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2025	Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities Critical Reviews in Microbiology Sajid Iqbal, Farida Begum, Ihsan Ullah, Nasir Jalal, Peter Shaw
2024	Valid publication of names of two domains and seven kingdoms of prokaryotes International Journal of Systematic and Evolutionary Microbiology Markus Göker, Aharon Oren
2024	Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation Water Research Kyohei Kuroda, Ryota Maeda, Futaba Shinshima, Kampachiro Urasaki, Kengo Kubota, Masaru K. Nobu, Taro Q.P. Noguchi, Hisashi Satoh, Masahito Yamauchi, Takashi Narihiro, Masayoshi Yamada
2023	Candidatus List. Lists of names of prokaryotic Candidatus phyla International Journal of Systematic and Evolutionary Microbiology Aharon Oren, Markus Göker
2023	A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry Genome Biology Yuji Sekiguchi, Kanae Teramoto, Dieter M. Tourlousse, Akiko Ohashi, Mayu Hamajima, Daisuke Miura, Yoshihiro Yamada, Shinichi Iwamoto, Koichi Tanaka
2023	Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park Astrobiology Carl Snyder, Jakob P. Centlivre, Shrikant Bhute, Gözde Shipman, Ariel D. Friel, Tomeu Viver, Marike Palmer, Konstantinos T. Konstantinidis, Henry J. Sun, Ramon Rossello-Mora, Jay Nadeau, Brian P. Hedlund
2022	Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology Bioresource Technology Lei Zhang, Yiyang Yuan, Yingdi Zhang, Yang Liu
2022	Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach Microbes and Environments Shuka Kagemasa, Kyohei Kuroda, Ryosuke Nakai, Yu-You Li, Kengo Kubota
2022	Exploring Key Factors in Anaerobic Syntrophic Interactions: Biomass Activity, Microbial Community, and Morphology SSRN Electronic Journal Lei Zhang, Yiyang Yuan, Yingdi Zhang, Yang Liu
2022	Encapsulins Annual Review of Biochemistry Tobias W. Giessen
2022	Technology status and trends of industrial wastewater treatment: A patent analysis Chemosphere Guozhu Mao, Yixin Han, Xi Liu, John Crittenden, Ning Huang, Umme Marium Ahmad
2021	Environmental stressors alter the composition of seagrass phyllosphere microbial communities Climate Change Ecology Margaret A. Vogel, Olivia U. Mason, Thomas E. Miller
2021	Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes PLOS ONE Beverly E. Flood, Deon C. Louw, Anja K. Van der Plas, Jake V. Bailey
2021	Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge Water Research Chenjing Jiang, Simon Jon McIlroy, Rong Qi, Francesca Petriglieri, Erika Yashiro, Zivile Kondrotaite, Per Halkjær Nielsen
2021	Large-scale computational discovery and analysis of virus-derived microbial nanocompartments Nature Communications Michael P. Andreas, Tobias W. Giessen
2021	Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors Frontiers in Microbiology Patricia Bovio-Winkler, Angela Cabezas, Claudia Etchebehere
2021	Sequence and evolutionary analysis of bacterial ribosomal S1 proteins Proteins: Structure, Function, and Bioinformatics Evgeniya Deryusheva, Andrey Machulin, Maxim Matyunin, Oxana Galzitskaya
2020	Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant Frontiers in Microbiology Hirotsugu Fujitani, Kengo Momiuchi, Kento Ishii, Manami Nomachi, Shuta Kikuchi, Norisuke Ushiki, Yuji Sekiguchi, Satoshi Tsuneda
2020	Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing Water Research Theo Y.C. Lam, Ran Mei, Zhuoying Wu, Patrick K.H. Lee, Wen-Tso Liu, Po-Heng Lee
2020	Lists of names of prokaryotic Candidatus taxa International Journal of Systematic and Evolutionary Microbiology Aharon Oren, George M. Garrity, Charles T. Parker, Maria Chuvochina, Martha E. Trujillo
