Featured
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Technology Feature |
The search for microbial dark matter
Researchers are developing technologies to find and grow microbes that biologists have struggled to culture in the lab.
- Amber Dance
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Technology Feature |
Microbial matters: modelling the complex web of host–microbiome interactions
Computational approaches help to map the extensive biochemical chatter between bacteria and their human hosts.
- Michael Eisenstein
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Article |
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis
A cross-sectional analysis of participants in the MetaCardis Body Mass Index Spectrum cohort finds that the higher prevalence of gut microbiota dysbiosis in individuals with obesity is not observed in those who take statin drugs.
- Sara Vieira-Silva
- , Gwen Falony
- & Jeroen Raes
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Article |
Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells
The secondary bile acid 3β-hydroxy-deoxycholic (isodeoxycholic) acid, produced by gut bacteria, promotes the generation of colonic extrathymic regulatory T cells, whose immunosuppressive activities are known to be essential for intestinal health.
- Clarissa Campbell
- , Peter T. McKenney
- & Alexander Y. Rudensky
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Article |
The stepwise assembly of the neonatal virome is modulated by breastfeeding
The infant gut is colonized first by temperate bacteriophages induced from pioneer bacteria and later by viruses that replicate in human cells, the populations of which are modulated by breastfeeding.
- Guanxiang Liang
- , Chunyu Zhao
- & Frederic D. Bushman
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Article |
A plant genetic network for preventing dysbiosis in the phyllosphere
Mutations in genes involved in immune signalling and vesicle trafficking cause defects in the leaf microbiome of Arabidopsis thaliana that result in damage to leaf tissues, suggesting mechanisms by which terrestrial plants control the level and diversity of endophytic phyllosphere microbiota.
- Tao Chen
- , Kinya Nomura
- & Sheng Yang He
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Article |
Recycling and metabolic flexibility dictate life in the lower oceanic crust
Analyses of microbial communities that live 10–750 m below the seafloor at Atlantis Bank, Indian Ocean, provide insights into how these microorganisms survive by coupling energy sources to organic and inorganic carbon resources.
- Jiangtao Li
- , Paraskevi Mara
- & Virginia P. Edgcomb
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Article |
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.
- Gregory D. Poore
- , Evguenia Kopylova
- & Rob Knight
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Article |
Global chemical effects of the microbiome include new bile-acid conjugations
Metabolomics data from germ-free and specific-pathogen-free mice reveal effects of the microbiome on host chemistry, identifying conjugations of bile acids that are also enriched in patients with inflammatory bowel disease or cystic fibrosis.
- Robert A. Quinn
- , Alexey V. Melnik
- & Pieter C. Dorrestein
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Research Highlight |
How gut bacteria make broccoli a superfood
Scientists reveal the pathway used by one gut microbe to transform vegetable components into anti-cancer compounds.
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Article
| Open AccessClades of huge phages from across Earth’s ecosystems
Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.
- Basem Al-Shayeb
- , Rohan Sachdeva
- & Jillian F. Banfield
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Outlook |
The gut microbiome
Microorganisms live in the human digestive system and affect our health — scientists are trying to work out how.
- Herb Brody
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Outlook |
Therapeutic microbes to tackle disease
Modified bacteria and carefully formulated microbial communities could form the basis of new living treatments.
- Claire Ainsworth
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Outlook |
Could a bacteria-stuffed pill cure autoimmune diseases?
Researchers are investigating how the community of microbes living in the gut might help people with multiple sclerosis, lupus and type 1 diabetes.
- Eric Bender
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Outlook |
Homing in on the molecules from microbes
Bioengineer Michael Fischbach wants to find out everything he can about the short-chain fatty acids produced by microbes.
- Andrew Scott
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Outlook |
Diet should be a tool for researchers, not a treatment
Peter J. Turnbaugh explains why scientists can’t tell you what to eat to prevent disease.
- Peter J. Turnbaugh
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Outlook |
The hunt for a healthy microbiome
Despite evidence of the gut microbiome’s role in human health, researchers are still working out what shapes the community of microbes.
- Michael Eisenstein
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Outlook |
Could the gut microbiome be linked to autism?
Researchers are hoping to understand whether the microbes in our guts have a role in the disorder.
- Elizabeth Svoboda
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Outlook |
The complex relationship between drugs and the microbiome
Scientists know that the microbiome has an effect on pharmaceuticals, and vice versa, but they are still trying to work out the various mechanisms involved.
- Neil Savage
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Outlook |
Rich data sets could end costly drug discovery
Eran Segal explains why deep phenotyping of study volunteers could transform therapy development.
- Eran Segal
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Outlook |
Highlights from studies on the gut microbiome
Researchers strive to understand how microbes affect health and disease.
- Liam Drew
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Outlook |
Fighting cancer with microbes
Targeting the microbiome could hold the key to combating a range of malignant diseases.
- Elie Dolgin
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Technology Feature |
Technologies to watch in 2020
Thought leaders predict the tech developments that could have a big impact in the coming year.
- Esther Landhuis
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Article |
Microbiota-targeted maternal antibodies protect neonates from enteric infection
Neonatal mice are protected against infection with the enteric pathogen enterotoxigenic Escherichia coli by maternally derived natural antibodies as well as by maternal commensal microbiota that induce antibodies that recognize antigens expressed by Enterobacteriaceae.
- Wen Zheng
- , Wenjing Zhao
- & Dennis L. Kasper
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Article |
Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis
Both dietary and microbial factors influence the composition of the gut bile acid pool, which in turn modulates the frequencies and functionalities of RORγ-expressing colonic FOXP3+ regulatory T cells, contributing to protection from inflammatory colitis.
- Xinyang Song
- , Ximei Sun
- & Dennis L. Kasper
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Research Highlight |
The meal plan that hinders the gut’s recovery from antibiotics
Experiments in mice show that a regimen of low-fibre foods keeps the gut microbiome from bouncing back.
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Article |
Human gut bacteria contain acquired interbacterial defence systems
An interbacterial defence strategy, involving clusters of immunity genes against toxins released by the type VI secretion system of the same or different species, is widespread among Bacteroides species, and transfer of these gene clusters confers resistance to toxins in vitro and in the mammalian gut.
- Benjamin D. Ross
- , Adrian J. Verster
- & Joseph D. Mougous
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News & Views |
Fungi accelerate pancreatic cancer
The impact of fungi on human health is under-studied and underappreciated. One genus of fungus, Malassezia, has now been linked to the progression of pancreatic cancer.
- Ivy M. Dambuza
- & Gordon D. Brown
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Technology Feature |
Microbial chemistry gains fresh focus
The tools of chemical biology, genomics and data mining can yield insights into the metabolites of the microbiome.
- Esther Landhuis
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News |
C-section babies are missing key microbes
UK study provides the best evidence yet that the way infants are born can alter their microbiomes — but the health effects are unclear.
- Ewen Callaway
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Letter |
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Delivery via caesarean section, maternal antibiotic prophylaxis and colonization by opportunistic pathogens associated with the hospital environment affect the composition of the gut microbiota of children from birth until infancy.
- Yan Shao
- , Samuel C. Forster
- & Trevor D. Lawley
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Research Highlight |
How to spot a hardy opportunistic infection
Gut-dwelling bacteria produce molecules that could reveal who is prone to a life-threatening consequence of antibiotic treatment.
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Letter |
Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus
The gut commensal Blautia producta secretes a lantibiotic that reduces colonization of the gut by the major pathogen vancomycin-resistant Enterococcus faecium, and transplantation of microbiota with high abundance of the lantibiotic gene enhances resistance to colonization in mice.
- Sohn G. Kim
- , Simone Becattini
- & Eric G. Pamer
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News |
Do C-section babies need mum’s microbes? Trials tackle controversial idea
Swabbing infants with mothers’ vaginal bacteria could affect the children’s health, but critics warn of sparse data and high risk.
- Sara Reardon
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News & Views |
No bacteria found in healthy placentas
Analysis of hundreds of placentas provides convincing evidence that this organ does not harbour microorganisms that can enter the fetal gut — a key finding for research into how the human microbiota is established.
- Nicola Segata
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Nature Podcast |
Podcast: The placental microbiome, and advances in artificial intelligence
Tune into the latest from the world of science, with Nick Howe and Noah Baker.
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Article |
Human placenta has no microbiome but can contain potential pathogens
The human placenta does not have a microbiota, suggesting that bacterial infection of the placenta is not a common cause of adverse pregnancy outcome, but group B Streptococcus is found in approximately 5% of placental samples.
- Marcus C. de Goffau
- , Susanne Lager
- & Gordon C. S. Smith
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Research Highlight |
Gut bacteria foil a potent treatment for a devastating disease
Bacteria reduce the effectiveness of a remedy for Parkinson’s disease — and might amplify the drug’s side effects.
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Research Highlight |
Gut microbes react to a meal — but have no use for nutrition labels
Changes in microbial populations are more closely associated with food type than the nutrient profile listed on the packet.
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Article |
Mapping human microbiome drug metabolism by gut bacteria and their genes
High-throughput genetic analyses combined with mass spectrometry reveal that the gene products of diverse human gut bacteria affect a wide range of oral drugs, as well as drug metabolism in mice.
- Michael Zimmermann
- , Maria Zimmermann-Kogadeeva
- & Andrew L. Goodman
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Editorial |
After the Integrative Human Microbiome Project, what’s next for the microbiome community?
The latest phase of this ambitious undertaking has provided important insights into inflammatory bowel disease, the onset of type 2 diabetes and preterm birth. But fully integrated multidisciplinary collaborations are now needed to convert knowledge of the microbiome into clinical applications.
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Comment |
Priorities for the next 10 years of human microbiome research
The dream of microbiome-based medicine requires a fresh approach — an ecological and evolutionary understanding of host-microbe interactions — argues Lita Proctor.
- Lita Proctor
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News & Views |
Tracking humans and microbes
The Human Microbiome Project put the health-associated microbes found in humans on centre stage. The project’s second phase shows how microbial disturbance in disease is linked to host processes.
- Verónica Lloréns-Rico
- & Jeroen Raes
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Perspective
| Open AccessThe Integrative Human Microbiome Project
Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.
- Lita M. Proctor
- , Heather H. Creasy
- & Curtis Huttenhower
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Article
| Open AccessMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases
The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.
- Jason Lloyd-Price
- , Cesar Arze
- & Curtis Huttenhower
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Letter |
A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes
A newly identified lineage of apicomplexans, named corallicolids, are intracellular symbionts of many coral species, and possesses a plastid that retains genes for chlorophyll biosynthesis despite lacking photosystem genes.
- Waldan K. Kwong
- , Javier del Campo
- & Patrick J. Keeling
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News |
Virus tricks the immune system into ignoring bacterial infections
The finding could explain why the body tolerates some microbes ― and lead to better treatments for chronic infections.
- Sara Reardon
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Article |
Structural variation in the gut microbiome associates with host health
The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.
- David Zeevi
- , Tal Korem
- & Eran Segal
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Research Highlight |
Baby’s mouth might hold sway over breast-milk microbiome
The bacterial content of breast milk differs between mothers who pump and those who nurse.