Section snippets Main textA microbiologist’s lexicon is filled with words focused on the life cycle of their favorite microorganism, such as growth, replication, and fitness. Researchers log hours at the bench counting PFUs, CFUs, titers, and plotting growth curves and survival. These metrics are key to understanding microbes and how these tiny inhabitants interact with their environments, whether

A Nature Medicine paper by Sawhney et al.1 presents a strain-resolved analysis of the gut microbiome from infancy through eight years of age, identifying weaning as an evolutionary trigger for microbial adaptation. Their findings refine the timeline of microbiome development and highlight human milk as a pacemaker of microbial succession.

The gut microbiome plays a pivotal role in human health, particularly in cancer prevention and treatment. Diet can significantly influence microbiome composition, but individual variability complicates intervention outcomes. We review the microbiome’s influence on cancer development and therapy outcomes and evaluate dietary strategies that modulate microbial composition and metabolites. To address

Probiotics, prebiotics, synbiotics, and postbiotics are required, by definition, to confer a health benefit on the host. It is often presumed the host microbiome plays a central role in the mechanism of action of these substances, collectively referred to here as “biotics.” However, the definitions of both probiotics and postbiotics do not include an associated mechanism nor the involvement of the

Many plants and animals, including humans, host diverse communities of microbes that provide many benefits. A key challenge in understanding microbiomes is that the species composition often differs among individuals, which can thwart generalization. Here, we argue that the key to identifying general principles for microbiome science lies in microbial metabolism. In the human microbiome and in other

Daily oscillations in microbiota composition and function are emerging as an important element in host-microbiota interactions. Here, we summarize features of the microbiota that undergo diurnal rhythms, their development, their impact on the biology of the host, and their relevance to human health and disease. In particular, we focus on the intrinsic and extrinsic factors that regulate microbiota

Human milk represents a highly evolved bioactive system that promotes colonization by infant microbial pioneers, supports immune maturation, and fosters infant development. Beyond providing nutrition, human milk contains key bioactive components, such as microbes, metabolites, human milk oligosaccharides, immunoglobulins, lactoferrin, and antimicrobial peptides. These factors influence colonization

Parasitic protists belonging to the Apicomplexa and Trypanosomatidae are the cause of important diseases and life-long chronic infections in humans. Several of these parasites replicate within intracellular niches in their mammalian host, including specialized vacuoles, as well as endo-lysosomal compartments or the cytosol of infected cells. These parasites are highly dependent on nutrient salvage

Plants and microbiomes have co-evolved for millennia. Through this co-evolution, microbiomes have become essential for plant nutrient acquisition, which involves plant signaling, microbial sensing, and acquiring and sharing nutrients. In this review, we synthesize recent advancements in the complex associations of molecular, physiological, and eco-evolutionary mechanisms that underpin microbe-facilitated

Gut colonization by opportunistic or pathogenic microbes is a critical step in infection, but strategies to displace these organisms without perturbing the commensal microbiota remain scarce. In a recent Science article, Lentsch et al. combine oral vaccination with a niche-competing strain to selectively eliminate Salmonella spp. and related Escherichia coli.

Plant hormone pathways can be regulated by microbes. In a recent issue of Cell, Zhang et al. demonstrate manipulation of rice strigolactone signaling by root bacteria in field conditions and reveal the molecular mechanism of rhizosphere microbiota that affect rice tillering and yield.

How plants respond to shade is crucial for optimizing crop yield under high-density planting. In this issue of Cell Host & Microbe, Lu et al. revealed that rhizosphere microbes regulate shade avoidance response in Arabidopsis via the host FLS2/BAK1 immune complex and the MYC2/PIFs/HY5 transcription factors.

In this issue, Brenes and Laub screen temperate phages for defenses against other temperate phages. This uncovers an array of prophage-encoded immune systems in E. coli. The work expands the concept of phage-phage conflict, reveals context dependency of defense, and highlights temperate phages as both targets and carriers of anti-phage immunity.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent liver disease worldwide. The liver communicates with the intestine, in large part through the gut microbiota. Microbial enzymes are key mediators that affect the progression of MASLD and the more severe metabolic dysfunction-associated steatohepatitis (MASH). These enzymes contribute to the metabolism or biosynthesis

A new study published in Science1 reveals a crucial connection between our neonatal gut microbiota composition and the long-term health of our pancreas, specifically focusing on β-cell development and the subsequent lifelong impact microbe-induced β-cell expansion has on metabolic health, including prevention of, and even potential reversal of, diabetes.

What enables certain microbes to successfully colonize the mammalian gut? In a recent issue of Cell, Liu et al. present a microbial cross-species genomic framework that identifies conserved genetic determinants of gut residency. This study provides a roadmap for developing more effective microbiome-based therapeutics, advancing our understanding of host-microbe interactions.

Bacteria deploy many distinct mechanisms to resist protist predation in natural environments. In a recent study published in Cell, Zhang et al. discover a chemical radar used by the plant pathogen Pseudomonas syringae to sense and kill an amoeba predator.

The Western equine encephalitis virus (WEEV), an alphavirus causing severe neurological disease, exhibits fluctuating epidemic patterns and enigmatic host adaptability. Recent studies by Raju et al. and Fan et al. in Cell reveal glycoprotein modifications enabling receptor switching, explaining its reduced human pathogenicity while underscoring re-emergence risks.

Antiviral defense requires signal transmission that connects the perception of viral infection to activation of plant immunity. Findings in Nature by Huang et al. describe key players whereby RING1-IBR-RING2-type ubiquitin ligase (RBRL) recognizes viral coat proteins to release NINJA3-mediated suppression of jasmonate signaling and initiate broad-spectrum antiviral responses in rice.

Species-level uniformity on the skin surface masks substantial strain-level diversity modulated by ecological dynamics. In this issue of Cell Host & Microbe, Jacob et al. uncover dynamic intraspecies behaviors, revealing different patterns of colonization and persistence for two important skin commensals.

In this issue of Cell Host & Microbe, Feng et al. find that broad-spectrum antibiotics perturbed the ecology of the gut microbiome in individuals receiving a rabies vaccine, resulting in systemic inflammatory responses. Such inflammation is hypothesized to alter immune homeostasis with consequences for immunological responsiveness to vaccination.

(Cell Host & Microbe 32, 1365–1379.e1–e10; August 14, 2024)

Plant phenolic glycosides are thought to be beneficial for human health. In a recent issue of Cell, Kuziel et al. identified that Bacteroides species, the dominant symbiotic bacteria in the gut, harbor a unique multi-enzyme system that processes dietary plant glycosides into various aglycone metabolites with antimicrobial or immunomodulatory activities.

Three studies recently published in Cell reveal distinct ACE2 binding interactions across the merbecoviruses, uncovering how HKU5 can use ACE2s of many non-human hosts and identifying a novel HKU5 lineage capable of using human ACE2. These findings highlight merbecovirus receptor plasticity and caution for preparedness against potential merbecovirus threats.

Immunoglobulin A (IgA) antibodies maintain homeostasis between the host and its microbiota, by exerting luminal control over fungi and bacteria. In this issue of Cell Host & Microbe, Lisicka et al. show that IgA antibodies also control the population of specific members of our virome.

Plasmodium liver infection is limited by type I interferons (IFN-I) but the mechanisms remain unknown. In this issue of Cell Host & Microbe, Marques-da-Silva et al. reveal two IFN-I-induced pathways that trigger the fusion of lysosomes with, and the disruption of, the membranes surrounding the parasites, leading to their clearance.

In this issue of Cell Host & Microbe, Honda et al. identify an antiviral defense system in fungi. Mycoviruses trigger the expression of RNA-editing enzymes, which catalyze the editing of mRNAs encoding zinc finger transcription factors. This system differs from the RNA interference and is conserved in filamentous fungi.

Staphylococcus aureus is a major pathogen with rising antibiotic resistance. In this issue of Cell Host & Microbe, Shekhar et al. find that quinoxalinediones reduce S. aureus lung infections through α-hemolysin inhibition, offering a therapeutic strategy for S. aureus pneumonia.

The nose-to-brain pathway for drug delivery holds promising therapeutic outcomes. In a recent issue of Cell, Shen et al.1 successfully identified and characterized a commensal bacterial strain to enable the intranasal delivery of therapeutics, using obesity as a disease model.

Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially

In a recent article in Nature, Cook et al. demonstrate that an autoactive mutant of CNGC15 generates continuous low-frequency calcium (Ca2+) oscillations, enabling sustained flavonoid production and promoting endosymbiont attraction and root colonization. The mutant simultaneously enables endosymbiosis gene induction, even under high-nutrient conditions, offering avenues for improving crop-microbe

The mucosal immune response of the urinary bladder to bacterial infection is complex, as immune cells must efficiently neutralize and contain the infection while preventing harmful pathology. A recent Immunity paper by Li et al. illuminates the critical role of a resident macrophage subset in preventing invasive and life-threatening disease.