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HerbSprout Microbiome Blog -


Herbsprout is a webblog and podcast dedicated to sharing 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 of China (TCM), India (Ayurveda), and Japan (eJim & Kampo).

Green tea, esp. fermented, may prevent weight gain

Green tea, esp. fermented, ma...
Green tea, commonly consumed in Asia, has been reported to have an antiobesity activity, and the alteration of gut microbiota composition is a main means of action. According to an April 2019 report by scientists at China Pharmaceutical University (see description below) when sundried green tea was fermented, it restored the increased Bacteroides/Prevotella (B/P) ratio and significantly decreased the F/B (Firmicutes/Bacteroidetes) ratio in HFD (high fat diet) mice after 8 weeks of treatment. Epigallocatechin gallate (EGCG), the main type of catechin in green tea, could inhibit the formation of rat abdominal adipose tissue after a 4-week treatment regimen. The natural antioxidant catechin is an anti-inflammatory that repairs cell damage and helps fight cancer.

In their study, it was revealed that EGCG-treated rats showed a dramatic decrease of Clostridium spp. and an increase of Bacteroides in feces. Moreover, Chang et al. of China Pharmaceutical University (see source detail below) reported that a water extract of Ganoderma lucidum (Curtis) P. Karst. (WEGL) prevented weight gain and fat accumulation in HFD-induced obese mice. Furthermore, endotoxemia and insulin resistance were found to be improved by WEGL for the modification of gut dysbiosis. The F/B ratio and levels of endotoxin-bearing Proteobacteria were also restored to normal levels. However, several bacteria increased (Parabacteroides goldsteinii, Bacteroides spp., Anaerotruncus colihominis, Roseburia hominis, and Clostridium), which negatively correlated with obesity. The authors suggested that WEGL or polysaccharides could be used as prebiotic agents for the treatment of obesity and modulating obesity-related metabolic disorders.

Lonicerae japonicae flos is famous for its anti-inflammatory activity and has widely been used in Asia for years. In animal studies using HFD-fed animals, administration of unfermented Flos Lonicera (UFL) or fermented Flos Lonicera (FFL) significantly reduced body weight (BW) and adipose tissue weight and decreased lipid accumulation in the liver with ameliorated serum total cholesterol, HDL, and triglyceride levels. As suggested by the authors, alterations in the relative abundance of Lactobacillus spp., Bifidobacterium spp., and B/F ratio in the intestinal tract were supposed to be one of the mechanisms of UFL or FFL. In addition, the amount of Bifidobacterium spp. in the cecal pool of HFD-induced mice was increased by pomegranate peel extract (PPE), which is known for its beneficial effects, including anti-inflammatory and antimicrobial activities.

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.

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Key foods/ herbs for your daily health

Key foods/ herbs for your dai...
Probiotics such as fermented foods include yogurt, kefir, sauerkraut, kimchi, among others with live cultures support a healthy gut.

Prebiotics help feed the microbiome in the gut such as fruits, vegetables, beans, nuts, and whole grains. This is why vegans and vegetarians support a rich diversity of gut bacteria.

Mental health is as important as anything to your overall health. Stress and anxiety have been implicated in multiple aspects of health and disease. Keep your gut-brain axis healthy. Of course, the general consensus for a person to have adequate sleep is 7-9 hours regardless of age.

It's a good idea to keep clean, but it's equally important what you use to clean. If you use nondisinfectant, biodegradable cleaners, you can avoid damage to your microbiome. Studies found that test patients had high levels of a certain bacteria called Lachnospiraceae in their gut among those using disinfectants, which has been connected to obesity.

Vitamin D is a hormone we need to maintain healthy bones, and breast, prostate, and colon cells. There is growing evidence that it is also linked to a healthy gut microbiome. Our bodies produce Vitamin D when exposed to sunlight or adequate Vitamin C from other sources.

