| # | Title | Journal | Year | Citations |
|---|
| 1 | Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin | Microbiome | 2018 | 3,159 |
| 2 | Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data | Microbiome | 2018 | 1,729 |
| 3 | An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform | Microbiome | 2014 | 1,454 |
| 4 | Normalization and microbial differential abundance strategies depend upon data characteristics | Microbiome | 2017 | 1,434 |
| 5 | MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis | Microbiome | 2018 | 1,098 |
| 6 | Gut microbiota dysbiosis contributes to the development of hypertension | Microbiome | 2017 | 1,086 |
| 7 | Microbiome definition re-visited: old concepts and new challenges | Microbiome | 2020 | 903 |
| 8 | Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study | Microbiome | 2017 | 901 |
| 9 | Microbial interactions within the plant holobiont | Microbiome | 2018 | 833 |
| 10 | Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis | Microbiome | 2014 | 816 |
| 11 | The vocabulary of microbiome research: a proposal | Microbiome | 2015 | 778 |
| 12 | A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome | Microbiome | 2017 | 744 |
| 13 | Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health | Microbiome | 2019 | 708 |
| 14 | New evidences on the altered gut microbiota in autism spectrum disorders | Microbiome | 2017 | 668 |
| 15 | Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut | Microbiome | 2013 | 621 |
| 16 | The gut mycobiome of the Human Microbiome Project healthy cohort | Microbiome | 2017 | 609 |
| 17 | The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women | Microbiome | 2014 | 607 |
| 18 | Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses | Microbiome | 2018 | 541 |
| 19 | Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals | Microbiome | 2016 | 533 |
| 20 | MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm | Microbiome | 2014 | 521 |
| 21 | Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem | Microbiome | 2018 | 514 |
| 22 | Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling | Microbiome | 2013 | 493 |
| 23 | VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences | Microbiome | 2020 | 482 |
| 24 | Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family | Microbiome | 2019 | 481 |
| 25 | Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank | Microbiome | 2021 | 479 |
| 26 | Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis | Microbiome | 2017 | 467 |
| 27 | DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data | Microbiome | 2018 | 462 |
| 28 | Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota | Microbiome | 2016 | 447 |
| 29 | VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses | Microbiome | 2021 | 441 |
| 30 | Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants | Microbiome | 2014 | 437 |
| 31 | VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data | Microbiome | 2017 | 433 |
| 32 | The sponge holobiont in a changing ocean: from microbes to ecosystems | Microbiome | 2018 | 426 |
| 33 | Optimizing methods and dodging pitfalls in microbiome research | Microbiome | 2017 | 420 |
| 34 | Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees | Microbiome | 2017 | 406 |
| 35 | Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases | Microbiome | 2019 | 404 |
| 36 | Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming | Microbiome | 2018 | 399 |
| 37 | Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort | Microbiome | 2017 | 390 |
| 38 | Diet shapes the gut microbiome of pigs during nursing and weaning | Microbiome | 2015 | 387 |
| 39 | Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems | Microbiome | 2018 | 368 |
| 40 | The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term | Microbiome | 2014 | 361 |
| 41 | Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation | Microbiome | 2013 | 355 |
| 42 | The structure and diversity of human, animal and environmental resistomes | Microbiome | 2016 | 355 |
| 43 | Microbial shifts in the aging mouse gut | Microbiome | 2014 | 354 |
| 44 | Root exudates drive the soil-borne legacy of aboveground pathogen infection | Microbiome | 2018 | 354 |
| 45 | Community differentiation of the cutaneous microbiota in psoriasis | Microbiome | 2013 | 353 |
| 46 | VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data | Microbiome | 2015 | 352 |
| 47 | Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle | Microbiome | 2016 | 348 |
| 48 | Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems | Microbiome | 2017 | 347 |
| 49 | Viruses in the Built Environment (VIBE) meeting report | Microbiome | 2020 | 345 |
| 50 | Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers | Microbiome | 2018 | 344 |
