Tami D. Lieberman
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View article: Intraspecies associations from strain-rich metagenome samples
Intraspecies associations from strain-rich metagenome samples Open
Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides informati…
View article: De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen
De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen Open
Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-huma…
View article: Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing
Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing Open
Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass samples. Here, we systemically compare …
View article: The microbiome of the human facial skin is unique compared to that of other hominids
The microbiome of the human facial skin is unique compared to that of other hominids Open
The human facial skin microbiome is remarkably similar across all people sampled to date, dominated by facultative anaerobe Cutibacterium . The origin of this genus is unknown, with no close relatives currently described from samples of pr…
View article: Intraspecies dynamics underlie the apparent stability of two important skin microbiome species
Intraspecies dynamics underlie the apparent stability of two important skin microbiome species Open
Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific comm…
View article: Intraspecies associations from strain-rich metagenome samples
Intraspecies associations from strain-rich metagenome samples Open
Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides informati…
View article: Reversions mask the contribution of adaptive evolution in microbiomes
Reversions mask the contribution of adaptive evolution in microbiomes Open
When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit strong…
View article: Reversions mask the contribution of adaptive evolution in microbiomes
Reversions mask the contribution of adaptive evolution in microbiomes Open
When examining bacterial genomes for evidence of past selection, the results obtained depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhib…
View article: Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin
Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin Open
Commensal bacteria on skin may limit the ability of pathogenic bacteria to cause clinically significant infections. The bacteria on healing acute wounds, which might provide such a protective effect, have not been described using culture-i…
View article: Detecting bacterial adaptation within individual microbiomes
Detecting bacterial adaptation within individual microbiomes Open
The human microbiome harbours a large capacity for within-person adaptive mutations. Commensal bacterial strains can stably colonize a person for decades, and billions of mutations are generated daily within each person's microbiome. Adapt…
View article: No evidence that synonymous mutations in yeast genes are mostly deleterious
No evidence that synonymous mutations in yeast genes are mostly deleterious Open
In a recent paper 1 , Shen et al . reported that most mutations in the coding regions of 21 yeast genes were strongly deleterious, and that the distributions of fitness effects were similar for synonymous and nonsynonymous mutations. Taken…
View article: Cutaneous surgical wounds have distinct microbiomes from intact skin
Cutaneous surgical wounds have distinct microbiomes from intact skin Open
Infections are relatively rare following cutaneous surgical procedures, despite the potential for wound exposure to pathogens both during surgery and throughout the healing process. Although gut commensals are believed to reduce the risk o…
View article: The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment
The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment Open
Background Atopic dermatitis (AD) is characterized by an altered skin microbiome dominantly colonized by S. aureus . Standard treatment includes emollients, anti-inflammatory medications and antiseptics. Objectives To characterize changes …
View article: Anatomy promotes neutral coexistence of strains in the human skin microbiome
Anatomy promotes neutral coexistence of strains in the human skin microbiome Open
What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes , the most abundant species on human skin. We reconstruct on-person evolution …
View article: On-person adaptive evolution of<i>Staphylococcus aureus</i>during treatment for atopic dermatitis
On-person adaptive evolution of<i>Staphylococcus aureus</i>during treatment for atopic dermatitis Open
Genetic variation among bacterial strains can contribute to heterogeneity in the severity of chronic inflammatory diseases 1,2 , but the degree of variation created by de novo mutation during colonization is not well understood. The inflam…
View article: Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events Open
Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individua…
View article: Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events
Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events Open
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we …
View article: Seven Billion Microcosms: Evolution within Human Microbiomes
Seven Billion Microcosms: Evolution within Human Microbiomes Open
Rational microbiome-based therapies may one day treat a wide range of diseases and promote wellness. Yet, we are still limited in our abilities to employ such therapies and to predict which bacterial strains have the potential to stably co…
View article: Adaptive evolution within the gut microbiome of individual people
Adaptive evolution within the gut microbiome of individual people Open
Individual bacterial lineages stably persist for years in the human gut microbiome 1–3 . However, the potential of these lineages to adapt during colonization of healthy people is not well understood 2,4 . Here, we assess evolution within …