Biology subjects

Lieberman, T. D.

Publications and source records attributed to Lieberman, T. D..

11 recordsLinked to original sources

bioRxiv2025

High Precision Binary Trait Association on Phylogenetic Trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial GWAS (mGWAS) methods have been developed to account for the fact that genome-wide linkage in bacteria creates strong evolutionary-induced associations, these methods have high false discovery rates or lack statistical power, have poor performance on negative interactions, and face computational limits at the scale required for pangenome-wide study of gene-gene interactions. Here, we present SimPhyNI, a computationally optimized framework for efficient and rigorous mGWAS studies. SimPhyNI builds null co-occurrence distributions by independently simulating traits using phylogenetically-informed parameters, novelly including time to first event. The constrained variation in these simulations, combined with log odds ratio scoring for comparing across traits, robustly identifies both positive and negative associations. Using synthetic datasets mimicking both gene-gene and gene-trait associations, we demonstrate that SimPhyNI achieves high precision and recall for both positive and negative interactions. We demonstrate SimPhyNIs utility by detecting interactions between phage defense systems in E. coli and gene-gene interactions across the entire E. coli pangenome (>9 million tests). Though developed here for binary traits, SimPhyNIs design supports extension to multi-state and continuous traits using generalized models of stochastic simulation. SimPhyNIs performance and scalability enable genome-wide discovery of genetic interactions that drive microbial function, ecology, and disease. Impact StatementUnderstanding how bacterial genes associate with traits and with one another is essential for predicting disease outcomes, antibiotic resistance, and future evolution. However, identifying these interactions is challenging because shared ancestry creates false correlations. SimPhyNI overcomes this through an ancestry-informed statistical simulation process, achieving near-zero false positive rates while maintaining computational efficiency for large scale analyses. This efficiency enables systematic mapping of gene-gene interaction networks across large datasets containing thousands of genes and genomes. As microbial genomic datasets continue to expand, SimPhyNIs scalability and precision will accelerate discovery of the mechanistic principles underlying infectious disease, microbiome function, and microbial evolution and ecology.

microbiology↗

bioRxiv2025

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one system to systematically characterize how the phage-bacteria arms race shapes C. acnes evolution and community composition on individual people. Our analysis reveals a surprising lack of phage-mediated selection despite global prevalence of C. acnes phages. Analysis of anti-phage defense systems across 3,205 bacterial genomes revealed a limited, phylogenetically restricted defense repertoire under weak selective pressure to diversify or be maintained. Functional assays did not reveal alternative phage resistance mechanisms or fitness costs associated with defense gene carriage that could explain this limited immune arsenal. This lack of pressure to maintain phage resistance could not be explained by lack of phage colonization, as examination of 471 global human facial skin metagenomes demonstrated that even in samples with high virus-to-microbe ratio, phage-sensitive clades dominate on-person populations. Together, these findings indicate that phage pressure, while present, does not play a critical role in determining strain fitness and success within C. acnes populations on human skin. We propose that this observed weak phage-mediated selective pressure can be explained by the anatomy of skin: C. acnes growth is thought to occur at the bottom of pores, where exposure to phage may be limited by physical barriers. Together, this portrait of a static arms race provides a strong contrast with other microbial species in different ecosystems and expands understanding of phage-bacteria interactions in the human microbiome.

genomics↗

bioRxiv2025

Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing

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 microbiome analysis methods --16S rRNA sequencing, shallow metagenomics, and qPCR PMP panels--as well as extraction methods across skin swab samples and mock community dilutions. While extraction method minimally impacted results, with no significant signal for method-specific contamination or bias, we observed critical differences in inferred composition across analysis methods for low biomass samples. Metagenomic sequencing and qPCR revealed concordant, diverse microbial communities on low biomass leg skin samples, whereas 16S amplicon sequencing exhibited extreme bias toward the most abundant taxon. Both qPCR and metagenomics showed that female genital tract bacteria dominated the leg skin microbiome in about half of female subjects. Metagenomics also enabled sub-species analysis, which demonstrated that individuals have consistent within-species diversity across high-biomass forehead and low-biomass leg skin sites. This work illustrates that shallow metagenomics provides the necessary sensitivity and taxonomic resolution to characterize species and strain-level diversity in extremely low biomass samples, opening possibilities for microbiome discovery in previously unexplored niches. ImportanceDespite the importance of the skin microbiome in health and disease, there have been far fewer studies characterizing the microbiome of skin compared to that of the gut. In part, this is because microbiome methods were initially developed for bacteria-rich samples like stool and these methods perform poorly on bacteria-poor samples like skin swabs. The perceived difficulty of getting reliable data from such low biomass sites has limited the scope and types of analyses performed. Here we demonstrate that shotgun, whole-genome, metagenomic sequencing recovers the full input from even very dilute control community samples, and reveals a highly diverse population even on very low biomass skin sites. We describe a streamlined sample processing and analysis pipeline which can be applied broadly to characterize low biomass microbiome samples and reveal new host-microbiome interactions.

