Biology subjects

Petri, W. A.

Publications and source records attributed to Petri, W. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Antibiotics promote susceptibility to C. difficile infection through a CCR5-dependent immune response

Antibiotics (ABXs) represent the current standard of care for treating Clostridioides difficile infection (CDI). Paradoxically, ABX-induced dysbiosis is the primary risk factor for CDI, as disruption of the colonic microbial ecosystem creates an opportunity for C. difficile colonization. Given that ABXs can also alter immune responses, we investigated whether ABXs prime the colonic immune milieu for CDI susceptibility. Here, we implicate ABXs in driving CDI severity through the emergence of pathogenic CCR5-reliant immune populations in the mouse colon. High-throughput immune cell profiling revealed that ABXs shift the colonic immune compartment toward a CCR5-associated type I immunity signature, marked by an expansion of CCR5+ ILC1s and CCR5+ Th1 cells. A partial genetic deletion of CCR5 reversed CDI severity, alleviating colonic inflammation and improving survival. Pharmacological inhibition of the CCL3/4/5-CCR5 circuit also recapitulated these favorable disease outcomes, which we attribute to reduced colonic CCR5+ ILC1, CCR5+ Th1, and CCR5+ CD8 T cell populations during CDI. Together, our findings extend beyond dysbiosis as the canonical CDI risk factor and establish ABX-induced immune imbalance as an underappreciated determinant of CDI susceptibility.

immunology↗

bioRxiv2026

REGULATION OF COLONIC MACROPHAGES AND TYPE-17 AND REGULATORY T CELLS IN DSS-COLITIS BY IBD-ASSOCIATED TRANSCRIPTION FACTOR, CREM

BackgroundRecent genome wide association studies (GWAS) performed by our laboratory identified polymorphisms at the locus containing the gene, cAMP-responsive element modulator (CREM), that influence Entamoeba histolytica+ diarrheal disease susceptibility in children. CREM is a cAMP-responsive transcription factor that regulates genetic expression and epigenetic modulation in a context- and cell-specific manner. Polymorphisms at this locus have been previously associated with IBD susceptibility, suggesting CREM regulates enteric inflammation in infectious and autoimmune colitis. MethodsMice were generated with either a tamoxifen-inducible global deletion or an intestinal epithelial cell (IEC)-specific deletion of Crem. Dextran-sodium sulfate (DSS) was administered to chemically induce colitis and mice were assayed for weight loss, clinical score, spectral flow cytometry of colonic lamina propria and mesenteric lymph node white blood cells, and shallow shotgun whole genome sequencing of fecal samples. ResultsTamoxifen-inducible global deletion of Crem significantly ameliorated DSS-colitis severity as measured by clinical scoring and weight loss over the course of disease (p = 2.29 x 10-15, p = 2.24 x 10-21, respectively). Protection was not phenocopied when Crem was deleted exclusively in IECs. When sampled during acute colitis, protection seen in Crem-deleted mice was associated with a significant increase in macrophages, and ROR{gamma}t+ regulatory (pTregs) and T helper (Th17) cells in the colonic lamina propria, along with an increase of T-follicular like helper cells in the mesenteric lymph node. ConclusionsInducible global deletion of Crem reduced the severity of DSS colitis while increasing colonic macrophages, ROR{gamma}t+ regulatory (pTregs) and T helper (Th17) cells. Future work will investigate the aforementioned cell types to determine the mechanism by which CREM aggravates DSS-colitis, thereby defining the immunoregulatory role of CREM in intestinal inflammation with the goal of identifying new therapeutic targets for IBD.

immunology↗

bioRxiv2025

The hyaluronan receptor CD44 drives COVID-19 severity through its regulation of neutrophil migration

The novel respiratory disease COVID-19 caused by the coronavirus SARS-CoV-2 continues to be a public health emergency worldwide, and there is a need for more effective therapy for patients. The relationship between the extracellular matrix and the host immune response to infection is severely understudied. Deposition of the polysaccharide hyaluronan (HA) into the lungs is associated with more severe COVID-19 disease outcomes. HA is a major component of the extracellular matrix in connective tissues and is abundant in many parts of the body, including cartilage, skin, brain, and vitreous body. CD44 is the primary receptor for HA and is found on almost all immune cells in the lung. Known functions of CD44 include mediation of immune cell migration, activation, and differentiation. We hypothesized that increased HA deposition during COVID-19 increases CD44-mediated immune cell infiltration into lungs and results in more severe pathology. Here, we report that in mice infected with a mouse-adapted strain of SARS-CoV-2, treatment with a combination of two anti-CD44 monoclonal antibodies confers a significant survival benefit and reduces weight loss and clinical score of the mice on Day 4 post infection. We show that anti-CD44 treatment decreases many key cytokines and chemokines in the bronchoalveolar lavage fluid on Day 4. With flow cytometry, we show that anti-CD44 reduces the numbers of neutrophils in infected lungs. We also show through immunofluorescence that treatment with anti-CD44 antibodies reduces colocalization of HA and CD45 in lung sections, indicating that HAs interaction with immune cells contributes to pathology. Our findings demonstrate that disruption of HA-receptor interactions is a way to prevent inflammatory pathology in pulmonary infection.

