Chloroplasts are the home of innumerable metabolic pathways for plant growth and environmental responses. Recently, in an issue of Cell, Medina-Puche et al. revealed a novel mechanism by which plant pathogens dampened host defense responses, orchestrated from chloroplasts. This mechanism encompassing the plasma membrane and chloroplasts has likely been established via host-pathogen co-evolution.

Although bacteriophages are highly abundant in the gut microbiome, little is known about their potential effects on gut bacteria. In this issue of Cell Host & Microbe, Hryckowian et al. (2020) and Fujimoto et al. (2020) combined metagenomic analysis and experiments to study phage-bacteria associations in order to develop future research tools and therapies.

How do we explain the co-existence of bacteria and bacteriophages in complex environments? In this issue of Cell Host & Microbe, Lourenço et al. highlight the importance of spatial structure in facilitating the persistence of sensitive bacterial hosts and their virulent bacteriophages in the mammalian gut.

In this issue of Cell Host & Microbe, publications from Bushman et al. (2020) and Knippel et al. (2020) outline elements of host epithelial damage or inflammation that Clostridioides difficile subverts, enabling continued growth. These mechanisms provide insight into how this important pathogen influences the gut environment to promote its metabolic strategy during infection.

In this issue of Cell Host & Microbe, three papers describe the pseudotyping of vesicular stomatitis virus (VSV) with the SARS-CoV-2 spike. This VSV-CoV-2-S platform allows virus neutralization assays to be performed at BSL-2 and also has applications as a candidate vectored vaccine to elicit protective immunity against SARS-CoV-2.

The explosive spread of SARS-CoV-2 suggests that a vaccine will be required to end this global pandemic. Progress in SARS-CoV-2 vaccine development to date has been faster than for any other pathogen in history. Multiple SARS-CoV-2 vaccine candidates have been evaluated in preclinical models and are currently in clinical trials. In this Perspective, we discuss three topics that are critical for SARS-CoV-2

Every animal is in constant communication with populations of microbes. In a recent study, O’Donnell and colleagues (2020) uncover an inter-domain conversation, defining a relationship in which a non-pathogenic microbe directly synthesizes a signal that alters host behavior for a mutually beneficial outcome.

In this issue of Cell Host & Microbe, Adebayo et al. (2020) examine the urobiome of older community-dwelling women within the TwinUK Cohort. They define a core genitourinary microbiome for older women with many heritable microbial taxa. Some taxa appear to co-occur, suggesting the existence of specific microbial consortia.

Human milk harbors its own microbiota, but whether the microbes seed the infant gut and are modified by breastfeeding practices is unresolved. In this issue, Fehr et al. (2020) sequence breastmilk and infant stool samples from mother-infant dyads to investigate the co-occurrence of milk-gut bacteria and the impact of breastfeeding practices.

The story of twentieth century biomedical breakthroughs could be told through cholesterol. Revolutions in genetics, molecular biology, genomics, and antibody-based therapies defined cholesterol’s impact on human health and cholesterol-lowering strategies. In this issue, Kenny et al. (2020) bring a key twenty-first century biomedical development—the microbiome revolution—to cholesterol.

Gut microbes exhibit diurnal rhythmicity, and disruptions in this rhythmicity potentially impact host health. In this issue of Cell Host & Microbe, Reitmeier et al. (2020) employ timestamped gut microbiome sequencing data from human subjects coupled with machine learning to identify microbial rhythmicity patterns that predict Type 2 Diabetes incidence.

The mouth presents a multiplicity of local environments in communication with one another via saliva. The spatial organization of microbes within the mouth is shaped by opposing forces in dynamic equilibrium—salivary flow and adhesion, shedding and colonization—and by interactions among and between microbes and the host. Here we review recent evidence confirming that oral microbes are specialized for

Vaccines are the most effective means available for preventing infectious diseases. However, vaccine-induced immune responses are highly variable between individuals and between populations in different regions of the world. Understanding the basis of this variation is, thus, of fundamental importance to human health. Although the factors that are associated with intra- and inter-population variation

The gut microbiota changes with age, but it is not clear to what degree these changes are due to physiologic changes, age-associated inflammation or immunosenescence, diet, medications, or chronic health conditions. Observational studies in humans find that there are profound differences between the microbiomes of long-lived and frail individuals, but the degree to which these differences promote or

The skin microbiome is an ecosystem comprised of a multitude of microbial species interacting with their surroundings, including other microbes and host epithelial and immune cells. These interactions are the basis of important roles within the skin microbiome that provide benefit to the host, boosting multiple aspects of barrier function, a critical function of this essential organ. However, with

The gut microbiome is increasingly implicated in modifying susceptibility to and progression of neurodegenerative diseases (NDs). In this review, we discuss roles for the microbiome in aging and in NDs. In particular, we summarize findings from human studies on microbiome alterations in Parkinson’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis, and Huntington’s disease. We assess animal

Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play

The liver communicates with the intestine via the portal vein, biliary system, and mediators in the circulation. Microbes in the intestine maintain liver homeostasis but can also serve as a source of pathogens and molecules that contribute to fatty liver diseases. We review changes in the gut microbiota that can promote development or progression of alcohol-associated and non-alcoholic fatty liver

In this issue of Cell Host & Microbe, two papers by Osuna et al. describe the characterization of AcrIIA1, an anti-CRISPR protein distributed widely among Listeria phages. AcrIIA1 functions as an anti-CRISPR and as a dynamic repressor of acr loci, suggesting it may play an important role in lysogeny.

Ketogenic diets (KDs) are popularly used to aid a myriad of conditions. KDs induce metabolic changes, but how microbiome alterations contribute to these changes remains unexplored. In a recent Cell paper, Ang et al. identify KD-specific changes to the gut microbiota linked to a reduction in pro-inflammatory Th17 cells.

In this issue of Cell Host & Microbe, Bruggisser et al. show that Clostridium perfringens β-toxin (CPB) binds platelet endothelial cell adhesion molecule-1 (PECAM-1) (also known as CD31) to induce membrane pores. The discovery explains the cell type specificity for CPB and, in large part, the basic pathophysiology of disease.

Little is known about the mechanism that regulates the core steps of antiviral RNA interference (RNAi) pathway in plants and animals. In this issue of Cell Host & Microbe, Yang et al. (2020) provide compelling evidence for the regulation of antiviral RNAi by the jasmonate hormone signaling in plants.

Plasmacytoid DCs (pDCs) are typically thought to be key in antiviral defense. In this issue of Cell Host & Microbe, Guo, Kasahara et al. (2020) reveal a critical role for pDCs in antifungal immunity. Aspergillus-infected monocyte-derived DCs and neutrophils recruit pDCs, which promote neutrophil fungicidal activity.

Mammalian gut microbiomes profoundly influence host fitness, but the processes that drive the evolution of host-microbiome systems are poorly understood. Recent studies suggest that mammals and their individual gut symbionts can have parallel evolutionary histories, as represented by their congruent phylogenies. These “co-phylogenetic” patterns are signatures of ancient co-speciation events and illustrate