Article
Computer Science, Artificial Intelligence
Jesper N. Tegner
Summary: Machine translation now enables automatic detection of different cell types from single-cell transcriptomic data, allowing for the potential to dissect complex clinical samples like heterogeneous tumors at a large scale.
NATURE MACHINE INTELLIGENCE
(2023)
Review
Chemistry, Multidisciplinary
Jackson K. B. Cahn, Jorn Piel
Summary: This review discusses available and emerging techniques for targeted single-cell analysis, with a particular focus on applications to the discovery and study of natural products.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Anna Kuchina, Leandra M. Brettner, Luana Paleologu, Charles M. Roco, Alexander B. Rosenberg, Alberto Carignano, Ryan Kibler, Matthew Hirano, R. William DePaolo, Georg Seelig
Summary: microSPLiT is a high-throughput single-cell RNA sequencing method that can resolve heterogeneous transcriptional states in Gram-negative and Gram-positive bacteria. Researchers used microSPLiT to process Bacillus subtilis cells and obtained detailed information on changes in metabolism and lifestyle, as well as identified new gene expression states in the bacterial population.
Article
Biology
John A. Lees, Gerry Tonkin-Hill, Zhirong Yang, Jukka Corander
Summary: Microbial population genomics has advanced rapidly in the past decade, with the ability to sequence thousands or even tens of thousands of strains in a single study. The availability of hundreds of thousands of genomes for a single bacterial species calls for innovative methods to explore population structure. Mandrake is an efficient implementation of a dimensional reduction method that visualizes population structure from millions of whole genomes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Junhui Li, Paul Dijkstra, Qihong Lu, Shanquan Wang, Shaohua Chen, Deqiang Li, Zhiheng Wang, Zhenglei Jia, Lu Wang, Hojae Shim
Summary: The study identified 952 genomes carrying genes associated with DMF degradation, expanding the known diversity of bacteria with this metabolic capability. Both aerobic and anaerobic pathways for DMF degradation were found, with microbial consortia potentially more advantageous than pure culture in degrading DMF in wastewater.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2021)
Review
Microbiology
Emily C. Pierce, Rachel J. Dutton
Summary: Microbial interactions are crucial in the biology of microbiomes. By studying interactions in representative contexts, common mechanisms have been identified across diverse microbial systems, providing insights into the impact of these interactions on microbiomes. Technological advancements in genetics, metabolomics, imaging, and microfluidics have facilitated interdisciplinary research in understanding the mechanisms of microbial interactions.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Chemistry, Physical
Vasan Sivalingam, Vafa Ahmadi, Omodara Babafemi, Carlos Dinamarca
Summary: This study conducted a series of experiments to test the integration of syngas fermentation into a single-cell microbial electrosynthesis process, aiming to improve gas-liquid mass transfer. The study was divided into three phases, with the second phase demonstrating higher gas consumption and acetic acid production.
Article
Biochemistry & Molecular Biology
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation and disease occurrence and progression. HUSCH is a large-scale database that integrates high-quality single-cell transcriptomic datasets from different tissues, providing comprehensive visualization and analysis of gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Wenbing Chen, Changling Zuo, Chundi Wang, Tengteng Zhang, Liping Lyu, Yu Qiao, Fangqing Zhao, Miao Miao
Summary: Using single-cell genomics, eight high-quality Euplotia genomes were obtained, revealing the underestimated genomic diversity of Euplotia. The extensive gene expansion events in Euplotia genomes are closely related to phenotypic evolution and environmental adaptation of individual species. This study provides valuable insights into the evolutionary history and genetic diversity of ciliates.
Review
Biochemistry & Molecular Biology
Sebastiano Rontauroli, Chiara Carretta, Sandra Parenti, Matteo Bertesi, Rossella Manfredini
Summary: Myeloproliferative neoplasms (MPNs) are clonal disorders caused by somatic mutations in hematopoietic stem/progenitor cells. Different types of MPNs can progress to secondary myelofibrosis or acute myeloid leukemia. This review focuses on the genomic heterogeneity in MPNs and discusses the impact of single cell studies on disease progression and leukemic transformation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Multidisciplinary Sciences
Christian Rinke
Summary: This passage describes how microorganisms store some genetic information on non-chromosomal elements and mentions the emergence of a surprising version of these elements, which shifts our understanding of their diversity and potential roles.
Article
Biology
Monica F. Sentmanat, J. Michael White, Evguenia Kouranova, Xiaoxia Cui
Summary: In this study, we propose an improved method for floxing genomic regions of any desired size using electroporation of fertilized eggs, which is highly reliable and predictable in terms of timeline.
Article
Biochemical Research Methods
Mengqi Zhang, F. Richard Guo
Summary: Single-cell sequencing has revolutionized the identification of differentially expressed genes (DEGs) by providing high resolution for heterogeneous cell tissues. However, current analysis mainly focuses on comparing different cell types within the same individual. This study proposes a nonparametric method called barycenter single-cell differential expression (BSDE) to identify DEGs in case-control studies. The method overcomes the limitations of parametric approaches and accurately detects differential expressions. It is demonstrated through simulations and real data analysis that BSDE can effectively identify cell type-specific DEGs. The availability of the R package and datasets further facilitate its application in research.
