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A roadmap to mammalian oral microbiome evolution with dental calculus
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Long‐Term Temporal and Spatial Dynamics of Food Availability for Endangered Mountain Gorillas in Volcanoes National Park, Rwanda
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Tooth wear and feeding ecology in mountain gorillas from Volcanoes National Park, Rwanda
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Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus
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The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models
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Long‐term breeding phenology shift in royal penguins
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Cultural legacies, fire ecology, and environmental change in the Stone Country of Arnhem Land and Kakadu National Park, Australia
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The Microbiology of Primary Dental Caries in Humans
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A Mathematical Theory of Communication
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A Mathematical Theory of Communication
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The Statistical Analysis of Compositional Data
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Molecular detection of bacteria associated to caries activity in dentinal lesions
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Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy
inferredcites →https://doi.org/10.1016/j.cell.2015.11.004openalex-snapshot
Gut Microbiota Orchestrates Energy Homeostasis during Cold
inferredcites →https://doi.org/10.1016/j.chom.2014.11.010openalex-snapshot
Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota
inferredcites →https://doi.org/10.1016/j.chom.2017.08.013openalex-snapshot
Host Genetic Control of the Oral Microbiome in Health and Disease
inferredcites →https://doi.org/10.1016/j.cub.2018.05.058openalex-snapshot
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
inferredcites →https://doi.org/10.1016/j.cub.2018.11.055openalex-snapshot
Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas
inferredcites →https://doi.org/10.1016/j.jhevol.2014.10.016openalex-snapshot
Ancient human microbiomes
inferredcites →https://doi.org/10.1016/j.tig.2017.05.005openalex-snapshot
Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
inferredcites →https://doi.org/10.1016/j.tree.2016.06.008openalex-snapshot
Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?
inferredcites →https://doi.org/10.1016/j.vetmic.2014.11.019openalex-snapshot
The feline oral microbiome: A provisional 16S rRNA gene based taxonomy with full-length reference sequences
inferredcites →https://doi.org/10.1016/j.ympev.2012.08.023openalex-snapshot
MITOS: Improved de novo metazoan mitochondrial genome annotation
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/ismej.2013.16openalex-snapshot
Habitat degradation impacts black howler monkey ( Alouatta pigra ) gastrointestinal microbiomes
inferredcites →https://doi.org/10.1038/nature10842openalex-snapshot
Insights into hominid evolution from the gorilla genome sequence
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nature12228openalex-snapshot
Great ape genetic diversity and population history
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Insights into the phylogeny and coding potential of microbial dark matter
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Biogeography and individuality shape function in the human skin metagenome
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Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
inferredcites →https://doi.org/10.1038/nature23292openalex-snapshot
The evolution of the host microbiome as an ecosystem on a leash
inferredcites →https://doi.org/10.1038/nature23889openalex-snapshot
Strains, functions and dynamics in the expanded Human Microbiome Project
inferredcites →https://doi.org/10.1038/nbt.4229openalex-snapshot
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
inferredcites →https://doi.org/10.1038/ncomms14319openalex-snapshot
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
inferredcites →https://doi.org/10.1038/ng.2536openalex-snapshot
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
inferredcites →https://doi.org/10.1038/ng.2906openalex-snapshot
Pathogens and host immunity in the ancient human oral cavity
inferredcites →https://doi.org/10.1038/nmeth.1650openalex-snapshot
Bayesian community-wide culture-independent microbial source tracking
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
inferredcites →https://doi.org/10.1038/nrd4572openalex-snapshot
ESKAPEing the labyrinth of antibacterial discovery
inferredcites →https://doi.org/10.1038/s41467-019-10191-3openalex-snapshot
Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
inferredcites →https://doi.org/10.1038/s41559-017-0446-6openalex-snapshot
Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
inferredcites →https://doi.org/10.1038/s41559-018-0654-8openalex-snapshot
Partial genomic survival of cave bears in living brown bears
inferredcites →https://doi.org/10.1038/s41559-018-0778-xopenalex-snapshot
Direct estimation of mutations in great apes reconciles phylogenetic dating
inferredcites →https://doi.org/10.1038/s41564-017-0012-7openalex-snapshot
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