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The Health of Silicon Valley's health disruptors amid uBiome bankruptcy

In the wake of uBiome's filing for Chapter 11 and then closing its doors on October 31, 2019, it's timely to review the status of startups in healthcare.

The uBiome bankruptcy appears to be a mere hiccup due to mismanagement, although this year's health startups were largely health services such as cloud services. Apertiva and ChronicCareIQ topped the 2019 list of CIO magazine. Also making the list were other Saas health tech companies Duxlink Tele-Hospital, a platform that integrates clinical data with wearable tech and remote access. Finpay also tops the list as a financial management platform. The range of services is capped off by PatientPop which bills itself as a complete practice growth solution for health practitioners.

Health service startups aside, disruptors in healthcare include well known entrepreneurs like Mark Zuckerberg’s $600 million funded biotechnology center in Silicon Valley.

Biohub made a big splash a few years ago. BioHub’s premier project is to create a vast directory of human cells, which it calls a “cell atlas.” (source: Antonio Regalado, MIT Technology Review, October 31, 2016). Stanford researcher and BioHub Co-President Steven Quake and BioHub are also part of a consortium of researchers around the globe who are collaborating to map the millions of cells in the human body. Scientists at BioHub and elsewhere are inspecting tens of millions of human cells for their molecular signatures, among other things, to track the body’s specific immune system responses to different treatments such as radiation.

Like other venture funded companies collecting gut samples (Viome), uBiome claimed a database of nearly 100,000 gut samples collected from its early adopter consumers the company refers to as “citizen scientists”, according to a 2016 TechCrunch article (Sara Buhr, November 01, 2016). “The GI tract is teeming with bacteria and research suggests the wrong kind may play a role in diabetes, multiple sclerosis, cancer, liver disease, obesity, irritable bowel syndrome and a number of other maladies.”
Apparantly the company owed millions of dollars to insurance companies related to illegal billing practices for which they are under criminal investigation, according to a Business Insider article (see ). It appears the company seeks to come out of bankruptcy with new management.

UBiome features a new SmartGut screening test kit that you can buy online for an estimated $89 which aims to identify “dozens of microbial genera and species” using a 16S rRNA gene sequencing method. However, the 16s rRNA gene sequencing is a twenty year old technology that offers very limited insights and is prone to inaccuracies, claims competitor company CEO Viome's Naveen Jain.
The above example are just a snapshot of disruptive innovators in the healthcare space.
#healthtech #healthstartups #funding #healthinnovation #datascience #disruptors #unicorncompany

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Institutional Innovations - DNA sequencing issues

Institutional Innovations - DNA ...
A November 15, 2019 report published by calls for a multiplatform approach for researching structural variation (SV) in genome interpretation. "Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies," says the report. Detection methods have helped scientists discover thousands of SVs, showing their relationship to disease and possible effects on our biology. (see ). By multiplatform, the article recommends testing on a variety of platforms and approaches, not relying on a single one, comparing results from different research labs and institutions around the world.

So much focus particularly in tech media has been about disruptive innovators and startups in the healthcare field. What about innovations by these more traditional institutions such as research institutions and hospitals?

Highly customizable and personalized healthcare solutions are at the cutting edge of disruptive innovation. You do not need to be an established entity to drive these disruptions, but you can be. The innovative applications of a person’s DNA sequence such as the tool for synthesizing DNA invented by biologist Leroy Hood’s Institute for Systems Biology, offer customizable health care at a genetic level, called genotyping. Seattle area’s Swedish Health Services has been recognized nationally for providing personalized health care using Dr. Hood’s DNA sequencing.

Another example, the creator of the CRISPR Cas9 technology, CRISPR Caribou Biosciences CEO, Dr. Jennifer Doudna invented the ability to edit our genetic code. Doudna showed how CRISPR, or "clustered regularly-interspaced short palindromic repeats", "bacteria’s natural defense system could be turned into a 'gene editing' tool to cut DNA strands", according to the Genetic Literacy Project. In addition to founding CRISPR, she teaches chemistry and molecular biology at University of California Berkeley. Both Hood and Doudna are said by peers to be viable candidates for the Nobel Prize.

