| # | Title | Journal | Year | Citations |
|---|
| 1 | The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 | Nature Microbiology | 2020 | 5,799 |
| 2 | Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses | Nature Microbiology | 2020 | 2,585 |
| 3 | A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology | Nature Microbiology | 2020 | 2,291 |
| 4 | A new view of the tree of life | Nature Microbiology | 2016 | 1,823 |
| 5 | Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life | Nature Microbiology | 2017 | 1,465 |
| 6 | The importance of anabolism in microbial control over soil carbon storage | Nature Microbiology | 2017 | 1,288 |
| 7 | Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly | Nature Microbiology | 2018 | 1,268 |
| 8 | The neuroactive potential of the human gut microbiota in quality of life and depression | Nature Microbiology | 2019 | 1,206 |
| 9 | Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans | Nature Microbiology | 2020 | 1,115 |
| 10 | Gut microbiome structure and metabolic activity in inflammatory bowel disease | Nature Microbiology | 2019 | 1,094 |
| 11 | Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy | Nature Microbiology | 2018 | 906 |
| 12 | Dynamics of the human gut microbiome in inflammatory bowel disease | Nature Microbiology | 2017 | 830 |
| 13 | Continental-scale pollution of estuaries with antibiotic resistance genes | Nature Microbiology | 2017 | 812 |
| 14 | Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic | Nature Microbiology | 2020 | 772 |
| 15 | MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis | Nature Microbiology | 2016 | 761 |
| 16 | The physiology and habitat of the last universal common ancestor | Nature Microbiology | 2016 | 739 |
| 17 | Culture of previously uncultured members of the human gut microbiota by culturomics | Nature Microbiology | 2016 | 735 |
| 18 | Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships | Nature Microbiology | 2017 | 727 |
| 19 | Enterotypes in the landscape of gut microbial community composition | Nature Microbiology | 2018 | 717 |
| 20 | Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis | Nature Microbiology | 2016 | 704 |
| 21 | Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus | Nature Microbiology | 2019 | 699 |
| 22 | Stress and stability: applying the Anna Karenina principle to animal microbiomes | Nature Microbiology | 2017 | 661 |
| 23 | Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets | Nature Microbiology | 2020 | 661 |
| 24 | Relic DNA is abundant in soil and obscures estimates of soil microbial diversity | Nature Microbiology | 2017 | 660 |
| 25 | The current and future global distribution and population at risk of dengue | Nature Microbiology | 2019 | 645 |
| 26 | Defining and combating antibiotic resistance from One Health and Global Health perspectives | Nature Microbiology | 2019 | 614 |
| 27 | Combating multidrug-resistant Gram-negative bacteria with structurally nanoengineered antimicrobial peptide polymers | Nature Microbiology | 2016 | 610 |
| 28 | GABA-modulating bacteria of the human gut microbiota | Nature Microbiology | 2019 | 590 |
| 29 | Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes | Nature Microbiology | 2017 | 562 |
| 30 | The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets | Nature Microbiology | 2021 | 556 |
| 31 | Next-generation probiotics: the spectrum from probiotics to live biotherapeutics | Nature Microbiology | 2017 | 553 |
| 32 | Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies | Nature Microbiology | 2020 | 553 |
| 33 | The continued threat of emerging flaviviruses | Nature Microbiology | 2020 | 520 |
| 34 | Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease | Nature Microbiology | 2019 | 517 |
| 35 | Persister formation in Staphylococcus aureus is associated with ATP depletion | Nature Microbiology | 2016 | 508 |
| 36 | Global diversity and biogeography of bacterial communities in wastewater treatment plants | Nature Microbiology | 2019 | 491 |
| 37 | Recovery of gut microbiota of healthy adults following antibiotic exposure | Nature Microbiology | 2018 | 483 |
| 38 | Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread | Nature Microbiology | 2019 | 476 |
| 39 | The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota | Nature Microbiology | 2016 | 465 |
| 40 | Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota | Nature Microbiology | 2016 | 459 |
| 41 | Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans | Nature Microbiology | 2019 | 455 |
| 42 | Phage puppet masters of the marine microbial realm | Nature Microbiology | 2018 | 438 |
| 43 | REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes | Nature Microbiology | 2019 | 437 |
| 44 | Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype | Nature Microbiology | 2016 | 436 |
| 45 | Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes | Nature Microbiology | 2018 | 436 |
| 46 | Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome | Nature Microbiology | 2016 | 433 |
| 47 | A reference gene catalogue of the pig gut microbiome | Nature Microbiology | 2016 | 416 |
| 48 | An insider's perspective: Bacteroides as a window into the microbiome | Nature Microbiology | 2017 | 416 |
| 49 | Dynamics of metatranscription in the inflammatory bowel disease gut microbiome | Nature Microbiology | 2018 | 408 |
| 50 | Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom | Nature Microbiology | 2016 | 384 |
