Mouth Microbes transmitted to gut Could Help Diagnose gastrointestinal Cancers

Amazing stuff! Cancer is history (soon)!

Is this maybe another good reason to do daily tongue scraping?

"... In a new study, researchers have shown that mouth bacteria migrate through the gastrointestinal tract in certain types of cancer.1 The findings raise hope that the breakdown of these carefully sectioned-off compartments in the body could be an indicator of disease, leading to easier and quicker diagnostic tests for gastrointestinal cancers. ..."

"... In a study ... researchers report that by analyzing the make-up of oral microbes, they may be able to detect signals associated with gastric (stomach) and colorectal cancer. These findings could lead to the development of new, less-invasive screening tests for gastrointestinal cancers. ...

To conduct the study, the researchers recruited 507 volunteers to donate both oral and fecal samples, using a highly standardized collection process. The cohort included 129 healthy individuals; 215 people with metabolic disorders such as metabolic syndrome, hypertension, hyperlipidemia, and type 2 diabetes; 77 people with gastric cancer; and 86 people with colorectal cancer. For the volunteers with cancer, samples were collected before the start of any treatment.  ...

The findings were more nuanced than a simple cancer-versus-healthy comparison. The MF index was significantly elevated in patients with gastric or colorectal cancer but not in people with metabolic disorders. After accounting for alcohol consumption, regular exercise, and BMI, the association remained robust for both gastric and colorectal cancers. ..."

From the highlights and abstract:

"Highlights

• Mouth and gut microbial compartmentalization is disrupted in gastrointestinal cancers

• Mouth-to-gut transmitted bacteria correlate with metabolic and inflammatory markers

• Oral-fecal transmission signatures enable cancer classification by oral microbiome alone

• Transmission-based classifier surpasses microbiota models and fecal occult blood testing

Summary

The human microbiome is spatially compartmentalized, yet oral bacteria can ectopically colonize distal sites such as the gut, potentially influencing disease.

By analyzing paired oral and fecal microbiomes from 507 participants across healthy controls and patients with metabolic disorders or gastrointestinal cancers, we established a quantitative mouth-to-feces (MF) index to measure MF microbial transmission.

The MF index revealed elevated mouth-to-gut transmission in cancer and a strong association with host metabolic and inflammatory indicators.

Using transmitted taxa, we developed a random forest classifier that accurately distinguished gastric/colorectal cancer from healthy controls across seven independent cohorts, even when trained solely on oral microbiome data.

When benchmarked against the conventional screening test, the MF-based model achieved markedly higher sensitivity than the fecal occult blood test.

These findings uncover disease-specific transmission signatures and highlight MF microbial profiling as a generalizable, non-invasive framework for gastrointestinal cancer diagnosis and risk stratification."

Mouth Microbes Could Help Diagnose Gastric Cancers | The Scientist "Some mouth bacteria migrate to the gut in gastrointestinal cancers, opening possibilities for more convenient cancer diagnostic tests."

Mouth and gut microbes could help detect gastrointestinal cancers

Mouth-to-gut microbial transmission signatures enable robust, non-invasive diagnosis of gastrointestinal cancers (open access)

Graphical abstract

Figure 2. MF transmission index as an assessment of the mouth-gut microbiome axis

More evidence that plants are not passive and defenseless

Amazing stuff! There is much more than thorns to plant defenses!

"Dying [attacked] plants can protect their successors from the same fate

Plants might look like passive life forms, quietly enduring drought, disease or parasites. But they are actually great at fighting back. A new study reveals an intricate feedback system that allows cowpeas attacked by herbivores to protect future plants from the same fate.

Previous studies have documented how some plants ‘call for help’ when being eaten: When caterpillars start to chew on the leaves, they release a chemical into the air that attracts predators, like wasps, which then feed on the caterpillars. But scientists have now uncovered a more complex mechanism, one that triggers protective capabilities across plant generations.

“The major finding is that a mechanism under the soil can impact the response to predators,” ... “This has never been seen before.” ...

found that when attacked by insects called leafminers, cowpea plants—in addition to releasing an airborne chemical to attract wasps—also release chemicals called flavonoids into the soil from their roots. Those flavonoids, in turn, cultivate a particular community of soil bacteria, which influences the next plants to grow in that soil: They cause the new plants to trigger that airborne alarm system before they’re attacked, as a protective measure.

The finding can have direct implications for the development of green pest management ..."

From the highlights and abstract:

"Highlights

• Leaf herbivory leaves a persistent soil-borne defensive legacy

• Jasmonate-dependent flavonoids restructure the rhizosphere microbiome

• The rhizosphere microbiome acts as a soil-borne legacy for subsequent plants

• Soil-borne legacy reconfigures volatile emission and enhances parasitoid attraction

Summary

How organisms convert short-term stress into long-term defense is a key ecological question. Classic herbivore-induced plant volatiles recruit natural enemies but act briefly only in damaged tissues.

Here, we report that leaf herbivory establishes a persistent soil defensive legacy to help uninfested subsequent plants attract parasitoids.

During the conditioning phase, herbivory systemically activates jasmonate signaling, which reprograms root metabolism and promotes the exudation of specific flavonoids, notably daidzein and genistein.

These compounds selectively restructure the rhizosphere microbiome, enriching functionally specialized bacterial taxa that constitute the soil-borne legacy. During the feedback phase, these enriched rhizosphere bacteria, in turn, increase jasmonate signaling in succeeding plants, boosting emission of the key parasitoid-attracting volatile (Z)-3-hexenyl acetate in the absence of herbivory.

Together, our findings reveal plant-soil feedback as an active ecological process that extends the spatial and temporal reach of plant defenses, with broad implications for plant-enemy interactions and sustainable pest management."

