Reported gut microbiome associations with diet and disease are frequently inconsistent between studies and interventions. Ruple et al. show that a high-fiber diet and time-restricted feeding induce si...

Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of or...

Background Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbio...

The upper gastrointestinal (uGI) microbiota has been implicated in infectious, metabolic, and immunological conditions, yet remains poorly characterized due to invasive sampling and low microbial b...

In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...

In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...

The gut microbiota plays a critical role in human health, yet its taxonomic complexity, interpersonal variability, and resistance to change in adulthood present challenges for understanding the factors driving shifts in its composition and function. Here,…

Background The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcome...

As many inflammatory and metabolic disorders have been associated with structural deficits of the human gut microbiota, the principles and mechanisms …

The etiology of inflammatory bowel disease (IBD) remains unclear, treatment options unsatisfactory and disease development difficult to predict for individual patients. Dysbiosis of the gastrointes...

Is it possible to restore the human gut microbiome in industrialized settings and reintroduce microbial species that have been lost? In healthy adults, Li et al. found that consuming a diet mimicking ...

Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host me...

The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative a…