microbiology↗

bioRxiv2025

Intraspecies associations from strain-rich metagenome samples

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 information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.

microbiology↗

bioRxiv2024

De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen

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-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, diverse parallel mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization revealed that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.

microbiology↗

bioRxiv2023

Commensal skin bacteria exacerbate inflammation and delay skin healing

The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, application of commensals-- including the mouse commensal Staphylococcus xylosus, three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic-wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.

microbiology↗

bioRxiv2023

Reversions mask the contribution of adaptive evolution in microbiomes

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 exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale-dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with exactly opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally-fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long-time scales with caution, as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short time scales.

evolutionary biology↗

bioRxiv2022

No evidence that synonymous mutations in yeast genes are mostly deleterious

In a recent paper1, 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 at face value, these results would conflict with well-established findings from a broad range of fields and approaches. Here, we argue that these results arose from a lack of appropriate controls for the impacts of background genetic effects in edited strains. A re-examination of the data in Shen et al. strongly suggests that it is entirely consistent with the expectation that most nonsynonymous and nearly all synonymous mutations have no detectable effects on fitness. We present analyses which show that the data is inconsistent with the proposed explanation that pervasive fitness effects of synonymous mutations arise from their effects on mRNA levels, that the sequence-based fitness assay overestimates fitness effects compared to the growth-based fitness assay, and that the observed wide fitness distributions for nonsense mutations are consistent with off-target effects or other uncontrolled sources of biological variation contributing to measured fitness. We conclude by discussing the essential controls and other experimental design considerations that are required to produce interpretable results regarding the fitness effects of mutations in large-scale screens.

genetics↗

bioRxiv2021

Anatomy promotes neutral coexistence of strains in the human skin microbiome

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 and migration using 947 C. acnes colony genomes acquired from 16 subjects, including from individual skin pores, and find that pores maintain diversity by limiting competition. Although strains with substantial fitness differences coexist within centimeter-scale regions, each pore is dominated by a single strain. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks during migration into pores and subsequently blocks new migrants; the resulting population fragmentation reduces competition and promotes coexistence. Our findings imply that therapeutic interventions involving pore-dwelling species should focus on removing resident populations over optimizing probiotic fitness.

microbiology↗

bioRxiv2021

On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity

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 inflamed skin of people with atopic dermatitis (AD) is frequently colonized with Staphylococcus aureus, an opportunistic pathogen associated with both asymptomatic colonization of nasal passages and invasive disease 3-6. While genetic risk and barrier disruption are critical to AD initiation 7,8, S. aureus colonization is thought to worsen disease severity by promoting skin damage9 1,4,5,10. Here we show, from tracking 23 children treated for AD over 9 months, that S. aureus adapts via de novo mutations during colonization. Patients S. aureus populations are typically dominated by a single lineage, with infrequent invasion by distant lineages. Variants emerge within each lineage with mutation accumulation rates similar to S. aureus in other contexts. Some of these variants replace their ancestors across the body within months, with signatures of adaptive, rather than neutral, forces. Most strikingly, the capsule synthesis gene capD obtained four parallel mutations within one patient and was involved in mutational sweeps in multiple patients. We confirm that selection for capD negativity is common in AD, but not in other contexts, via reanalysis of public S. aureus genomes from 276 people. Our finding of disease-specific selection raises the possibility that adaptation of pathobionts during colonization prolongs the positive feedback cycle of inflammation.

microbiology↗

bioRxiv2017

Adaptive evolution within the gut microbiome of individual people

Individual bacterial lineages stably persist for years in the human gut microbiome1-3. However, the potential of these lineages to adapt during colonization of healthy people is not well understood2,4. Here, we assess evolution within individual microbiomes by sequencing the genomes of 602 Bacteroides fragilis isolates cultured from 12 healthy subjects. We find that B. fragilis within-subject populations contain substantial de novo nucleotide and mobile element diversity, which preserve years of within-person evolutionary history. This evolutionary history contains signatures of within-person adaptation to both subject-specific and common selective forces, including parallel mutations in sixteen genes. These sixteen genes are involved in cell-envelope biosynthesis and polysaccharide utilization, as well as yet under-characterized pathways. Notably, one of these genes has been shown to be critical for B. fragilis colonization in mice5, indicating that key genes have not already been optimized for survival in vivo. This lack of optimization, given historical signatures of purifying selection in these genes, suggests that varying selective forces with discordant solutions act upon B. fragilis in vivo. Remarkably, in one subject, two B. fragilis sublineages coexisted at a stable relative frequency over a 1.5-year period despite rapid adaptive dynamics within one of the sublineages. This stable coexistence suggests that competing selective forces can lead to B. fragilis niche-differentiation even within a single person. We conclude that B. fragilis adapts rapidly within the microbiomes of individual healthy people, providing a new route for the discovery of key genes in the microbiome and implications for microbiome stability and manipulation.

evolutionary biology↗