immunology↗

bioRxiv2025

Human immune response to primary cryptosporidiosis parallels murine infection models

Cryptosporidium is a protozoan parasite that causes cryptosporidiosis, an enteric infection associated with diarrhea, malnutrition, and impaired childhood development in low- and middle-income countries. Both humoral and cell-mediated immune responses have been implicated in protection, but the durability and quality of human immune responses in immunocompetent adults remain poorly defined. We investigated the development of immunity in two healthy US adults following primary cryptosporidiosis acquired during travel to Bangladesh. Longitudinal plasma samples were analyzed for antibody responses to Cryptosporidium antigens Cp17 and Cp23 and for circulating cytokine profiles. Circulating antibody peaked at three weeks post-infection but declined rapidly thereafter, approaching baseline within 16 weeks. In contrast, antibody avidity increased steadily over time, consistent with ongoing affinity maturation in germinal centers. While affinity maturation occurred, the composition memory B cells specific to Cryptosporidium antigens was skewed toward IgM+ cells across timepoints suggesting extrafollicular responses dominated and germinal center-derived, class-switched memory was limited. Cytokine profiling revealed an acute Th1-skewed response, with elevations in CXCL9, CXCL10, IL-27, IFN{gamma}, IL-12, and IL-18 during early infection. These signatures mirrored protective pathways identified in murine models, underscoring the importance of type I immunity in parasite clearance. Together, these findings highlight that while antibody responses to Cryptosporidium are short-lived, avidity maturation persists, and Th1-driven cytokine responses dominate during acute infection. This work provides rare longitudinal data on immune responses in naive adults following natural cryptosporidiosis and offers insight into mechanisms that may inform vaccine development and strategies to mitigate recurrent infection in vulnerable populations.

immunology↗

bioRxiv2024

The IL-33/ST2 signaling axis drives pathogenesis in acute SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a significant threat to global public health. Immunopathological damage plays a role in driving pneumonia, acute respiratory distress syndrome (ARDS), and multiorgan failure in severe COVID-19. Therefore, dissecting the pulmonary immune response to SARS-CoV-2 infection is critical to understand disease pathogenesis and identify immune pathways targetable by therapeutic intervention. Considering that the type 2 cytokine IL-13 enhances COVID-19 disease severity, therapeutic targeting of upstream signals that drive type 2 immunity may confer further protection. In this study, we investigate the role of the IL-33/ST2 signaling axis, a potent inducer of type 2 immunity in the lung, in a mouse model of COVID-19. Upon infection with mouse-adapted SARS-CoV-2 MA10, ST2-/- mice had significantly improved weight loss and survival (69.2% vs 13.3% survival; P = 0.0005), as compared to wild-type mice. In a complementary pharmacologic approach, IL-33/ST2 signaling was inhibited using HpBARI_Hom2, a helminth derived protein that binds to mouse ST2 and blocks IL-33 signaling. In SARS-CoV-2 MA10 infection, HpBARI_Hom2-treated mice had significantly improved weight loss and survival (60% vs 10% survival; P = 0.0035), as compared to inert control-treated mice. These data demonstrate that loss of IL-33/ST2 signaling confers protection during acute SARS-CoV-2 MA10 infection, implicating the IL-33/ST2 signaling axis as an enhancer of COVID-19 disease severity. The protection conferred by pharmacologic blockade of IL-33/ST2 signaling was independent of viral control, as HpBARI_Hom2-treated mice had no reduction in viral titers. This finding suggests an immunopathogenic role for IL-33/ST2 signaling. One potential mechanism through which IL-33/ST2 signaling may drive severe disease is through enhancement of type 2 immune pathways including IL-5 production, as pulmonary IL-5 concentrations were found to depend on IL-33/ST2 signaling in acute SARS-CoV-2 MA10 infection.

immunology↗

bioRxiv2024

Enhanced immunogenicity of a Clostridioides difficile TcdB vaccine adjuvanted with a synthetic dual-TLR ligand adjuvant.

We report a comprehensive evaluation of the toxin B (TcdB) vaccine adjuvanted with a dual Toll-like receptor ligand liposome adjuvant for Clostridioides difficile infection (CDI). The vaccine completely protected mice from a lethal infection. Compared to alum adjuvanted TcdB, it generated functionally superior systemic antibodies and supported strong memory B cell and gut IgA responses. This pharmaceutically acceptable adjuvant platform holds promise for developing a next-generation CDI vaccine.

immunology↗

bioRxiv2024

IL-33 protects from recurrent C. difficile infection by restoration of humoral immunity

Clostridioides difficile infection (CDI) recurs in one of five patients. Monoclonal antibodies targeting the virulence factor TcdB reduce disease recurrence, suggesting that an inadequate anti-TcdB response to CDI leads to recurrence. In patients with CDI, we discovered that IL-33 measured at diagnosis predicts future recurrence, leading us to test the role of IL-33 signaling in the induction of humoral immunity during CDI. Using a mouse recurrence model, IL-33 was demonstrated to be integral for anti-TcdB antibody production. IL-33 acted via ST2+ ILC2 cells, facilitating germinal center T follicular helper (GC-Tfh) cell generation of antibodies. IL-33 protection from reinfection was antibody-dependent, as MT KO mice and mice treated with anti-CD20 mAb were not protected. These findings demonstrate the critical role of IL-33 in generating humoral immunity to prevent recurrent CDI. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/623943v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@9ec4aeorg.highwire.dtl.DTLVardef@1827bd3org.highwire.dtl.DTLVardef@18f761dorg.highwire.dtl.DTLVardef@19396d4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO IL-33 restoration induces toxin-B-specific antibody production via the ILC2-TFH axis. In the left panel, IL-33 remediation increases ILC2s, subsequently inducing TFH directly or indirectly. TFH cell induction is pivotal for the production of antibodies. IL-33 also downregulates type 1 and type 3 immunity, favoring type 2 immunity to enhance host survival and reduce morbidity. The middle panel illustrates antibiotic-induced dysbiosis, resulting in decreased IL-33 levels and reduced antibody production. The right panel demonstrates the protective effect in reinfection, attributed to toxin-specific antibodie generated by IL-33 remediation. C_FIG

immunology↗

bioRxiv2024

Examining the relationship between psychosocial adversity and inhibitory control: an fMRI study of children growing up in extreme poverty

Exposure to psychosocial adversity (PA) is associated with poor behavioral, physical, and mental health outcomes in adulthood. As these outcomes are related to alterations in developmental processes, growing evidence suggests that deficits in executive functions-inhibitory control in particular-may, in part, explain this relationship. However, literature examining the development of inhibitory control has been based on children in higher resource environments, and little is known how low resource settings might exacerbate the link between inhibitory control and health outcomes. In this context, we collected fMRI data during a Go/No-Go inhibitory control task and PA variables for 68 children 5 to 7 years of age living in Dhaka, Bangladesh, an area with a high prevalence of PA. The childrens mothers completed behavioral questionnaires to assess the childs PA and their own PA. Whole-brain activation underlying inhibitory control was examined using the No-Go versus Go contrast, and associations with PA variables were assessed using whole-brain regressions. Childhood neglect was associated with weaker activation in the right posterior cingulate, whereas greater family conflict, economic stress, and maternal PA factors were associated with greater activation in the left medial frontal gyrus, right superior and middle frontal gyri, and left cingulate gyrus. These data suggest that neural networks supporting inhibitory control processes may vary as a function of exposure to different types of PA, particularly between those related to threat and deprivation. Furthermore, increased activation in children with greater PA may serve as a compensatory mechanism, allowing them to maintain similar behavioral task performance.

