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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
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- Nenad Macesic & Jane Hawkey & Ben Vezina & Jessica A. Wisniewski & Hugh Cottingham & Luke V. Blakeway & Taylor Harshegyi & Katherine Pragastis & Gnei Zweena Badoordeen & Amanda Dennison & Denis W. Spe, 2023. "Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Sébastien Bridel & Valérie Bouchez & Bryan Brancotte & Sofia Hauck & Nathalie Armatys & Annie Landier & Estelle Mühle & Sophie Guillot & Julie Toubiana & Martin C. J. Maiden & Keith A. Jolley & Sylvai, 2022. "A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Minghui Cheng & Yingjie Xu & Xiao Cui & Xin Wei & Yundi Chang & Jun Xu & Cheng Lei & Lei Xue & Yifan Zheng & Zhang Wang & Lingtong Huang & Min Zheng & Hong Luo & Yuxin Leng & Chao Jiang, 2024. "Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Nils Giordano & Marinna Gaudin & Camille Trottier & Erwan Delage & Charlotte Nef & Chris Bowler & Samuel Chaffron, 2024. "Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Ling Zhong & Menghan Zhang & Libing Sun & Yu Yang & Bo Wang & Haibing Yang & Qiang Shen & Yu Xia & Jiarui Cui & Hui Hang & Yi Ren & Bo Pang & Xiangyu Deng & Yahui Zhan & Heng Li & Zhemin Zhou, 2023. "Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Joachim Johansen & Damian R. Plichta & Jakob Nybo Nissen & Marie Louise Jespersen & Shiraz A. Shah & Ling Deng & Jakob Stokholm & Hans Bisgaard & Dennis Sandris Nielsen & Søren J. Sørensen & Simon Ras, 2022. "Genome binning of viral entities from bulk metagenomics data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Roxana Zamudio & Patrick Boerlin & Racha Beyrouthy & Jean-Yves Madec & Stefan Schwarz & Michael R. Mulvey & George G. Zhanel & Ashley Cormier & Gabhan Chalmers & Richard Bonnet & Marisa Haenni & Inga , 2022. "Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Daniel R. Colman & Lisa M. Keller & Emilia Arteaga-Pozo & Eva Andrade-Barahona & Brian Clair & Anna Shoemaker & Alysia Cox & Eric S. Boyd, 2024. "Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
- Akuzike Kalizang’oma & Damien Richard & Brenda Kwambana-Adams & Juliana Coelho & Karen Broughton & Bruno Pichon & Katie L. Hopkins & Victoria Chalker & Sandra Beleza & Stephen D. Bentley & Chrispin Ch, 2024. "Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Xiyang Dong & Yongyi Peng & Muhua Wang & Laura Woods & Wenxue Wu & Yong Wang & Xi Xiao & Jiwei Li & Kuntong Jia & Chris Greening & Zongze Shao & Casey R. J. Hubert, 2023. "Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Jean-Sebastien Gounot & Minghao Chia & Denis Bertrand & Woei-Yuh Saw & Aarthi Ravikrishnan & Adrian Low & Yichen Ding & Amanda Hui Qi Ng & Linda Wei Lin Tan & Yik-Ying Teo & Henning Seedorf & Niranjan, 2022. "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Helen R. Davison & Jack Pilgrim & Nicky Wybouw & Joseph Parker & Stacy Pirro & Simon Hunter-Barnett & Paul M. Campbell & Frances Blow & Alistair C. Darby & Gregory D. D. Hurst & Stefanos Siozios, 2022. "Genomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Vincent Somerville & Nadine Thierer & Remo S. Schmidt & Alexandra Roetschi & Lauriane Braillard & Monika Haueter & Hélène Berthoud & Noam Shani & Ueli Ah & Florent Mazel & Philipp Engel, 2024. "Genomic and phenotypic imprints of microbial domestication on cheese starter cultures," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- Xin Fan & Rong-Chen Dai & Shu Zhang & Yuan-Yuan Geng & Mei Kang & Da-Wen Guo & Ya-Ning Mei & Yu-Hong Pan & Zi-Yong Sun & Ying-Chun Xu & Jie Gong & Meng Xiao, 2023. "Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Lucie Semenec & Amy K. Cain & Catherine J. Dawson & Qi Liu & Hue Dinh & Hannah Lott & Anahit Penesyan & Ram Maharjan & Francesca L. Short & Karl A. Hassan & Ian T. Paulsen, 2023. "Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Xiao Luo & Xiongbin Kang & Alexander Schönhuth, 2022. "VeChat: correcting errors in long reads using variation graphs," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Conor Feehily & Ian J. O’Neill & Calum J. Walsh & Rebecca L. Moore & Sarah Louise Killeen & Aisling A. Geraghty & Elaine M. Lawton & David Byrne & Rocio Sanchez-Gallardo & Sai Ravi Chandra Nori & Ida , 2023. "Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Xuanji Li & Asker Brejnrod & Jonathan Thorsen & Trine Zachariasen & Urvish Trivedi & Jakob Russel & Gisle Alberg Vestergaard & Jakob Stokholm & Morten Arendt Rasmussen & Søren Johannes Sørensen, 2023. "Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Corentin Hochart & Lucas Paoli & Hans-Joachim Ruscheweyh & Guillem Salazar & Emilie Boissin & Sarah Romac & Julie Poulain & Guillaume Bourdin & Guillaume Iwankow & Clémentine Moulin & Maren Ziegler & , 2023. "Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Max E. Schön & Vasily V. Zlatogursky & Rohan P. Singh & Camille Poirier & Susanne Wilken & Varsha Mathur & Jürgen F. H. Strassert & Jarone Pinhassi & Alexandra Z. Worden & Patrick J. Keeling & Thijs J, 2021. "Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- David J. Williams & Patrick A. D. Grimont & Adrián Cazares & Francine Grimont & Elisabeth Ageron & Kerry A. Pettigrew & Daniel Cazares & Elisabeth Njamkepo & François-Xavier Weill & Eva Heinz & Matthe, 2022. "The genus Serratia revisited by genomics," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Aleksandar Stanojković & Svatopluk Skoupý & Hanna Johannesson & Petr Dvořák, 2024. "The global speciation continuum of the cyanobacterium Microcoleus," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Sanjam S. Sawhney & Rhiannon C. Vargas & Meghan A. Wallace & Carol E. Muenks & Brian V. Lubbers & Stephanie A. Fritz & Carey-Ann D. Burnham & Gautam Dantas, 2023. "Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Yuval Bussi & Ruti Kapon & Ziv Reich, 2021. "Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-27, October.
