Author,Title,Year,Method,Description of Method,Doi,
Fierer et al.,"The influence of sex, handedness, and washing on the diversity of hand surface bacteria",2008,Proportion of Replicates,"""commonly found"" across all samples",10.1073/pnas.0807920105,
Zaura et al.,"Defining the healthy ""core microbiome"" of oral microbial communities",2009,Proportion of Replicates,"84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes",10.1186/1471-2180-9-259,
Benson et al.,Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors,2010,Hard cut off,30 sequence reads for a given taxon,doi.org/10.1073/pnas.1007028107,
Junji Qin,A human gut microbial gene catalogue established by metagenomic sequencing,2010,Proportion of Replicates,"present in all individuals, 57 in ≥90% and 75 in ≥50% of individuals",10.1038/nature08821,
Caporaso et al.,Moving pictures of the human microbiome,2011,Proportion of Replicates + Temporal aspect,time series to define core (using 90% over time series),10.1186/gb-2011-12-5-r50,
Lundberg et al.,Defining the core Arabidopsis thaliana root microbiome,2012,Hard cut off,At least 25 reads in 5 samples,10.1038/nature11237,
Krych et al.,"Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome",2013,Cumulative Proportion of Sequence Reads,a cut off threshold (0.19%) for the low abundant taxa,10.1371/journal.pone.0062578,
Li et al.,Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome,2013,Proportion of Reads and Replicates,"abundance and ubiquity: 75% of the cohort, let the definition of a “majority” of the population be a more loosely required ubiquity at >50% ",10.1371/journal.pone.0063139,
Petri et al.,Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge,2013,Venn diagram,Shared OTUs across treatments,10.1371/journal.pone.0083424,
De Filippis et al.,A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures,2014,Cumulative Proportion of Sequence Reads,13 of them had a relative abundance higher than 1% in at least one sample,10.1371/journal.pone.0089680,
Zhang et al.,Mongolians core gut microbiota and its correlation with seasonal dietary changes,2014,Proportion of Replicates,"""among all or the vast majority of samples""",10.1038/srep05001,
Henderson et al.,"Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range",2015,Cumulative Proportion of Sequence Reads,"were all found in over 90% of samples, and together comprised 89.4% of all sequence data",10.1038/srep14567,
Ainsworth et al.,The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts,2015,Proportion of Replicates,OTU abundance in the core at 2% intervals from 0% to 100% of samples,10.1038/ismej.2015.39,
Givens et al.,Comparison of the gut microbiomes of 12 bony fish and 3 shark species,2015,Proportion of Replicates,present in all samples,10.3354/meps11034,
Zachow et al.,Endemic plants harbour specific Trichodermacommunities with an exceptional potential for biocontrol of phytopathogens,2016,Proportion of Replicates,OTUs were only considered when they occurred in 10 of all 12 samples,10.1016/j.jbiotec.2016.03.049,
Debnath et al.,Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang,2016,Proportion of Replicates,compute_core_microbiome.py at 100%,10.3389/fpls.2016.01345,
Segata et al.,The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers,2016,Proportion of Replicates,present in all samples,10.1038/srep24207,
Yuan et al.,Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity,2016,Venn diagram,,10.1038/srep32467,
Hammer et al.,Caterpillars lack a resident gut microbiome,2017,Hard cut off,100 reads in 3 samples,10.1073/pnas.1707186114,
Khan et al.,Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree,2017,Hard cut off,OTUs kept only if they had at least two reads in at least three samples (ITS data) or at least seven reads in at least three samples. (Different cut off but cite Lundberg),10.1371/journal.pone.0186939,
Beckers et al.,Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees,2017,Cumulative Proportion of Sequence Reads,10 most abundant OTUs of each of the plant compartment,10.1186/s40168-017-0241-2,
Pfeiffer et al.,Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development,2017,Proportion of Reads and Replicates,detected in at least 3 of 5 of rhizosphere replicates and relative abundance of minimum 0.1%,10.1093/femsec/fiw242,
Astudillo‐García et al.,Evaluating the core microbiota in complex communities: A systematic investigation,2017,Proportion of Replicates,"specific core 12–100% and overall core 5–100% both with no minimum abundance threshold, 0.01% and 0.1% relative abundance threshold",doi.org/10.1111/1462-2920.13647,
Liete et al.,Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont,2017,Proportion of Replicates,set of bacterial taxa universally present in all samples,10.1002/ece3.3717,
