| 1 | Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin | Microbiome | 2018 | 3,400 |
| 2 | Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data | Microbiome | 2018 | 1,708 |
| 3 | Normalization and microbial differential abundance strategies depend upon data characteristics | Microbiome | 2017 | 1,273 |
| 4 | An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform | Microbiome | 2014 | 1,269 |
| 5 | Microbiome definition re-visited: old concepts and new challenges | Microbiome | 2020 | 1,166 |
| 6 | Gut microbiota dysbiosis contributes to the development of hypertension | Microbiome | 2017 | 1,163 |
| 7 | Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study | Microbiome | 2017 | 963 |
| 8 | Microbial interactions within the plant holobiont | Microbiome | 2018 | 872 |
| 9 | Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health | Microbiome | 2019 | 812 |
| 10 | The vocabulary of microbiome research: a proposal | Microbiome | 2015 | 786 |
| 11 | 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 | 767 |
| 12 | A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome | Microbiome | 2017 | 733 |
| 13 | New evidences on the altered gut microbiota in autism spectrum disorders | Microbiome | 2017 | 705 |
| 14 | The gut mycobiome of the Human Microbiome Project healthy cohort | Microbiome | 2017 | 632 |
| 15 | The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women | Microbiome | 2014 | 576 |
| 16 | Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut | Microbiome | 2013 | 569 |
| 17 | VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses | Microbiome | 2021 | 531 |
| 18 | VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences | Microbiome | 2020 | 512 |
| 19 | Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family | Microbiome | 2019 | 492 |
| 20 | Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis | Microbiome | 2017 | 477 |
| 21 | Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals | Microbiome | 2016 | 471 |
| 22 | MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm | Microbiome | 2014 | 464 |
| 23 | Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems | Microbiome | 2018 | 460 |
| 24 | Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling | Microbiome | 2013 | 454 |
| 25 | Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming | Microbiome | 2018 | 410 |
| 26 | Root exudates drive the soil-borne legacy of aboveground pathogen infection | Microbiome | 2018 | 409 |
| 27 | Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota | Microbiome | 2016 | 398 |
| 28 | Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons | Microbiome | 2019 | 392 |
| 29 | VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data | Microbiome | 2017 | 385 |
| 30 | Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis | Microbiome | 2021 | 384 |
| 31 | Optimizing methods and dodging pitfalls in microbiome research | Microbiome | 2017 | 382 |
| 32 | Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses | Microbiome | 2018 | 381 |
| 33 | Microbiome–host systems interactions: protective effects of propionate upon the blood–brain barrier | Microbiome | 2018 | 379 |
| 34 | Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort | Microbiome | 2017 | 378 |
| 35 | Review: microbial transformations of human bile acids | Microbiome | 2021 | 375 |
| 36 | The sponge holobiont in a changing ocean: from microbes to ecosystems | Microbiome | 2018 | 367 |
| 37 | Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees | Microbiome | 2017 | 366 |
| 38 | Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation | Microbiome | 2013 | 355 |
| 39 | Uncovering the trimethylamine-producing bacteria of the human gut microbiota | Microbiome | 2017 | 355 |
| 40 | Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers | Microbiome | 2018 | 354 |
| 41 | Diet shapes the gut microbiome of pigs during nursing and weaning | Microbiome | 2015 | 351 |
| 42 | The structure and diversity of human, animal and environmental resistomes | Microbiome | 2016 | 347 |
| 43 | Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants | Microbiome | 2014 | 337 |
| 44 | Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease | Microbiome | 2017 | 330 |
| 45 | Specialized metabolic functions of keystone taxa sustain soil microbiome stability | Microbiome | 2021 | 330 |
| 46 | Community differentiation of the cutaneous microbiota in psoriasis | Microbiome | 2013 | 329 |
| 47 | Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems | Microbiome | 2017 | 323 |
| 48 | Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions | Microbiome | 2016 | 322 |
| 49 | Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain | Microbiome | 2018 | 320 |
| 50 | The hologenome concept of evolution after 10 years | Microbiome | 2018 | 314 |