2020	Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01 Microbiological Research Apurvasinh C. Puvar, Neelam M. Nathani, Inayatullah Shaikh, Arpan D. Bhatt, Poonam Bhargava, Chaitanya G. Joshi, Madhvi N. Joshi
2019	Charles Thomas Parker, George M Garrity
2019	Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria Frontiers in Microbiology Yu Zheng, Ayana Saitou, Chiung-Mei Wang, Atsushi Toyoda, Yohei Minakuchi, Yuji Sekiguchi, Kenji Ueda, Hideaki Takano, Yasuteru Sakai, Keietsu Abe, Akira Yokota, Shuhei Yabe
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters Environmental Technology Sonda Guermazi-Toumi, Rakia Chouari, Abdelghani Sghir
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Genomic Characteristics of Desulfonema ishimotonii Tokyo 01T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria Frontiers in Microbiology Miho Watanabe, Hisaya Kojima, Kazuhiro Umezawa, Manabu Fukui
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge Frontiers in Microbiology Lachlan B. M. Speirs, Daniel T. F. Rice, Steve Petrovski, Robert J. Seviour
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2019	Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach Frontiers in Microbiology Sam Lambrechts, Anne Willems, Guillaume Tahon
2019	Charles Thomas Parker, George M Garrity
2019	Charles Thomas Parker, George M Garrity
2018	A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Microbiome Charlotte D. Vavourakis, Adrian-Stefan Andrei, Maliheh Mehrshad, Rohit Ghai, Dimitry Y. Sorokin, Gerard Muyzer
2018	A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Nature Biotechnology Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz
2018	Molecular Docking Evaluation of (E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors Molecules Mihaela Ileana Ionescu, Ovidiu Oniga
2018	Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities Environmental Science & Technology Yu Deng, Bing Li, Tong Zhang
2018	Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes Frontiers in Microbiology Lily Momper, Heidi S. Aronson, Jan P. Amend
2018	New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Frontiers in Microbiology Marie E. Kroeger, Tom O. Delmont, A. M. Eren, Kyle M. Meyer, Jiarong Guo, Kiran Khan, Jorge L. M. Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clovis D. Borges, James M. Tiedje, Siu M. Tsai, Klaus Nüsslein
2018	Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat PLOS ONE Jackson Z. Lee, R. Craig Everroad, Ulas Karaoz, Angela M. Detweiler, Jennifer Pett-Ridge, Peter K. Weber, Leslie Prufert-Bebout, Brad M. Bebout
2018	Genomic Approaches in Earth and Environmental Sciences
2018	Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity Frontiers in Microbiology Norisuke Ushiki, Hirotsugu Fujitani, Yu Shimada, Tomohiro Morohoshi, Yuji Sekiguchi, Satoshi Tsuneda
2017	Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Nature Microbiology Donovan H. Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J. Woodcroft, Paul N. Evans, Philip Hugenholtz, Gene W. Tyson
2017	Exposure to Microbiological Agents in Indoor and Occupational Environments Mark A. Barnes
2017	Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5 T , a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria Genome Announcements Yan-Ling Qiu, Dieter M. Tourlousse, Norihisa Matsuura, Akiko Ohashi, Yuji Sekiguchi
