/microbiome

A — hopefully — ever-up-to-date collection of articles and studies on the human microbiome.

A — hopefully — ever-up-to-date collection of articles and studies on the human microbiome.

The emerging and surprising view of how the enteric nervous system in our bellies goes far beyond just processing the food we eat

The bacteria in our guts can influence the working of the mind, says Frank Swain. So could they be upgraded to enhance brainpower?

Researchers at Johns Hopkins think they might have come up with a novel way to manage blood pressure. Hint: Microbes.

Each year, as bears prepare to hibernate, they gorge themselves on food to pack on fat. And yet, despite the rapid weight gain, the animals somehow avoid the health consequences so often associated with obesity in humans. Now, researchers show that the bears' shifting metabolic status is associated with significant changes in their gut microbes.

Symbiotic gut bacteria evolved and diverged along with ape and human lineages, researchers find.

Sience writer Sonia Shah explains why it’s really not your fault you’re attracted to that terrible person.

A new study adds to a growing body of research that suggests we might have been thinking about Parkinson's disease wrong this whole time.

The bacteria in our guts can break down food the body can't digest, produce important nutrients, regulate the immune system, and protect against harmful germs. And while we can't control all the factors that go into maintaining a healthy gut microbiome, we can manipulate the balance of our microbes by paying attention to what we eat. Shilpa Ravella shares the best foods for a healthy gut.

For a healthy body full of ‘good’ bacteria, you may need to do a lot more than eat a probiotic yoghurt, as Adam Rutherford discovered when he took a rather uncomfortable test.

By suppressing or increasing cravings, microbes help the brain decide what foods the body “needs”.

Ever wonder how we poop? Learn about the gut -- the system where digestion (and a whole lot more) happens -- as doctor and author Giulia Enders takes us inside the complex, fascinating science behind it, including its connection to mental health. It turns out, looking closer at something we might shy away from can leave us feeling more fearless and appreciative of ourselves.

Kidneys sniff out signals from gut bacteria for cues to moderate blood pressure after meals. Our understanding of how symbiotic microbes affect health is becoming much more molecular.

One day, you might be able to eat microbes — yes, microbes — to help you lose weight.

A plethora of conditions, from obesity to anxiety, appear to be linked to the microbes inside us. Nicola Davis explains why the microbiome is such a hot topic of research.

Researchers say they noticed changes in the gut microbiome after six weeks of exercise. The gut makeup returned to normal after exercise was dropped.

Genetic mutations, which occur in both the brain and gut, could be a main cause of autism. Using mouse models of ASD, researchers discovered the neuroligin-3 R451C mutation affects neural communication in the brain and causes dysfunction in the gut. The findings strengthen the gut-brain hypothesis of autism.

Manipulating gut bacteria in mice before chemotherapy reduces the mental fog of “chemo brain.”

Oligomannate, derived from a compound in seaweed, suppresses neural inflammation caused by gut bacteria in mice.

Knowing how dietary fibre nourishes gut microorganisms might suggest ways to boost health-promoting bacteria. A method developed to pinpoint bacteria that consume particular types of dietary fibre could advance such efforts.

New studies help to explain how microbes in the gut can shape a host’s fear responses.

The barrier between mind and body appears to be crumbling. Clinical practice and public perception need to catch up

Parkinson's disease (PD) is a debilitating neurodegenerative disorder, impairing the motor functions of millions of elderly people worldwide. Often, people with PD will experience disturbances in gastrointestinal function, such as constipation, years before motor symptoms set in.

Changes in gut mucus may contribute to Alzheimer’s, Parkinson’s, and other neurological disorders. Researchers noted changes in types of gut mucus bacteria in those with a range of neurological disorders compared to their healthy peers. Findings suggest those with reduced gut mucus protection may be more susceptible to gastrointestinal problems.

The gut microbiome is more malleable in the first two years after birth, allowing probiotics to make their mark. Can we exploit this to improve infants’ health?

Hand-washing aside, James Hamblin has not used soap for five years. He warns that our obsession with being clean is harming the microbiome that keeps us healthy.

IgA cells that originate in the gut play a role appear to have neuroprotective properties against diseases associated with neuroinflammation, such as meningitis.

