HerbSprout Microbiome Blog -



Herbsprout is a webblog and podcast dedicated to sharing about the health benefits of herbs, food, innovations, and our gut microbiome. Herbsprout seeks to bridge the vast chasm dividing the mainstream medical community, alternative medicine, and Asian medicine, especially TCM (China), Ayurveda (India), and eJIM (Japan).

Profile: Viome’s Genetic Code Principles

Viome expands on the genetic code principles. Viome is a personalized “life optimization” healthcare solution using complex biological data and the most advanced, cutting edge technology originating from Los Alamos Laboratory. Viome takes highly customized information about how the body functions at a molecular and microscopic level. In addition to the aforementioned data driven analyses, there are three pillars to the Viome solution, according to their website (see http://viome.com), using microbiome gene expression, gut metabolites, metabolome, and genetics. Here is a step-by-step overview of the Viome solution:

1) SCIENCE: Viome conducts a comprehensive metabolome and microbiome analysis (of their customer’s stool sample) resulting in high resolution complex biological data at a molecular level using a cost effective proprietary process.

2) DATA: Viome processes the customer's samples in their state- of- the- art facilities to help generate a picture of your body at a molecular level. The company combines that with their doctor-trained artificial intelligence (AI) engine to generate actionable diet, exercise, and nutrient recommendations.

3) INSIGHT: Viome offers an artificially intelligent, contextually relevant recommendation engine.

Why Viome is a leader in healthcare innovation is partly because it recognizes that the lion's share of a person's genetics resides in their gut, a whopping upwards of 90%! No other company has achieved the breadth of genetic makeup in the gut that Viome has and nor as deep and extensive data analysis of the microbial content of the body.

1. Outside Disruptors - Besides the revolutionary disruptive nature of their research, a few business takeaways here are that marketplace disruptions as in the case of Viome, can come from industry outsiders like Naveen Jain.

1. Research Incubation - Technologies such as the military from Los Alamos labs and other major research-based institutions and universities are evolving to become leading incubators to driving the entrepreneurial innovations. Pre-existing technologies and creations at the academic and laboratory level are common sources of marketplace innovations in healthcare, as in the case of Jain’s Viome, Silicon Valley's CRISPR Caribou Biosciences, and BioHub. This again reinforces the assertion that disruptive innovations can come from anywhere.

1. D2C Applications - Direct-to-consumer (D2C) applications which remove middlemen such as those of Viome and Ubiome offer more efficient and cost effective solution for health care consumers. It is not always about "reinventing the wheel" as it is "'repurposing' or 're- imagining' the wheel", as Jain likes to say. Technology and ideas can be repurposed for another business sector and be a disruptive innovation.

Circling back to the original themes of this chapter, Viome and the study of the enteric nervous system, gut microbiome research, and applying it to personalized healthcare, has effectively created what may be greatest disruptive innovation of this generation.

Viome’s Metatranscriptome Sequencing.
It is easy for a consumer to confuse different approaches to microbiome testing. Hopefully, the following chart will shed some light on the key differences. Viome has invested extensively in a new form of microbiome sequencing called Metatranscriptome Sequencing as opposed to competitor like Ubiome (now in bankruptcy), Illumina and other 16S Sequencing companies:

Head-to-Head Comparison of Microbiome Testing:

16S Sequencing:

● Identifies only a fraction of your gut bacteria; unable to identify nonbacterial microorganisms
● Low resolution (genus level only)
● Does not determine microbe function
● Unreliable; sequencing the same sample twice can yield very different results
● Unable to identify microbial metabolites, which are key for maintaining health
● Low resolution and lack of functional data preclude any actionable recommendations

Viome’s Meta-Transcriptome Sequencing:

● Identifies all bacteria and all other living organisms in your gut: viruses, archaea, yeast, fungi, parasites, and bacteriophages2
● High resolution (species & strain level)
● Quantifies the biochemical activities of all gut microorganisms
● Unbiased analysis, minimized variation in results
● Identifies which metabolites are being produced and which are missing
● Allows correlation of microbes and their functions with common chronic conditions, so actionable recommendations can be made


Links between gut health and mania/ bi-polar disorder

Links between gut health and ...
A September 04, 2019 article in the New Scientist suggests that eating a proper amount of psychobiotics, a derivation of probiotics, can improve one's mental health. (see
https://www.newscientist.com/article/mg24332460-500-how-what-you-eat-directly-influences-your-mental-health/ ). Probiotics may help improve a variety of mental health conditions, in part due to an anti-inflammatory effect, including those suffering from manic depression and bi-polar (BP) disorders. Psychobiotics are believed to mitigate chemical imbalance in the brain, and offer an alternative to drug treatment, claims the article.