ScienceAdviser

Herbivory leaves a soil-borne defensive legacy that recruits parasitoids (open access)

Graphical abstract

Figure 1 Leaf herbivory attracts parasitoids via systemic jasmonate signaling-mediated plant-soil feedbacks

How neurons in C. Elegans sense bacteria in the gut

Amazing stuff!

"... In the new open-access study  ... identifies the specific chemicals that a key neuron in C. elegans senses, both in the bacteria that it eats and in the bacteria that it needs to avoid ingesting. ...

C. elegans a “bacterial specialist” because the tiny, transparent worm has evolved to eat bacteria as its diet, while also needing to avoid pathogenic bacteria that can prove to be its undoing. This has led it to develop a nervous system especially well-attuned to sorting out what is food and what is foe. ...

what the ion channels are detecting in the bacteria. To get started, they exposed worms to 20 different kinds of bacteria the worms are known to encounter and found that they all activated NSM activity to varying extents. Then they broke the bacteria down into more and more specific chemical components to see which one or ones triggered NSM. The experiments ruled out many components, including DNA, lipids, proteins, and simple sugars, and instead found that it’s specifically the polysaccharide sugars that coat many bacteria that drive NSM activation. In particular, in gram-positive bacteria, a chemical called peptidoglycan activated NSM. In gram-negative bacteria, a different polysaccharide was apparently in play. ...

Having shown what exactly triggers the worms to recognize their bacterial food, the researchers wondered whether they could also pinpoint a danger sign the worm finds in harmful bacteria.

For these experiments, they carefully used Serratia marcescens, a bacterium that’s also infectious for humans. Some strains of the bacteria have a red color, while others do not. The red ones, which have a pigment called prodigiosin, tend to be much more lethal for worms. In their testing, the researchers found that when NSM detected the non-pigmented bacteria, the neuron still activated and the worms still ingested the bacteria, but when prodigiosin was present, NSM did not activate and the worm did not pump it in or slow down to eat. ..."

From the highlights and abstract:

"Highlights

• The enteric sensory neuron NSM is activated by ingestion of diverse bacteria

• Bacterial polysaccharides, including peptidoglycans, are sufficient to activate NSM

• Bacterial polysaccharides drive serotonin-dependent changes in foraging behaviors

• Prodigiosin, produced by pathogenic S. marcescens, inhibits NSM activity

Summary

The bacterial microbiome influences many aspects of animal health and disease. Bacteria can have beneficial functions, for example providing nutrients, whereas others can act as pathogens.

Bacteria are sensed by host cells to induce adaptive changes in physiology and behavior. While immune and intestinal cells detect bacterial signals through well-characterized mechanisms, recent studies indicate that neurons can also directly sense bacteria.

However, the bacterial sensory mechanisms in neurons are less well understood. In Caenorhabditis elegans, the enteric sensory neuron NSM innervates the pharyngeal lumen and is directly activated by bacterial ingestion; in turn, NSM releases serotonin to induce feeding-related behaviors.

However, the molecular identities of the bacterial signals that activate NSM are unknown.

To identify them, we probed bacterial macromolecules from nutritive bacteria using biochemical approaches. We find that polysaccharides from bacteria are sufficient to activate NSM.

We further identify peptidoglycans from Gram-positive bacteria as specific components capable of activating NSM. NSM responses to polysaccharides require the acid-sensing ion channels DEL-3 and DEL-7, which localize to NSM's sensory dendrite in the pharyngeal lumen.

Ingestion of bacterial polysaccharides enhances feeding and reduces locomotion, matching the known effects of NSM on behavior.

We also examine signals produced by pathogenic bacteria. This approach identifies prodigiosin, from pathogenic Serratia marcescens, as a metabolite that prevents NSM activation by nutritive bacterial signals.

This study identifies molecular signals that underlie neuronal recognition of nutritive bacteria in the alimentary canal and competing signals from a pathogenic bacterial strain that can mask this form of recognition."

How neurons sense bacteria in the gut | MIT News | Massachusetts Institute of Technology "Neural interaction with bacteria has important effects on animal brains. A new study investigates how neurons sense bacteria by revealing, in nematodes, the bacterial signals that a key neuron detects."

Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans (open access)

Figure 1 Bacterial polysaccharides activate the enteric sensory neuron NSM

Figure 5 A Serratia marcescens metabolite, prodigiosin, inhibits NSM activity and associated behaviors

One of cholera’s great enemies is found in the human gut, a bacteriophage

Recommendable!

"... found that in the Ganges Delta, cholera bacteria rapidly gain and lose special armour that protects against attacks from the virus, known as bacteriophage ICP1.

The new research ... highlighted that maintaining these anti-viral defences leads to lower disease severity of cholera in humans and reduced ability to spread outside the country for this bacterial strain. ...

By looking at the ecology of cholera in South Asia, this study challenges the long-held belief that the Ganges Delta is the global source of cholera. Knowing more about the strains and the factors that influence the spread of cholera bacteria in different regions could help provide an early warning system, identifying high-risk strains before they escalate and allowing for early intervention. ...

Globally, we are in the seventh cholera pandemic, which started in 1961, with an estimated 1.3 to 4 million cases and up to 143,000 deaths per year from the condition worldwide. It has been shown that the seventh pandemic is caused by V. cholerae strain 7PET O1, originating from the Bay of Bengal, which borders Bangladesh and India, and it was thought that the Ganges Delta was the global source of cholera.

This new research sequenced bacterial samples from across Bangladesh and North India, creating the most comprehensive dataset of cholera in this area to date, containing over 2,300 genomes collected across approximately 20 years. They found that it was the Ganges Basin, not the Ganges Delta, that was the primary global source of cholera in that time.

By tracking the bacterial spread, they also uncovered that the bacteria do not simply follow the flow of rivers. Instead, they tend to stay within national borders, suggesting that human travel and population density are more important for cholera transmission than the natural environment.

They also found V. cholerae in Bangladesh, strain 7PET O1, rapidly gain and lose genetic elements known as defence systems, which act like armour helping them survive against their viral nemesis, the bacteriophage ICP1. ..."

From the abstract:

"The seventh pandemic of cholera, caused by the seventh pandemic El Tor lineage of Vibrio cholerae, was previously shown to have emanated in three global waves from the Bay of Bengal, bordering Bangladesh and India.

However, the respective roles of the Ganges Delta and Basin regions in seeding these global pandemic waves were not known.

Here we show that, although transmission events occur between Bangladesh and India, V. cholerae in the two countries has largely evolved separately over the past 20 years, apparently constrained by national borders rather than by hydrological features, such as the Ganges Delta and Basin.

Evolution within Bangladesh was distinct from that seen in India, involving rapid gain and loss of genes and mobile genetic elements, particularly those involved in phage defence. The loss of these systems was associated with increased risk of severe disease and transmission outside Bangladesh.

Lineage replacement in Bangladesh in 2018, resulting in a major change in phage defence systems, was accompanied by a rapid change in the lineage and anti-defence system of lytic phage ICP1.

Here we show that the Ganges Basin, falling across Bangladesh and Northern India, rather than the Ganges Delta, probably acts as a global launch pad for pandemic disease. This shifts our understanding of Bangladesh as the purported global source of cholera and underscores the potential role of phage in controlling spread of lineages within the current seventh pandemic."

One of cholera’s great enemies is found in the human gut "Cholera-causing bacteria are locked in an evolutionary arms race with a viral nemesis, according to a new genomic study."

Evolution of pandemic cholera at its global source (open access)

Fig. 1: Dynamics of V. cholerae sublineages in Bangladesh and their genetic profiles over time.

Gut bacteria influence mice social behavior through smell

Amazing stuff! Why do humans use perfume and deodorants?

When one metabolite molecule regulates aggressiveness of individuals!

"In a new study, Northwestern University neurobiologists discovered that gut bacteria and the nose work together to shape social behavior in mice, including who fights and who backs down. Using a combination of genetic and behavioral experiments, the scientists found gut microbes produce a pungent odor that other animals can smell. When detected, these scents trigger aggression and shape social hierarchies. The discovery reveals a previously unknown way the microbiome influences social interactions. ...

"Over the past 20 years, there's been a growing realization that microbes in the gut have profound influences on behavior and physiology," ... "They produce bioactive chemicals that affect the function of many organ systems, including the immune system, and can even cross the blood-brain barrier to affect behavior. These chemicals can also affect social behaviors through the sense of smell. While species use microbiome-derived chemicals for social communication, our study is the first to uncover the underlying mechanism." ...

In the new study, ... team focused on trimethylamine (TMA), a molecule produced in the gut that smells like dead, rotten fish. When gut bacteria break down choline-rich foods, such as eggs and meat, they generate TMA as a byproduct. The body's liver then converts TMA into an odorless metabolite. But in adult male mice, testosterone suppresses the liver enzyme that typically neutralizes TMA, allowing it to accumulate in urine.

"It seemed like mice use TMA as a male-specific odor," ...

To better understand why adult male mice produce this odor, ... team imaged the olfactory bulb within the brain to see which neurons respond to TMA. They specifically focused on trace amine-associated receptors (TAARs), a small family of odor detectors that are especially sensitive to strong-smelling molecules. Among the 14 TAARs in mice, the team found that TAAR5 is the most sensitive receptor to TMA and plays a central role in detecting the odor. ...

From scent to social hierarchy

When mice detect this scent, it changes how they behave. Dominant animals initiate fights, while subordinate mice adopt defensive postures—patterns that quickly establish a social hierarchy. 

But when ... team disabled TAAR5 in mice, those distinctions blurred. Mice still interacted with one another, but their behavior became more evenly matched. Without this signal, it took longer for clear dominant-subordinate relationships to emerge. ..."

From the highlights and abstract:

"Highlights

• TAAR5 deletion alters aggression and social dominance in male mice

• The effect of TAAR5 on social behavior occurs via the main olfactory pathway

• Blocking production of the TAAR5 ligand TMA by gut microbes reduces aggression

• A microbiome-derived chemical cue shapes mammalian social behavior via olfaction

Summary

Many species use microbiome-derived metabolites as chemosensory cues, yet the chemicals involved and the sensory pathways that detect and process them remain poorly understood.

Trimethylamine (TMA) is a volatile metabolite that is produced by the gut microbiome and selectively accumulated in the urine of sexually mature male mice.

Here, we show that TMA regulates inter-male aggression and social dominance by activating trace amine-associated receptor 5 (TAAR5) in the main olfactory system.

In wild-type mice, early aggressive behavior during male-male encounters strongly predicts eventual social status: dominant males initiate more attacks, whereas subordinate males display more defensive behaviors.

Deletion of TAAR5 eliminated this asymmetry, with dominant and subordinate mice showing similar levels of aggressive and defensive behaviors.

Strikingly, restoring TAAR5 expression in olfactory sensory neurons (OSNs) rescued the behavioral asymmetry, indicating that this effect is mediated by the main olfactory system and arguing against contributions from proposed TAAR5 expression in the brain.

Finally, pharmacological suppression of microbial TMA production reduced inter-male aggression, and this effect was reversed by painting treated males with TMA, showing that microbiome-derived TMA is the key volatile ligand for TAAR5 in this context.

Taken together, our findings identify TMA as a critical olfactory cue that signals the presence of sexually mature males and facilitates social hierarchy formation. More broadly, our results demonstrate that a microbiome-derived metabolite can shape mammalian social interactions through the main olfactory system and uncover a previously unrecognized role for the TAAR family in regulating social behavior."

Gut bacteria may influence social behavior through smell

A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice (open access)

Graphical abstract

The microbiome is basically an undiscovered organ of the human body

Amazing stuff!

"... A growing body of research now suggests that the microbiome’s medical significance may be even broader than imagined — extending not just to gastrointestinal conditions but also to the immune system, metabolism, and even the brain. The progress has come not from moving fast, but from moving carefully.

“The microbiome has basically been an undiscovered organ of the human body,” ...  “It’s difficult to study, but it’s incumbent upon us to understand it.” ..."

The Long Game of Microbiome Science | Harvard Medicine Magazine "Looking beyond the hype, three experts explain what research on the gut microbiome might actually deliver"

Faecal transplants boost immunotherapy

Good news! Fecal transplants keep on giving!

"Three trials provide compelling evidence that faecal microbiota transplantation (FMT) can boost the effectiveness of immunotherapy in advanced solid tumors ... in an analysis of three studies ... But challenges for safety, donor selection and product development remain.

Tumours partially or completely shrunk in 75% of FMT-treated people who underwent immunotherapy with melanoma, 80% of those with non-small cell lung cancer and 50% with metastatic renal cell carcinoma (RCC) across the studies. The only randomized, placebo-controlled trial, which evaluated immunotherapy plus an oral drug with or without FMT in individuals with metastatic RCC, did not find statistically significant 12-month progression-free survival. But it did find that FMT increased the proportion of people whose tumours shrunk (52% versus 32%)."

Nature Briefing: Translational Research

Microbiome modulation in cancer immunotherapy (no public access) "Three landmark trials confirm that fecal microbiota transplantation is a promising approach to enhancing immunotherapy efficacy in advanced solid tumors. The trials also provide insights with major implications for microbiome therapeutic development."

Three studies suggest that FMT improves immunotherapy responsiveness not only by bolstering the growth of good bacteria, which improves the microbiome to help the immune system respond to cancer, but also by killing off bad bacteria.

High resolution mouse study shows a gut microbe can promote memory loss

Amazing stuff!

"... In a study published today in Nature, scientists show how a bacterium that is particularly common in older animals can drive memory loss. This microbe makes compounds that impair signaling along neurons connecting the gut with the brain, dampening activity in brain regions associated with learning and memory, the team found. ...

Research on the so-called gut-brain axis has exploded in recent decades. Multiple studies have identified differences in microbiome composition between healthy people and those with cognitive disorders such as Alzheimer’s disease. This kind of research can’t establish cause and effect, though, and the literature is rife with conflicting results. ..."

From the abstract:

"Ageing is accompanied by declining memory function, with extremely heterogeneous manifestation in the human population.

Brain-extrinsic factors influencing cognitive decline, such as gastrointestinal signals, have emerged as attractive targets for peripheral interventions, but the underlying mechanisms remain largely unclear.

Here, by charting a high-resolution map of microbiome ageing and its functional consequences throughout the lifespan of mice, we identify a mechanism by which inhibition of gut–brain signalling during ageing results in impaired neuronal activation in the hippocampus and loss of memory encoding. Specifically, accumulation of gut bacteria that produce medium-chain fatty acids, such as Parabacteroides goldsteinii, can drive peripheral myeloid cell inflammation through GPR84 signalling. As a result, the function of vagal afferent neurons is impaired, the interoceptive signal received by the brain is weakened and hippocampal function declines.

We leverage this pathway to define interventions that enhance memory in aged mice, such as phage targeting of Parabacteroides, GPR84 inhibition and restoration of vagal activity. These findings indicate a key role for interoceptive dysfunction in brain ageing and suggest that interoceptomimetics that stimulate gut–brain communication may counteract age-associated cognitive decline."

‘Tour de force’ mouse study shows a gut microbe can promote memory loss | Science | AAAS "Research suggests the microbiome may contribute to cognitive decline—but its relevance in humans is unclear"

Intestinal interoceptive dysfunction drives age-associated cognitive decline (open access)

Fig. 1: Microbiome impact on age-associated cognitive decline.

Mouth microbiome linked to obesity and metabolic health

Amazing stuff!

"... But a new study published in Cell Reports suggests the mouth may be carrying its own metabolic fingerprint. In saliva samples from 628 adults, researchers at New York University Abu Dhabi found that people living with obesity host a distinct oral microbiome, one that differs not just in species, but in what those microbes are actively doing. ...

For the study participants with obesity, bacteria were more active in pathways linked to sugar fermentation and lactate production, while showing reduced capacity to generate certain essential nutrients. Across all participants, body mass index stood out as one of the strongest drivers of oral microbial variation, suggesting the microbiome of the mouth may reflect a broader metabolic state. These changes were not random, but instead pointed in a consistent metabolic direction. Species linked to inflammation and lactate production became more prominent, including proinflammatory Streptococcus parasanguinis and Actinomyces oris, along with the lactate-producing Oribacterium sinus, while others associated with nutrient synthesis receded. A shift that went deeper than simple taxonomy. ..."

From the highlights and abstract:

"Highlights

• Oral microbiome composition and functions differ significantly in obesity

• Obesity is linked to proinflammatory and lactate-producing oral bacteria

• Obese individuals show disrupted oral metabolism and altered energy balance

• Obesity-linked metabolites correlate with cardiometabolic disease markers

Summary

Obesity is a leading global health challenge and risk factor for cardiometabolic disorders, driven in part by industrialization and low-fiber, ultra-processed diets. While the gut microbiome has been implicated in obesity, the contribution of the oral microbiome—the body’s second largest microbial ecosystem—remains underexplored. We analyze a prospective cohort of 628 Emirati adults, including multi-omics profiling of 97 obese individuals and 95 matched controls, generating the most comprehensive oral microbiome analysis to date.

Obese participants show altered microbial diversity, composition, functions, and metabolites with enrichment of proinflammatory Streptococcus parasanguinis, Actinomyces oris, and lactate-producing Oribacterium sinus. Pathways for carbohydrate metabolism, histidine degradation, and obesogenic metabolites are upregulated, whereas B-vitamin and heme biosynthesis are depleted. Corresponding metabolites—including lactate, histidine derivatives, choline, uridine, and uracil—are elevated and correlate with obesity-linked cardiometabolic markers.

These findings reveal mechanistic oral microbiome-metabolite shifts, highlighting oral microbiome-host interactions as novel targets for obesity prevention and intervention."

Mouth microbiome linked to obesity and metabolic health

NYU Abu Dhabi Researchers Reveal an Association Between Mouth Bacteria and Obesity and Metabolic Health (original news release)

Integrative multi-omics analysis reveals oral microbiome-metabolome signatures of obesity (open access)

Graphical abstract

Microbes in tree bark remove greenhouse gases from the atmosphere

As I have said on my blog several times before plant some more trees if you are really concerned with greenhouse gases and climate change!

Remember, global warming is a hoax and climate change is a religion! One can safely assume that until recently the microbiota living on tree bark and their effect on climate was unknown! What little we still know about such a complex natural phenomenon like climate (Corollary: climate models are largely junk)!

"... New research shows that microbes living in tree bark also help clean the air by taking up vast amounts of other climate-active gases too.

The study ... sampled the bark of 8 tree species in freshwater wetland, coastal and upland forest biomes of eastern Australian to determine the microbial species present and how they consumed and produced key gases. ..."

From the abstract of the Perspective:

"Ecosystems exchange gases with the atmosphere, influencing its chemical composition and temperature. Trace gases are present at very low concentrations in the atmosphere but have important effects.

For decades, soil was thought to be the only surface that exchanges trace gases with the atmosphere.  ... 

Tree bark biogeochemistry (life-mediated chemical cycling and exchange between air, water, and land) has been almost completely ignored, despite bark having a global surface area of ~143 million km2, almost as large as the global land surface. ... Leung et al. report that bark microbes process methane, hydrogen, and carbon monoxide, showing that bark is an important component of global trace gas dynamics."

From the editor's summary and abstract:

"Editor’s summary

Tree trunks comprise a huge area of habitat for metabolically active microorganisms. Not only do the trunks provide a substrate for many epiphytic species, but tree bark also shelters specific communities of bacteria. Leung et al. sampled the bark of several eastern Australian trees to investigate the species present and their metabolic capacities. Depending on locality, prevailing conditions, and species and their microbiota, tree trunk communities can be net producers or consumers of climate active gases. While planning a planting scheme, it is therefore important to assess specific settings for the potential role that trees can play, through their trunk communities, in climate mitigation ...

Structured Abstract

INTRODUCTION

The global surface area of tree bark is similar to that of terrestrial Earth. These substantial tree surfaces are increasingly recognized for mediating the exchange of atmospheric gases along the soil-tree-atmosphere continuum. They also represent a potential habitat for microorganisms, with recent metabarcoding studies indicating a possible role for bark microbes in the cycling of methane (CH4). However, a general understanding of the metabolism and ecosystem roles of these potentially globally pervasive microbiota remains lacking.

RATIONALE

At the soil-atmosphere interface, we predicted that tree bark microbiota use diverse gas substrates to sustain growth and in turn may mediate an important role in global atmospheric gas cycling. However, previous metabarcoding approaches have only provided limited and indirect inference for the lifestyle of bark microorganisms. Numerous traits, such as microbial oxidation of the climate-active gases hydrogen (H2) and carbon monoxide (CO), cannot be reliably predicted by taxonomic affiliation. A functional understanding of the bark microbiota requires direct evidence from genomic characterization and functional validation. Here we integrated genome-resolved metagenomic analysis with in situ and ex situ biogeochemical assays to study the capabilities, metabolism, and ecosystem importance of bark microbiota in Australian forests.

RESULTS

We examined bark microbiota of eight prevalent Australian tree species, spanning freshwater wetland, coastal, and upland forest biomes.

All tree species were found to harbor abundant endophytic microbial populations, estimated at up to 6 trillion cells per square meter of bark.

Gene-centric and genome-resolved metagenomics revealed that bark microbial communities were distinct from surrounding soils and waters and included diverse metabolically flexible gas cycling and facultatively anaerobic bacteria. Predominant bacteria were predicted to consume hydrogen through aerobic respiration and fermentatively produce this gas during hypoxia.

Bacteria encoding enzymes for aerobic and anaerobic metabolism of other gases, including CO, CH4, and volatile organic compounds, were also abundant, with methanogenic archaea present in some wetland trees.

Consistently, microcosm assays showed that bark microorganisms aerobically consume CH4, H2, and CO but switched to production of these gases under anoxia.

In situ measurements further showed that fluxes of multiple climate-active gases occur at tree bark surfaces. In particular, net H2 uptake was consistently observed across all tree species and bark heights, indicating that bark may be an overlooked H2 sink, where robust microbial activity could account for annual removal of atmospheric H2 at the teragram scale.

CONCLUSION

Our results provided genome-resolved insights into the abundant bark microbiota, revealing their ability to flexibly metabolize gases and adapt to substrate and redox conditions within trees.