Depression may be a new biomarker for the onset of specific bowel conditions, researchers report. The study found those with digestive disorders such as IBS, Crohn’s disease, and ulcerative colitis were more likely to be diagnosed with depression up to nine years prior to being diagnosed with bowel conditions.

The gastrointestinal tracts of people with major depressive disorder harbor a signature composition of viruses, bacteria, and their metabolic products, according to the most comprehensive genomic and metabolomic analysis in depression to date.

A new “organ on a chip” system helps researchers uncover how bacteria in the human digestive tract can impact neurological diseases.

Neanderthals' gut microbiota included beneficial microorganisms that are also found in the modern human microbiome. An international research group led by the University of Bologna achieved this result by extracting and analyzing ancient DNA from 50,000-year-old fecal sediments sampled at the archaeological site of El Salt, near Alicante (Spain).

Both wisdom and loneliness appear to be influenced by microbial diversity within the gut, a new study reports.

Previous research has found links between gut bacteria and degenerative brain disorders, such as Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis (ALS). A new study in tiny worms provides the first evidence that “pathogenic” bacteria can promote the misfolding of proteins that is a characteristic of these conditions. Other bacteria that produce a fatty acid called butyrate prevented protein misfolding in the worms. The research adds to evidence that a history of antibiotic treatments may play a role in the early development and course of Parkinson’s disease.

  • 2021 May-July

    Plants, like other multicellular lifeforms, are colonized by microorganisms. How plants respond to their microbiota is currently not well understood. We used a phylogenetically diverse set of 39 endogenous bacterial strains from Arabidopsis thaliana leaves to assess host transcriptional and metabolic adaptations to bacterial encounters. We identified a molecular response, which we termed the general non-self response (GNSR) that involves the expression of a core set of 24 genes. The GNSR genes are not only consistently induced by the presence of most strains, they also comprise the most differentially regulated genes across treatments and are predictive of a hierarchical transcriptional reprogramming beyond the GNSR. Using a complementary untargeted metabolomics approach we link the GNSR to the tryptophan-derived secondary metabolism, highlighting the importance of small molecules in plant–microbe interactions. We demonstrate that several of the GNSR genes are required for resistance against the bacterial pathogen Pseudomonas syringae. Our results suggest that the GNSR constitutes a defence adaptation strategy that is consistently elicited by diverse strains from various phyla, contributes to host protection and involves secondary metabolism.

    The plant microbiota consists of a multitude of microorganisms that can affect plant health and fitness. However, it is currently unclear how the plant shapes its leaf microbiota and what role the plant immune system plays in this process. Here, we evaluated Arabidopsis thaliana mutants with defects in different parts of the immune system for an altered bacterial community assembly using a gnotobiotic system. While higher-order mutants in receptors that recognize microbial features and in defence hormone signalling showed substantial microbial community alterations, the absence of the plant NADPH oxidase RBOHD caused the most pronounced change in the composition of the leaf microbiota. The rbohD knockout resulted in an enrichment of specific bacteria. Among these, we identified Xanthomonas strains as opportunistic pathogens that colonized wild-type plants asymptomatically but caused disease in rbohD knockout plants. Strain dropout experiments revealed that the lack of RBOHD unlocks the pathogenicity of individual microbiota members driving dysbiosis in rbohD knockout plants. For full protection, healthy plants require both a functional immune system and a microbial community. Our results show that the NADPH oxidase RBOHD is essential for microbiota homeostasis and emphasizes the importance of the plant immune system in controlling the leaf microbiota.

    Not only animals and humans host a complex community of microorganisms—plants do this as well. Researchers at ETH Zurich have recently published two new studies that shed light on fundamental aspects of these close—and often overlooked—relationships.

Not only animals and humans host a complex community of microorganisms – plants do this as well. Researchers at ETH Zurich have recently published two new studies that shed light on fundamental aspects of these close – and often overlooked – relationships.

When it comes to hunger and satiety, nerve cells in the vagus nerve fulfill opposing tasks.

Most strains of bacteria in the microbiome are persistent within families and geographical regions, with the chance for a strain persisting up to a year at 90%.

The billions of microbes living in your gut could play a key role in supporting the formation of new nerve cells in the adult brain, with the potential to possibly prevent memory loss in old age and help to repair and renew nerve cells after injury, an international research team spanning Singapore, UK, Australia, Canada, US, and Sweden has discovered.

Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.

Millions of people worldwide suffer from neurological disorders such as Alzheimer's disease (AD), Parkinson's disease, and amyotrophic lateral sclerosis (ALS). By gradually destroying motor abilities, communication skills, memory, and clear thinking, these devastating diseases rob patients of their independence and take a heavy toll on family members and caregivers.

  • 2021 July, Gut-microbiota-targeted diets modulate human immune status

    Diet modulates the gut microbiome, which in turn can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading carbohydrate active enzymes (CAZymes) despite stable microbial community diversity. Although cytokine response score (primary outcome) was unchanged, three distinct immunological trajectories in high-fiber consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society.

    A diet rich in fermented foods, such as yogurt and kimchi, can help to improve gut microbiome diversity and reduce symptoms of chronic inflammation, a new study reports.

    Researchers have shown that the gut microbiome is connected to overall health and that diet can alter the microbiome. In a recent small-scale preliminary study, researchers compared the effects of two diets on the gut microbiome. They found that a fermented food diet increased the diversity of the gut microbiome and lowered markers of inflammation.

    Gut-boosting foods are popping up on supermarket shelves, but are they more than just a trendy side dish?

  • 2021 July, Gut Microbiome Affects a Specific Set of Neurons Responsible For Proper Social Function

Researchers identified the gut bacteria E. faecalis as a mediator of social behavior and corticosterone levels in mice.

The results of studies in mice by University of Iowa (UI) scientists suggest that the metabolism of plant-based dietary compounds by specific gut bacteria that are lacking in patients with multiple sclerosis (MS) may provide protection against the immune-mediated disease.

We have known for a while that obesity has a microbial component. Now, a team of scientists led by Patrice D. Cani reports a novel bacterium isolated from the human gut that counteracts diet-induced obesity, inflammation and glucose dysregulation in mice.

A team of researchers from SAHMRI and Flinders University has found a link between the type of microbiome that repopulates the gut following antibiotics and shortened lifespan in mice.

With age, a diet lacking in the essential amino acid tryptophan — which has a key role in our mood, energy level, and immune response — makes the gut microbiome less protective and increases inflammation body-wide, investigators report.

Can this newly discovered bacterium really help you lose weight? We interview a nutritionist to find out.

Emerging evidence is revealing that alterations in gut microbiota are associated with colorectal cancer (CRC). However, very little is currently known about whether and how gut microbiota alterations are causally associated with CRC development. Here we show that 12 faecal bacterial taxa are enriched in CRC patients in two independent cohort studies. Among them, 2 Porphyromonas species are capable of inducing cellular senescence, an oncogenic stress response, through the secretion of the bacterial metabolite, butyrate. Notably, the invasion of these bacteria is observed in the CRC tissues, coinciding with the elevation of butyrate levels and signs of senescence-associated inflammatory phenotypes. Moreover, although the administration of these bacteria into ApcΔ14/+ mice accelerate the onset of colorectal tumours, this is not the case when bacterial butyrate-synthesis genes are disrupted. These results suggest a causal relationship between Porphyromonas species overgrowth and colorectal tumourigenesis which may be due to butyrate-induced senescence.

Human-associated microorganisms play a vital role in human health, and microbial imbalance has been linked to a wide range of disease states. In this Review, we explore recent efforts to progress from correlative studies that identify microorganisms associated with human disease to experiments that establish causal relationships between microbial products and host phenotypes. We propose that successful efforts to uncover phenotypes often follow a chain of evidence that proceeds from (1) association studies; to (2) observations in germ-free animals and antibiotic-treated animals and humans; to (3) fecal microbiota transplants (FMTs); to (4) identification of strains; and then (5) molecules that elicit a phenotype. Using this experimental ‘funnel’ as our guide, we explore how the microbiota contributes to metabolic disorders and hypertension, infections, and neurological conditions. We discuss the potential to use FMTs and microbiota-inspired therapies to treat human disease as well as the limitations of these approaches.

Plant-based diets cause men to fart more and have larger stools, researchers have found – but that seems to be a good thing, because it means these foods are promoting healthy gut bacteria.

