Biology subjects

Barkal, L. J.

Publications and source records attributed to Barkal, L. J..

4 recordsLinked to original sources

bioRxiv2024

Discovery and engineering of the antibody response against a prominent skin commensal

The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8+ T cell response pre-emptively, in the absence of an infection1. However, the scope and purpose of this anti-commensal immune program are not well defined, limiting our ability to harness it therapeutically. Here, we show that this colonist also induces a potent, durable, and specific antibody response that is conserved in humans and non-human primates. A series of S. epidermidis cell-wall mutants revealed that the cell surface protein Aap is a predominant target. By colonizing mice with a strain of S. epidermidis in which the parallel {beta}-helix domain of Aap is replaced by tetanus toxin fragment C, we elicit a potent neutralizing antibody response that protects mice against a lethal challenge. A similar strain of S. epidermidis expressing an Aap-SpyCatcher chimera can be conjugated with recombinant immunogens; the resulting labeled commensal elicits high titers of antibody under conditions of physiologic colonization, including a robust IgA response in the nasal mucosa. Thus, immunity to a common skin colonist involves a coordinated T and B cell response, the latter of which can be redirected against pathogens as a novel form of topical vaccination.

microbiology↗

bioRxiv2023

Bacteriophage populations mirror those of bacterial pathogens at sites of infection

Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophage are highly specific to their bacterial host species and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly-available cell-free DNA generated using next generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from E. coli, Streptococcus, and S. aureus are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues. ImportanceBacteriophages are an active area of investigation in microbiome research but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available dataset to study bacteriophage populations in cell free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell free DNA.

microbiology↗

bioRxiv2022

Microbial Community Interactions on a Chip

Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here we report a Microbial Community Interaction (CI) device to advance the systematic study of chemical and biological interactions within a microbial community. The CI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing GFP provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables". The CI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased growth of B. cereus. The CI device enables both strain-level and community-level insight. The scalable geometric design of the CI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.

microbiology↗

bioRxiv2022

The circulating phageome reflects bacterial infections

Bacteriophage, viruses that infect bacteria, are abundant in the human body but the relationship between the phageome and bacterial population dynamics is unclear. Because bacteriophage are often highly specific to bacterial host strains and species, we asked whether bacteriophage present in cell-free DNA (cfDNA) reflect bacterial infections in sepsis. To address this, we generated a workflow for identifying and interpreting bacteriophage sequences in cfDNA and a bacteriophage characteristic dictionary. In two independent cohorts of infected patients and asymptomatic controls, we demonstrate that all individuals, septic and healthy, have a circulating phageome. Moreover, infection associates with overrepresentation of pathogen-specific phage, allowing for the study of bacterial pathogens. We further show that phage can identify pathovariant Escherichia coli infections and distinguish between closely-related pathogenic bacterial species such as Staphylococcus aureus and frequent contaminants such as coagulase-negative Staphylococcus. Phage DNA may have utility in studying bacteriophage ecology in infection.

microbiology↗