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Here, the authors use detailed temporal nutrition intake data captured through real-time food logging via a smartphone app and gut microbiota profiles from ~1,000 participants of a digital cohort on personalized nutrition to associate dietary regularity and quality with gut microbiome diversity.

Nine experts discuss the challenges in translating current research on the human microbiome into strategies for disease prediction, diagnosis and therapy.

Here, Blaser, Bork, Fraser, Knight and Wang highlight the most exciting findings in the field of microbiome research and discuss what will be necessary to obtain a better understanding of the role of the microbiota in human health and disease, and to develop microbiota-based therapies.

Here, in a representative cohort of 7,095 Finnish adults, the authors reveal that gut antibiotic resistance is shaped not only by antibiotic use but also by the microbiome, diet, lifestyle, household income—and is linked to higher long-term mortality.

Here, the authors apply novel pangenome indexes created from diverse human references to facilitate computationally efficient removal of host genetic information, preserving biological accuracy and protecting patient privacy in metagenomic sequencing analyses.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Here, the authors investigate associations of vitamin D metabolites with gut microbiome in a cross-sectional analysis of 567 elderly men enrolled in the Osteoporotic Fractures in Men (MrOS) Study and find larger alpha-diversity correlates with high 1,25(OH)2D and high 24,25(OH)2D and higher ratios of activation and catabolism.

Demand for steady output stymies discovery. To pursue the most important research, scientists must be allowed to shift their focus, say Tolu Oni and colleagues.

Using an international collection of population-based microbiome studies of participants in the MicroCardio Consortium, a cross-cohort meta-analysis identified several phylogenetically diverse, species- and strain-level microbial features as well as community-level functional shifts encompassing diverse pathways to type 2 diabetes.

Soils from 30 grasslands across Europe were subjected to 4 contrasting extreme climatic events under drought, flood, freezing and heat conditions, with the results suggesting that soil microbiomes from different climates share unified responses to extreme climatic events.

Novel technologies including AI are becoming widely available and transforming healthcare and precision medicine. In this Perspective, the authors discuss how some of these technologies and innovations can help advance maternal and child health by complementing existing methods and enabling nutritional assessment on a larger scale and at an affordable cost in low-resource settings.

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Neuroinflammation is observed in Alzheimer’s disease. Here the authors show that 15 proteins related to inflammation found in CSF can potentially be used as a prognostic biomarker.

Studies of the composition, dynamics and function of the human microbiome have taken off in the past two years thanks to the development of new sequencing technologies and advanced algorithms. This article provides a guide to the experimental and analytical best practices in this flourishing field.

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

Stig Bojesen, Georgia Chenevix-Trench, Alison Dunning and colleagues report common variants at the TERT-CLPTM1L locus associated with mean telomere length measured in whole blood. They also identify associations at this locus to breast or ovarian cancer susceptibility and report functional studies in breast and ovarian cancer tissue and cell lines.

To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.

Effective interventions may come before all the research is in

Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.

The authors build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on 381 markers. The results indicate a remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that used fewer “core” genes, such as the ribosomal proteins.

In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.

Most microbiome studies make conclusions based on changes in relative abundance of taxa, inferred from sequencing data. Here, the authors highlight common pitfalls in comparing relative abundance across samples, and identify solutions that reveal microbial changes without the need to estimate total microbial load.

A new, publicly available, collection of cultured bacterial species from the mouse gut, the Mouse Intestinal Bacterial Collection, opens up opportunities for deepening microbiome research. Cultured isolates allow the functions of specific species and controlled consortia to be determined through in vitro experimentation.

Douglas Easton, Per Hall and colleagues report meta-analyses of genome-wide association studies for breast cancer, including 10,052 cases and 12,575 controls, followed by genotyping using the iCOGS array in an additional 52,675 cases and 49,436 controls from studies within the Breast Cancer Association Consortium (BCAC). They identify 41 loci newly associated with susceptibility to breast cancer.

Available evidence supports the existence of functional connections between resident microorganisms and the kidney that are altered in the context of specific kidney diseases. This Roadmap article describes current understanding of the mechanisms by which microorganisms regulate host organ function, highlighting key knowledge gaps that remain to be addressed and opportunities for future research.

Gamification of the multiple sequence alignment problem improves microbial phylogeny estimates.

The microbial community in the intestine can affect other organs such as the skin but it is not clear if the opposite can occur. Here the authors show that skin wounding affects the microbial composition of the intestinal flora which then enhances DSS induced colitis and intestinal inflammation.

Gut microbiome composition is associated with phenotypes as revealed by a dimensionality reduction tool.

Methods for error correction and classification of metagenomic datasets suggest that the rare biosphere is not as large as previously assumed.

A new study explores the ancient oral microbiome from the well-preserved dental calculus samples of four human individuals who lived during medieval times, using a suite of genomic, proteomic and microscopic approaches. The authors investigate the evolution of dental pathogens by reconstructing the genome of the periodontal pathogen Tannerella forsythia and also identify antibiotic resistance genes, bacterial virulence factors and host immune defense proteins.