inferredcites →https://doi.org/10.1038/s41592-018-0176-yopenalex-snapshot
Species-level functional profiling of metagenomes and metatranscriptomes
inferredcites →https://doi.org/10.1038/s41598-018-23276-8openalex-snapshot
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
inferredcites →https://doi.org/10.1038/s41598-018-24497-7openalex-snapshot
Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
inferredcites →https://doi.org/10.1038/s41598-018-26045-9openalex-snapshot
Dental calculus and isotopes provide direct evidence of fish and plant consumption in Mesolithic Mediterranean
inferredcites →https://doi.org/10.1038/s41598-018-28091-9openalex-snapshot
Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
inferredcites →https://doi.org/10.1038/sj.bdj.2016.865openalex-snapshot
The oral microbiome – an update for oral healthcare professionals
inferredcites →https://doi.org/10.1038/srep08026openalex-snapshot
Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway
inferredcites →https://doi.org/10.1038/srep15161openalex-snapshot
Dental calculus evidence of Taï Forest Chimpanzee plant consumption and life history transitions
inferredcites →https://doi.org/10.1073/pnas.1016868108openalex-snapshot
Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium)
inferredcites →https://doi.org/10.1073/pnas.1218525110openalex-snapshot
Animals in a bacterial world, a new imperative for the life sciences
inferredcites →https://doi.org/10.1073/pnas.1314445110openalex-snapshot
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
inferredcites →https://doi.org/10.1073/pnas.1707279114openalex-snapshot
Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers
inferredcites →https://doi.org/10.1080/1745039x.2012.676817openalex-snapshot
Effect of the rumen ciliatesEntodinium caudatum, Epidinium ecaudatumandEudiplodinium maggii, and combinations thereof, on ruminal fermentation and total tract digestion in sheep
inferredcites →https://doi.org/10.1093/bib/bbs033openalex-snapshot
Functional assignment of metagenomic data: challenges and applications
inferredcites →https://doi.org/10.1093/bioinformatics/btm098openalex-snapshot
UniRef: comprehensive and non-redundant UniProt reference clusters
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btt193openalex-snapshot
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
inferredcites →https://doi.org/10.1093/bioinformatics/btu739openalex-snapshot
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/database/baq013openalex-snapshot
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
inferredcites →https://doi.org/10.1093/jn/128.12.2712sopenalex-snapshot
Periodontal Disease and Diet in Domestic Pets
inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkt371openalex-snapshot
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkw1004openalex-snapshot
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
inferredcites →https://doi.org/10.1093/nar/gkx935openalex-snapshot
The MetaCyc database of metabolic pathways and enzymes
inferredcites →https://doi.org/10.1098/rsbl.2016.0137openalex-snapshot
‘Disperse abroad in the land’: the role of wildlife in the dissemination of antimicrobial resistance
inferredcites →https://doi.org/10.1098/rstb.2013.0624openalex-snapshot
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1101/gr.213611.116openalex-snapshot
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
inferredcites →https://doi.org/10.1111/1365-2664.12596openalex-snapshot
Antimicrobial resistance in wildlife
inferredcites →https://doi.org/10.1111/1755-0998.12699openalex-snapshot
Whole mitochondrial genome capture from faecal samples and museum‐preserved specimens
inferredcites →https://doi.org/10.1111/1755-0998.13009openalex-snapshot
Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies
inferredcites →https://doi.org/10.1111/1755-0998.13011openalex-snapshot
Laboratory contamination over time during low‐biomass sample analysis
inferredcites →https://doi.org/10.1111/2041-210x.12410openalex-snapshot
popart : full‐feature software for haplotype network construction
inferredcites →https://doi.org/10.1111/cmi.12308openalex-snapshot
Defining dysbiosis and its influence on host immunity and disease
inferredcites →https://doi.org/10.1111/j.1600-051x.1998.tb02419.xopenalex-snapshot
Microbial complexes in subgingival plaque
inferredcites →https://doi.org/10.1111/j.2041-1014.2010.00587.xopenalex-snapshot
Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing
inferredcites →https://doi.org/10.1111/mec.13038openalex-snapshot
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears
inferredcites →https://doi.org/10.1111/mec.13239openalex-snapshot
Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear
inferredcites →https://doi.org/10.1111/mec.13529openalex-snapshot
Natural history collections as windows on evolutionary processes
inferredcites →https://doi.org/10.1111/mec.14435openalex-snapshot
Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet
inferredcites →https://doi.org/10.1111/mec.14473openalex-snapshot
Rates of gut microbiome divergence in mammals
inferredcites →https://doi.org/10.1111/mec.14860openalex-snapshot
Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
inferredcites →https://doi.org/10.1126/science.1203043openalex-snapshot
Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin
inferredcites →https://doi.org/10.1126/science.aaa3952openalex-snapshot
Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
inferredcites →https://doi.org/10.1128/aac.41.10.2265openalex-snapshot