Dr. Hood helped his associates at Swedish Health Services (Swedish Hospital and Providence Health Systems) play a leadership role in innovation, according to former Swedish CEO Anthony Armada in my interview with him for the Northwest Asian Weekly. “On the clinical side, for example, Swedish is the first to apply truly ‘personalized medicine’ using genotyping. Genotyping is a fingerprint of who you are genetically,” he adds. “For example, there can be five potential cures for a particular cancer. Genotyping can test and determine which of the five offers the best results, the least risk, and the best course of action for that particular patient” (source: NW Asian Weekly, Chris Beer). Thanks to help from Dr. Hood, the founding father of genomics, the hospital is lead the country in the medical and scientific applications of genomics.
#DNAsequencing #genomics #structuralvariance #gutmicrobiome #bacteria #healthinnovation #datascience #ai #artificialintelligence #machinelearning #mindbody #healthtech

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Microbial treatments for Parkinson's still premature

Microbial treatments for Parki...
While scientists found a direct connection between Parkinson's disease and our gut microbiome, a November 11, 2019 report by the Journal of Parkinson's Disease and Neuroscience News concluded "there is currently no consensus on PD-specific changes in microbiome composition and their pathophysiological implications due to inconsistent results, differences in methodologies and unaddressed confounders,” observed Dr. Scheperjans, MD, PhD, Department of Neurology, Helsinki University Hospital, Helsinki, Finland.

While several findings were replicated in various studies, such as an increase of Verrucomicrobiaceae and Akkermansia and a decrease of Prevotellaceae, the investigators also found numerous differences.

There is no standard procedure established for clinical research on the subject, making the results difficult to collectively evaluate. "Procedures for collection, storage and shipment of the stool samples varied considerably; almost all studies used different DNA extraction kits; different DNA sequencing protocols were used; and different bioinformatics and statistical methods can further lead to different results." In addition, the study populations differed considerably between studies in terms of age, percentage of females and Parkinson’s disease characteristics, such as disease duration and the clinical subtype.

"It is important to emphasize that no microbiota-based treatment for PD exists to date," says Dr. Scherperjans. "We advise PD patients not to start self-treatment with probiotics or undergo fecal microbiota transplantation without consulting with their doctors in order to avoid potential harm.”

However, research has determined a connection between gut microbiome and PS progression, though further studies are needed to identify how they are connected. This blog is a continuation of the earlier blog entry, "Parkinson's may originate in the gut":
#Braindiseases #microbiomes #autism #effectormolecules #molecules #neurotransmitters #Parkinsonsdisease #mentalhealth

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Who will be the next "Lebron James" or "MJ"?

Who will be the next "Lebron ...
“I was asked whether we could use genomics to predict the next Michael Jordan," said Jonathan Scheiman, Ph.D. This question was posed to researchers at the 254th National Meeting & Exposition of the American Chemical Society (ACS), August 20, 2017. "My response was that a better question is: Can you extract Jordan's biology and give it to others to help make the next Michael Jordan?" To answer that question, microbes seemed like a good place to start, according to the Science Daily News reporting on the same ACS conference.

"We are more bacteria than we are human," says Scheiman, a postdoctoral fellow in the laboratory of George Church, Ph.D., Harvard Medical School. "The bugs in our gut affect our energy metabolism, making it easier to break down carbohydrates, protein and fiber. They are also involved in inflammation and neurological function. So perhaps the microbiome could be relevant for applications in endurance, recovery and maybe even mental toughness."

The research on stool samples of athletes found for one that a particular microbe breaks down lactic acid, which spikes during long distance running or intense exercise and can cause soreness and fatigue. Another study of Olympic athletes found another gut microbiome that breaks down carbohydrates and fiber.

