标题/作者	年份
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks Bioinformatics 36 (6), 1925-1927	2020
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae J Zheng, S Wittouck, E Salvetti, CMAP Franz, HMB Harris, P Mattarelli, ... International journal of systematic and evolutionary microbiology 70 (4 …	2020
Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle E Pasolli, F Asnicar, S Manara, M Zolfo, N Karcher, F Armanini, F Beghini, ... Cell 176 (3), 649-662. e20	2019
A new genomic blueprint of the human gut microbiota A Almeida, AL Mitchell, M Boland, SC Forster, GB Gloor, A Tarkowska, ... Nature 568 (7753), 499-504	2019
A complete domain-to-species taxonomy for Bacteria and Archaea DH Parks, M Chuvochina, PA Chaumeil, C Rinke, AJ Mussig, ... Nature biotechnology 38 (9), 1079-1086	2020
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth Y Shao, SC Forster, E Tsaliki, K Vervier, A Strang, N Simpson, N Kumar, ... Nature 574 (7776), 117-121	2019
A unified catalog of 204,938 reference genomes from the human gut microbiome A Almeida, S Nayfach, M Boland, F Strozzi, M Beracochea, ZJ Shi, ... Nature biotechnology 39 (1), 105-114	2021
The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations A Tett, KD Huang, F Asnicar, H Fehlner-Peach, E Pasolli, N Karcher, ... Cell host & microbe 26 (5), 666-679. e7	2019
metaFlye: scalable long-read metagenome assembly using repeat graphs M Kolmogorov, DM Bickhart, B Behsaz, A Gurevich, M Rayko, SB Shin, ... Nature Methods 17 (11), 1103-1110	2020
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 F Asnicar, AM Thomas, F Beghini, C Mengoni, S Manara, P Manghi, ... Nature communications 11 (1), 1-10	2020
Giant virus diversity and host interactions through global metagenomics F Schulz, S Roux, D Paez-Espino, S Jungbluth, DA Walsh, VJ Denef, ... Nature 578 (7795), 432-436	2020
Diversity within species: interpreting strains in microbiomes T Van Rossum, P Ferretti, OM Maistrenko, P Bork Nature Reviews Microbiology 18 (9), 491-506	2020
Genomic diversity landscape of the honey bee gut microbiota KM Ellegaard, P Engel Nature communications 10 (1), 1-13	2019
The population genetics of pathogenic Escherichia coli E Denamur, O Clermont, S Bonacorsi, D Gordon Nature Reviews Microbiology 19 (1), 37-54	2021
Minimal standards for the description of new genera and species of rhizobia and agrobacteria PM De Lajudie, M Andrews, J Ardley, B Eardly, E Jumas-Bilak, ... International journal of systematic and evolutionary microbiology 69 (7 …	2019
Charting the complexity of the marine microbiome through single-cell genomics MG Pachiadaki, JM Brown, J Brown, O Bezuidt, PM Berube, SJ Biller, ... Cell 179 (7), 1623-1635. e11	2019
A genus definition for bacteria and archaea based on a standard genome relatedness index RA Barco, GM Garrity, JJ Scott, JP Amend, KH Nealson, D Emerson MBio 11 (1), e02475-19	2020
Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids S Redondo-Salvo, R Fernández-López, R Ruiz, L Vielva, M de Toro, ... Nature communications 11 (1), 1-13	2020
Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome E Pasolli, F De Filippis, IE Mauriello, F Cumbo, AM Walsh, J Leech, ... Nature communications 11 (1), 1-12	2020
Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder MHK Johansson, V Bortolaia, S Tansirichaiya, FM Aarestrup, AP Roberts, ... Journal of Antimicrobial Chemotherapy 76 (1), 101-109	2021

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