Claire Shaw’s research while affiliated with University of California, Davis and other places

Staphylococcus aureus is a versatile zoonotic pathogen capable of causing a wide range of infections. Due to the organism’s ability to persist, recalcitrant and recurring infections are a major concern for public and animal health. This study investigated the establishment of persistence using two S. aureus strains—ATCC 29740, a bovine mastitis isolate, and USA300, a human clinical isolate—under substrate depletion. This stress established a persistence phenotype where the strains remained persistent for >120 days at notable concentrations and developed persister-like growth, including small colony variant formations. With qRT-PCR we found the cell density was higher than represented by the plate count while the intracellular ATP remained constant during the persistence phase. These findings indicate that S. aureus has complex survival strategies to support its persistent state, providing a host-specific perspective when addressing recurrent infections in human and animal infectious disease.

The cat oral microbiome plays an important role in maintaining host health, yet little is known about how to apply microbial data in a clinical setting. One such use of microbiome signatures is in cases of feline chronic gingivostomatitis (FCGS), a severe debilitating complex disease of the oral cavity. FCGS-afflicted cats have limited treatment options, and individual patient responses to treatment are needed. In this work, we used deep sequencing of total RNA of the oral microbiome to chronicle microbial changes that accompanied an FCGS-afflicted cat’s change from treatment-non-responsive to treatment-responsive within a 17-month span. The oral microbiome composition of the two treatment-non-responsive time points differed from that of the treatment-responsive point, with notable shifts in the abundance of Myscoplasmopsis, Aspergillus, and Capnocytophaga species. Intriguingly, the presence of the fungal groups Aspergillus and Candida primarily differentiated the two non-responsive microbiomes. Associated with responder status were multiple Capnocytophaga species, including Capnocytophaga sp. H2931, Capnocytophaga gingivalis, and Capnocytophaga canimorsus. The observation that the oral microbiome shifts in tandem by response to treatment in FCGS suggests a potential use for microbiome evaluations in a clinical setting. This work contributes to developing improved molecular diagnostics for enhanced efficacy of individualized treatment plans to improve oral disease.

Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this approach remain unclear, in part because pathogen reduction appears to be both strain and ecology dependent. Here we tested the ability of five probiotic strains, including some from common probiotic genera Lactobacillus and Bifidobacterium, to reduce binding of Salmonella enterica sv. Typhimurium to epithelial cells in vitro. Bifidobacterium longum subsp. infantis emerged as a promising strain; however, S. Typhimurium infection outcome in epithelial cells was dependent on inoculation order, with B. infantis unable to rescue host cells from preceding or concurrent infection. We further investigated the complex mechanisms underlying this interaction between B. infantis, S. Typhimurium, and epithelial cells using a multi-omics approach that included gene expression and altered metabolism via metabolomics. Incubation with B. infantis repressed apoptotic pathways and induced anti-inflammatory cascades in epithelial cells. In contrast, co-incubation with B. infantis increased in S. Typhimurium the expression of virulence factors, induced anaerobic metabolism, and repressed components of arginine metabolism as well as altering the metabolic profile. Concurrent application of the probiotic and pathogen notably generated metabolic profiles more similar to that of the probiotic alone than to the pathogen, indicating a central role for metabolism in modulating probiotic-pathogen-host interactions. Together these data imply crosstalk via small molecules between the epithelial cells, pathogen and probiotic that consistently demonstrated unique molecular mechanisms specific probiotic/pathogen the individual associations.

Feline chronic gingivostomatitis (FCGS) is a debilitating inflammatory oral mucosal disease with a multifactorial etiology. The clinical diagnosis of FCGS is made based on inspection of severe inflammatory lesions and histological confirmation rather than a molecular diagnostic outcome. This gap limits the ability to provide an early diagnosis. In this report, we seek to provide additional diagnostic tools using genomics to aid in providing clinically relevant information. The use of in-depth diagnostic tools, like transcriptomics of diseased tissues, to diagnose FCGS and stratify patients into predictive treatment response groups would dramatically improve both clinical decisions and patient outcomes. In this study, we addressed the gap in diagnostic options using transcriptomic analysis of caudal oral mucosal swab specimens coupled to detailed medical record linkage of FCGS-affected cats undergoing tooth extractions and in some cases administration of mesenchymal stromal cells (MSCs). To better identify markers of disease and potential response to treatment, the transcriptomes of FCGS-afflicted cats were compared to those of healthy cats and those with chronic periodontitis to clearly establish diagnostic biomarker signal transduction connections. Phosphatidylinositol 3-kinase/Ak strain transforming (PI3K/AKT) and stress-activated protein kinases/Jun N-terminal kinase (SAP/JNK) signaling pathways were significantly differentially regulated in FCGS-afflicted cats. Activation of these pathways also differed in the treatment response groups. In conjunction, the enzymes Caspase 4 (CASP4), matrix metalloproteinase-8 (MMP8), and prostaglandin-endoperoxide synthase 2 (PTGS2) were identified as potential biomarkers for the prediction of treatment response outcomes. The observations in the case study support the use of transcriptomics of FCGS patients to contribute to improved molecular diagnostics for the diagnosis and treatment of FCGS.

