Genome-Resolved Metagenomics Reveals Site-Specific Diversity of Episymbiotic CPR Bacteria and DPANN Archaea in Groundwater Ecosystems
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Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). -
The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism Elizabeth Waters†‡, Michael J. Hohn§, Ivan Ahel¶, David E. Graham††, Mark D. Adams‡‡, Mary Barnstead‡‡, Karen Y. Beeson‡‡, Lisa Bibbs†, Randall Bolanos‡‡, Martin Keller†, Keith Kretz†, Xiaoying Lin‡‡, Eric Mathur†, Jingwei Ni‡‡, Mircea Podar†, Toby Richardson†, Granger G. Sutton‡‡, Melvin Simon†, Dieter So¨ ll¶§§¶¶, Karl O. Stetter†§¶¶, Jay M. Short†, and Michiel Noordewier†¶¶ †Diversa Corporation, 4955 Directors Place, San Diego, CA 92121; ‡Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182; §Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universita¨tsstrasse 31, D-93053 Regensburg, Germany; ‡‡Celera Genomics Rockville, 45 West Gude Drive, Rockville, MD 20850; Departments of ¶Molecular Biophysics and Biochemistry and §§Chemistry, Yale University, New Haven, CT 06520-8114; and ʈDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, August 21, 2003 (received for review July 22, 2003) The hyperthermophile Nanoarchaeum equitans is an obligate sym- (6–8). Genomic DNA was either digested with restriction en- biont growing in coculture with the crenarchaeon Ignicoccus. zymes or sheared to provide clonable fragments. Two plasmid Ribosomal protein and rRNA-based phylogenies place its branching libraries were made by subcloning randomly sheared fragments point early in the archaeal lineage, representing the new archaeal of this DNA into a high-copy number vector (Ϸ2.8 kbp library) kingdom Nanoarchaeota. The N. equitans genome (490,885 base or low-copy number vector (Ϸ6.3 kbp library). DNA sequence pairs) encodes the machinery for information processing and was obtained from both ends of plasmid inserts to create repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide ‘‘mate-pairs,’’ pairs of reads from single clones that should be biosyntheses. -
University of Oklahoma Graduate College Development of High
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE DEVELOPMENT OF HIGH-THROUGHPUT EXPERIMENTAL AND COMPUTATIONAL TECHNOLOGIES FOR ANALYZING MICROBIAL FUNCTIONS AND INTERACTIONS IN ENVIRONMENTAL METAGENOMES A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By ZHOU SHI Norman, Oklahoma 2017 DEVELOPMENT OF HIGH-THROUGHPUT EXPERIMENTAL AND COMPUTATIONAL TECHNOLOGIES FOR ANALYZING MICROBIAL FUNCTIONS AND INTERACTIONS IN ENVIRONMENTAL METAGENOMES A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Lee Krumholz, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Sridhar Radhakrishnan ______________________________ Dr. Yiqi Luo ______________________________ Dr. Jizhong Zhou © Copyright by ZHOU SHI 2017 All Rights Reserved. Dedication I dedicate this dissertation to my wife, Mengting Yuan, whom I met and married during the time period of this work and whose love, faith and support is the greatest gift that I can ever imagine in my life; to my son, Andrew Shi, who is always curious, energetic and wonderful, and is my lasting source of enlightenment and true happiness; to my parents, Yiping Shi and Aiping Zeng, whose selfless love and care transcended the distance and time, and carried me whenever I need; to my aunt, Cindy Shi, whose unwavering support and encouragement instilled in me the spirit of striving for excellence; to my friend, Su Xu, who boarded on the same plane with me to the U.S. seven years ago and then has witnessed all parts of this work as my best friend, and Dian Zou, who passed away in an accident during the time period of this work and is a friend I will forever miss. -
Cultivating the Macroalgal Holobiont: Effects of Integrated Multi-Trophic Aquaculture on the Microbiome of Ulva Rigida (Chlorophyta)
fmars-07-00052 February 10, 2020 Time: 15:0 # 1 ORIGINAL RESEARCH published: 12 February 2020 doi: 10.3389/fmars.2020.00052 Cultivating the Macroalgal Holobiont: Effects of Integrated Multi-Trophic Aquaculture on the Microbiome of Ulva rigida (Chlorophyta) Gianmaria Califano1, Michiel Kwantes1, Maria Helena Abreu2, Rodrigo Costa3,4,5 and Thomas Wichard1,6* 1 Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany, 2 ALGAplus Lda, Ílhavo, Portugal, 3 Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal, 4 Centre of Marine Sciences, University of Algarve, Faro, Portugal, 5 Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, University of California, Berkeley, Berkeley, CA, United States, 6 Jena School for Microbial Communication, Jena, Germany Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi-Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to Edited by: their high productivity and environmental sustainability. Complex host–microbiome Bernardo Antonio Perez Da Gama, interactions play a decisive role in macroalgal development, especially in Ulva spp. Universidade Federal Fluminense, due to algal growth- and morphogenesis-promoting factors released by associated Brazil bacteria. However, our current understanding of the microbial community assembly and Reviewed by: Alejandro H. Buschmann, structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent University of Los Lagos, Chile IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) Henrique Fragoso Santos, to explore the dynamics of beneficial microbes to algal growth and development under Universidade Federal Fluminense, Brazil IMTA settings, and (iii) to improve current knowledge of host–microbiome interactions. -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
Identical Bacterial Populations Colonize Premature Infant Gut, Skin, and Oral Microbiomes And
Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates Matthew R. Olm1, Christopher T. Brown1, Brandon Brooks1, Brian Firek2, Robyn Baker3, David Burstein4, Karina Soenjoyo1, Brian C. Thomas4, Michael Morowitz2 and Jillian F. Banfield4,5,6* 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 2Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. 3Division of Newborn Medicine, Children’s Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States 4Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 5Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 6Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. *Corresponding author Running title Metagenomics of infant skin, mouth, and gut Keywords Microbiome, metagenomics, growth rates, premature infants, strains Corresponding author contact info Jillian Banfield Department of Environmental Science, Policy, & Management UC Berkeley 130 Mulford Hall #3114 Berkeley, CA 94720 [email protected] (510) 643-2155 1 Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth and gut of two hospitalized premature infants during the first month of life. -
Libros Sobre Enfermedades Autoinmunes: Tratamientos, Tipos Y Diagnósticos- Profesor Dr
- LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS . AUTOR: PROFESOR DR. ENRIQUE BARMAIMON.- - Doctor en Medicina.- - Cátedras de: - Anestesiología - Cuidados Intensivos - Neuroanatomía - Neurofisiología - Psicofisiología - Neuropsicología. - 9 TOMOS - - TOMO VI - -AÑO 2020- 1ª Edición Virtual: (.2020. 1)- - MONTEVIDEO, URUGUAY. 1 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - Queda terminantemente prohibido reproducir este libro en forma escrita y virtual, total o parcialmente, por cualquier medio, sin la autorización previa del autor. -Derechos reservados. 1ª Edición. Año 2020. Impresión [email protected]. - email: [email protected].; y [email protected]; -Montevideo, 15 de enero de 2020. - BIBLIOTECA VIRTUAL DE SALUD del S. M.U. del URUGUAY; y BIBLIOTECA DEL COLEGIO MÉDICO DEL URUGUAY. 0 0 0 0 0 0 0 0. 2 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - TOMO V I - 3 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - ÍNDICE.- - TOMO I . - - ÍNDICE. - PRÓLOGO.- - INTRODUCCIÓN. - CAPÍTULO I: -1)- GENERALIDADES. -1.1)- DEFINICIÓN. -1.2)- CAUSAS Y FACTORES DE RIESGO. -1.2.1)- FACTORES EMOCIONALES. -1.2.2)- FACTORES AMBIENTALES. -1.2.3)- FACTORES GENÉTICOS. -1.3)- Enterarse aquí, como las 10 Tipos de semillas pueden mejorar la salud. - 1.4)- TIPOS DE TRATAMIENTO DE ENFERMEDADES AUTOINMUNES. -1.4.1)- Remedios Naturales. -1.4.1.1)- Mejorar la Dieta. -
Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. .................................................................... -
How Do Pesticides Influence Gut Microbiota? a Review
International Journal of Environmental Research and Public Health Review Toxicology and Microbiota: How Do Pesticides Influence Gut Microbiota? A Review Federica Giambò 1,†, Michele Teodoro 1,† , Chiara Costa 2,* and Concettina Fenga 1 1 Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Occupational Medicine Section, University of Messina, 98125 Messina, Italy; [email protected] (F.G.); [email protected] (M.T.); [email protected] (C.F.) 2 Clinical and Experimental Medicine Department, University of Messina, 98125 Messina, Italy * Correspondence: [email protected]; Tel.: +39-090-2212052 † Equally contributed. Abstract: In recent years, new targets have been included between the health outcomes induced by pesticide exposure. The gastrointestinal tract is a key physical and biological barrier and it