The organizational principles of the root immune system are largely uncharacterized. In the February 6, 2020 issue of Cell, Zhou et al. showed roots are built entirely by immunocompetent cells that require distinct instructions to unlock cell-autonomous immune programs. A root cell’s developmental identity combined with its spatial distribution fine-tunes immune signal sensitivity, enabling sector-specific

The mechanisms by which Mycobacterium tuberculosis evades host immunity remain enigmatic. In a recent study in the journal Nature, Wang et al. report that an enzyme acting in the bacterial cytoplasm to degrade lipids also acts as an effector protein in the host cell cytoplasm to suppress inflammation.

How gut cells distinguish between beneficial symbionts and deleterious pathobionts is a central question. In this issue of Cell Host & Microbe, Kim et al. (2020) demonstrate that the nucleoside catabolism pathway controlling bacterial uracil and ribose production is an essential trigger of the commensal to pathogen transition.

Intestinal epithelial absorption of dietary lipids is a major determinant of animal energy balance and metabolic health. Recent studies uncovered significant roles for intestinal microbiota in this process, but underlying mechanisms remain unresolved. Araújo et al. (2020) identify two end-products of bacterial fermentation that regulate intestinal lipid absorption and metabolism.

Pathogens rely on nutrient assimilation, particularly essential metal incorporation, to successfully survive in the host. In this issue of Cell Host & Microbe, Riedelberger et al. (2020) convincingly demonstrate that type I interferons (IFNs-I) promote dysregulation of iron homeostasis in macrophages upon infection with Candida glabrata and exacerbate infection.

The microbiota is necessary for the induction of intestinal immunoglobulin A (IgA). In this issue of Cell Host & Microbe, Yang et al. (2020) show that the ability to induce or suppress IgA is characteristic of specific strains of Bacteroides ovatus. Immunogenicity and IgA induction by the microbiota is determined by inter-bacterial interaction.

The intestine is an essential physical and immunological barrier comprised of a monolayer of diverse and specialized epithelial cells that perform functions ranging from nutrient absorption to pathogen sensing and intestinal homeostasis. The intestinal barrier prevents translocation of intestinal microbes into internal compartments. The microbiota is comprised of a complex community largely populated

If, as we all know, only the strong survive, why do bacterial viruses (phages) encode weak suppressors of a bacterial immune system? In this issue of Cell Host & Microbe, Chevallereau et al. (2019) expertly demonstrate how, in the context of competition with other phages, weakness can be a strength.

Bacteriophages shape bacterial ecosystems, including community membership and their metabolic function. In this issue of Cell Host & Microbe, Mirzaei et al. (2020) identify harbored bacteriophages among a Proteobacteria-dominant community unique to toddlers with stunted growth from Bangladesh, and that confer the capacity to similarly tailor microbiota profiles in vitro.

Invertebrates molt, furry mammals shed, and human skin exfoliates. In this issue of Cell Host & Microbe, Zingl et al. describe a virulence mechanism in which the bacterial pathogen Vibrio cholerae jettisons outer membrane proteins and lipids in vesicles as it enters the mammalian intestine.

Ebolavirus disease is a global threat. In this issue, Khurana et al. reveal the antibody response against all ebolavirus proteins by analyzing longitudinal antibody repertoires of an Ebola survivor from disease onset. Antibodies against VP40 and GP are found to predominate and two protective antigenic sites in GP identified.

Recent studies show that neutrophils mediate both tissue damage and host protection in response to multicellular parasites. In this issue of Cell Host & Microbe, Bouchery et al. demonstrate the importance of neutrophil extracellular traps in helminth damage after primary infections.

Restoration of the gut microbiome is a promising preventive and therapeutic strategy in a number of clinical scenarios. We discuss here the scientific and clinical challenges of engineering and implementing these strategies.

Fecal microbiota for transplantation (FMT) is being studied as a potential intervention for numerous conditions. The regulation of FMT by the FDA is discussed along with FMT donor screening and manufacturing considerations. The FDA is committed to ensuring that FMT products can be safely tested in clinical trials.

Biological rhythms appear to be an elegant solution to the challenge of coordinating activities with the consequences of the Earth's daily and seasonal rotation. The genes and molecular mechanisms underpinning circadian clocks in multicellular organisms are well understood. In contrast, the regulatory mechanisms and fitness consequences of biological rhythms exhibited by parasites remain mysterious

An in-depth annotation of the newly discovered coronavirus (2019-nCoV) genome has revealed differences between 2019-nCoV and severe acute respiratory syndrome (SARS) or SARS-like coronaviruses. A systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may have caused functional and pathogenic divergence of 2019-nCoV.

The role of gut bacteria in complications of heart inflammation has previously not been fully understood. Gil-Cruz et al. (2019) demonstrate a commensal Bacteroides species that triggers a cross-immune response against a bacterial protein and heart epitope, causing cardiomyopathy. This study links commensal bacteria with heart inflammation mechanistically in mice and correlatively in patients.

Despite decades of study, the molecular basis for granuloma formation and restriction of chronic pathogens remains murky. Three articles reveal how Salmonella rewires macrophage polarization (Panagi et al. and Gibbs et al.) to shift the balance between M1 and M2 granuloma macrophages and resist TNF-mediated clearance (Pham et al.).

Bacteroides genomes encode a large repertoire of proteins dedicated to the utilization of diverse plant polysaccharides and host glycans. In this issue of Cell Host & Microbe, Glowacki et al. (2020) show that B. thetaiotaomicron can also extract the monosaccharide ribose from nucleosides and characterize proteins necessary for its utilization.

In this issue of Cell Host & Microbe, Hancock et al., 2020 show that latent HCMV infection, and specifically miR-US5-2, induces TGF-β secretion, which inhibits myelopoiesis in uninfected HPCs. They also show that HCMV-infected cells become resistant to TGF-β signaling through targeting of SMAD3 by miR-UL22-A-3p and -5p.

The neonatal gut microbiome undergoes dynamic changes in response to many nutritional and environmental variables. A recent study by Singer et al. in Nature Medicine elucidates several mechanisms to inhibit the expansion of gut-derived pathobionts in a dysbiotic neonatal gut and prevent these pathobionts from disseminating systemically and causing sepsis in neonatal mice.

Humoral immunity is an essential component of the protective immune response to flavivirus infection. Typically, primary infection generates a robust neutralizing antibody response that mediates viral control and protection. It is becoming increasingly apparent that secondary infection with a closely related flavivirus strain can result in immunological cross-reactivity; however, the consequences to