(The TQCC of Microbiome is 75. The table below lists those papers that are above that threshold based on CrossRef citation counts. The publications cover those that have been published in the past four years, i.e., from 2019-03-01 to 2023-03-01.)
Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health490
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis342
Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family330
Optimizing methods and dodging pitfalls in microbiome research314
Host-microbiota interactions: from holobiont theory to analysis200
Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons183
Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils181
Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria179
Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing178
Understanding microbial community dynamics to improve optimal microbiome selection170
Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome170
Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization166
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease150
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling146
Alterations in the gut microbiome and metabolism with coronary artery disease severity145
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle144
Suppressed N fixation and diazotrophs after four decades of fertilization142
Maize synthesized benzoxazinoids affect the host associated microbiome129
A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016120
Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota120
Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids118
Advancing functional and translational microbiome research using meta-omics approaches117
Fungi stabilize connectivity in the lung and skin microbial ecosystems113
Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia109
Gut microbiota from NLRP3-deficient mice ameliorates depressive-like behaviors by regulating astrocyte dysfunction via circHIPK2108
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces108
Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children104
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms102
The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome99
Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning99
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle98
Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis96
Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model94
Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem94
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments93
Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench92
The skin microbiome of vertebrates91
Microbial indicators of environmental perturbations in coral reef ecosystems88
Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems85
Competitive interaction with keystone taxa induced negative priming under biochar amendments85
Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth84
CAMISIM: simulating metagenomes and microbial communities84
Diversities and potential biogeochemical impacts of mangrove soil viruses82
Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies81
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month81
Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome81
Gut microbiota trajectory in early life may predict development of celiac disease80
Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin80
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals79
Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters79
Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases79
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model78
Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites77
Ochratoxin A induces liver inflammation: involvement of intestinal microbiota76
A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis76
Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage75