Featured
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Article
| Open Access
Streptomyces umbrella toxin particles block hyphal growth of competing species
Streptomyces are discovered to produce antibacterial protein complexes that selectively inhibit the hyphal growth of related species, a function distinct from that of the small-molecule antibiotics they are known for.
- Qinqin Zhao
- , Savannah Bertolli
- & Joseph D. Mougous
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News |
Gut bacteria break down cholesterol — hinting at probiotic treatments
Species in the human microbiome have enzymes that can metabolize a potentially dangerous lipid.
- Julian Nowogrodzki
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Article |
A host–microbiota interactome reveals extensive transkingdom connectivity
A new technology for proteome-scale assessment of human exoproteome–microbiome interactions exposes an extensive network of transkingdom connectivity.
- Nicole D. Sonnert
- , Connor E. Rosen
- & Noah W. Palm
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Outlook |
Could the gut give rise to alcohol addiction?
Microorganisms in the gut might make a person more vulnerable to substance-use disorders.
- Tammy Worth
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Article |
Bile salt hydrolase acyltransferase activity expands bile acid diversity
Acyltransferase activity of the enzyme bile salt hydrolase is identified and shown to mediate microbial bile acid conjugation, diversifying the bile acid pool and expanding their role in gut physiology.
- Douglas V. Guzior
- , Maxwell Okros
- & Robert A. Quinn
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Article
| Open Access
Bile salt hydrolase catalyses formation of amine-conjugated bile acids
We find that bile salt hydrolase N-acyltransferase activity can form bacterial bile acid amidates that are positively correlated with the colonization of gut bacteria that assist in the regulation of the bile acid metabolic network.
- Bipin Rimal
- , Stephanie L. Collins
- & Andrew D. Patterson
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Research Briefing |
Synthesizing and identifying potential biomarkers to explore uncharted biochemistry
Public repositories of metabolomics data are expanding rapidly and can be leveraged to uncover previously undescribed metabolites. Reverse metabolomics is a workflow in which thousands of small compounds are synthesized using combinatorial chemistry, and their molecular ‘fingerprints’ are then used to discover where they are localized in tissues and biological fluids and how they are associated with health and disease in humans.
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News & Views Forum |
The journey to understand previously unknown microbial genes
The analysis of DNA sequences sheds light on microbial biology, but it is difficult to assess the function of genes that have little or no similarity to characterized genes. Here, scientists discuss this challenge from genomic and microbial perspectives.
- Jakob Wirbel
- , Ami S. Bhatt
- & Alexander J. Probst
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News |
‘Wildly weird’ RNA bits discovered infesting the microbes in our guts
Rod-shaped structures named ‘obelisks’ are even smaller than viruses but can still transmit instructions to cells.
- Saima Sidik
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News |
How does chronic stress harm the gut? New clues emerge
A bacterium in the intestines of stressed mice interferes with cells that protect against pathogens.
- Max Kozlov
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Comment |
Boosting microbiome science worldwide could save millions of children’s lives
Studies of the microbes living on and in our bodies are conducted mainly in a few rich countries, squandering opportunities to improve the health of people globally.
- Hilary P. Browne
- , Najeeha Talat Iqbal
- & Samuel Kariuki
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Article
| Open Access
Bioactive glycans in a microbiome-directed food for children with malnutrition
Two Prevotella copri metagenome-assembled genomes that are positively associated with ponderal growth are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2—a microbiome-directed complementary food.
- Matthew C. Hibberd
- , Daniel M. Webber
- & Jeffrey I. Gordon
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News |
This group of bizarre gut microbes is unexpectedly complex
Protists’ food preferences shape their interactions with bacteria and affect host immunity.
- McKenzie Prillaman
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Article
| Open Access
Reverse metabolomics for the discovery of chemical structures from humans
A new discovery strategy, ‘reverse metabolomics’, facilitates high-throughput matching of mass spectrometry spectra in public untargeted metabolomics datasets, and a proof-of-concept experiment identified an association between microbial bile amidates and inflammatory bowel disease.
- Emily C. Gentry
- , Stephanie L. Collins
- & Pieter C. Dorrestein
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News |
Inflammation in severe COVID linked to bad fungal microbiome
An overabundant ‘mycobiota’ in the gut might be involved in triggering harmful immune responses.
- McKenzie Prillaman
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Research Highlight |
Placenta forms with aid of mother’s microbiome
The organ that nourishes the developing embryo does not develop properly in mice that lack the usual gut microbes.
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News |
COVID lockdowns altered babies’ microbiomes
Isolation can have lasting effects on the composition of microbes in the gut, but links to other health conditions are still poorly understood.
- Lilly Tozer
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Article
| Open Access
Gut microbial carbohydrate metabolism contributes to insulin resistance
Faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines.
- Tadashi Takeuchi
- , Tetsuya Kubota
- & Hiroshi Ohno
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Article
| Open Access
Persistent equatorial Pacific iron limitation under ENSO forcing
An assessment of variations in phytoplankton nutrient limitation in the tropical Pacific over the past two decades finds that phytoplankton iron limitation is more stable in response to ENSO dynamics than models predict.
- Thomas J. Browning
- , Mak A. Saito
- & Alessandro Tagliabue
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Matters Arising |
Revisiting the intrinsic mycobiome in pancreatic cancer
- Ashley A. Fletcher
- , Matthew S. Kelly
- & Peter J. Allen
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Technology Feature |
Foldseek gives AlphaFold protein database a rapid search tool
The structural search program makes finding proteins with similar 3D shapes easy.
- Matthew Hutson
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Article |
Gut microbial fatty acid isomerization modulates intraepithelial T cells
A diet–microorganism pathway involving conjugated linoleic acid, interleukin-18, intraepithelial lymphocytes and the transcription factor hepatocyte nuclear factor 4γ modulates the host mucosal immune system.
- Xinyang Song
- , Haohao Zhang
- & Dennis L. Kasper
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News |
Hunter-gatherer lifestyle fosters thriving gut microbiome
Samples from the Tanzanian Hadza group included species previously unknown to science.
- Gemma Conroy
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Career Q&A |
How I mixed microbiome research with public-health advocacy
Evolutionary geneticist Aashish Jha studies the gut microbiome of infants while advocating for better hygiene and health care in their marginalized communities.
- Saugat Bolakhe
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News |
Mum’s microbes might boost brain development of c-section babies
Vaginal seeding is safe and seems to benefit infants delivered by the surgery — but larger trials are needed.
- Ewen Callaway
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Spotlight |
Mapping the Chinese microbiome: it’s time for a united effort
Much has been done to investigate the human microbiome. Now, it’s time for countries to dig deeper.
- Ju-Sheng Zheng
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News |
Could endometriosis be caused by bacteria? Study offers fresh clues
Link to bacterial infection suggests a potential way to treat the painful disorder.
- Heidi Ledford
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Article
| Open Access
Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma
Tumour-infiltrating lymphocytes from glioblastoma can recognize bacterial and gut microbial peptides.
- Reza Naghavian
- , Wolfgang Faigle
- & Roland Martin
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Article
| Open Access
Profiling the human intestinal environment under physiological conditions
Variations in microbial composition, phage induction, antimicrobial resistance genes and bile acid profiles are identified by using an ingestible device for site-specific sampling along the intestines.
- Dari Shalon
- , Rebecca Neal Culver
- & Kerwyn Casey Huang
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Article
| Open Access
Structural atlas of a human gut crassvirus
A cryo-electron microscopy reconstruction of the virus ΦcrAss001 provides insights into the functions of the viral gene products in capsid assembly and infection.
- Oliver W. Bayfield
- , Andrey N. Shkoporov
- & Alfred A. Antson
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Perspective |
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
This Perspective reviews the evidence for and against the existence of a fetal microbiome and concludes that detected microbial signals are most likely the result of contamination, suggesting that the ‘sterile womb’ hypothesis is correct.
- Katherine M. Kennedy
- , Marcus C. de Goffau
- & Jens Walter
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News |
How antidepressants help bacteria resist antibiotics
A laboratory study unravels ways non-antibiotic drugs can contribute to drug resistance.
- Liam Drew
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News |
How our microbiome is shaped by family, friends and even neighbours
Social contacts throughout a person’s lifetime seed the body with microbes that could influence health and disease.
- Ewen Callaway
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Article
| Open Access
The person-to-person transmission landscape of the gut and oral microbiomes
Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.
- Mireia Valles-Colomer
- , Aitor Blanco-Míguez
- & Nicola Segata
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Research Highlight |
Plagued by hay fever? Blame your nasal microbes
People with hay fever have a higher proportion of a certain bacterial species in their noses.
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Article |
A microbiome-dependent gut–brain pathway regulates motivation for exercise
It is demonstrated that the brain circuitry involved in regulating the motivation for physical activity is not strictly central nervous system autonomous but is shaped by peripheral influences that originate in the intestinal microbial community.
- Lenka Dohnalová
- , Patrick Lundgren
- & Christoph A. Thaiss
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Article |
Enterococci enhance Clostridioides difficile pathogenesis
Enterococci enhance the fitness and pathogenesis of Clostridioides difficile in the gut by altering the amino acid composition and providing signals that increase its virulence towards the host.
- Alexander B. Smith
- , Matthew L. Jenior
- & Joseph P. Zackular
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Article |
Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation
Dietary inulin fibre alters the composition and metabolism of gut microbiota, resulting in elevated levels of bile acids that subsequently trigger mucosal type 2 inflammation characterized by eosinophilia, with clinical implications for allergy and anti-helminth defence.
- Mohammad Arifuzzaman
- , Tae Hyung Won
- & David Artis
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News |
Do fungi lurking inside cancers speed their growth?
Studies that scrutinized thousands of tumour samples provide the clearest link yet between cancer and fungi — but more research is needed.
- Max Kozlov
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Article
| Open Access
Identification of trypsin-degrading commensals in the large intestine
Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.
- Youxian Li
- , Eiichiro Watanabe
- & Kenya Honda
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News Feature |
How gut bacteria could boost cancer treatments
Faecal transplants have helped some people to overcome resistance to powerful immunotherapies. Now dozens of trials are taking aim at the cancer–microbiome connection.
- Jeanne Erdmann
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Article |
Within-host evolution of a gut pathobiont facilitates liver translocation
Within-host evolution is a critical regulator of commensal pathogenicity that provides a unique source of stochasticity in the development and progression of microbiota-driven disease.
- Yi Yang
- , Mytien Nguyen
- & Noah W. Palm
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Research Highlight |
Even glaciers have a microbiome — including unique bacteria
Glaciers on the Tibetan Plateau boast a wide diversity of microorganisms, including species found nowhere else.
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Research Briefing |
A wealth of new biosynthetic pathways from the global ocean microbiome
DNA from more than 1,000 marine microbial communities around the world was used to reconstruct around 26,000 genomes. The analyses identified a highly biosynthetically diverse family of bacteria in the open ocean, as well as new enzymes and biochemical compounds.
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World View |
The human microbiome: there is much left to do
It’s time to make the survey of humanity’s ‘second genome’ more complete.
- Ruth Ley
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Article |
Discovery of bioactive microbial gene products in inflammatory bowel disease
A computational system termed MetaWIBELE (workflow to identify novel bioactive elements in the microbiome) is used to identify microbial gene products that are potentially bioactive and have a functional role in the pathogenesis of inflammatory bowel disease.
- Yancong Zhang
- , Amrisha Bhosle
- & Eric A. Franzosa
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Article |
ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs
The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
- Hui Yang
- , Jinyuan Wu
- & Lusheng Huang
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Article |
Environmental factors shaping the gut microbiome in a Dutch population
A study in which gut microbiomes of 8,208 individuals from 2,756 families were characterized and correlated to 241 host and environmental factors defines microbiome patterns shared across diverse diseases and shows that the microbiome is shaped largely by environment and cohabitation.
- R. Gacesa
- , A. Kurilshikov
- & R. K. Weersma
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Career Guide |
How gut reactions are shaping cancer treatment
An explosion of interest in the workings of the gut microbiome is fuelling career and funding opportunities in a wide array of fields.
- Bianca Nogrady
Exploring the lung microbiome’s role in disease