Microbiome

In this study, Ratiner et al. examine the advantages, challenges and future perspectives of utilizing microbiome data in personalized medicine for optimal patient care.

In this Review, Motta and Moran explore recent research investigating the role of the gut microbiota in honeybee biology and health, as well as the environmental factors that can impair the microbiota and the potential strategies to restore a perturbed microbiota in honeybees.

In this Review, Segata, Waldron and colleagues discuss important key concepts of machine learning that are relevant to microbiologists and provide them with a set of tools essential to apply machine learning in microbiology research.

In this Review, McCallum and Tropini discuss physical and biological factors that affect microbiota biogeography and organization at different scales, starting with an overview of the whole gut at the macroscale and then zooming in to the scale of host and microbial interactions.

In this Review, He and co-workers explore the structure and diversity of the oral microbiota, and they discuss the role of the oral microbiota in the pathology of both oral and systemic diseases.

In this Review, Fishbein, Mahmud and Dantas discuss factors that influence restructuring of the gut microbiome on antibiotic exposure, and they explore promising therapeutic avenues aimed at minimizing antibiotic-induced damage to the microbiome or restoring the community structure post-treatment.

In this Review, de Nies, Kobras and Stracy examine the detrimental effects of antibiotics on the microbiota and the resulting associated infections. They delve into the interplay between antibiotic therapy, loss of colonization resistance, overgrowth of resistant bacteria and subsequent infections. They also discuss strategies to mitigate these risks and reduce antibiotic-associated infections.

In this Review, Hsu and Schnabl examine the role of the gut microbiota in liver and intestine function, and how gut microorganisms contribute to liver diseases, and explore different microbiota-based strategies for the treatment of liver disease.

In this Review, Carmody and Bisanz examine the role of the gut microbiome in energy metabolism, the two-way relationship between the gut microbiome and weight management strategies and opportunities and challenges in the development of microbiome-directed therapies targeting energy balance.

Over the course of the lifespan of a host, the gut microbiota undergoes evolutionary changes and is shaped by ecological interactions with the host and other microbial species. In this Review, Barreto and Gordo explore mechanisms of evolution of the gut microbiota, intrahost evolution of strains and communities and implications of intrahost evolution for disease and microbiota-based therapies.

In this Review, Baldrian et al. discuss the effects of global change on the forest ecosystem and its microbiome across boreal, temperate and tropical climatic zones, and present different strategies aimed at reducing global change impact on forests.

In this Review, Caballero-Flores, Pickard and Núñez explore how the microbiota limits colonization by pathogens and the strategies used by pathogens to counter colonization resistance.

Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. In this Review, Jansson and Wu explore our current understanding of soil viral diversity and ecology, and how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses.

Like the gut, the lung harbours a diverse, interacting assortment of microbiota. In this review, Natalini, Singh and Segal examine the role of the lung microbiome in health and disease and discuss future work that is needed to produce novel diagnostic and therapeutic tools aimed at improving lung health.

The gut microbiota metabolizes bile acids, thereby influencing human health and diseases including obesity, colitis and cancer. In this Review, Patterson and colleagues discuss host–microbiota interactions and their influence on the bile acid pool as well as therapeutic implications.

One health links human, animal and environmental health, and microorganisms have a central role in this connection. In this Review, Banerjee and van der Heijden outline the central role of the soil microbiome for one health and its detrimental or beneficial effects.

The human microbiota can undergo dramatic changes during different phases of life (for example, during colonization after birth, after disturbances or in old age). In this Review, Knight and colleagues discuss the microbiota successions that occur from the cradle to the grave.

The human gut microbiota produces an extensive array of carbohydrate-active enzymes to degrade carbohydrates derived from the diet, host and other microorganisms. Withers and colleagues discuss the vast diversity and activities of these enzymes and their potential applications.

Soil microorganisms shape global element cycles in life and death. In this Review, Sokol and colleagues explore how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. They also discuss incorporating microbial life and death into trait-based models that predict soil biogeochemical dynamics.

We take up a multitude of foreign substances, so called xenobiotics, such as medications, food additives and pollutants, which affect the composition and function of the gut microbiota. In this Review, Lindell, Zimmermann-Kogadeeva and Patil discuss these reciprocal interactions and their mechanisms.

Microbiome-based therapeutics hold great promise for reducing disease susceptibility and enhancing disease resistance. In this Review, Sorbara and Pamer explore the major bacterial phyla associated with health benefits and the potential of microbiome-based therapeutics, including faecal microbiota transplantation, bacterial consortia, engineered symbiotic bacteria, diet and prebiotics, and microbiome-derived proteins and metabolites. They also discuss the challenges confronting therapeutic development as well as the regulatory hurdles for clinical trials and manufacturing.