neuroscience↗

bioRxiv2023

Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection

Fecal Microbiota Transplant (FMT) is an emerging therapy that has had remarkable success in treatment and prevention of recurrent Clostridioides difficile infection (rCDI). FMT has recently been associated with adverse outcomes such as inadvertent transfer of antimicrobial resistance, necessitating development of more targeted bacteriotherapies. To address this challenge, we developed a novel systems biology pipeline to identify candidate probiotic strains that would be predicted to interrupt C. difficile pathogenesis. Utilizing metagenomic characterization of human FMT donor samples, we identified those metabolic pathways most associated with successful FMTs and reconstructed the metabolism of encoding species to simulate interactions with C. difficile. This analysis resulted in predictions of high levels of cross-feeding for amino acids in species most associated with FMT success. Guided by these in silico models, we assembled consortia of bacteria with increased amino acid cross-feeding which were then validated in vitro. We subsequently tested the consortia in a murine model of CDI, demonstrating total protection from severe CDI through decreased toxin levels, recovered gut microbiota, and increased intestinal eosinophils. These results support the novel framework that amino acid cross-feeding is likely a critical mechanism in the initial resolution of CDI by FMT. Importantly, we conclude that our predictive platform based on predicted and testable metabolic interactions between the microbiota and C. difficile led to a rationally designed biotherapeutic framework that may be extended to other enteric infections.

systems biology↗

bioRxiv2021

IL-13 promotes recovery from C. difficile infection

Clostridioides difficile infection (CDI) is the leading hospital-acquired infection in North America. We have previously discovered that antibiotic disruption of the gut microbiota decreases intestinal IL-33 and IL-25 and increases susceptibility to CDI. We further found that IL-33 promotes protection through type 2 Innate Lymphoid Cells (ILC2s), which produce IL-13. However, the contribution of IL-13 to disease has never been explored. We found that administration of IL-13 protected, and anti-IL-13 exacerbated CDI as measured by weight loss and clinical score, particularly during disease resolution. Additionally, concordant with IL-13 being important for M2 macrophage polarization, we saw a decrease in M2 macrophages (CD11B+CD64+CD206+) cells following neutralization of IL-13. We also observed monocyte accumulation as early as day three post-infection following IL-13 neutralization, suggesting IL-13 may be directly or indirectly important for their recruitment or transition into macrophages. Neutralization of the decoy receptor IL-13R2 resulted in protection from disease, likely through increased available endogenous IL-13. Our data highlight the protective role of IL-13 in promoting recovery from CDI and the association of poor responses with a dysregulated monocytemacrophage compartment. These results increase our understanding of type 2 immunity in CDI and may have implications for treating disease in patients.

immunology↗

bioRxiv2021

Clostridioides difficile binary toxin binding component (CDTb) increases virulence in a hamster model

Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infection, in part due to the existence of binary toxin (CDT)-expressing hypervirulent strains. We have previously shown that CDT interacts with the TLR2/6 heterodimer to induce inflammation, and in this study we further explore this interaction as well as the contribution of the separate components of CDT, CDTa and CDTb. We found that the binding component, CDTb, is capable of inducing inflammation. Additionally, complementation of a CDT-deficient C. difficile strain with CDTb alone restored virulence in a hamster model of C. difficile infection. Overall, this study demonstrates that the binding component of C. difficile binary toxin contributes to virulence during infection.

microbiology↗

bioRxiv2021

Fecal Microbiota Transplantation Drives Colonic Expression of Immune Activation Genes in a Mouse Model of Antibiotic Use

Clostridioides difficile infection (CDI) is the leading hospital acquired infection in North America. While the standard treatment for CDI remains antibiotics, fecal microbiota transplantation (FMT) has gained attention as an effective therapy to prevent relapse. Previous work has focused on colonization resistance mounted against C. difficile by FMT-delivered commensals, but the effects of FMT on the gut mucosal immune response are poorly understood. Better understanding of the molecular mechanisms driven by FMT would allow for more targeted therapy against CDI. To address this important gap in knowledge, microbial community structure and host gene expression were assessed after FMT in a mouse model of antibiotic use. Administration of FMT led to a significant increase in microbial diversity and partial restoration of community structure within 48 hours of treatment. RNA sequencing of cecal tissue identified large changes in gene expression between FMT recipient and vehicle control groups. Strikingly, genes upregulated after FMT treatment were enriched in immune activation pathways, many of which were associated with pro-inflammatory immune responses. FMT also upregulated several genes associated with type 2 immunity while repressing several associated with type 3 immunity, trends that are associated with improved response to CDI. These results highlight the interplay between the intestinal microbiota and host transcriptome and identify pathways of interest for exploring the role of FMT on treatment of recurring CDI.