Article
Microbiology
Jiayu Zhang, Xiaoyan Li, Uli Klumper, Huaxin Lei, Thomas U. Berendonk, Fangliang Guo, Ke Yu, Chao Yang, Bing Li
Summary: This study elucidates the comprehensive biotransformation pathway, key metabolic enzymes, and interspecies interactions of chloramphenicol in an activated sludge-enriched consortium using integrated multi-omics and cultivation-based approaches. The discovery of a new biotransformation pathway and key enzymes, as well as the understanding of synergistic interactions and substrate exchange among microbes, provides valuable resources and knowledge for enhanced bioremediation of chloramphenicol-contaminated sites and environmental microbiology.
Article
Biochemical Research Methods
Pinar Demetci, Rebecca Santorella, Bjoern Sandstede, William Stafford Noble, Ritambhara Singh
Summary: Single-cell alignment using optimal transport (SCOT) is an unsupervised algorithm that aligns single-cell multiomics data by constructing k-nearest neighbor (k-NN) graphs and using coupling matrices.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Ecology
Eric D. Becraft, Maggie C. Y. Lau Vetter, Oliver K. I. Bezuidt, Julia M. Brown, Jessica M. Labonte, Kotryna Kauneckaite-Griguole, Ruta Salkauskaite, Gediminas Alzbutas, Joshua D. Sackett, Brittany R. Kruger, Vitaly Kadnikov, Esta van Heerden, Duane Moser, Nikolai Ravin, Tullis Onstott, Ramunas Stepanauskas
Summary: Recent research has found that the genomes of sulfate-reducing bacteria CDA from Africa, North America, and Eurasia are highly conserved, suggesting minimal evolution in these populations since their separation. This is likely due to high-fidelity DNA replication and repair mechanisms.
Article
Microbiology
J. Goordial, T. D'Angelo, J. M. Labonte, N. J. Poulton, J. M. Brown, R. Stepanauskas, G. L. Fruh-Green, B. N. Orcutt
Summary: This study reveals the diversity and metabolic potential of microbial communities in the marine lithospheric subsurface, showing that the biosphere in this environment is not fueled by active serpentinization reactions. Despite low abundance, distinct rock-associated microorganisms were identified, with a prevalence of heterotrophic and aerobic carbon cycling metabolisms.
Article
Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Article
Multidisciplinary Sciences
Clara Martinez-Perez, Chris Greening, Sean K. Bay, Rachael J. Lappan, Zihao Zhao, Daniele De Corte, Christina Hulbe, Christian Ohneiser, Craig Stevens, Blair Thomson, Ramunas Stepanauskas, Jose M. Gonzalez, Ramiro Logares, Gerhard J. Herndl, Sergio E. Morales, Federico Baltar
Summary: Using a multi-omics approach, this study provides insights into the microbial communities beneath the Ross Ice Shelf in coastal Antarctica. The findings reveal a taxonomically distinct microbial community adapted to a highly oligotrophic marine environment, with aerobic lithoautotrophic archaea and bacteria driving the production of new organic carbon, and aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Timothy D'Angelo, Jacqueline Goordial, Nicole J. Poulton, Lauren Seyler, Julie A. Huber, Ramunas Stepanauskas, Beth N. Orcutt
Summary: The application of redox-sensitive fluorescent molecules for flow cytometric sorting of cells allows for single cell genomic sequencing from low biomass crustal fluid, providing a powerful tool for studying microbial biospheres in low biomass systems or sites with limited sample volumes available for analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Svetlana Lyalina, Ramunas Stepanauskas, Frank Wu, Shomyseh Sanjabi, Katherine S. Pollard
Summary: By using flow cytometry and low-coverage sequencing, we captured and identified the genomes of the mouse gut microbiome, significantly enriching the gene catalog and phylogenetic breadth of this community. We also discovered previously invisible microbial functional pathways.
Article
Multidisciplinary Sciences
Marianne Acker, Shane L. Hogle, Paul M. Berube, Thomas Hackl, Allison Coe, Ramunas Stepanauskas, Sallie W. Chisholm, Daniel J. Repeta
Summary: This study reveals that a small fraction of microbial producers in the ocean sustain the presence of phosphonates and allocate a significant portion of their phosphorus quota for phosphonate production. The phosphonates may be associated with cell-surface glycoproteins, mediating ecological interactions between the cell and its surrounding environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Biochemistry & Molecular Biology
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjami Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene Koonin, Uri Gophna
Summary: High-throughput RNA sequencing allows us to explore the diversity of RNA viruses on Earth. By analyzing diverse metatranscriptomes and RNA-dependent RNA polymerases, we discovered a 5-fold increase in the known diversity of RNA viruses, as well as new protein domains and virus-host interactions. Additionally, we identified two new bacteriophage phyla and potential new classes and orders.
