Biology subjects

Gu Liu, C.

Publications and source records attributed to Gu Liu, C..

3 recordsLinked to original sources

bioRxiv2020

Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species

Pathogenic bacteria take host nutrients to support their growth, division, survival, and pathogenesis. The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we employed a quantitative measurement of the number of reducing equivalents as a function of growth on hundreds of different sources of carbon to gauge the "culinary preferences" of three distinct Bacillus species, and related Staphylococcus aureus. We show that each species had widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. In addition, carbohydrates are shown to be the preferred sources of carbon when grown under ideal in vitro conditions. Rather unexpectedly, these metabolic utilizations did not correspond one-to-one with an increase in biomass, which brings to question what cellular activity should be considered productive when it comes to virulence. Finally, we applied this system to the growth and survival of B. anthracis in a blood-based environment and find that amino acids become the preferred source of energy while demonstrating the possibility of applying this approach to identifying xenobiotics or host compounds that can promote or interfere with bacterial metabolism during infection. Author summarySuccessful organisms must make nutritional adaptations to thrive in their environment. Bacterial pathogens are no exception, having evolved for survival inside their hosts. The host combats these pathogens by depriving them of potential biochemical resources, termed nutritional immunity. This places pathogens under pressure to utilize their resources efficiently and strategically, and their metabolism must in turn be tailored for this situation. In this study, we examined the carbon metabolism of three human pathogens of varying virulence (Bacillus anthracis, Bacillus cereus, and Staphylococcus aureus) and one nonpathogenic Bacillus (Bacillus subtilis) via a phenotype microarray that senses reducing equivalents produced during metabolism. Our analysis shows the existence of distinct preferences by these pathogens towards only a select few carbohydrates and implies reliance on specific metabolic pathways. These metabolic signatures obtained could be distinguished from one bacterial species to another, and we conclude that nutrient preferences offer a new perspective into investigating how pathogens can thrive during infection despite host-induced starvation.

microbiology↗

bioRxiv2020

Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

The human mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. Bacteriophage parasitize the prokaryotes but are not known to associate with eukaryotic cells. In the gastrointestinal tract, the interaction of these two domains influences the health of the host, especially colonization with invasive pathobionts. Antibiotics may be used but they also kill protective commensals and lack the physio-chemical properties to be specifically and optimally active in this complex milieu. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The enhanced activity is encoded in its tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, thereby positioning it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing epithelial-targeting phage to selectively remove invasive pathobiont species from mucosal surfaces. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/212829v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@13219f6org.highwire.dtl.DTLVardef@469d7borg.highwire.dtl.DTLVardef@d31e0org.highwire.dtl.DTLVardef@458e14_HPS_FORMAT_FIGEXP M_FIG C_FIG Model showing (1) mucins from the intestinal mucus layer inhibit phage infection, (2) phage ES17 can bind to mucin and utilize other intestinal glycans as a receptor to infect and kill mucus-coated bacteria, and (3) phages like ES17 can be utilized to coat the intestinal epithelium by binding heparan sulfate glycans to protect from invasive pathogen infection.

microbiology↗

bioRxiv2020

Phage-Antibiotic Synergy Is Driven By A Unique Combination Of Antibacterial Mechanism Of Action And Stoichiometry

The continued rise in antibiotic resistance is precipitating a medical crisis. Bacteriophage (phage) has been hailed as one possible therapeutic option to augment the efficacy of antibiotics. However, only a handful of studies have addressed the synergistic relationship between phage and antibiotics. Here, we report a comprehensive analysis of phage-antibiotic interaction that evaluates synergism, additivism, and antagonism for all classes of antibiotics across clinically achievable stoichiometries. We combined an optically-based real-time microtiter plate readout with a matrix-like heatmap of treatment potencies to measure phage and antibiotic synergy (PAS), a process we term synography. Phage-antibiotic synography was performed against a pandemic drug-resistant clonal group of E. coli (ExPEC) with antibiotic levels blanketing the minimum inhibitor concentration (MIC) across seven orders of viral titers. Our results suggest that, under certain conditions, phages provide an adjuvating effect by lowering the MIC for drug-resistant strains. Furthermore, synergistic and antagonistic interactions are highly dependent on the mechanism of bacterial inhibition by the class of antibiotic paired to the phage, and when synergism is observed, it suppresses the emergence of resistant cells. Host conditions that simulate the infection environment, including serum and urine, suppress PAS in a bacterial growth-dependent manner. Lastly, phage burst size seems to be a significant driver of synergism. Collectively, this data suggests lytic phages can resuscitate an ineffective antibiotic for previously resistant bacteria, while also synergize with antibiotics in a class-dependent manner, processes that may be dampened by lower bacterial growth rates found in host environments. Significance StatementBacteriophage (phage) therapy is a promising approach to combat the rise of multi-drug resistant bacteria. Currently, the preferred clinical modality is to pair phage with an antibiotic, a practice thought to improve efficacy. However, antagonism between phage and antibiotics has been reported, the choice of phage and antibiotic is not often empirically determined, and the effect of the host factors on the effectiveness is unknown. Here, we interrogate phage-antibiotic interactions across antibiotics with different mechanisms of action. Our results suggest that phage can lower the working MIC for bacterial strains already resistant to the antibiotic, is dependent on the antibiotic class and stoichiometry of the pairing, and is dramatically influenced by the host microenvironment.

microbiology↗