francesca D'Angelo, Elena Fernandez-Fueyo, Pierre Simon Garcia, Helena Shomar, Martin Pelosse, Rita Rebelo Manuel, Ferhat Buke, Siyi Liu, Niels van den Broek, Nicolas Duraffourg, Carol de Ram, Martin Pabst, Emmanuelle Bouveret, Simonetta Gribaldo, Beatrice Py, Sandrine Ollagnier de Choudens, Frederic Barras, Gregory Bokinsky
Summary: Iron-sulfur (Fe-S) clusters play crucial roles in various metabolic and regulatory processes, but Fe-S enzymes often fail to function in non-native host species. By studying the compatibility of non-native Fe-S enzymes, we found a significant correlation between phylogenetic distance and probability of functional expression. Coexpression of heterologous Fe-S biogenesis pathways can expand the range of compatible orthologs. Moreover, Fe-S enzymes requiring specific electron carrier proteins usually require their taxon-specific reducing partners for successful expression.
Article
Microbiology
Jerzy Witwinowski, Anna Sartori-Rupp, Najwa Taib, Nika Pende, To Nam Tham, Daniel Poppleton, Jean-Marc Ghigo, Christophe Beloin, Simonetta Gribaldo
Summary: A comprehensive analysis of the distribution and evolution of the main outer membrane tethering systems across bacteria, coupled with experimental deletion of one of these systems in Veillonella parvula, provide insights into the transition from diderm to monoderm bacteria.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Alexander L. Jaffe, Maxime Fuster, Marie C. Schoelmerich, Lin-Xing Chen, Jonathan Colombet, Hermine Billard, Telesphore Sime-Ngando, Jillian F. Banfield
Summary: Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. Using genomics and microscopy, the study found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. The results provide insights into possible interactions within a complex lake ecosystem.
Review
Microbiology
Pierre Simon Garcia, Simonetta Gribaldo, Guillaume Borrel
Summary: Methane is a crucial greenhouse gas on Earth, and the only organisms capable of using methane as an energy source are archaea. New research has revealed a wide diversity of methane-related pathways in archaea, challenging established theories on the origin and evolution of methanogenesis.
ANNUAL REVIEW OF MICROBIOLOGY
(2022)
Article
Biology
Raphael Meheust, Cindy J. Castelle, Alexander L. Jaffe, Jillian F. Banfield
Summary: Archaea play important roles in the environment, and recent genomic analyses have provided new insights into their distribution and functionalities. This study identified representative genomes of Archaea and analyzed the co-occurring proteins that distinguish major lineages. The results highlighted the presence of new eukaryotic signature proteins in Asgard and the dominance of hypothetical proteins in lineage-specific families.
Article
Microbiology
Mathilda Fatton, Sevasti Filippidou, Thomas Junier, Guillaume Cailleau, Matthieu Berge, Daniel Poppleton, Thorsten B. Blum, Marek Kaminek, Adolfo Odriozola, Jochen Blom, Shannon L. Johnson, Jan Pieter Abrahams, Patrick S. Chain, Simonetta Gribaldo, Elitza Tocheva, Benoit Zuber, Patrick H. Viollier, Pilar Junier
Summary: This study discovered the production of spore-like structures in Kurthia strain 11kri321, which was previously considered as asporogenic. These cryptospores, however, did not offer protection against heat or UV damage and were lost after successive sub-culturing. These findings suggest that cryptosporulation might have been a prevalent ancestral developmental state in Firmicutes under harsh environmental conditions.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Courtney M. Thomas, Elie Desmond-Le Quemener, Simonetta Gribaldo, Guillaume Borrel
Summary: By analyzing 250 species of animals, the authors demonstrate that archaea are common constituents of the animal gut throughout the animal kingdom. They identify six main genera/families of gut archaea and reveal that their abundance and diversity are driven by host diet, evolutionary history, and physiology.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Helena Chan, Najwa Taib, Michael C. Gilmore, Ahmed M. T. Mohamed, Kieran Hanna, Johana Luhur, Hieu Nguyen, Elham Hafiz, Felipe Cava, Simonetta Gribaldo, David Rudner, Christopher D. A. Rodrigues
Summary: Cell envelope remodeling is critical for bacteria growth and division, especially during the development of highly resistant endospores. This study identifies two new factors, YrvJ and MurAB, that are required for efficient envelope remodeling during sporulation, highlighting the importance of peptidoglycan precursor synthesis for engulfment efficiency in B. subtilis and likely other endospore-forming bacteria.
Correction
Microbiology
Daniela Megrian, Najwa Taib, Alexander L. L. Jaffe, Jillian F. F. Banfield, Simonetta Gribaldo
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pierre Simon Garcia, Frederic Barras, Simonetta Gribaldo
Summary: Understanding the origin of mitochondria and plastids is crucial for studying the early evolution of eukaryotes. Recent advancements in microbial diversity and phylogenomics indicate that mitochondria originated from Alphaproteobacteria and plastids from Cyanobacteria. This study provides strong support for these hypotheses by analyzing the machinery for iron-sulfur cluster assembly in eukaryotic cells.
Article
Microbiology
Jett Liu, Alexander L. Jaffe, Linxing Chen, Batbileg Bor, Jillian F. Banfield
Summary: This study analyzed the CRISPR-Cas systems in Gracilibacteria, Absconditabacteria, and Saccharibacteria, and predicted the phages that infect these bacteria. Some phages were found to infect both standard-coded and alternatively coded CPR bacteria. Additionally, spacers encoded in Actinobacteria were predicted to target some phages of Saccharibacteria.