Microbial life can thrive in extreme environments such as terrestrial hot springs and deep sea hydrothermal vents, glaciers and permafrost, hypersaline habitats, acid mine drainage and the subsurface. In this Review, Shu and Huang explore the diversity, functions and evolution of bacteria and archaea inhabiting Earth’s major extreme environments.

Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota and to understand the functional role of these microbial metabolites. In this Review, Dorrestein and colleagues review common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis.

The order and timing of the arrival (priority effects) of members of a microbiome can influence microbiome composition and function. In this Review, Debray and colleagues provide an overview of the mechanisms of priority effects, highlight examples in host-associated and environmental communities, and discuss methods to detect priority effects in microbial communities.

Small antibacterial molecules termed bacteriocins can influence microbiome composition by providing an advantage to bacteriocin producers over bacteriocin-sensitive strains. In this Review, Peschel and colleagues provide an overview of the types of bacteriocins, their costs and benefits, and how they may provide new avenues for antibacterial drug development.

In this Review, Mallott and Amato summarize the prevalence of phylosymbiosis across the animal kingdom and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. They find that phylosymbiosis is less prevalent in taxonomically richer microbiomes across the animal kingdom, except in mammals, perhaps owing to a unique combination of mammalian traits that influence the microbiota.

In this Review, Mizrahi and colleagues describe the composition, ecology and metabolism of the rumen microbiome, and the impact on host physiology and the environment. They also discuss the most pertinent methane mitigation strategies that emerged to balance food security and environmental impact.

In this Review, Brito discusses methods that are available to study how horizontal gene transfer shapes the function of natural microbial communities and explores questions to which some of these tools can be applied.

The human body hosts vast numbers of different viruses, collectively termed the virome. In this Review, Liang and Bushman provide an overview of research on the human virome and highlight recent studies that explore the assembly and composition of the human virome as well as host–virome interactions in health and disease.

In this Review, Morais, Schreiber and Mazmanian discuss emerging and exciting evidence of intricate and potentially important connections between the gut microbiota and the brain involving multiple biological systems, and possible contributions by the gut microbiota to complex behaviours.

Viruses are extremely diverse and not all of this diversity has been captured so far. In this Review, Martínez Martínez, Martinez-Hernandez and Martinez-Garcia explore the potential and limitations of single-virus genomics and how this emerging technology can complement other methods.

In this Review, Fan and Pedersen discuss how the gut microbiota and derived microbial compounds may contribute to human metabolic health and to the pathogenesis of common metabolic diseases, and highlight examples of microbiota-targeted interventions aiming to optimize metabolic health.

The gut microbiota contributes to host physiology through the production of a myriad of metabolites. In this Review, Bäckhed and colleagues discuss the major classes of microbial metabolites, highlight examples of how microbial metabolites affect host health and provide a potential framework for integration of discovery-based metabolite studies with mechanistic work.

In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.

Large-scale metagenomic analyses are vastly increasing the rate of discovery of variation within species but they are also leading to scientific and semantic challenges. Bork and colleagues highlight the advances and challenges that are resulting from the use of metagenomic data to study within-species diversity.

In this Review, Ruff, Greiling and Kriegel discuss the mechanisms through which the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases, and explore the therapeutic avenues that either target the microbiota, the barrier surfaces or the host immune system to restore tolerance and homeostasis.

The schooner Tara sailed 140,000 km across the global oceans to sample diverse marine ecosystems and plankton communities. In the Review, members of the Tara Oceans project highlight how resulting data can be used for an integrated understanding of ocean biology.

In this Review, Hatzenpichler et al. introduce next-generation physiology, which is a suite of new techniques that enable investigation into the phenotypes of individual cells in a non-destructive manner. Next-generation physiology complements genomics and culturing and provides new insights into microbiome function.

In this Review, Jansson and Hofmockel explore the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems and the potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.

Going from description of the diversity and disease associations of the human gut microbiota towards functional understanding and applications is challenging. In this Review, Raes and colleagues present synthetic ecology approaches that reduce the complexity and advance translation of human gut microbiota research.

Microbiome engineering has many potential applications, ranging from agriculture to medicine. In this Review, Lawson, McMahon and colleagues guide us through the design–build–test–learn cycle that has been successful in many disciplines and explain how it applies to microbiome engineering.

In this Review, Kolodziejczyk, Zheng and Elinav describe the latest advances in understanding diet–microbiota interactions, the individuality of gut microbiota composition and how this knowledge could be harnessed for personalized nutrition strategies to improve human health.

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.

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.

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.