- Daniel P. Morreale & Eric A. Porsch & Brad K. Kern & Joseph W. Geme & Paul J. Planet, 2023. "Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Rathanin Seng & Chalita Chomkatekaew & Sarunporn Tandhavanant & Natnaree Saiprom & Rungnapa Phunpang & Janjira Thaipadungpanit & Elizabeth M. Batty & Nicholas P. J. Day & Wasun Chantratita & T. Eoin W, 2024. "Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Wenxiu Wang & Weizhi Song & Marwan E. Majzoub & Xiaoyuan Feng & Bu Xu & Jianchang Tao & Yuanqing Zhu & Zhiyong Li & Pei-Yuan Qian & Nicole S. Webster & Torsten Thomas & Lu Fan, 2024. "Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Jean F. Power & Carlo R. Carere & Holly E. Welford & Daniel T. Hudson & Kevin C. Lee & John W. Moreau & Thijs J. G. Ettema & Anna-Louise Reysenbach & Charles K. Lee & Daniel R. Colman & Eric S. Boyd &, 2024. "A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Kang-Hua Chen & Jiao Feng & Paul L. E. Bodelier & Ziming Yang & Qiaoyun Huang & Manuel Delgado-Baquerizo & Peng Cai & Wenfeng Tan & Yu-Rong Liu, 2024. "Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Jordy Evan Sulaiman & Jaron Thompson & Yili Qian & Eugenio I. Vivas & Christian Diener & Sean M. Gibbons & Nasia Safdar & Ophelia S. Venturelli, 2024. "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Wanting Dong & Xinyue Fan & Yaqiong Guo & Siyi Wang & Shulei Jia & Na Lv & Tao Yuan & Yuanlong Pan & Yong Xue & Xi Chen & Qian Xiong & Ruifu Yang & Weigang Zhao & Baoli Zhu, 2024. "An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- M. C. Rühlemann & C. Bang & J. F. Gogarten & B. M. Hermes & M. Groussin & S. Waschina & M. Poyet & M. Ulrich & C. Akoua-Koffi & T. Deschner & J. J. Muyembe-Tamfum & M. M. Robbins & M. Surbeck & R. M. , 2024. "Functional host-specific adaptation of the intestinal microbiome in hominids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Xiyang Dong & Chuwen Zhang & Yongyi Peng & Hong-Xi Zhang & Ling-Dong Shi & Guangshan Wei & Casey R. J. Hubert & Yong Wang & Chris Greening, 2022. "Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Harold P. Hodgins & Pengsheng Chen & Briallen Lobb & Xin Wei & Benjamin J. M. Tremblay & Michael J. Mansfield & Victoria C. Y. Lee & Pyung-Gang Lee & Jeffrey Coffin & Ana T. Duggan & Alexis E. Dolphin, 2023. "Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Ruobing Wang & Anru Zhang & Shijun Sun & Guankun Yin & Xingyu Wu & Qi Ding & Qi Wang & Fengning Chen & Shuyi Wang & Lucy Dorp & Yawei Zhang & Longyang Jin & Xiaojuan Wang & Francois Balloux & Hui Wang, 2024. "Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Georges P. Schmartz & Jacqueline Rehner & Madline P. Gund & Verena Keller & Leidy-Alejandra G. Molano & Stefan Rupf & Matthias Hannig & Tim Berger & Elias Flockerzi & Berthold Seitz & Sara Fleser & Sa, 2024. "Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Shaojun Pan & Chengkai Zhu & Xing-Ming Zhao & Luis Pedro Coelho, 2022. "A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Lucas Serra Moncadas & Cyrill Hofer & Paul-Adrian Bulzu & Jakob Pernthaler & Adrian-Stefan Andrei, 2024. "Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.