Widespread detection of PER-1-type extended-spectrum beta-lactamases among nosocomial Acinetobacter and Pseudomonas aeruginosa isolates in Turkey: a nationwide multicenter study
inferredcites →https://doi.org/10.1128/aem.02167-10openalex-snapshot
Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
inferredcites →https://doi.org/10.1128/aem.02385-15openalex-snapshot
Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen
inferredcites →https://doi.org/10.1128/aem.02812-07openalex-snapshot
Structure of the Archaeal Community of the Rumen
inferredcites →https://doi.org/10.1128/genomea.00578-15openalex-snapshot
Draft Genome Sequence of Pseudomonas psychrophila MTCC 12324, Isolated from the Arctic at 79°N
inferredcites →https://doi.org/10.1128/msystems.00080-18openalex-snapshot
Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
inferredcites →https://doi.org/10.1139/z06-016openalex-snapshot
Major components of grizzly bear diet across North America
inferredcites →https://doi.org/10.1177/0022034510379602openalex-snapshot
The Role of Bacteria in the Caries Process
inferredcites →https://doi.org/10.1177/089875649801500104openalex-snapshot
Dental Health Status and Endodontic Treatment of Captive Brown Bears ( Ursus Arctos ssp.) Living in the Bernese Bear Pit
inferredcites →https://doi.org/10.1177/1357034x14561341openalex-snapshot
Antibiotic Resistance and the Biology of History
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1183/23120541.00013-2016openalex-snapshot
Influenza: from zoonosis to pandemic
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2164-11-523openalex-snapshot
Study of inter- and intra-individual variations in the salivary microbiota
inferredcites →https://doi.org/10.1186/1944-3277-10-18openalex-snapshot
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12859-015-0788-5openalex-snapshot
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
inferredcites →https://doi.org/10.1186/s12915-014-0087-zopenalex-snapshot
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
inferredcites →https://doi.org/10.1186/s13059-015-0759-1openalex-snapshot
Host genetic variation impacts microbiome composition across human body sites
inferredcites →https://doi.org/10.1186/s13059-016-0918-zopenalex-snapshot
EAGER: efficient ancient genome reconstruction
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.1186/s13567-016-0333-1openalex-snapshot
The microbiome associated with equine periodontitis and oral health
inferredcites →https://doi.org/10.1186/s13756-018-0352-yopenalex-snapshot
Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
inferredcites →https://doi.org/10.1186/s40168-018-0605-2openalex-snapshot
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
inferredcites →https://doi.org/10.1371/journal.pcbi.1004557openalex-snapshot
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot
Population Structure and Eigenanalysis
inferredcites →https://doi.org/10.1371/journal.pgen.1003345openalex-snapshot
Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
inferredcites →https://doi.org/10.1371/journal.pone.0036067openalex-snapshot
The Canine Oral Microbiome
inferredcites →https://doi.org/10.1371/journal.pone.0101229openalex-snapshot
Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups
inferredcites →https://doi.org/10.1371/journal.pone.0110808openalex-snapshot
Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data
inferredcites →https://doi.org/10.2307/1270335openalex-snapshot
The Statistical Analysis of Compositional Data
inferredcites →https://doi.org/10.2307/3872911openalex-snapshot
Variability of Dental Diseases in Two Populations of Great Lakes Black Bears
inferredcites →https://doi.org/10.2307/4278openalex-snapshot
Comparative Summer Feeding Strategies of Arctic and Alpine Rangifer
inferredcites →https://doi.org/10.32614/cran.package.veganopenalex-snapshot
vegan: Community Ecology Package
inferredcites →https://doi.org/10.3389/fmicb.2016.00579openalex-snapshot
Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem
inferredcites →https://doi.org/10.3389/fmicb.2016.01234openalex-snapshot
Bacterial Communities: Interactions to Scale
inferredcites →https://doi.org/10.3389/fmicb.2017.00725openalex-snapshot
Evolutionary Biology Needs Wild Microbiomes
inferredcites →https://doi.org/10.3389/fmicb.2017.01020openalex-snapshot
Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach
inferredcites →https://doi.org/10.3389/fmicb.2017.02224openalex-snapshot
Microbiome Datasets Are Compositional: And This Is Not Optional
inferredcites →https://doi.org/10.3390/genes9120598openalex-snapshot
The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis
inferredcites →https://doi.org/10.4103/0974-777x.68538openalex-snapshot
Multidrug resistant Acinetobacter
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7557/2.13.1.1067openalex-snapshot
The introduction of reindeer to Brøggerhalvøya, Svalbard: grazing preference and effect on vegetation
inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.archoralbio.2020.104835openalex-snapshot
Tusks, the extra-oral teeth
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.145246openalex-snapshot
Heavy metal (PTE) ecotoxicology, data review: Traditional vs. a compositional approach
inferred← citeshttps://doi.org/10.1098/rstb.2019.0580openalex-snapshot
Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico
inferred← citeshttps://doi.org/10.1128/mra.00850-20openalex-snapshot
Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus
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