How gut bacteria controls gene expression through “interspecies communication”

Imagine a tiny microbe living inside you with the power to control the activity of your DNA. Scientists are increasingly discovering how much control our gut bacteria may actually have over us, with a new study describing how individual bacteria can secrete a molecule that literally turns genes off or on.

Epigenetics is a field of study looking at what mechanisms turn specific genes on or off. Separate to our hard-coded DNA, certain external influences can either enhance the expression of a gene or silence it altogether. We know that gut bacteria can modulate the expression of certain genes, potentially influencing the onset of a variety of autoimmune diseases. However, it is unclear exactly how these tiny microbes actually do this.

A fascinating new study has revealed for the first time that certain bacteria can secrete a compound called nitric oxide which is known to regulate gene expression. The researchers describe this interaction between host and bacteria as a form of “interspecies communication.”

Nitric oxide is a gas molecule fundamental to cellular signaling and health. It was only recently, back in 2013, that scientists discovered the molecule’s epigenetic role. The new research set out to understand whether bacteria uses this same network to alter its hosts DNA.

The study used C. elegans worms to examine how this process could work. The worms were administered bacteria known to produce nitric oxide and then the researchers set their focus on a specific protein called ALG-1. This protein is known to play a crucial role in controlling the expression of several genes.

The study revealed that when the bacteria produced excessive volumes of nitric oxide it fundamentally impaired the function of ALG-1 and disrupted the worm’s healthy development. The worm essentially grew deformed reproductive organs and died.

Jonathan Stamler, senior author on the new study, suggests in the real world such an extreme outcome would not pragmatically happen. It’s obviously not in the best interests of either the host or the bacteria to stimulate a biological mechanism that would cause both organisms to die.

“The worm is going to be able to stop eating the bacteria that make the nitric oxide, or it will begin to eat different bacteria that makes less nitric oxide, or change its environment, or countless other adaptations,” says Stamler. “But by the same token, too much nitric oxide produced by our microbiome may cause disease or developmental problems in the fetus.”

As with much microbiome research these days, the study raises more questions that it answers, and it is not entirely clear how this specific mechanism can be harnessed into a useful clinical treatment. Stamler suggests that now this mechanism has been identified, researchers can potentially home in on specific human health outcomes it may be influencing. From that point, future treatments could conceivably modulate this nitric oxide pathway in the gut to benefit human health.

“I now think of this therapeutically, as a drug,” says Stamler. “There are tremendous opportunities to manipulate nitric oxide to improve human health.”

The new study was published in the journal Cell.

Almost 2,000 previously unknown bacteria discovered in the human gut

Nearly 2,000 previously unknown species of gut bacteria have been discovered by a team of international researchers using novel metagenomic data. The discovery greatly expands our knowledge of the microbial species living inside us, and establishes new computational methods to help reconstruct and identify undiscovered bacterial genomes.

Inside all of us there lies a vast population of trillions of microorganisms. Our gut in particular plays host to the largest microbial population and is home to potentially trillions of microbes. Although the vast majority of this bacteria consists of just 30 or 40 different species, it is still very much unknown exactly how many different kinds of bacteria live inside us.

Different estimates in bacterial species diversity range from 1,000 to 40,000, many of which are still yet to be identified. These undiscovered species may not survive well outside of the gut, or may be unique to geographical populations. This latest study set out to characterize undiscovered bacteria using new metagenomic analysis – a method that tracks potential unidentified genomic traces in human microbiome samples.

“Computational methods allow us to understand bacteria that we cannot yet culture in the lab,” explains Rob Finn, one of the researchers working on the project. “Using metagenomics to reconstruct bacterial genomes is a bit like reconstructing hundreds of puzzles after mixing all the pieces together, without knowing what the final image is meant to look like, and after completely removing a few pieces from the mix just to make it that bit harder.”

The research ultimately homed in on 1,952 unclassified metagenomic samples indicating previously unknown bacterial species. Almost half of these could not be classified to a known genus, meaning they may be entirely new families or genera. A great deal of the new data was also noted as coming from diverse geographical populations, suggesting future research needs to better study broader populations of people.

“We are seeing a lot of the same bacterial species crop up in the data from European and North American populations,” says Finn. “However, the few South American and African datasets we had access to for this study revealed significant diversity not present in the former populations. This suggests that collecting data from underrepresented populations is essential if we want to achieve a truly comprehensive picture of the composition of the human gut.”

Little is known about the newly discovered bacteria, and they are still yet to be cultured in laboratory conditions or properly classified. However, these new computational methods are undeniably allowing scientists to identify bacterial species that previously remained hidden from the usual analysis methods. Microbiome research may revolutionize medicine in the future but it is still certainly in a nascent stage, and the first step we need to complete is comprehensively identifying the diversity of bacteria that live inside us.

“Research such as this is helping us create a so-called blueprint of the human gut, which in the future could help us understand human health and disease better and could even guide diagnosis and treatment of gastrointestinal diseases,” adds group leader on the project, Trevor Lawley.

The new researcher was published in the journal Nature.

EM and its Impact on the Quality of Compost

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When composting organic materials we are looking to re-purpose large amounts of waste by-products and also have an end product that is going to enhance soils. Composting is the decomposition of organic solid wastes. The composting process involves decomposition of organic material into a humus-like material, which provides food for our soils and nutrients for plants.

Traditional composting requires four ingredients to work:

Carbon — for energy; the microbial oxidation of carbon produces the heat, if included at suggested levels. High carbon materials tend to be brown and dry.
Nitrogen — to grow and reproduce more organisms to oxidize the carbon. High nitrogen materials tend to be green (or colorful, such as fruits and vegetables) and wet.
Oxygen — for oxidizing the carbon, the decomposition process.
Water — in the right amounts to maintain activity without causing anaerobic conditions.
EM can also be used in compost to enhance the process and the decomposition of the organic materials. In traditional compost EM will effectively enhance your aerobic compost system. It will give you a more complete breakdown of organic matter in your compost and also give you a higher quality. This means you will get a higher growth index and therefore better growth rate from plants as a result. What I want to highlight is a study which aims to assess the effect of EM application on the composting process of rice straw with goat manure and green waste and to evaluate the quality of both compost treatments. There are two treatment piles in this study, in which one pile was applied with EM and another pile without EM. Each treatment was replicated three times with 90 days of composting duration.

The results showed that the application of EM in compost increases the macro and micronutrient content. The following parameters support this conclusion: compost applied with EM has more N, P and K content (P < 0.05) compared to compost without EM. Although the Fe in compost with EM is much higher (P < 0.05) than in the compost without EM, for Zn and Cu, there is no significant difference between treatments. This study suggests that the application of EM is suitable to increase the mineralisation in the composting process.

Changes in N content in composting mixtures with days.


Changes in P content in composting mixtures with days.

Changes in K content in composting mixtures with days.

Follow this link to the full trial:

EM can also be used to produce a anaerobic compost. The EM anaerobic composting process is a fermentation gateway to very effective compost. The benefits over an aerobic composting system are that it doesn’t generate heat so therefore retains all of the energy usually lost. This makes it very effective and more digestible to the soil. More on Anaerobic composting here.


Effect of EM on Fungal Infections in the Soil

I stumbled across this paper recently as a client was asking about the effect of EM on Fusarium and I thought it would be relevant to a lot of our growers. This trial published in the Polish Journal of Natural Sciences in 2008 looked at the Effect of fungal infection and the application of the biological agent EM on the rate of photosynthesis and transpiration in pea (pisum sativum l.) leaves.

Field experiments conducted during the years 2003-2005 showed that the rate of photosynthesis and transpiration decreased as a result of pea infection by Peronospora viciae which set up the trial to see what the effect of different treatsments would be. The results showed that:

1. The tested biological agent (EM) reduced the incidence of pea diseases.

2. Foliar application of EM significantly increased the rate of photosynthesis in pea.

3. Soil application of EM, seed dressing and chemical control decreased the rate of photosynthesis in pea.

4. Seed dressing with the tested biological agent (EM) and chemical control caused a significant decrease in molar transpiration values in pea.

5. The occurrence of downy mildew of peas significantly reduced the rate of photosynthesis.

6. The occurrence of downy mildew and ascochytosis of peas decreased the rate of molar transpiration.



World’s Largest Study on the Human Gut Reveals Connection to These Mental Health Problems

The largest study of all time on the human gut has been underway since 2012 and they are discovering some remarkable things.

Scientists have been collecting fecal samples from around the world and tirelessly analyzing and comparing samples. Believe it or not, people have been paying $99 each to send their own stool samples along with oral and skin samples of bacteria to the research scientists. They also answer questions including those about their diet and lifestyle.

Three PhDs, Rob Knight, Jeff Leach, and Jack Gilbert founded the American Gut Project in 2012 on a quest to discover more about the human microbiome, more commonly referred to as ‘the gut’.

The microbiome is essentially a diverse world of different kinds of bacteria that live within our digestive system. These bacteria, some beneficial, some villainous, form a microscopic world of activity that can either fight disease, or give it the perfect atmosphere to thrive.

Many health problems have been linked to certain types of bacteria that live in our microbiome that are either foreign invaders or simply types that overgrow their beneficial bacterial counterpart and ruin the natural healthy balance.

So Far the American Gut Project Has Made the Following Discoveries

Firstly, they have noted that people who eat a wider variety of plants have a wider variety of bacteria in their microbiome. They haven’t necessarily stated that it’s better to have a more complex microbiome but they have noted that those people eating extra plants have less antibiotic resistance, which is noteworthy for sure.

This lack of antibiotic resistance could simply have to do with the subjects who favor a wide variety of plants eating fewer packaged and processed foods that contain animals raised with antibiotics.

The scientists have also discovered that people who have similar bacterial profiles tend to suffer from the same health problems. This was determined by matching subjects to controls with the same age, gender, and body mass index that did not suffer from the ailment.

Gut Bacteria and Mental Health

Some of the health problems that were found to have subjects in common with similar bacterial profiles were mental health problems, take PTSD for instance. Post-traumatic stress disorder (PTSD), schizophrenia, depression, or bipolar disorder have stood out in the study thus far as having a very strong link to gut bacteria diversity.

In other words, subjects who suffer from PTSD tend to have the same bacteria in their digestive tract. The same goes for depression and bipolar disorder.

When you consider how many mental and physical health symptoms are linked to nutritional deficiencies and also how vital a role our gut plays in absorbing and utilizing nutrients, this all starts to make a lot of sense.

Medical News Today puts it very well:

The results demonstrated that people who reported mental health issues had more bacteria in common with other people who reported similar problems than they did with the controls.

This association was strong regardless of gender, age, or geographical location. Also, the research suggests that some types of bacteria may be more prevalent in people who live with depression.

The MNT article also points out that a certain recent study found a connection between anxiety and a lack of healthy gut microbes. Another study discovered that certain bacteria are altered in people who suffer from PTSD.

“We observed a much greater microbial diversity than previous smaller studies found, and that suggests that if we look at more populations, we’ll see more diversity, which is important for defining the boundaries of the human microbiome,” said Daniel McDonald, PhD, the scientific director of the American Gut Project at UC San Diego School of Medicine.

The ultimate goal of the project is to map the human microbiome. Essentially it is to be able to tell people, ‘Alright, you’re suffering from this ailment, well here’s what is missing or different about your gut bacteria and here’s what you need to eat (or not eat) in order to fix it.’

Dr. Rob Knight said, “The human microbiome is complex, but the more samples we get, the sooner we will be able to unravel the many ways the microbiome is associated with various health and disease states.”


Links between gut microbes and depression strengthened

The once-wild idea that intestinal bacteria influence mental health has transformed into a major research pursuit.

Just ten years ago, the idea that microorganisms in the human gut could influence the brain was often dismissed as wild. Not any more.

Links between the central nervous system and the trillions of bacteria in the gut — the microbiota — are now a major focus of research, public interest and press coverage. But how does this ‘gut–brain axis’ work? The mechanisms by which microorganisms shape aspects of brain functioning such as memory and social behaviour, and how they might contribute to conditions such as depression and neurodegenerative disease, are tenuous and often controversial.

Much of what we know so far is based on studies showing correlations between specific gut bacteria, their metabolites and neurological symptoms. But these correlations do not prove cause and effect. Many studies use animal models, which don’t accurately mirror human traits or behaviours. Human studies have been limited: they’re usually based on relatively small numbers of people, and might not control for a wealth of confounding factors — such as unusual diets, antibiotics or antidepressants — that can affect the microbiota.

A study published this week in Nature Microbiology tackles some of these issues (M. Valles-Colomer et al. Nature Microbiol.; 2019). The authors used DNA sequencing to analyse microbiota in the faeces of more than 1,000 people enrolled in Belgium’s Flemish Gut Flora Project. The team then correlated different microbial taxa with the participants’ quality of life and incidence of depression, using self-reported and physician-supplied diagnoses. The researchers validated the findings in an independent cohort of 1,063 individuals in the Netherlands’ LifeLines DEEP project. Finally, they mined the data to generate a catalogue describing the microbiota’s capacity to produce or degrade molecules that can interact with the human nervous system.

The researchers found that two groups of bacteria, Coprococcus and Dialister, were reduced in people with depression. And they saw a positive correlation between quality of life and the potential ability of the gut microbiome to synthesize a breakdown product of the neurotransmitter dopamine, called 3,4-dihydroxyphenylacetic acid. The results are some of the strongest yet to show that a person’s microbiota can influence their mental health.

These are still correlations, not causes. Researchers know that the gut microbiota can produce or stimulate the production of neurotransmitters and neuroactive compounds, such as serotonin, GABA and dopamine, and that these compounds can modulate bacterial growth. The challenge now is to find out whether, and how, these microbe-derived molecules can interact with the human central nervous system, and whether that alters a person’s behaviour or risk of disease. At least now, answering these questions is a wise pursuit, not a wild one.

Nature 566, 7 (2019)


Workshop Bokashi maken voor de tuin

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Roeach organiseert twee informatieve workshops over Bokashi met de Bokashi-keukenemmer.

Bokashi is het Japanse woord voor “goed gefermenteerd organisch materiaal”. Het is een manier om je organische resten om te zetten tot een zeer rijke bodemverbeteraar. Bokashi is het resultaat van een eeuwenoude techniek: fermentatie. Janet Pasveer van Roeach legt uit: “Tine en ik werken al enige tijd met Bokashi. In onze perma-tuin voeden we de bodem met Bokashi. Je doet groenteafval in een Bokashi-emmer, voegt effectieve micro-organismen in de vorm van Bokashi-starter toe en drukt het allemaal goed aan. Door het verwerken van je resten zonder zuurstof, maak je van je eigen organische resten een waardevolle bodemverbeteraar. De firma Agriton is al 25 jaar, wereldwijd, bezig met dit mooie product. Simone Vos van EM Agriton Natuurlijk Actief komt, samen met ons, op twee avonden uitleg geven over deze manier om je groenteresten te verwerken tot voeding voor de bodem”. De kosten zijn € 5,- p.p. De avonden zijn op:

  • dinsdagavond 26 februari in Leeuwarden (hier is nog plek)
  • woensdagavond 6 maart in Joure (is al bijna volgeboekt)

Wil je komen? Meld je dan vóór 24 februari aan:
Voor Leeuwarden:
Voor Joure:

Voor meer info kijk ook op Roeach.