Lithium has become the most accepted remedy used for treating BP. Studies such as the 2020 Neuropsychobiology report have found little connection between lithium intake and Escherichia coli or Lactobacillus rhamnosus, except that it appears to support a stronger richness and diversity of these species. However, they found a noticeable increase in Clostridium, Peptoclostridium, Intestinibacter, and Christenellaceae following lithium treatment (see https://www.karger.com/Article/FullText/504496 ). These results suggest a connection between our gut microbiota and BP treatment using lithium.


Researchers from Johns Hopkins University School of Medicine did a study to determine if probiotics could help recently discharged manic patients, according to a Harvard Health Publishing blog of June 25, 2018. Two groups of 33 patients were given Lactobacillus and Bifidobacterium species to one group and a placebo to the second group over a 24 week period.

The results for the rates of rehospitalization were 51.1% in the placebo group and 24.2% in the group who took probiotics. On average, the reduction in readmission was 74% lower in the probiotic group, and a 90% reduction of hospitalization in the group with the highest inflammation score. Additionally, patients who took probiotics and were rehospitalized stayed in the hospital on average 2.8 days, compared with 8.3 days for those taking placebo.

A Nature article in February 2019 referenced human trials that found connections between coprococcus and dialister bacteria, with lower levels contributing to mental health issues and specifically depression (see article, https://www.nature.com/articles/s41564-018-0337-x ).

While tests on mice are less reliable than human trials, they can effectively make connections between similar human functions. For example, The Scientist article reported that study coauthor Julio Licinio, a psychiatrist at SUNY Upstate Medical University in Syracuse made fecal transplants of schizophrenic mice that verified lower glutamate, glutamine, and GABA in their hippocampi. These are key amino acid neurotransmitters that are essential for brain function (see https://www.the-scientist.com/news-opinion/gut-microbes-may-play-a-role-in-mental-health-disorders-66039/amp ).

What scientists can say with some accuracy is that there is a link between our gut bacteria and mental health. One step further, they've identified specific species of bacteria, keystone species such as bifidobacteria and lesser known species such as coprococcus and dialister bacteria. The next steps will be to prove efficacy and FDA approval as a form of treatment in mental health patients. When this might be achieved is still to be determined, but scientists are getting closer.
#herbs #herbalmedicine #plantnutrition #health #mentalhealth #spices #diet #gutmicrobiome #bacteria #healthinnovation #psychobiotics #probiotics #datascience #ai #healthtech


"I am who I am" because of my gut bugs?

"I am who I am" because of ...
A February 13, 2020 article published by Psychology Central claims that our personality is shaped by the bugs, or microbes, in our gut.

Microbial diversity seems to be the key indicator to a healthy personality. Strong microbial diversity supports good mental health while a low microbial diversity points toward mental health problems such as autism or neuroticism. "Personality is both inherited and influenced by one’s environment. And the environment inside humans may matter just as much as the external environment", says Katerina Johnson in the Inverse article, and a research associate at Oxford. It is believed based on ongoing research that a lack of the Akkermansia, Lactococcus, and Osciollospir bacteria in our gut shows a tendency to autism, says the report (source: https://www.inverse.com/mind-body/microbiome-mental-health-study-links-gut-bacteria-personality/amp ). Conversely, a study of primates shows that social interactions can promote gut microbiome diversity, adds Dr. Johnson (see https://psychcentral.com/news/2020/02/13/gut-bacteria-may-be-linked-to-personality-traits/154172.html ). So the research suggests it goes both ways, even though it is not explicitly stated in these articles. We are predisposed in part to being social or anti-social based on the pre-existing level of microbiome diversity in our gut, but we can promote healthy microbiome diversity in our gut by being more social.

BBC Science reported in December 2019 that probiotics and prebiotics by nurturing and nourishing our gut bugs can help ease stress and anxiety, even aid in reducing other mental health risks. (See article, https://www.sciencefocus.com/the-human-body/psychobiotics-your-microbiome-has-the-potential-to-improve-your-mental-health-not-just-your-gut-heath/amp/ ). So yes, be at ease; the bottom line is we do have self determination; we can steer and shape and mold our own personality. . . with a little help from our microbiome friends.