Their activities substantially modulate fluxes of major climate-active gases, such as CH4, and the often-overlooked indirect greenhouse gases H2, CO, and volatile organic compounds.

Bark microbiota may contribute to the climate benefits of trees by removing multiple climate-active gases, although their metabolic flexibility indicates a potential to switch to a source, depending upon environmental conditions. Collectively, these results suggest that trees and their microbiota contribute to regulating global atmospheric cycles and should be considered in biogeochemical models, forest management, and conservation efforts."

Microbes in tree bark remove greenhouse gases from the atmosphere | News | ConnectSci

Tree bark microbes for climate management (Perspective, no public access)

Bark microbiota modulate climate-active gas fluxes in Australian forests (no public access)

Bark microbiota modulate climate-active gas fluxes in Australian forests

Gut microbes use common nutrient choline to fight type 2 diabetes

Good news! Is a choline dietary supplement a good idea?

"... Earlier this year, for example, it was found that an antibiotic primarily used in veterinary medicine was able to convince the microbes in mouse guts to produce colonic acid, a life-extending compound.

Now, a team led by a researcher ... has figured out another powerful way our gut microbes can help us out – this time by tamping down inflammation caused by a fatty diet, keeping our insulin response in check and, in turn, warding off diabetes. ...

The researchers found that one of the chemicals involved in this cascade of negative effects is the immune-system protein IRAK4, which triggers inflammation in the presence of a high-fat diet as a sort of alarm bell. When that protein is expressed for an extended period of time, it leads to insulin resistance and diabetes. ...

Using mice, human cell models, and molecular target-screening, the scientists found that when the nutrient choline hits the gut, microbes convert it into a metabolite called trimethylamine (TMA). TMA, in turn, binds to IRAK4, blocks its activity, reduces inflammation, and restores insulin sensitivity. ..."

"An international research team ... has uncovered a surprising ally in the fight against insulin resistance and type 2 diabetes: a microbial metabolite called trimethylamine (TMA). ... the study reveals that TMA, produced by gut bacteria from dietary choline can block a key immune pathway and improve blood sugar control. ..."

From the abstract:

"The global type 2 diabetes epidemic is a major health crisis. Although the microbiome has roles in the onset of insulin resistance (IR), low-grade inflammation and diabetes, the microbial compounds controlling these processes remain to be discovered.
Here, we show that the microbial metabolite trimethylamine (TMA) decouples inflammation and IR from diet-induced obesity by inhibiting interleukin-1 receptor-associated kinase 4 (IRAK4), a central kinase in the Toll-like receptor pathway sensing danger signals. TMA blunts TLR4 signalling in primary human hepatocytes and peripheral blood monocytic cells and rescues mouse survival after lipopolysaccharide-induced septic shock.
Genetic deletion and chemical inhibition of IRAK4 result in metabolic and immune improvements in high-fat diets.

Remarkably, our results suggest that TMA—unlike its liver co-metabolite trimethylamine N-oxide, which is associated with cardiovascular disease—improves immune tone and glycemic control in diet-induced obesity. Altogether, this study supports the emerging role of the kinome in the microbial–mammalian chemical crosstalk."

Gut microbes use common nutrient to fight type 2 diabetes

Microbial molecule offers new hope for diabetes (original news release)

Inhibition of IRAK4 by microbial trimethylamine blunts metabolic inflammation and ameliorates glycemic control (open access)

Fig. 1: Choline supplementation improves glucose homoeostasis and inflammation after 5 months of HFD [high fat diet]. 

Human oral Microbiome Evolution with Christina Warinner

Very recommendable! Excellent talk! Fascinating research!

Some newly discovered bacteria of the human mouth/teeth vanished suddenly about 200 years ago after having been with humans for about 40,000 years or so.

Microbiome may determine the temperament of babies

Amazing stuff! I am not sure this study resolved the chicken and egg issue or what came first. Did the microbiome influence the temperament or vice versa.

"... a new preprint, may be differences in their microbiomes.

Previous studies have drawn connections between microbiome composition and certain temperament traits. 

But it’s hard to tell the chicken from the egg: Do kids who behave certain ways end up with a specific mix of microbes, or do some microbes influence the way kids behave? ...

They gathered four exuberant 2.5-year-old toddlers and four more inhibited ones. ... The team obtained fecal samples from all the toddlers, then prepared a bunch of rats for a poo transfusion by essentially rinsing the microbes from their bowels before giving them a filtered stool sample or a sham control, followed by booster inoculations 2 and 3 days later.

Rats that received exuberant toddler poo were more exploratory in standard lab tests than both the rats that received samples from the inhibited kids and the control rats. 

Intriguingly, although the rats that received the inhibited kids’ stools didn’t show significant behavioral differences from the controls, a part of their brains showed reduced dopamine signaling, which could indicate that they felt less “reward” from joyful activities. ..."

From the abstract:

"Background

Behavioural phenotypes have previously been transferred via faecal microbiota transplantation (FMT) from patients with psychiatric disorders to rodents. Studies indicate that the gut microbiota composition may be linked to certain temperament traits, defined as biologically-based differences in emotional reactivity and self-regulation. Here, we aimed to determine if the gut microbiota plays a role in temperament using an FMT approach. We focused on the temperament traits of exuberance, defined as positive reactivity, decreased behavioural inhibition, and high behavioural approach tendencies.

Methods

Faeces from 2.5-year-old toddlers from FinnBrain Birth Cohort Study with high exuberance/approach or high behavioural inhibition in the LabTAB bubbles-episode was transferred to juvenile male Sprague Dawley rats (age 22/23 days). Behaviour of the rat recipients (n=53) was assessed using the novel non-social arena, novel social arena, hole board test for exploratory behaviour, social approach-avoidance test, and forced swim test. The faecal pellets collected from the rodents were analyzed with 16s rRNA sequencing and faecal samples from the sample of toddlers (which included the donors, n=176) were analysed using short-read metagenomic sequencing. The striatum and prefrontal cortex from the rodents’ brains were analysed post-mortem using RNAseq.

Results

Microbiome from toddlers with high exuberance traits induced increased exploratory behaviour compared to vehicle-controls and rats receiving faeces from inhibited toddlers.

Locomotor activity, social, and depressive-like behaviour remained unaffected. We noted a downregulation of the dopamine synapse pathway within the striatum of the rats that received faeces from the inhibited trait donors compared with vehicle-controls. Faecal microbiota of rats receiving faeces from the same donor resembled more each other than rats from a different cage. Clostridium species AM29 11AC in toddler microbiome was positively related to exuberance, but there were no cross-sectional associations between faecal metabolites in the human sample.

Conclusions

FMT from exuberant toddlers lead to altered exploratory-related behaviour in rats."

ScienceAdviser

Faecal transplantation from exuberant toddlers increases exploratory behaviour in rats (preprint, open access)

Figure 1. Schematic of the animal experiment timeline. 

Figure 3. Pathway analysis of differentially expressed genes in striatum in recipients of inhibited toddler’s faeces vs controls were not statistically significant.

Study finds link between gut microbiome and the placenta in pregnant women

Amazing stuff!

"New research in mice shows that a species of gut bacteria, Bifidobacterium breve, regulates the placental production of hormones which are critical for healthy pregnancy.

Pregnant mice without B. breve in their guts were also found to experience a higher rate of complications and increased early foetal loss.

B. breve occurs naturally in the human and mouse gut microbiome and increases in late pregnancy in both species. But stress or obesity in pregnant [mice or women] can alter its abundance. ..."

"Pregnant women with plenty of 'good' gut bacteria may have stronger, healthier pregnancies, according to new research.  

For the first time, scientists have shown that beneficial bacteria helps regulate placental hormones essential for supporting a developing baby. ..."

From the abstract:

"Background

Recent studies have shown that the maternal gut microbiota can regulate placental growth, particularly the transport region, in association with fetal growth. However, the specific role of certain microorganisms in modulating the hormonal production of the placenta, which is critical for supporting fetal development and maintaining a healthy pregnancy, remains largely unexplored. In this context, the objective of this study is to determine whether the maternal colonisation with the early life gut bacterium Bifidobacterium breve UCC2003 regulates placental endocrine function.

Methods

Pregnant germ-free mice were colonized with or without Bifidobacterium breve UCC2003 (BIF) during pregnancy. The endocrine region of the placenta (junctional zone, Jz) was collected to assess its metabolic profile using metabolomics, the expression of key nutrient uptake genes, hormones and synthetic genes by qPCR, and proteome using LC-MS/MS.

Results

BIF colonised dams had increased lactate and taurine concentrations in the placental Jz. BIF presence was also associated with upregulated expression of nutrient carriers, particularly those involved in large neutral amino acid and monocarboxylate uptake (e.g., Slc7a8 and Slc16a4).

Additionally, key hormones, such as prolactins and pregnancy-specific glycoproteins, were upregulated. The Jz proteome was changed in BIF colonised dams, with over 400 proteins dysregulated. Pathway analysis revealed more than 150 biological processes were altered, including transcriptional activity, protein synthesis, cell cycle progression, and metabolic regulation. Proteins regulated by BIF in the placental Jz were correlated with fetal growth and nutrient levels (namely glucose). Notably, maternal-associated BIF reduced the number of fetal resorptions (early fetal loss).

Conclusions

In germ-free mice, maternal-associated gut Bifidobacterium breve UCC2003 regulates placental endocrine capacity, by altering its metabolic profile and ability to produce endocrine factors. This study provides the first clear evidence that the maternal gut microbiota not only influences placental transport function, but also regulates its endocrine outputs."

Study finds link between gut microbiome and the placenta

‘Good’ gut bacteria boosts placenta for healthier pregnancy (original news release) "Cambridge scientists discover how probiotics may help prevent miscarriages, gestational diabetes and preeclampsia"

Placental endocrine function is controlled by maternal gut Bifidobacterium in germ-free mice (open access)

Fig. 1 Maternal B. breve supplementation induces changes in specific metabolites and nutrient carriers in the endocrine zone of the mouse placenta.

27 oral microbes linked to a greater risk of developing pancreatic cancer by 3.5 times

Amazing stuff! Cancer is history (soon)!

Does a daily mouthwash with antiseptics help? We need another study! 😊

"For the first time, scientists have identified 27 bacteria and fungi living in our mouths that are implicated in the development of pancreatic cancer. Collectively, housing all of the bad microbes increases one’s risk of the deadly disease by 250% – or 3.5 times higher – compared to the general population.

Researchers ... sampled the saliva of 122,000 healthy US men and women, who took part in the American Cancer Society Cancer Prevention Study II and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Samples were collected at baseline, and participants were followed for an average of nine years, with any records of tumors added to the data. ..."

"Among the hundreds of species of bacteria and fungi that live in people’s mouths, 27 have been collectively tied to a 3.5 times greater risk of developing pancreatic cancer ...

Experts have long observed that those with poor oral health are more vulnerable to pancreatic cancer than those with healthier mouths. More recently, scientists have uncovered a mechanism that could help explain this connection, finding that bacteria can travel through swallowed saliva into the pancreas, an organ that helps with digestion. ...

Last year, the same team of scientists uncovered a link between certain oral bacteria and a heightened risk of developing head and neck squamous cell carcinoma, a group of cancers that arise in the mouth and throat.

The researchers had also conducted a small study in 2016 that tied microbes living in the mouth to pancreatic cancer, but could not identify precise bacterial species. ..."

From the key points and abstract:

"Key Points

Question

Is the prediagnostic oral bacterial and fungal microbiome associated with the subsequent development of pancreatic cancer?

Findings

In this cohort study including 122 000 individuals, 3 oral bacterial periodontal pathogens, an additional 20 bacteria, and 4 fungi were identified, which together conferred a more than 3-fold increase in the risk for pancreatic cancer.

Meaning

The oral fungal and bacterial microbiotas may serve as readily accessible, noninvasive biomarkers for subsequent pancreatic cancer risk to identify individuals at high risk of pancreatic cancer.

Abstract

Importance

The oral microbiota may be involved in the development of pancreatic cancer, yet current evidence is largely limited to bacterial 16S amplicon sequencing and small retrospective case-control studies.

Objective

To test whether the oral bacterial and fungal microbiome is associated with the subsequent development of pancreatic cancer.

Design, Setting, and Participants

This cohort study used data from 2 epidemiological cohorts: the American Cancer Society Cancer Prevention Study-II Nutrition Cohort and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Among cohort participants who provided oral samples, those who prospectively developed pancreatic cancer were identified during follow-up.

Control participants who remained free of cancer were selected by 1:1 frequency matching on cohort, 5-year age band, sex, race and ethnicity, and time since oral sample collection.

Data were collected from August 2023 to September 2024, and data were analyzed from August 2023 to January 2025.

Exposures

The oral bacterial and fungal microbiome were characterized via whole-genome shotgun sequencing and internal transcribed spacer (ITS) sequencing, respectively.

The association of periodontal pathogens of the red complex (Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia) and orange complex (Fusobacterium nucleatum, F periodonticum, Prevotella intermedia, P nigrescens, Parvimonas micra, Eubacterium nodatum, Campylobacter shower, and C gracilis) with pancreatic cancer was tested via logistic regression.

The association of the microbiome-wide bacterial and fungal taxa with pancreatic cancer was assessed by Analysis of Compositions of Microbiomes With Bias Correction 2 (ANCOM-BC2).

Microbial risk scores (MRS) for pancreatic cancer were calculated from the risk-associated bacterial and fungal species.

Main Outcomes and Measures

Pancreatic cancer incidence.

Results

Of 122 000 cohort participants who provided samples, 445 developed pancreatic cancer over a median (IQR) follow-up of 8.8 (4.9-13.4) years and were matched with 445 controls.

Of these 890 participants, 474 (53.3%) were male, and the mean (SD) age was 67.2 (7.5) years.

Three oral bacterial periodontal pathogens—P gingivalis, E nodatum, and P micra—were associated with increased risk of pancreatic cancer.

A bacteriome-wide scan revealed 8 oral bacteria associated with decreased and 13 oral bacteria associated with increased risk of pancreatic cancer (false discovery rate–adjusted Q statistic less than .05).

Of the fungi, genus Candida was associated with increased risk of pancreatic cancer.

The MRS, based on 27 oral species, was associated with an increase in pancreatic cancer risk (multivariate odds ratio per 1-SD increase in MRS, 3.44; 95% CI, 2.63-4.51).

Conclusions and Relevance

In this cohort study, oral bacteria and fungi were significant risk factors for pancreatic cancer development. Oral microbiota hold promise as biomarkers to identify individuals at high risk of pancreatic cancer, potentially contributing to personalized prevention."

Oral bacteria linked to higher pancreatic cancer risk "27 oral microbes drive 250% rise in pancreatic cancer risk"

Oral Microbes Linked to Increased Risk of Pancreatic Cancer

Oral Bacterial and Fungal Microbiome and Subsequent Risk for Pancreatic Cancer (no public access)

Giant DNA chunks found inside bacteria in the oral microbiome of human saliva surprise scientists

Amazing stuff! I am scratching my head and wonder why this was never before investigated or discovered! Lack of technology/methods?

"... These ... genetic pieces are known as extrachromosomal DNA (ecDNA) and, while they can play a role in the development and growth of cancerous tumors, they can also help maintain our telomeres, protective caps at the ends of our chromosomes involved in the aging process. ...

Seeking to explore the possibility of ecDNA existing in human saliva, researchers ... got a "big" surprise as they carried out a new study. Not only did they find ecDNA in the oral microbiome hidden inside bacteria known as Streptococcus salivarius, they found comparatively giant chunks of it. They named these chunks "Inocles." ..."

"Researchers ... have made a surprising discovery hiding in people’s mouths: Inocles, giant DNA elements that had previously escaped detection. These appear to play a central role in helping bacteria adapt to the constantly changing environment of the mouth. The findings provide fresh insight into how oral bacteria colonize and persist in humans, with potential implications for health, disease and microbiome research. ...

“We know there are a lot of different kinds of bacteria in the oral microbiome, but many of their functions and means of carrying out those functions are still unknown,” ... “By exploring this, we discovered Inocles, an example of extrachromosomal DNA — chunks of DNA that exist in cells, in this case bacteria, but outside their main DNA. ..."

From the abstract:

"Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown.

Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly.

Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population.

These ECEs, which we named, “Inocles”, are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium.

Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells.

Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment."

Huge DNA chunks found in human saliva surprise scientists

Giant DNA discovered hiding in your mouth Three-quarters of all people may host newly identified genetic material called Inocles, which could impact research on oral health, immunity, and even cancer risk (original news release)

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome (open access)

Functional characterization of Inocle. A schematic describing what Inocles do and where they’re found. It shows the kinds of roles its genes might have, and how those jobs could be connected to things happening in the human body.

Fig. 3: Identification and characterizations of the four Inocle taxa.