Kristopher A. Kerns
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View article: Identifying essential genes in <i>Schaalia odontolytica</i> using a saturated transposon library
Identifying essential genes in <i>Schaalia odontolytica</i> using a saturated transposon library Open
The unique epibiotic-parasitic relationship between Nanosynbacter lyticus type strain TM7x, a member of the newly identified candidate phyla radiation, now referred to as Patescibacteria , and its basibiont, Schaalia odontolytica strain XH…
View article: Episymbiotic Saccharibacteria suppresses epithelial immunoactivation through Type IV pili and TLR2 dependent endocytosis
Episymbiotic Saccharibacteria suppresses epithelial immunoactivation through Type IV pili and TLR2 dependent endocytosis Open
Summary Saccharibacteria are episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing …
View article: Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples
Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples Open
Oral bacteria have been found in the colon in pathologies such as inflammatory bowel disease. To ascertain niche coalescence, 2 elements are essential: (i) paired oral/fecal samples and (ii) strain-level resolution. We profiled the microbi…
View article: Complete genome sequence of <i>Veillonella parvula</i> strain PK1910
Complete genome sequence of <i>Veillonella parvula</i> strain PK1910 Open
Here, we announce the complete genome sequence of Veillonella parvula strain PK1910, obtained from a frozen stock. The genome is composed of one closed contig with a length of 2,213,486 bp, resulting in 98.0× coverage containing 1,979 prot…
View article: Complete genome of <i>Nanosynbacter</i> sp. strain BB002, isolated and cultivated from a site of periodontal disease
Complete genome of <i>Nanosynbacter</i> sp. strain BB002, isolated and cultivated from a site of periodontal disease Open
Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris . As a member of the Saccharibacteria within the candidate phy…
View article: Training a rural oral health workforce: Effects of rural background on dentist practice choice
Training a rural oral health workforce: Effects of rural background on dentist practice choice Open
Purpose The Regional Initiatives in Dental Education (RIDE) program is an educational track of the University of Washington School of Dentistry that aims to produce leaders who practice in rural areas of the Pacific Northwest. This study a…
View article: Identifying essential genes in<i>Schaalia odontolytica</i>using a highly-saturated transposon library
Identifying essential genes in<i>Schaalia odontolytica</i>using a highly-saturated transposon library Open
The unique epibiotic-parasitic relationship between Nanosynbacter lyticus type strain TM7x, a member of the newly identified Candidate Phyla Radiation, now referred to as Patescibacteria , and its basibiont, Schaalia odontolytica strain XH…
View article: Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults
Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults Open
View article: Marker genes
Marker genes Open
Clade-specific marker genes for niche-overlapping species
View article: Taxa relative abundances and metadata
Taxa relative abundances and metadata Open
Specie-level taxonomic data (relative abundances) and metadata. Opens with R.
View article: Marker gene presence/absence
Marker gene presence/absence Open
Database of clade-specific marker gene presence/absence. Opens with R.
View article: R code
R code Open
R code
View article: Ultrasmall epibiont <i>Nanosynbacter lyticus</i> strain TM7x and host bacteria transcriptional activity after initial host parasitism
Ultrasmall epibiont <i>Nanosynbacter lyticus</i> strain TM7x and host bacteria transcriptional activity after initial host parasitism Open
As TM7× is a member of the broadly distributed Candidate Phyla Radiation with small genomes lacking numerous biosynthetic pathways, this study provides further insights into how these epibionts interact and modulate their host bacteria.
