Simple animal models are emerging as valuable tools for microbiome research. In this Review, Douglas discusses the opportunity for microbiome research on the traditional biomedical models Drosophila melanogaster, Caenorhabditis elegans and zebrafish. Other systems, for example, hydra, squid and the honeybee, are valuable alternative models to address specific questions.
One of the most revolutionary advances in the biological sciences in recent years has been the realization that microbial communities occupy virtually every environment and have central roles in human health and disease, as well as in the biogeochemical processes that sustain life on our planet. Moving beyond cataloguing the species and genes that are present in these diverse environments, the microbiome field is now focusing on defining the mechanisms underpinning the interactions between microorganisms and their environment. One of the main goals is to elucidate how the composition and functions of the human microbiota influence the initiation and progression of important human diseases, such as diabetes and cancer, with a view towards improving their diagnosis and treatment. Progress in the field has been driven by multi'omic technologies, combined with new computational tools and models to interpret the vast complexity of this fascinating research area.
In this series of articles, Nature Reviews Microbiology explores the latest developments in the study of environmental and host-associated microbiomes, highlighting the tools and methods that are propelling the field forward, the novel mechanistic insights into the composition and functions of these microbial communities, and the complex interplay between the microbiota and its surroundings.
Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). In this Review, Xavier and colleagues highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.
Hydrothermal vents are unique habitats for chemosynthetic bacteria and archaea and the animals that live in symbiosis with them. In this Review, Dick explores the challenges and opportunities that vent ecosystems provide for microbial life and their relationship to biogeography.
Fungi are enormously diverse, not the least in potential genetic markers that can be used for high-throughput sequencing studies of the mycobiome. In this Review, Nilsson and colleagues provide advice for leveraging next-generation technologies to explore mycobiome diversity in different habitats.
The dynamic and polymicrobial oral microbiota is a direct precursor of diseases such as dental caries and periodontitis. In this Review, Lamont, Koo and Hajishengallis discuss the mechanisms by which oral microbial communities develop and become functionally specialized. They also examine the progression of polymicrobial communities towards pathogenicity.
In this Review, Gilbert and Stephens outline the history of the field of microbiology of the built environment and discuss insights into microbial ecology, adaptation and evolution. They consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.
The microbiota can influence host behaviour through the gut–brain axis. In this Opinion, Johnson and Foster explore the evolution of this relationship and propose that adaptations of competing gut microorganisms may affect behaviour as a by‑product, leading to host dependence.
Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut. In this Review, Raoult and colleagues discuss the development of culturomics and how it has extended our understanding of bacterial diversity, and highlight the potential implications for human health.
The first line of host defence against both encroaching commensal bacteria and invading enteric pathogens is the intestinal mucosal barrier, which is composed of epithelial cells and a host-secreted mucous layer. In this Review, Martens and colleagues discuss the complex interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier.
Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.
In this Opinion article, Banerjee et al. explore the importance of microbial keystone taxa and keystone guilds in microbiome structure and functioning, describe challenges in the characterization and manipulation of such taxa, and propose a definition of keystone taxa in microbial ecology.
Interactions among organisms are not limited to the exchange of electron donors. Most microorganisms are auxotrophs and thus rely on external nutrients for growth. In this Opinion article, Zengler and Zaramela postulate that auxotrophies and nutrient requirements among members of complex communities have profound implications for microbial interactions and thus the overall microbial network.
Our skin is home to millions of bacteria, fungi and viruses that comprise the skin microbiota. In this Review, Byrd and colleagues discuss recent insights into skin microbial communities, including their composition in health and disease, dynamics between species and interactions with the immune system.
In this Opinion article, Byndloss and Bäumler propose that host control over the microbial ecosystem in the large bowel is critical for the composition and function of its resident microbial organ, while disruption of host control triggers microbial organ dysfunction. This concept provides a theoretical framework for linking the gut microbiota to non-communicable diseases.
The interplay between nutrient intake, gut microbial metabolism and microorganism-driven engagement of host receptors contributes to the pathogenesis of cardiovascular disease. In this Review, Brown and Hazen discuss the gut microbial mechanisms that drive cardiovascular disease, with special emphasis on therapeutic interventions.
Soil contains a vast diversity of microorganisms that can directly or indirectly modulate soil processes and terrestrial ecosystems. In this Review, Fierer summarizes the challenges in characterizing the composition and functions of the soil microbiome, and discusses key future research directions.
The resilience of the microbiota can protect us from disease, but a resilient dysbiotic microbiota may also cause disease. This Opinion article discusses the concepts and mechanisms of microbial resilience against dietary, antibiotic or bacteriotherapy-induced perturbations and the implications these have for human health.
The transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. In this Review, Browne and colleagues discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota.
The microbiota influences the development of cancer and the effect of cancer therapies. In this Review, the authors summarize the interactions between the microbiota, the immune system and tumours and how manipulation of the microbiota can be used therapeutically.
The human gut is host to a dense microbial community that includes a large bacteriophage population. This Review summarizes bacteria and phage dynamics in health and disease, and considers how phages may be harnessed as novel therapeutics to improve disease outcomes.
The respiratory tract spans from the nostrils to the lung alveoli and these distinct niches host a diverse microbiota. In this Review, Man, de Steenhuijsen Piters and Bogaert discuss the role of the respiratory microbiota in the maintenance of human health.
The microbiota is central for host homeostasis and affects not only the gut but also other organs, including the lungs. In this Opinion article, Hansbro and colleagues explore the role of the microbiota in the gut–lung axis and lung disease.
Metagenome-wide association studies (MWAS) are designed to detect associations between the human microbiome and disease. In this Review, Jia and Wang describe the principal findings of MWAS of human diseases, and consider how these findings might be integrated into medical research and practice.
Molecular-based studies of fungal biodiversity have revealed fundamental differences from the biodiversity of bacteria, plants and animals. In this Review, Peay and colleagues consider the roles of ecology and fungal biology in determining fungal biodiversity at different spatial scales.
The gut of honey bees is inhabited by a small group of highly host-adapted bacteria. In this Review, Kwong and Moran detail the composition and functions of the microbiota of honey bees and highlight similarities and differences to the human microbiota.
In this Review, Turnbaugh and colleagues discuss several mechanisms by which the human gut microbiome affects the metabolism of xenobiotics, including drugs and dietary compounds, and explore how this knowledge can be applied to improve the treatment of human disease.
In this Progress article, Stephanie Karst describes how the gut microbiota promotes intestinal infection by enteric viruses. She discusses direct mechanisms by which bacteria stabilize viral particles and facilitate viral attachment to host cells, and indirect mechanisms by which the microbiota suppresses antiviral immune responses.
The gut microbiota has a strong impact on host physiology. In this Review, Mazmanian and colleagues describe the mechanisms that control the biogeography of bacteria in the gut and discuss the importance of the spatial localization of the gut microbiota during health and disease.
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology
In this Opinion article, James Prosser considers the conceptual limitations of metagenomics and metatranscriptomics in contributing to our understanding of soil microbial ecology, and also explores potential opportunities for using these techniques to address specific ecological questions.
In this Review, Huttenhower and colleagues discuss how integrating multi-omic data types — including genomics, transcriptomics, proteomics and metabolomics — enables a better characterization of the composition and function of human-associated and environmental microbial communities.