The rumen contains a complex mixture of microbes, crucial for the animal’s ability to degrade feed. Some of the feed-derived carbon is released as methane, a potent greenhouse gas, into the atmosphere. There is growing interest in reducing the loss of feed-derived carbon, making it available to the animal and improving animal productivity. Artificial rumen systems (ARSs) have been widely used to evaluate novel feed additives in terms of their ability to reduce methane production in the rumen and their effect on the rumen microbiome function prior to conducting resource-intensive animal trials. While the value of ARSs is widely acknowledged, it remains unclear which of these in vitro systems simulate the natural system most accurately. Here, we evaluated three different ARSs and compared them to in vivo rumen metrics. The results showed that all systems were capable of maintaining stable pH, redox potential, and temperature over time. The batch-style ARS simulated the rumen over 48 h. The semi-continuous ARS mimicked the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 h. Similarly, all ARSs maintained the prokaryotic and eukaryotic rumen populations over the duration of the study, with the semi-continuous ARS maintaining the natural rumen microbiome more accurately and for up to 120 h. In sum, our results suggest that three of the widely used ARSs simulate the rumen ecosystem adequately for many short-term rumen microbiome studies, with the more advanced semi-continuous ARS being more accurate when rumen simulation is extended to over 48 h.

The gut microbiome provides the host access to otherwise indigestible nutrients, which are often further metabolized by the microbiome into bioactive components. The gut microbiome can also shift the balance of host-produced compounds, which may alter host health. One precursor to bioactive metabolites is the essential aromatic amino acid tryptophan. Tryptophan is mostly shunted into the kynurenine pathway but is also the primary metabolite for serotonin production and the bacterial indole pathway. Balance between tryptophan-derived bioactive metabolites is crucial for neurological homeostasis and metabolic imbalance can trigger or exacerbate neurological diseases. Alzheimer’s, depression, and schizophrenia have been linked to diverging levels of tryptophan-derived anthranilic, kynurenic, and quinolinic acid. Anthranilic acid from collective microbiome metabolism plays a complex but important role in systemic host health. Although anthranilic acid and its metabolic products are of great importance for host–microbe interaction in neurological health, literature examining the mechanistic relationships between microbial production, host regulation, and neurological diseases is scarce and at times conflicting. This narrative review provides an overview of the current understanding of anthranilic acid’s role in neurological health and disease, with particular focus on the contribution of the gut microbiome, the gut–brain axis, and the involvement of the three major tryptophan pathways.

Methicillin-resistant Staphylococcus aureus (MRSA) is a pervasive and persistent threat that requires the development of novel therapies or adjuvants for existing ones. Aptamers, small single-stranded oligonucleotides that form 3D structures and can bind to target molecules, provide one possible therapeutic route, especially when presented in combination with current antibiotic applications. BALB/c α-1, 3-galactosyltransferase (−/−) knockout (GTKO) mice were infected with MRSA via tail vein IV and subsequently treated with the αSA31 aptamer (n = 4), vancomycin (n = 12), or αSA31 plus vancomycin (n = 12), with split doses in the morning and evening. The heart, lungs, liver, spleen, and kidneys were harvested upon necropsy for histological and qPCR analysis. All mice treated with αSA31 alone died, whereas 5/12 mice treated with vancomycin alone and 7/12 mice treated with vancomycin plus αSA31 survived the course of the experiment. The treatment of MRSA-infected mice with Vancomycin and an adjuvant aptamer αSA31 reduced disease persistence and dispersion as compared to treatment with either vancomycin SA31 alone, indicating the combination of antibiotic and specifically targeted αSA31 aptamer could be a novel way to control MRSA infection. The data further indicate that aptamers may serve as a potential therapeutic option for other emerging antibiotic resistant pathogens.