Can these specific microbiome strains be extracted and transferred to another person? Yes, it's been tried but results have been mixed. More testing and research is needed.

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Our gut on diet and nutrition- a Japanese model- the good and bad

Our gut on diet and nutrition- ...
There still is debate about the impact of our diet on our health by the medical community. A report published May 29, 2019 by Edzard Ernst MD, suggests Japan has seen conflicting results particularly as western pharmaceuticals and Kampo herbal remedies are jointly applied (consult your primary care provider). So one must use extra caution when consuming herbs, food, and medications together. A key to one’s health is proper diet and nutrition, an assertion which countries like Japan have long held. In the past few decades Japan has been considered the world’s healthiest country, according to World Health Organization metrics such as combined world’s highest life expectancy and lowest infant mortality.

Despite these indicators over decades, Japanese health care spending per capita remains far below that of the west, especially the United States. The argument is that proper diet and nutrition by itself can fight off the chronic diseases to which most people are susceptible. A growing amount of data and research points toward the critical role microorganisms play relative to nutrition in our individual health. Research at MIT, Harvard, UCLA, UCSD, UCSF, Stanford, Rockefeller University, to name a few, back claims with substantive research in different areas.

A January 31, 2018 article in the Nikkei Asian Review by Annu Nishioka, says herbal remedies are not only favored among the growing numbers of elderly Japanese that are keen on the products, an increasingly health-conscious younger generation is also starting to favor herbal remedies. However, it has created a sizable gap in the supply chain showing on the above graph. With supply from China capped out, experts say the gap must be filled domestically.

You do have doubters, but most agree that a better diet and nutrition leads to a healthier life. As quoted from a INC Magazine article (“A Space Entrepreneur has Launched Another Moonshot Venture . . . by Kevin Ryan, May 24, 2017), "If, for example, you follow 1,000 people who have a healthy lifestyle and 1,000 who don't," says Dr. Edward Giovannucci, a professor at Harvard's T.H. Chan School of Public Health, "without question there will be many more chronic diseases that develop in the 1,000 who don't have a healthy lifestyle.

But we have limited ability to predict specifically who will or will not develop diseases," according to Dr. Giovannucci. Giovannucci does agrees that healthy dieting generally leads to better health and fewer chronic conditions.
The bacteria inside our guts— which collectively make up the so-called gut microbiome— are incredibly diverse, with countless species and strains, he agrees. But they also differ depending on the individual, with one person’s microbiome having little to do with another’s.

As in all things, one must be cautious about applications of medicine, even in relation to Kampo herbal medicine. The May 29 study found conflicts between medicine and herbal remedies. It found that pseudoaldosteronism-related events, which are induced by Glycyrrhizae Radix, included several events related to muscle injury, heart failure, and arrhythmia. Events related to mesenteric phlebosclerosis, believed to be induced by long-term use of Kampo formulas containing Gardeniae Fructus, increased remarkably during the study period. Among the events related to drug eruption, approximately 35% were suspected to be induced by Kampo formulations containing Ephedrae Herba. See Dr. Enprnst report at .

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Impact of Cooked vs. Raw Food on Gut Microbiota

Impact of Cooked vs. Raw Foo...
An October 10, 2019 study reported by Andrew Padros of Gut Microbiota for Health demonstrated that raw and cooked diets have a distinct effect on the structure and metabolic activities of the gut microbiome in mice and humans. Dr. Rachel Carmody at Harvard University (USA), Dr. Peter Turnbaugh at University of California San Francisco (USA) and colleagues found that raw and cooked versions of the same foods affected the gut microbiome differently in mice.

Their research came up with that varied results between food types. It suggests that cooking sweet and white potatoes is a good idea, while consuming raw or cooked beef, carrots and beets is nearly the same. For example, consuming raw sweet potatoes led to lower microbiome diversity, a higher expression of genes and enzymes for metabolizing starch, sugar and xenobiotics. It also altered metabolic byproducts when compared with cooked-fed mice. However, raw and cooked lean beef had similar impacts on the gut microbiome; there was not much difference.