microbiology↗

bioRxiv2021

The IL-33-ILC2 pathway protects from amebic colitis

Entamoeba histolytica is a pathogenic protozoan parasite that causes intestinal colitis, diarrhea, and in some cases, liver abscess. Through transcriptomics analysis, we observed that E. histolytica infection was associated with increased expression of IL-33 mRNA in both the human and murine colon. IL-33, the IL-1 family cytokine, is released after cell injury to alert the immune system of tissue damage during infection. Treatment with recombinant IL-33 protected mice from amebic infection and colonic tissue damage; moreover, blocking IL-33 signaling made mice more susceptible to infection and weight loss. IL-33 limited the recruitment of inflammatory immune cells and decreased the pro-inflammatory cytokine IL-6 in the colon. Type 2 immune responses, which are known to be involved in tissue repair, were upregulated by IL-33 treatment during amebic infection. Interestingly, administration of IL-33 protected RAG2-/- mice but not RAG2-/-{gamma}c-/- mice, demonstrating that IL-33 mediated protection occurred in the absence of T or B cells but required the presence of innate lymphoid cells (ILCs). IL-33 induced recruitment of ILC2 but not ILC1 and ILC3 in RAG2-/- mice. Adoptive transfer of ILC2s to RAG2-/-{gamma}c-/- mice restored IL-33 mediated protection. These data reveal that the IL-33-ILC2 pathway is an important host defense mechanism against amebic colitis.

immunology↗

bioRxiv2020

Genome-scale metabolic reconstruction analysis of Clostridioides difficile identifies conserved patterns of virulence-related metabolic reprogramming

The pathogen Clostridioides difficile causes toxin-mediated diarrhea and is the leading cause of hospital-acquired infection in the US. Due to growing antibiotic resistance and recurrent infection, targeting C. difficile metabolism presents a new approach to combat this infection. Genome-scale metabolic network reconstructions (GENREs) have been used to identify therapeutic targets and uncover properties that determine cellular behaviors. Thus, we constructed C. difficile GENREs for a hyper-virulent isolate (str. R20291) and a historic strain (str. 630), validating both with in vitro and in vivo datasets. Growth simulations revealed significant correlations with measured carbon source usage (PPV [≥] 92.7%), and single-gene deletion analysis showed >89.0% accuracy. Next, we utilized each GENRE to identify metabolic drivers of both sporulation and biofilm formation. Through contextualization of each model using transcriptomes generated from in vitro and infection conditions, we discovered reliance on the Pentose Phosphate Pathway as well as increased usage of cytidine and N-acetylneuraminate when virulence expression is reduced, which was subsequently supported experimentally. Our results highlight the ability of GENREs to identify novel metabolite signals in bacterial pathogenesis. ImportanceClostridioides difficile is a Gram-positive, sporulating anaerobe that has become the leading cause of hospital-acquired infections. Numerous studies have demonstrated the importance of specific metabolic pathways in aspects of C. difficile pathophysiology, from initial colonization to regulation of virulence factors. In the past, genome-scale metabolic network reconstruction (GENRE) analysis of bacteria has enabled systematic investigation of the genetic and metabolic properties that contribute to downstream virulence phenotypes. With this in mind, we generated and extensively curated C. difficile GENREs for both a well-studied laboratory strain (str. 630) as well as a more recently characterized hyper-virulent isolate (str. R20291). In silico validation of both GENREs revealed high degrees of agreement with experimental gene essentiality and carbon source utilization datasets. Subsequent exploration of context-specific metabolism during both in vitro growth and infection revealed consistent patterns of metabolism which corresponded with experimentally measured increases in virulence factor expression. Our results support that differential C. difficile virulence is associated with distinct metabolic programs related use of carbon sources and provides a platform for identification of novel therapeutic targets.

bioengineering↗

bioRxiv2020

Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

BackgroundThe protozoan parasites in the Cryptosporidium genus cause both acute diarrheal disease and subclinical (i.e. non-diarrheal) disease. It is unclear if the microbiota can influence the manifestation of diarrhea during a Cryptosporidium infection. MethodsTo characterize the role of the gut microbiota in diarrheal cryptosporidiosis, the microbiome composition of both diarrheal and surveillance Cryptosporidium-positive fecal samples was evaluated using 16S rRNA gene sequencing. Additionally, the microbiome composition prior to infection was examined to test whether a preexisting microbiome profile could influence the Cryptosporidium infection phenotype. ResultsFecal microbiome composition was associated with diarrheal symptoms at two timepoints. Megasphaera was significantly less abundant in diarrheal samples when compared to subclinical samples at the time of Cryptosporidium detection (log2(fold change) = -4.3, p=10-10) and prior to infection (log2(fold change) = -2.0, p=10-4). Random forest classification also identified Megasphaera abundance in the pre- and post-exposure microbiota.as predictive of a subclinical infection. ConclusionsMicrobiome composition broadly, and specifically low Megasphaera abundance, was associated with diarrheal symptoms prior to and at the time of Cryptosporidium detection. This observation suggests that the gut microenvironment may play a role in determining the severity of a Cryptosporidium infection. SummaryMegasphaera abundance in the stool of Bangladeshi infants is associated with the development of diarrhea upon infection with the Cryptosporidium parasite.