2017	Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Nature Biotechnology Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, Adam R Rivers, Emiley A Eloe-Fadrosh, Susannah G Tringe, Natalia N Ivanova, Alex Copeland, Alicia Clum, Eric D Becraft, Rex R Malmstrom, Bruce Birren, Mircea Podar, Peer Bork, George M Weinstock, George M Garrity, Jeremy A Dodsworth, Shibu Yooseph, Granger Sutton, Frank O Glöckner, Jack A Gilbert, William C Nelson, Steven J Hallam, Sean P Jungbluth, Thijs J G Ettema, Scott Tighe, Konstantinos T Konstantinidis, Wen-Tso Liu, Brett J Baker, Thomas Rattei, Jonathan A Eisen, Brian Hedlund, Katherine D McMahon, Noah Fierer, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi, Gene W Tyson, Christian Rinke, Alla Lapidus, Folker Meyer, Pelin Yilmaz, Donovan H Parks, A Murat Eren, Lynn Schriml, Jillian F Banfield, Philip Hugenholtz, Tanja Woyke
2017	Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation Environmental Science & Technology Rose S. Kantor, Robert J. Huddy, Ramsunder Iyer, Brian C. Thomas, Christopher T. Brown, Karthik Anantharaman, Susannah Tringe, Robert L. Hettich, Susan T. L. Harrison, Jillian F. Banfield
2017	Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome Current Biology Natasha K. Dudek, Christine L. Sun, David Burstein, Rose S. Kantor, Daniela S. Aliaga Goltsman, Elisabeth M. Bik, Brian C. Thomas, Jillian F. Banfield, David A. Relman
2017	Draft Genome Sequence of Paludibacter jiangxiensis NM7 T , a Propionate-Producing Fermentative Bacterium Genome Announcements Yan-Ling Qiu, Dieter M. Tourlousse, Norihisa Matsuura, Akiko Ohashi, Yuji Sekiguchi
2017	Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone Frontiers in Marine Science Cory C. Padilla, Anthony D. Bertagnolli, Laura A. Bristow, Neha Sarode, Jennifer B. Glass, Bo Thamdrup, Frank J. Stewart
2017	The impact of immigration on microbial community composition in full-scale anaerobic digesters Scientific Reports Rasmus H. Kirkegaard, Simon J. McIlroy, Jannie M. Kristensen, Marta Nierychlo, Søren M. Karst, Morten S. Dueholm, Mads Albertsen, Per H. Nielsen
2017	Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla Frontiers in Microbiology Eric D. Becraft, Tanja Woyke, Jessica Jarett, Natalia Ivanova, Filipa Godoy-Vitorino, Nicole Poulton, Julia M. Brown, Joseph Brown, M. C. Y. Lau, Tullis Onstott, Jonathan A. Eisen, Duane Moser, Ramunas Stepanauskas
2017	Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens Water Research Mahi M. Mohiuddin, Yasser Salama, Herb E. Schellhorn, G. Brian Golding
2016	Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1 T , an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae Genome Announcements Norihisa Matsuura, Akiko Ohashi, Dieter M. Tourlousse, Yuji Sekiguchi
2016	Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates Biotechnology for Biofuels Irena Maus, Daniela E. Koeck, Katharina G. Cibis, Sarah Hahnke, Yong S. Kim, Thomas Langer, Jana Kreubel, Marcel Erhard, Andreas Bremges, Sandra Off, Yvonne Stolze, Sebastian Jaenicke, Alexander Goesmann, Alexander Sczyrba, Paul Scherer, Helmut König, Wolfgang H. Schwarz, Vladimir V. Zverlov, Wolfgang Liebl, Alfred Pühler, Andreas Schlüter, Michael Klocke
2016	Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion Environmental Microbiology Inka Vanwonterghem, Paul D. Jensen, Korneel Rabaey, Gene W. Tyson
2016	Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JL T Genome Announcements Norihisa Matsuura, Akiko Ohashi, Dieter M. Tourlousse, Yuji Sekiguchi
2016	A review of practical tools for rapid monitoring of membrane bioreactors Water Research E. Scholes, V. Verheyen, P. Brook-Carter