By feeding the mice controlled diets with different raw and cooked low- and high-starch foods—including sweet potato, white potato, corn, peas, carrots, and beets—the authors confirmed that gut microorganisms were sensitive to starch digestibility.

The study found that low-digestibility starch when raw (sweet potato and white potato) led to the most profound changes in gut microbial community structure. However, low-starch foods (carrot and beet) or foods with a high amount of high-digestibility starch when raw (corn and peas) led to almost undetectable changes in gut microbes.

Cooked foods were mainly digested and absorbed in the small intestine (thus, processed by host enzymes), whereas raw foods reached the colon, where they had detrimental effects on microbes, attributable to antimicrobial compounds.

By quantifying microbial cell damage in gut samples, Carmody and colleagues found that the mice fed raw tubers had the same extent of microbial cell damage as the mice group treated with the oral antibiotic ampicillin.

A metabolomic analysis of the six plant foods used in the experiments revealed multiple compounds that were both sensitive to cooking and showed antimicrobial activity, thus supporting the high xenobiotic gene expression found in mice that were fed raw food.
See report from Gut Microbiota for Health,
#herbs #herbalmedicine #plantnutrition #health #spices #diet #food #gutmicrobiome #bacteria #healthinnovation #datascience #ai #artificialintelligence #machinelearning #mindbody #healthtech

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Mood and behavior - "a kick in the gut"

Mood and behavior - "a kick i...
There is growing evidence that the microbiome in our gut contribute not only to various body and brain diseases, but also to our mood and behaviour relevant to many psychiatric and neurological disorders, according to a February 19,2019 report by NIH's National Library of Medicine and Frontiers in Genetics (see ), and a separate article by the Microbiome Journal.

From the current findings in patients with major depressive disorders (MDD), sixteen studies analyzed by the NIH found increased levels of the following microbiota - phylum Actinobacteria, Bacteroidales (order), Enterobacteriaceae (family), Alistipes (genus) and Lachnospiraceae (deceased family), Faecalibacterium (genus) - which were associated with depression in most studies. However, the change of Bacteroidetes was not consistent among these studies, while the others were more consistent, according to the February 19, 2019 report.

While many antidepressants work to increase levels of serotonin in our brain, other neurotransmitters such as dopamine, norepinephrine, acetylcholine, and GABA, play a major role in our mood, anxiety, concentration, reward, and motivation, much of which originate in our gut.

It has been repeatedly demonstrated that manipulation of the gut microbiome modulates anxiety-like behaviours, and our response to fear. The neural circuits that underlie anxiety- and fear-related behaviours are complex and heavily depend on functional communication between the amygdala and prefrontal cortex (PFC). Research at the University of California Los Angeles (UCLA) found a link between our stomach and a region of our brain that regulates mood and behavior, according to’s Robin Andrews (Source: “Our Gut Microbes Strongly Influence Our Emotional Behaviors,” IFL Science, July 4, 2017). The UCLA study was the first to link this connection within humans, based on the study of 40 healthy woman showing “brain-gut-microbial interactions in healthy humans”, according to the American Psychosomatic Society, affecting their mood and behaviors. Women who consumed fermented probiotic yogurt demonstrated calm in their brain activity while the base group who did not, demonstrated the opposite hyper brain activity for the same emotional task.

Likewise, the Microbiome Journal reports that “transcriptional networks within the amygdala and PFC of Germ-Free mice are altered. MicroRNAs (miRNAs) act through translational repression to control gene translation and have been implicated in anxiety-like behaviours.” (See Microbiome Journal, August 25, 2017; These results suggest that the microbiome is necessary for appropriate regulation of mRNA expression in brain regions implicated in anxiety-like behaviors.

Youtube videos on gut microbiome's connection to depression:

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