View article: Effects of a stabilized stannous fluoride dentifrice on clinical, immunomodulatory, and microbial outcomes in a human experimental gingivitis model
Effects of a stabilized stannous fluoride dentifrice on clinical, immunomodulatory, and microbial outcomes in a human experimental gingivitis model Open
Background Stannous fluoride dentifrice is well established for its beneficial clinical effects. In this study, we evaluated the effects of stannous fluoride on inflammation and oral microbiome. Methods In this randomized, parallel‐arm, do…
View article: Localized microbially induced inflammation influences distant healthy tissues in the human oral cavity
Localized microbially induced inflammation influences distant healthy tissues in the human oral cavity Open
Variation in human immune response to the same bacterial or viral pathogen is well established in the literature. Variation in immune response to microbial challenge has also been observed within the human oral cavity. Our recent study foc…
View article: Specific host metabolite and gut microbiome alterations are associated with bone loss during spaceflight
Specific host metabolite and gut microbiome alterations are associated with bone loss during spaceflight Open
Understanding the axis of the human microbiome and physiological homeostasis is an essential task in managing deep-space-travel-associated health risks. The NASA-led Rodent Research 5 mission enabled an ancillary investigation of the gut m…
View article: Transcriptome of Epibiont Saccharibacteria <i>Nanosynbacter lyticus</i> Strain TM7x During the Establishment of Symbiosis
Transcriptome of Epibiont Saccharibacteria <i>Nanosynbacter lyticus</i> Strain TM7x During the Establishment of Symbiosis Open
Nanosynbacter lyticus type strain TM7x is the first cultivated member of the Saccharibacteria and the candidate phyla radiation (CPR). It was discovered to be ultrasmall in cell size with a highly reduced genome that establishes an obligat…
View article: Draft Genome Sequences of Nine “ <i>Candidatus</i> Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity
Draft Genome Sequences of Nine “ <i>Candidatus</i> Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity Open
Here, we report draft genome sequences for nine strains of “ Candidatus Nanosynbacter sp. HMT-352.” These strains and their sequences were used to interrogate strain-level variations in host range, gene content, and growth dynamics among t…
View article: Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria Open
Candidate phylum radiation (CPR) bacteria comprise a poorly understood phylum that is estimated to encompass ∼26% of all diversity of domain bacteria. Among CPR bacteria, the Saccharibacteria lineage (TM7) is of particular interest, as it …
View article: Transcriptome of epibiont Saccharibacteria <i>Nanosynbacter lyticus</i> strain TM7x during establishment of symbiosis
Transcriptome of epibiont Saccharibacteria <i>Nanosynbacter lyticus</i> strain TM7x during establishment of symbiosis Open
Saccharibacteria Nanosynbacter lyticus strain TM7x is a member of the broadly distributed Candidate Phylum Radiation. These bacteria have ultrasmall cell size, reduced genomes and live as epibionts on the surface of other bacteria. The mec…
View article: Specific Host Metabolite and Gut Microbiome Alterations are Associated with Bone-Loss During Spaceflight
Specific Host Metabolite and Gut Microbiome Alterations are Associated with Bone-Loss During Spaceflight Open
View article: Human variation in gingival inflammation
Human variation in gingival inflammation Open
Significance Experimental gingivitis studies where dental hygiene is withheld from select teeth, allowing natural bacterial accumulation, provide a unique opportunity to study the reversible transition from health to inflammatory disease i…
View article: Modified SHI medium supports growth of a disease‐state subgingival polymicrobial community in vitro
Modified SHI medium supports growth of a disease‐state subgingival polymicrobial community in vitro Open
Developing a laboratory model of oral polymicrobial communities is essential for in vitro studies of the transition from healthy to diseased oral plaque. SHI medium is an enriched growth medium capable of supporting in vitro biofilms with …
View article: Author response for "Modified SHI‐medium supports growth of a disease‐state subgingival polymicrobial community <i>in vitro</i>"
Author response for "Modified SHI‐medium supports growth of a disease‐state subgingival polymicrobial community <i>in vitro</i>" Open
View article: Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts Open
View article: Author response: Rapamycin rejuvenates oral health in aging mice
Author response: Rapamycin rejuvenates oral health in aging mice Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Periodontal disease is an age…
View article: Rapamycin rejuvenates oral health in aging mice
Rapamycin rejuvenates oral health in aging mice Open
Periodontal disease is an age-associated disorder clinically defined by periodontal bone loss, inflammation of the specialized tissues that surround and support the tooth, and microbiome dysbiosis. Currently, there is no therapy for revers…
View article: Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria
Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria Open
Recently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capab…
View article: Independent Acquisition and Adaptation of Ultra-Small Bacteria with Reduced Genomes from the Phylum Saccharibacteria to Human Hosts
Independent Acquisition and Adaptation of Ultra-Small Bacteria with Reduced Genomes from the Phylum Saccharibacteria to Human Hosts Open