Jin et al.,Taxonomic structure and functional association of foxtail millet root microbiome,2017,Proportion of Replicates,80% of the samples in each group and were statistically enriched in rhizoplane compared with rhizospher,10.1093/gigascience/gix089,
Blaustien et al.,Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease,2017,Proportion of Replicates,detected in at least 95% of the respective leaf or root samples,10.1128/AEM.00210-17,
Jiang et al.,Plant cultivars imprint the rhizosphere bacterial community composition and association networks,2017,Proportion of Replicates,present in all samples,10.1016/j.soilbio.2017.02.010,
Santhanam et al.,Specificity of root microbiomes in native-grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization,2017,Proportion of Replicates,shared among all root samples,10.1111/mec.14049,
Astudillo-García et al.,Evaluating the core microbiota in complex communities: A systematic investigation,2017,Proportion of Replicates,"Tested thresholds, saw differences in alpha but not beta diversity",10.1111/1462-2920.13647,
Mahoney et al.,"Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars",2017,Proportion of Replicates,compute_core_microbiome.py in 95% samples,10.3389/fpls.2017.00132,
Bierlich et al.,Temporal and Regional Variability in the Skin Microbiome of Humpback Whales along the Western Antarctic Peninsula,2017,Proportion of Replicates,present in 93% or more of all samples,10.1128/AEM.02574-17,
Liu et al.,A comparative study of gut microbiota profiles of earthworms fed in three different substrates,2017,Venn diagram,Shared OTUs across treatments,10.1007/s13199-017-0491-6,Do we want to call these OTHER and use the discription?
Rybakova et al.,The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens,2017,Venn diagram,OTUs in all three cultivars,10.1186/s40168-017-0310-6,
Colin et al.,Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence,2017,Venn diagram,OTUs present in all the rhizosphere samples when the three soil types were considered together,10.1038/s41598-017-07639-1,
Lawson et al.,"Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium",2018,Cumulative Proportion of Sequence Reads,"a single OTU (clustered at 97% using VSEARCH, see Supporting Information Appendix S1) must be present in 100% of samples and have a minimum abundance of 0.0001%, each OTU was then identified to the highest taxonomic resolution possible",10.1111/1758-2229.12599,
Hamonts et al.,Field study reveals core plant microbiota and relative importance of their drivers,2018,Cumulative Proportion of Sequence Reads,Top 75% reads,10.1111/1462-2920.14031,
Delgado-Baquerizo et al.,A global atlas of the dominant bacteria found in soil,2018,Proportion of Reads and Replicates,"10% of reads, 55% of samples",10.1126/science.aap9516,
Rubio-Portillo et al.,Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea,2018,Proportion of Replicates,"minimum fraction of samples set at 85 and 100%, lowest percentage at which core OTU abundance was stable across healthy and necrosed samples",10.3389/fmicb.2018.00022,
Williams et al.,A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters,2018,Proportion of Replicates,OTUs shared amongst 95% or more of the individuals,10.1371/journal.pone.0034242,
Kostric et al.,Development of a Stable Lung Microbiome in Healthy Neonatal Mice,2018,Proportion of Replicates,present in 100% of samples/group,10.1007/s00248-017-1068-x,
Chauhan et al.,Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes,2018,Proportion of Replicates,presence in at least 50% of the study samples,10.3389/fmicb.2018.00118,
Kohl et al.,Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.,2018,Proportion of Replicates,detected across all samples,10.1111/1365-2656.12692,
Sánchez-López et al.,Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria,2018,Proportion of Replicates + Temporal aspect,bacterial taxa occurring in at least 50% of the samples over three consecutive years,10.3390/ijms19010291,
Amorim et al.,Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals,2018,Venn diagram,Shared OTUs across treatments,10.1016/j.ecoenv.2017.09.060,
Li et al.,Specialized core bacteria associate with plants adapted to adverse environment with high calcium contents,2018,Venn diagram,OTUs that repeatedly appeared in these fourteen amplicon libraries,10.1371/journal.pone.0194080,
Dong et al.,"Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum",2018,Venn diagram,,10.3389/fmicb.2018.00267,
Search Terms:,"WOS: ""Core"" AND ""Microbiome"" in topic",,Number of results: 1034,,,
Search Terms:,"WOS: ""Core"" within Lundberg et al. 2012 citations on WOS",,Number of results: 58,Sorted by: Date,,