How long you live and how well you age rests on many factors beyond your control, but the discovery that gut microbes play a key role means what you eat can make a difference

Researchers’ painstaking examinations have begun to reveal how the virus wreaks havoc in multiple organs and tissues.

A study in humans indicates that certain bile acids that are produced by bacteria and commonly found in people over 100 boost gut health and protect against infection. These findings shed light on the contributors to healthy ageing.

The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.

The mammalian gut harbors a complex and dynamic microbial ecosystem: the microbiota. While emerging studies support that microbiota regulates brain function with a few molecular cues suggested, the overall biochemical landscape of the “microbiota-gut-brain axis” remains largely unclear. Here we use high-coverage metabolomics to comparatively profile feces, blood sera, and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera, and 58 for brain with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters. Multicompartmental comparative analyses single out microbiota-derived metabolites potentially implicated in interorgan transport and the gut-brain axis, as exemplified by indoxyl sulfate and trimethylamine-N-oxide. Gender-specific characteristics of these landscapes are discussed. Our findings may be valuable for future research probing microbial influences on host metabolism and gut-brain communication.

The role of gut bacteria in the progression of prostate cancer has been highlighted in a new study showing how the microbiome can influence hormone metabolism, which subsequently amplifies tumor growth and disrupts certain hormone treatments.

In this Special Feature, we examine a potential link between sleep apnea, hypertension, and gut bacteria. Although a link between the three may seem unlikely on the surface, scientists are unraveling the connections.

Microbe types in older people’s intestines are different and are linked to disease.

Study in animals suggests omega-3 supplement may reduce effects.

Researchers find 3 most common artificial sweeteners cause a ‘breakdown in communication’ among microbes, potentially raising risk of obesity, diabetes and digestive problems

The vascular barrier in the choroid plexus locks down access to the brain in response to gut inflammation that causes IBD. The dysregulated activity of the gut-brain vascular axis appears to protect the brain from inflammation. However, the mechanism may increase the risk of both cognitive and mental health problems associated with IBD.

Study identifies a significant way in which a disrupted circadian clock drives inflammation in the body’s immune cells.

A species of gut bacteria called Lactobacillus apis has been linked to enhanced memory and cognition in bumblebees.

A first-of-its-kind study investigating the effects of a common food additive on human gut bacteria has found the emulsifier carboxymethylcellulose can alter the quality and composition of the microbiome and potentially increase a person’s risk of chronic intestinal inflammation.

Scientists examine mailed-in samples and find that early risers share gut bacteria pattern, hope to replicate it to help others get up with the larks

Microglia, a key immune cell in the brain, appears to mediate the relationship between the gut microbiome and amyloid-beta deposits in male mouse models of Alzheimer’s disease.

Findings by Chinese University and University of Hong Kong show a type of probiotic bacteria in the gut can help enhance efficacy of Sinovac and BioNTech vaccines Researchers report that low antibody response corresponded to inadequate levels of the bacteria

Gut Week at INVERSE, October 2021

“DIGESTION CAN BE VERY PERSONAL.”

Treatment-resistant cancer may be driven — at least in part — by the makeup of the gut microbiome.

WHAT MAKES YOU? Is it your genes, your experiences, or the trillion of microorganisms inside you that shape the person you are today?

Competing ideas on how to collect and study our microbiota raise a vital question: Who benefits?

“By restoring the microbiome, we’re targeting it through this transplantation, we’re able to reverse age-related cognitive deficits.”

GUT STUDY UNCOVERS A SURPRISING ROLE FOR IMMUNE CELLS IN NUTRIENT ABSORPTION

MAYBE YOUR PANTS ARE TIGHTER than usual or you’ve exhausted yourself walking up the stairs, but it’s never too late to get in shape. Unfortunately, all of the advice on the internet promising quick and easy results in less than 30 days is overwhelming at best, unhelpful and misleading at worst. If you’re unsure of where to start, try to listen to your gut.

Fungi are important members of the microbiome — but they can also hurt human health.

Your microbiome’s diversity may depend on your mood.

THIS ONE NUTRITIONAL STRATEGY CAN BENEFIT GUT HEALTH — AND FIGHT INFLAMMATION

A controversial doctor thinks he has the answer.

“Maintaining a healthy microbiome through healthy diet would definitely benefit in fighting against Covid-19.”