Article
Biochemistry & Molecular Biology
Thomas Hackl, Raphael Laurenceau, Markus J. Ankenbrand, Christina Bliem, Zev Cariani, Elaina Thomas, Keven D. Dooley, Aldo A. Arellano, Shane L. Hogle, Paul Berube, Gabriel E. Leventhal, Elaine Luo, John M. Eppley, Ahmed A. Zayed, John Beaulaurier, Ramunas Stepanauskas, Matthew B. Sullivan, Edward F. DeLong, Steven J. Biller, Sallie W. Chisholm
Summary: Horizontal gene transfer plays a crucial role in microbial evolution, and the newly discovered tycheposons, a family of DNA transposons, are found to be key drivers of genomic remodeling. Tycheposons are widely distributed in the marine environment and are dispersed through vesicles and phage particles. Similar elements are also found in microbes co-existing with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.
Article
Multidisciplinary Sciences
Jacob H. Munson-McGee, Melody R. Lindsay, Eva Sintes, Julia M. Brown, Timothy D'Angelo, Joe Brown, Laura C. Lubelczyk, Paxton Tomko, David Emerson, Beth N. Orcutt, Nicole J. Poulton, Gerhard J. Herndl, Ramunas Stepanauskas
Summary: The respiration rates of marine microbes vary significantly among different prokaryoplankton genera. Minority members of prokaryoplankton perform the majority of respiration, while the most prevalent lineages have extremely low respiration rates. Proteorhodopsin-based phototrophy is likely an important source of energy for prokaryoplankton, indicating a need to reevaluate the mechanistic understanding of the global carbon cycle.
Article
Ecology
Timothy D'Angelo, Jacqueline Goordial, Melody R. Lindsay, Julia McGonigle, Anne Booker, Duane Moser, Ramunas Stepanauskus, Beth N. Orcutt
Summary: The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms. These phyla are common inhabitants of marine and terrestrial subsurface environments and have diverse physiologies. Basal clades primarily inhabit these subsurface environments and have smaller, more densely coded genomes compared to later-branching clades. Both phyla share many traits inferred to be present in their respective common ancestors. Later-branching groups have genome expansions that include gene clusters performing unique nitrogen metabolisms. Modern subsurface environments represent a genomic repository for ancestral metabolic traits.
Article
Ecology
Anne E. Booker, Timothy D'Angelo, Annabelle Adams-Beyea, Julia M. Brown, Olivia Nigro, Michael S. Rappe, Ramunas Stepanauskas, Beth N. Orcutt
Summary: Through single cell genomics and metagenomics, we have revealed the life strategies of two uncultivated Aminicenantia bacteria lineages from the basaltic subseafloor oceanic crust. Both lineages scavenge organic carbon and have genetic potential to catabolize amino acids and fatty acids. Seawater recharge and necromass may serve as important carbon sources for microorganisms in this environment. Both lineages generate ATP through various mechanisms including substrate-level phosphorylation and electron transport. Genomic comparisons suggest extracellular electron transfer to iron or sulfur oxides. One lineage has small genomes and retains characteristics of early evolved life. Overall, Aminicenantia are well adapted to oceanic crust environments by utilizing simple organic molecules and extracellular electron transport.
Article
Multidisciplinary Sciences
Julia Anstett, Alvaro M. Plominsky, Edward F. DeLong, Alyse Kiesser, Klaus Juergens, Connor Morgan-Lang, Ramunas Stepanauskas, Frank J. Stewart, Osvaldo Ulloa, Tanja Woyke, Rex Malmstrom, Steven J. Hallam
Summary: Oxygen-deficient marine waters known as OMZs or AMZs are common oceanographic features that host microorganisms adapted to low oxygen conditions. The metabolic interactions of these microorganisms drive biogeochemical cycles and impact nitrogen loss and trace gas production and consumption. With the expansion and intensification of oxygen-deficient waters due to global warming, studying microbial communities in these areas is important for understanding the effects of climate change on marine ecosystem functions and services.
Article
Microbiology
Cale O. Seymour, Marike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian-Yu Jiao, Zheng-Shuang Hua, Lan Liu, Zheng-Han Lian, Wen-Jun Li, Maria Chuvochina, Brianna K. Finley, Benjamin J. Koch, Egbert Schwartz, Paul Dijkstra, Duane P. Moser, Bruce A. Hungate, Brian P. Hedlund
Summary: The candidate bacterial phylum Omnitrophota is poorly studied. By analyzing genomes and data from the Earth Microbiome Project, researchers found that Omnitrophota are ultra-small cells mainly found in water, sediments, and soils. These bacteria have reduced genomes but retain key metabolic pathways and symbiotic gene clusters, indicating a host-associated lifestyle. Additionally, stable-isotope probing identified certain Omnitrophota families as potential obligate bacterial predators. Overall, most Omnitrophota inhabit various ecosystems as predators or parasites.
NATURE MICROBIOLOGY
(2023)