The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSCs are likely to interact with microbes at sites of tissue damage and inflammation, like in the gastrointestinal system, the consequences of pathogenic association on MSC activities have yet to be elucidated. This study investigated the effects of pathogenic interaction on MSC trilineage differentiation paths and mechanisms using model intracellular pathogen Salmonella enterica ssp enterica serotype Typhimurium. The examination of key markers of differentiation, apoptosis, and immunomodulation demonstrated that Salmonella altered osteogenic and chondrogenic differentiation pathways in human and goat adipose-derived MSCs. Anti-apoptotic and pro-proliferative responses were also significantly upregulated (p < 0.05) in MSCs during Salmonella challenge. These results together indicate that Salmonella, and potentially other pathogenic bacteria, can induce pathways that influence both apoptotic response and functional differentiation trajectories in MSCs, highlighting that microbes have a potentially significant role as influencers of MSC physiology and immune activity.

Background The rumen contains a complex mixture of microbes, which are crucial for ruminant health and feed fermentation. During the fermentation process some of the feed-derived carbon becomes carbon dioxide and methane, which are released into the atmosphere where they act as greenhouse gases and contribute to climate change. There is growing interest in reducing the loss of feed-derived carbon and making it available to the animal, improving animal productivity, while also reducing the carbon footprint of the ruminant industry. To this end, artificial rumen systems (ARS) have been used for evaluating novel feed additives for their effect on the rumen microbiome and rumen function prior to conducting resource intensive animal trials. Whereas ARS are capable of predicting the response of the rumen and its microbiome, it is unclear how accurately different in vitro systems simulate the natural system and how results compare between the artificial systems that are being employed. Here we evaluated physical, chemical and microbiome metrics of three ARS over five days and compared them to those metrics in the in vivo rumen. Results Over a 48 hrs sampling period, the batch style platform (Ankom) was able to replicate pH, volatile fatty acid profile, and bacterial and fungal microbiome of the in vivo rumen, but its accuracy of mimicking in vivo metrics dropped significantly beyond 48 hrs. In contrast, the semi-continuous RUSITEC models, RUSITEC PP and RUSITEC prime, were able to mimic the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 hrs of rumen simulation. Comparison of gas production across vessel types demonstrated that the semi-continuous RUSITEC platforms display less variability among vessel replicates and time compared to the Ankom system. Conclusions In this study, we found that three widely used ARS were able to simulate the rumen ecosystem adequately for the first 48 hrs, with predictions from the more advanced semi-continuous ARS being more accurate when simulations extended over 48 hrs. Findings of this study will help to select the appropriate in vitro system for evaluating the response of the complex rumen microbiome to feed additives. Further work is necessary to improve the capabilities of these platforms and to standardize the methodology for large-scale application.

Two-component systems are ubiquitous signaling mechanisms in bacteria that enable intracellular changes from extracellular cues. These bacterial regulatory systems couple external stimuli to control genetic expression via an autophosphorylation cascade that transduces membrane signals to intracellular locations, thereby allowing bacteria to rapidly adapt to the changing environmental conditions. Well known to control basic cellular processes, it is evident that two-component systems also exercise control over virulence traits, such as motility, secretion systems, and stress responses that impact the complex cascade of networks that alter virulence traits. In the gastrointestinal system, cues for activation of virulence-related two-component systems include metal ions, host-derived metabolites, and gut conditions. The diversity and origin of these cues suggest that the host can exert control over enteric pathogenicity via regulation in the gastrointestinal system. With the rise in multi-drug resistant pathogens, the potential control of pathogenicity with host cues via two-component systems presents a potential alternative to antimicrobials. Though the signaling mechanism itself is well studied, to date there is no systematic review compiling the host-associated cues of two-component systems and virulence traits. This review highlights the direct link between the host gastrointestinal environment and pathogenicity by focusing on two-component systems that are associated with the genetic expression of virulence traits, and that are activated by host-derived cues. The direct link between the host gastrointestinal environment, metabolites, and pathogenicity established in this review both underscores the importance of host-derived cues on bacterial activity and presents an enticing therapeutic target in the fight against antimicrobial resistant pathogens.