2016	Environmental Footprints and Eco-design of Products and Processes Anthony Y.W. Ma, Billy K.W. Cheung, Katrina C.M. Kwok, Mingwei Cai, Patrick K.H. Lee
2016	Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Nature Communications Emiley A. Eloe-Fadrosh, David Paez-Espino, Jessica Jarett, Peter F. Dunfield, Brian P. Hedlund, Anne E. Dekas, Stephen E. Grasby, Allyson L. Brady, Hailiang Dong, Brandon R. Briggs, Wen-Jun Li, Danielle Goudeau, Rex Malmstrom, Amrita Pati, Jennifer Pett-Ridge, Edward M. Rubin, Tanja Woyke, Nikos C. Kyrpides, Natalia N. Ivanova
2016	Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology Liwei Sun, Mayu Toyonaga, Akiko Ohashi, Dieter M. Tourlousse, Norihisa Matsuura, Xian-Ying Meng, Hideyuki Tamaki, Satoshi Hanada, Rodrigo Cruz, Takashi Yamaguchi, Yuji Sekiguchi
2016	Microbial diversity in European alpine permafrost and active layers FEMS Microbiology Ecology Beat Frey, Thomas Rime, Marcia Phillips, Beat Stierli, Irka Hajdas, Franco Widmer, Martin Hartmann
2016	Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnology Advances Isabel Ferrera, Olga Sánchez
2016	Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor Frontiers in Microbiology Soe Myat Thandar, Norisuke Ushiki, Hirotsugu Fujitani, Yuji Sekiguchi, Satoshi Tsuneda
2016	Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage Molecular Biology and Evolution Yun Kit Yeoh, Yuji Sekiguchi, Donovan H. Parks, Philip Hugenholtz
2016	Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks Chemosphere Mariana P. Reis, Marcela F. Dias, Patrícia S. Costa, Marcelo P. Ávila, Laura R. Leite, Flávio M.G. de Araújo, Anna C.M. Salim, Mônica Bucciarelli-Rodriguez, Guilherme Oliveira, Edmar Chartone-Souza, Andréa M.A. Nascimento
2016	Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi International Journal of Systematic and Evolutionary Microbiology Liwei Sun, Mayu Toyonaga, Akiko Ohashi, Norihisa Matsuura, Dieter M. Tourlousse, Xian-Ying Meng, Hideyuki Tamaki, Satoshi Hanada, Rodrigo Cruz, Takashi Yamaguchi, Yuji Sekiguchi
2016	Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes mSystems Richard Allen White, Eric M. Bottos, Taniya Roy Chowdhury, Jeremy D. Zucker, Colin J. Brislawn, Carrie D. Nicora, Sarah J. Fansler, Kurt R. Glaesemann, Kevin Glass, Janet K. Jansson
2016	Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters The ISME Journal Rasmus Hansen Kirkegaard, Morten Simonsen Dueholm, Simon Jon McIlroy, Marta Nierychlo, Søren Michael Karst, Mads Albertsen, Per Halkjær Nielsen
2015	Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae ( Chloroflexi ) Genome Announcements Norihisa Matsuura, Dieter M. Tourlousse, Akiko Ohashi, Philip Hugenholtz, Yuji Sekiguchi
2015	Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan Genome Announcements Dieter M. Tourlousse, Takuya Honda, Norihisa Matsuura, Akiko Ohashi, Akio Tonouchi, Yuji Sekiguchi
2015	Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System Genome Announcements Dieter M. Tourlousse, Norihisa Matsuura, Liwei Sun, Mayu Toyonaga, Kyohei Kuroda, Akiko Ohashi, Rodrigo Cruz, Takashi Yamaguchi, Yuji Sekiguchi
2015	CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Research Donovan H. Parks, Michael Imelfort, Connor T. Skennerton, Philip Hugenholtz, Gene W. Tyson
2015	Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System Genome Announcements Norihisa Matsuura, Dieter M. Tourlousse, Liwei Sun, Mayu Toyonaga, Kyohei Kuroda, Akiko Ohashi, Rodrigo Cruz, Takashi Yamaguchi, Yuji Sekiguchi
2009	Charles Thomas Parker, Dorothea Taylor, George M Garrity
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