microbiology↗

bioRxiv2020

Evaluation of K18-hACE2 mice as a model of SARS-CoV-2 infection

Abstract/SummaryMurine models of SARS-CoV-2 infection are critical for elucidating the biological pathways underlying COVID-19 disease. Because human ACE2 is the receptor for SARS-CoV-2, mice expressing the human ACE2 gene have shown promise as a potential model for COVID-19. Five mice from the transgenic mouse strain K18-hACE2 were intranasally inoculated with SARS-CoV-2 Hong Kong/VM20001061/2020. Mice were followed twice daily for five days and scored for weight loss and clinical symptoms. Infected mice did not exhibit any signs of infection until day four, when weight loss, but no other obvious clinical symptoms were observed. By day five all infected mice had lost around 10% of their original body weight, but exhibited variable clinical symptoms. All infected mice showed high viral titers in the lungs as well as altered lung histology associated with proteinaceous debris in the alveolar space, interstitial inflammatory cell infiltration and alveolar septal thickening. Overall, these results show that symptomatic SARS-CoV-2 infection can be established in the K18-hACE2 transgenic background and should be a useful mouse model for COVID-19 disease.

pathology↗

bioRxiv2019

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

Protozoan parasites cause diverse diseases with large global impacts. Research on the pathogenesis and biology of these organisms is limited by economic and experimental constraints. Accordingly, studies of one parasite are frequently extrapolated to infer knowledge about another parasite, across and within genera. Model in vitro or in vivo systems are frequently used to enhance experimental manipulability, but these systems generally use species related to, yet distinct from, the clinically relevant causal pathogen. Characterization of functional differences among parasite species is confined to post hoc or single target studies, limiting the utility of this extrapolation approach. To address this challenge and to accelerate parasitology research broadly, we present a functional comparative analysis of 192 genomes, representing every high-quality, publicly-available protozoan parasite genome including Plasmodium, Toxoplasma, Cryptosporidium, Entamoeba, Trypanosoma, Leishmania, Giardia, and other species. We generated an automated metabolic network reconstruction pipeline optimized for eukaryotic organisms. These metabolic network reconstructions serve as biochemical knowledgebases for each parasite, enabling qualitative and quantitative comparisons of metabolic behavior across parasites. We identified putative differences in gene essentiality and pathway utilization to facilitate the comparison of experimental findings. This knowledgebase represents the largest collection of genome-scale metabolic models for both pathogens and eukaryotes; with this resource, we can predict species-specific functions, contextualize experimental results, and optimize selection of experimental systems for fastidious species.

systems biology↗

bioRxiv2018

Gut microbiome communication with bone marrow regulates susceptibility to amebiasis

The gut microbiome provides resistance to infection. However, the mechanisms for this are poorly understood. Colonization with the intestinal bacterium Clostridium scindens provided protection from the parasite Entamoeba histolytica via innate immunity. Introduction of C. scindens into the gut microbiota epigenetically altered and expanded bone marrow granulocyte-monocyte-progenitors (GMPs) and provided neutrophil-mediated protection against subsequent challenge with E. histolytica. Adoptive transfer of bone-marrow from C. scindens colonized-mice into naive-mice protected against ameba infection and increased intestinal neutrophils. Because of the known ability of C. scindens to metabolize the bile salt cholate, we measured deoxycholate and discovered that it was increased in the sera of C. scindens colonized mice, as well as in children protected from amebiasis. Administration of deoxycholate alone (in the absence of C. scindens) increased the epigenetic mediator JMJD3 and GMPs and provided protection from amebiasis. In conclusion the microbiota was shown to communicate to the bone marrow via microbially-metabolized bile salts to train innate immune memory to provide antigen-nonspecific protection from subsequent infection. This represents a novel mechanism by which the microbiome protects from disease.\n\nOne Sentence SummaryIntroduction of the human commensal bacteria Clostridium scindens into the intestinal microbiota epigenetically alters bone marrow and protects from future parasite infection.

microbiology↗