represents a primary site of exposure to toxic agents. Recently, the intestinal microbiota has emerged as a notable factor regulating pesticides’ toxicity. However, the specific mechanisms related to this interaction are not well known. In this review, we discuss the influence of pesticide exposure on the gut microbiota, discussing the factors influencing gut microbial diversity, and we summarize the updated literature. In conclusion, more studies are needed to clarify the host–microbial relationship concerning pesticide exposure and to define new prevention interventions, such as the identification of biomarkers of mucosal barrier function. Keywords: gut microbiota; microbial community; pesticides; occupational exposure; dysbiosis Citation: Giambò, F.; Teodoro, M.; Costa, C.; Fenga, C. Toxicology and Microbiota: How Do Pesticides Influence Gut Microbiota? A Review. 1. Introduction Int. J. Environ. Res. Public Health 2021, 18, 5510. https://doi.org/10.3390/ In recent years, the demand for food has risen significantly in relation to the world ijerph18115510 population’s increase. -
Bacterial, Archaeal, and Eukaryotic Diversity Across Distinct Microhabitats in an Acid Mine Drainage Victoria Mesa, José.L.R
Bacterial, archaeal, and eukaryotic diversity across distinct microhabitats in an acid mine drainage Victoria Mesa, José.L.R. Gallego, Ricardo González-Gil, B. Lauga, Jesus Sánchez, Célia Méndez-García, Ana I. Peláez To cite this version: Victoria Mesa, José.L.R. Gallego, Ricardo González-Gil, B. Lauga, Jesus Sánchez, et al.. Bacterial, archaeal, and eukaryotic diversity across distinct microhabitats in an acid mine drainage. Frontiers in Microbiology, Frontiers Media, 2017, 8 (SEP), 10.3389/fmicb.2017.01756. hal-01631843 HAL Id: hal-01631843 https://hal.archives-ouvertes.fr/hal-01631843 Submitted on 14 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-08-01756 September 9, 2017 Time: 16:9 # 1 ORIGINAL RESEARCH published: 12 September 2017 doi: 10.3389/fmicb.2017.01756 Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage Victoria Mesa1,2*, Jose L. R. Gallego3, Ricardo González-Gil4, Béatrice Lauga5, Jesús Sánchez1, Celia Méndez-García6† and Ana I. Peláez1† 1 Department of Functional Biology – IUBA, University of Oviedo, Oviedo, Spain, 2 Vedas Research and Innovation, Vedas CII, Medellín, Colombia, 3 Department of Mining Exploitation and Prospecting – IUBA, University of Oviedo, Mieres, Spain, 4 Department of Biology of Organisms and Systems – University of Oviedo, Oviedo, Spain, 5 Equipe Environnement et Microbiologie, CNRS/Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux, UMR5254, Pau, France, 6 Carl R. -
Metabolic Network Percolation Quantifies Biosynthetic Capabilities
RESEARCH ARTICLE Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome David B Bernstein1,2, Floyd E Dewhirst3,4, Daniel Segre` 1,2,5,6,7* 1Department of Biomedical Engineering, Boston University, Boston, United States; 2Biological Design Center, Boston University, Boston, United States; 3The Forsyth Institute, Cambridge, United States; 4Harvard School of Dental Medicine, Boston, United States; 5Bioinformatics Program, Boston University, Boston, United States; 6Department of Biology, Boston University, Boston, United States; 7Department of Physics, Boston University, Boston, United States Abstract The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems. *For correspondence: DOI: https://doi.org/10.7554/eLife.39733.001 [email protected] Competing interests: The authors declare that no Introduction competing interests exist. -
Genome-Reconstruction for Eukaryotes from Complex Natural Microbial Communities
Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Genome-reconstruction for eukaryotes from complex natural microbial communities ,$ Patrick T. West1, Alexander J. Probst2 , Igor V. Grigoriev1,5, Brian C. Thomas2, Jillian F. Banfield2,3,4* 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 2Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 4Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. * Corresponding Author $present address: Group for Aquatic Microbial Ecology, Biofilm Center, Department of Chemistry, University of Duisburg-Essen, Essen, Germany Running title Metagenomic Reconstruction of Eukaryotic Genomes Keywords metagenomics, eukaryotes, genome, gene prediction Corresponding author contact info Jillian Banfield Department of Environmental Science, Policy, & Management UC Berkeley 130 Mulford Hall #3114 Berkeley, CA 94720 [email protected] (510) 643-2155 1 Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer- based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential.