| 1 | Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis | 3.6 | 0 | Citations (PDF) |
| 2 | Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting | 4.6 | 0 | Citations (PDF) |
| 3 | The future is fermented: Microbial biodiversity of fermented foods is a critical resource for food innovation and human health | 15.4 | 4 | Citations (PDF) |
| 4 | Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities | 10.2 | 3 | Citations (PDF) |
| 5 | Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment | 3.3 | 32 | Citations (PDF) |
| 6 | Lord of the Diptera (and Moths and a Spider): Molecular Diet Analyses and Foraging Ecology of Indiana Bats in Illinois | 2.2 | 18 | Citations (PDF) |
| 7 | Effect of Bovine Milk Fat Globule Membrane and Lactoferrin in Infant Formula on Gut Microbiome and Metabolome at 4 Months of Age | 0.2 | 11 | Citations (PDF) |
| 8 | Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing | 3.9 | 52 | Citations (PDF) |
| 9 | Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences | 3.9 | 15 | Citations (PDF) |
| 10 | Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops | 3.3 | 2 | Citations (PDF) |
| 11 | Cigarette Smoking and Opium Use in Relation to the Oral Microbiota in Iran | 3.6 | 10 | Citations (PDF) |
| 12 | RESCRIPt: Reproducible sequence taxonomy reference database management | 3.3 | 397 | Citations (PDF) |
| 13 | Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran | 2.8 | 51 | Citations (PDF) |
| 14 | A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses | 2.0 | 42 | Citations (PDF) |
| 15 | Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? | 3.3 | 17 | Citations (PDF) |
| 16 | Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods | 4.2 | 47 | Citations (PDF) |
| 17 | Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity | 0.6 | 14 | Citations (PDF) |
| 18 | Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity | 0.6 | 7 | Citations (PDF) |
| 19 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | 18.1 | 12,543 | Citations (PDF) |
| 20 | Species abundance information improves sequence taxonomy classification accuracy | 14.1 | 97 | Citations (PDF) |
| 21 | Learning representations of microbe–metabolite interactions | 14.5 | 169 | Citations (PDF) |
| 22 | Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development | 2.8 | 76 | Citations (PDF) |
| 23 | Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles | 3.1 | 20 | Citations (PDF) |
| 24 | q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data | 4.6 | 201 | Citations (PDF) |
| 25 | Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women | 6.5 | 75 | Citations (PDF) |
| 26 | Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin | 11.5 | 3,400 | Citations (PDF) |
| 27 | q2-sample-classifier: machine-learning tools for microbiome classification and regression | 2.4 | 108 | Citations (PDF) |
| 28 | A communal catalogue reveals Earth’s multiscale microbial diversity | 40.1 | 1,683 | Citations (PDF) |
| 29 | mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking | 4.6 | 64 | Citations (PDF) |
| 30 | Antibiotics, birth mode, and diet shape microbiome maturation during early life | 13.1 | 1,017 | Citations (PDF) |
| 31 | Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics | 4.5 | 309 | Citations (PDF) |
| 32 | A new perspective on microbial landscapes within food production | 7.6 | 93 | Citations (PDF) |
| 33 | Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer | 25.6 | 705 | Citations (PDF) |
| 34 | Microbial biogeography of the transnational fermented milk matsoni | 4.4 | 46 | Citations (PDF) |
| 35 | The Soil Microbiome Influences Grapevine-Associated Microbiota | 4.5 | 677 | Citations (PDF) |
| 36 | Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate | 7.7 | 720 | Citations (PDF) |
| 37 | Indigenous Bacteria and Fungi Drive Traditional Kimoto Sake Fermentations | 3.6 | 86 | Citations (PDF) |
| 38 | The Microbiology of Malting and Brewing | 7.3 | 245 | Citations (PDF) |
| 39 | Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities | 3.6 | 416 | Citations (PDF) |
| 40 | Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing | 14.5 | 3,128 | Citations (PDF) |
| 41 | Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants | 3.6 | 228 | Citations (PDF) |
| 42 | Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance | 1.6 | 68 | Citations (PDF) |