#microbiome #guthealth #gutbacteria #braingutaxis #autism #mentalhealth


Our microbiota changes over time as we age

According to the PLOS Pathogens Journal July 25, 2019 article "Microbiome evolution during host aging ", our gut microbiota "undergoes dynamic changes through time as it integrates and responds to signals from the environment," and our genetics has very little to do with these changes. However, what we eat, what types of drugs we consume, even our social and physical environment have a significant impact on the microbial content of our gut.

These microbiota remain dynamic throughout our lives, continually changing as we grow older. It is possible, according to the report, that as we age, the changes in our gut microbiome may contribute to our aging and increased vulnerability to disease and frailty, thought our understanding of these changes are still not well understood. Just like our bodies age, so do our gut microbiome, and they weaken over time and incur damage. Our younger bacteria support a stronger immune defense, while the efficacy of aging bacteria is compromised. Younger bacterial strains carry adaptive variants and mutations, enabling it to adapt to changing environments.

More details around studies backing these assertions are available here, https://doi.org/10.1371/journal.ppat.1007727 .


Stress and "The Gut-Brain Connection”

The Gut- Brain axis (source: ... The Gut- Brain axis (source: deposit photos).
An October 2019 abstract published by the National Institute of Health (NIH) suggests that managing our stress levels in all phases of our lives from childhood to old age is key to a healthy microbiota gut-brain axis. As we grow up other factors affect our gut microbiome health such as infections, use of antibiotics, nutrition, stress, among others. Stress can particularly impact our latter years as our microbial diversity goes way down over time (see https://www.ncbi.nlm.nih.gov/pubmed/31460832 ).

The way we look at the brain and brain research has completely flipped on its head since a few decades ago when scientists first discovered that “messenger molecules” for the brain were circulating throughout the body in the bloodstream. None are more pervasive and penetrating than what scientists have found in the activities of microbiomes in the gut. Our bodies have more microbiome DNA than human DNA. The total human genome comprises around 20,000 genes, while the total microbiome DNA in our bodies total two to 20 million genes.

“Every cell is eavesdropping on the brain’s activity, sending and receiving messages identical to those that the brain processes,” says Deepak Chopra and contributing author Naveen Jain in their Huffington Post article “Will the Gut-Brain Connection Revolutionize Wellness?” (September 11, 2017; see http://www.huffingtonpost.com/entry/will-the-gut-brain-connection-revolutionize-wellness_us_59b6b598e4b0e4419674c375 ). In this article, Chopra goes so far as to say that all the common experiences we have are indicators of the brain’s connection to the gut -- “getting butterflies in your stomach when you feel nervous, overeating when you feel anxious, feeling dull and sluggish after taking an antibiotic, contracting stomach cramps before a competitive challenge, experiencing nausea or stomach upset from taking antidepressants.” Every major organ in the body from the heart to the stomach and liver combine to possess hundreds of millions of neurons with corresponding DNA, which again collectively makes up the “enteric nervous system”.

The bacteria inside our guts, microbiomes, include unlimited numbers of species and strains. They differ from person to person with limited or no relationship from person to person.” The known “messenger molecules” associated with the brain that circulate throughout the body in the bloodstream even produce neurotransmitters. Neurotransmitters are the chemicals our brain uses to communicate with the rest of the body. Every cell is eavesdropping on the brain’s activity, sending and receiving messages identical to those that the brain processes. For example, 90% of the well-known serotonin neurotransmitter is made in the body’s digestive tract, according to a 2015 report by CalTech (“Microbes Help Produce Serotonin in Gut”, April 09, 2015; http://m.caltech.edu/news/microbes-help-produce-serotonin-gut-46495 ). Serotonin is the chemical often referred to as the “happy chemical” and the balance of serotonin in our body influences our mood. A deficiency of serotonin can lead to depression.

Research is being administered about the influence of gut microbiomes on everything from autism, multiple sclerosis, PTSD, Parkinson’s Disease and brain health to cancer, obesity, diabetes and weight loss. It has become widespread as major research institutions and universities are conducting studies on the subject.

Scientists have found that differences in a person’s gut can be a clue to our specific health propensities, to cancers, but also something as immediate as our daily mood, behaviors, even happiness.

#gutmicrobiome #bacteria #healthinnovation #datascience #mindbody #brainresearch #neuroscience #healthtech


Benefits and Risks of taking probiotics

It is scientifically confirmed that microbes help us digest food, fight harmful bacteria, and regulate the immune system. But sometimes an imbalance of microbes occurs, leading to diarrhea and other health problems, so one should exercise caution when consuming Probiotic supplements. A January 20, 2020 article by Medical News Today warns that online misinformation about probiotics is common. It has become a $40 billion business and yet there remains a lack of scientific evidence to support the health benefits of certain probiotics, or their potential side effects. The article states that only "35% of online sites referenced scientific literature, only 25% listed potential side effects." (see article, https://www.medicalnewstoday.com/articles/amp/327510 ).

An August 20, 2019 report by Harvard University cautions the use of probiotic supplements, since they are not categorized as a drug by the FDA and do not undergo the same monitoring. The most common species of bacteria used in probiotics (among a potential 3,000 or so) are species of Lactobacillus or Bifidobacterium. These can be obtained by taking supplements or foods that have naturally live cultures in them such as sauerkraut, yogurt, kimchi and pickels. But it does not necessarily mean these foods or the supplements have the adequate amount of the key probiotics you might need that are unique to you. Symptoms may arise such as experiencing loose stool, but this should not be of major concern and should disappear in short order.



Diet and mindfulness therapy can help IBD patients, calls for further research

Diet and mindfulness therapy c...
A January 24, 2020 article in Healthline reveals a special "IBD-AID" diet that helps people with IBD (inflammatory bowel disease) who have a gut bacteria imbalance. The condition calls for eating a light protein diet such as fish, chicken, eggs, tofu, Greek yogurt, to be followed with refined grains, greens, beans, and well-cooked veggies. Herbsprout.com contacted Seattle Children's Hospital's Dr. David L. Suskind, a gastroenterologist, who agrees that "diet matters in both health and in disease." This means getting down to specifics; what herbs and foods address what health problems. Though not involved in the study himself, Dr. Suskind acknowledges ongoing research is needed on how gut health affects IBD. He said in Healthline, "diet has a huge impact for IBD." ( see https://www.healthline.com/health-news/microbiome-diet-may-help-ibd ).

Another study published by the Iranian Journal of Psychiatry, Tehran University of Medical Sciences, found basic advantages of mindfulness-based stress reduction therapy with emotion regulation on the quality of life and severity in patients IBS (irritable bowel syndrome).

The mindfulness included an increase in metacognitive awareness and employing techniques of one's increased acceptance of thoughts and emotions, rather than emotional regulation.

Seattle Children's Hospital's Dr. Suskind confirms that "we definitely need to focus on increasing the amount of research to better define what diet is the best for which individual and which condition." The Tehran University's test was a limited study of 24 patients and limited controls of patients such as diets, which can lead to inconclusive results. This is based on the July 2018 report, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178327/ .

An earlier blog by HerbSprout.com highlights clinical trials done by China Pharmaceutical University scientists pointing to how "Chinese herbs ginseng and coicis seed relieve ulcers, irritable bowel syndrome", https://en.bloguru.com/healthtech/357406/chinese-herbs-ginseng-and-coicis-seed .


Is there an Ayurveda, Gut Bacteria Connection?

An India Times article earlier this week had an interesting angle on Ayurveda and our gut microbiome. It suggests the three Ayurvedic states- vata, pitta, kapha - are connected to the state of our gut microbiome.

Yogesh Shouche, senior scientist at the National Centre for Cell Science (NCCS), Pune, asserts that vata people for example, have a higher amount of hydrogen sulphide (H2S) and methane gas in their body. Dr. Shouche says this is why people in the state of vata commonly carry the resulting symptoms such as upset stomach and gas.
(See https://punemirror.indiatimes.com/pune/others/ayurveda-gut-bacteria-correlated-experts/amp_articleshow/73621762.cms).

For your reference, here is a quick description of the three Ayurvedic states:

VATA is the sensory intake, communications and transport of information we receive from the outside world.

PITTA is the digesting, processing and metabolizing of that information.

KAPHA is the storing, growth, and memorizing of the information.


Chinese herbs ginseng and coicis seed relieve ulcers, irritable bowel syndrome

Coicix seed Coicix seed
Natural products play an important role in the improvement of gastrointestinal tract function. Several Chinese medicine products such as Red Ginseng and Semen Coicis were found to relieve the symptoms of ulcerative colitis (UC). After Red Ginseng and Semen Coicis treatment in rats, the structure of gut microbiota was altered, which may be beneficial for promoting the growth of probiotics, such as Bifidobacterium and Lactobacillus, and for inhibiting the growth of pathogenic bacteria. It is a Chinese medicine (TCM) and a nourishing food in China for the treatment of warts, chapped skin, rheumatism, neuralgia, inflammatory, and neoplastic diseases. Allay, or Coix seeds, Chinese pearl barley, pearl barley, semen coicis, yokuinin, 薏 苡仁 (yì yǐ rén), and 薏米 (yì mǐ), belongs to the family Gramineae.

In a double-blind, randomized clinical trial containing 54 patients, it was revealed that the combination of herbal medicine (Gwakhyangjeonggisan, GJS) and probiotics (Duolac7S, DUO) alleviated the symptoms of diarrhea-predominant irritable bowel syndrome (D-IBS) by changing the composition of gut microbiota. Beneficial intestinal microbe counts, including Bifidobacterium brevis, Bifidobacterium lactis, Streptococcus thermophilus, Lactobacillus rhamnosus, Lactobacillus plantarum, and Lactobacillus acidophilus, were synergistically enhanced by GJS combined with DUO, suggesting that a combined treatment of herbal medicine and probiotics might provide a promising implication for clinical treatment of D-IBS. GJS consists of 13 common crude herbs containing the ingredients naringin, hesperidin, thymol, honokiol and magnolol (source: State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China).

Of course, there is also the "stress factor". We produce cortisol when we are stressed, affecting every system in our body, especially the gut-brain axis (for more information about the impact of stress on the gut, see https://www.melbournemindbodypsychology.com/blog/help-for-ibs-the-microbiome-and-stress).
#herbs #herbalmedicine #plantnutrition #health #spices #diet #gutmicrobiome #bacteria #healthinnovation #chinesemedicine #easternmedicine #healthtech #stressfactor #gutbrainaxis


How do butyrate producing foods support mental health, longevity?

Foods that support butyrate pr... Foods that support butyrate production, a type of short chain fatty acid, include whole grains, raspberries, pears, apples, green peas, broccoli, and turnip greens.
A January 22, 2020 article in Science Magazine reports that a healthy mix of microbes in our gut can prevent many diseases better than our own genes can, and can even indicate risk of dying in the next 15 years.

The Science Magazine cited a review by Samuel Minot, a microbiome researcher at Seattle's Fred Hutchinson Cancer Research Center. He and his team analyzed 47 studies on collective genomes of gut microbes and their relationship with 13 common diseases. They compared these studies with 24 genome-wide association (GWA) studies dealing with human genomes and found that genetic signature of gut microbes was 20% more effective at "discriminating between a healthy and ill person" (source: see https://www.sciencemag.org/news/2020/01/microbes-your-gut-could-predict-whether-you-re-likely-die-next-15-years ).

A November 17, 2019 article in the New Atlas, reported a separate study that fecal transplants (in effect "microbial transplant") from young mice to older mice showed new neurons being produced called neurogenesis, a key to slowing aging. While testing in mice does not necessarily translate to the same results in humans, it is a significant factor suggesting possible solutions. The study found a greater volume of microbes produced short chain fatty acid called butyrate.

“We’ve found that microbes collected from an old mouse have the capacity to support neural growth in a younger mouse,” explains Sven Pettersson, lead on the research team from Nanyang Technological University in Singapore in the New Atlas article.

A January 06 2020 article in Neuroscience News says a study by a University of Kentucky consortium found similar results of tests for stroke victims. Researchers found that short chain fatty acids additive to the drinking water of mice showed better stroke recovery. (See https://neurosciencenews.com/gut-microbes-stroke-15425/amp/ ).

So much attention has been given to the influence of gut microbiomes on our mental health just in the past few weeks. These are a sampling of them.

While Pettersson acknowledges that further research is required, it suggests that healthy aging remedies such as herbs and good prebiotic and probiotic foods that enhance butyrate production can support longevity, and healthy living into our twilight years. To bring it home, examples of foods that support butyrate production include whole grains, raspberries, pears, apples, green peas, broccoli, and turnip greens.

#herbs #herbalmedicine #plantnutrition #health #spices #diet #gutmicrobiome #bacteria #healthinnovation #genomics #DNA #SCFA #butyrate #healthtech


  • ブログルメンバーの方は下記のページからログインをお願いいたします。
  • まだブログルのメンバーでない方は下記のページから登録をお願いいたします。