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Microbial strain gives Japanese Sushi-eating advantage

Jan

18

Japanese consume large amounts of raw fish and seaweed, in the form of sushi and nori. It is healthy for them partly due to a partnership with a seafaring bacteria friend found in their gut. Japanese gut bacteria aren’t just limited to the genes that they inherit from their ancestors. Bacteria native to the natural world can be introduced to our gut. Once ingested, individual bacteria can swap genes quite easily, both internal gut bacteria and externally introduced bacteria. This ‘horizontal gene transfer’ means that bacteria have an entire kingdom of genes, ripe for exchange. In the world’s oceans – a marine bacterium called Zobellia galactanivorans was introduced to the Japanese gut through consuming seaweed.

Zobellia is a seaweed-eater. It lives on, and digests, several species including those used to make nori. Nori, or seaweed, is commonly used in Japanese meals, in miso soup, sushi wrapping, for example. When you consume these algae with sushi and miso, marine bacteria is also consumed, and Zobellia is consumed. Zobellia mingles with our existing gut microbiota, "including those that allow them to break down the carbohydrates of their marine meals", according to research by the University of Victoria. The gut bacteria suddenly gained the ability to exploit an extra source of energy and those that retained their genetic loans prospered. This process is known as horizontal gene transfer. Six strains of of the human gut Bacteroides plebeius had been discovered that possess an unique gene from the aforementioned porphyran-breaking enzyme, all of them coming from the bowels of Japanese people.

See article for more information, https://www.nationalgeographic.com/science/phenomena/2010/04/07/gut-bacteria-in-japanese-people-borrowed-sushi-digesting-genes-from-ocean-bacteria/

#ai #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #plantnutrition #spices

Honeysuckle - Chinese remedy for common cold and more

Jan

7

The leaves and flower of honeysuckle have been used for several thousand years as a traditional Chinese medicine. It has been a challenge to discriminate between the variations of honeysuckle herbs, such as Lonicerae japonicae flos and Lonicera japonica thunb, according to a report published September 23, 2019 (see reference below). The leaves and dried flower buds of Lonicera japonica Thunb, also called Japanese honeysuckle or jīn yín huā has been widely used in traditional Chinese medicine to treat flu- like symptoms such as cough, fever, sore throat, and influenza infection. Tests have shown that Lonicerae japonicae flos exhibits a broader antimicrobial spectrum, more powerful antibacterial activity, and inhibition of drug-resistant bacteria. Pharmacologic studies have confirmed the bacteria and antibacterial effects of Lonicerae japonicae flos, says the study.

The following can be extracted from Lonicerae japonicae flos - water extract, alcohol extract, polysaccharide, and volatile oil. These ingredients can "extensively inhibit Gram-negative bacteria and Gram-positive bacteria including Streptococcus haemolyticus, Staphylococcus aureus, Salmonella Typhi, Klebsiella pneumoniae, Salmonella paratyphi, Vibrio cholerae, oral pathogens, Diplococcus intracellularis, Streptococcus pneumoniae, and Mycobacterium tuberculosis," according to a study by the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences (see article "Lonicerae Japonicae Flos and Lonicerae Flos: A Systematic Pharmacology Review", by Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Dongzhimen Nei Nanxiao Road, Dongcheng District, Beijing 100700, China; Department of Drug and Cosmetics Registration, China Food and Drug Administration, Xuanwumen Xidajie, Beijing 100053, China; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519546/).

The testing method used for determining the content of a key active ingredient, secologanic acid, was established using Ultra Performance Liquid Chromatography (HPLC) (see article, "A Simple, Rapid, and Practical Method for Distinguishing Lonicerae Japonicae Flos from Lonicerae Flos"; by Fang Zhang, Pengliang Shi, Hongyan Liu, Yongqing Zhang 1,Xiao Yu, Jing Li and Gaobin Pu; College of Pharmacy, Shandong University of Traditional Chinese medicine, Jinan 250355, China). Using HPLC makes it simple, fast, accurate, and cost effective to identify the different variations of Lonicerae Flos.

#ai #artificialintelligence #bacteria #chinesemedicine #datascience #diet #easternmedicine #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #naturopathichealth #plantnutrition #spices

A little history on the origins of Ayurveda

Jan

3

Dr. Vivek Shanbhag of Bastyr University explains that between 1,000 to 700 B.C. Ashrams gathered people together in India to discuss topics of the day such as health issues. Attendees of these open forums facilitated exchange of acquired knowledge; for example, about herbs and foods that help with certain health conditions. Out of these Ashrams evolved two main schools relating to health care, Atreya and Dhanvantari. Atreya became the school of physicians and Dhanvantari, the school of surgeons. Traditions such as chanting of mantras were gradually replaced by scientific thinking and solutions.

Veda means acquired knowledge and data research, which accumulated over thousands of years in India from the general Ashram meetings, according to Bastyr University's Professor of Ayurvedic Health Dr. Vivek Shanbhag.

The original text of Ayurveda are the trio - Charak Sambita, Sushrat Sambita, and Ashtang Hridaya Sambita.

Ayurveda achieved by pursuing these Four Goals of Life:

1. DHARMA - vocation, your calling, reaching your inner object of life
2. ARTHA - creating your resources, prosperity, attainment of outer objects, right possessionsof life
3. KAMA - enjoyment, achieving, fulfilling basic desires, emotional mind
4. MOKSHA - total freedom, not attached to anything, liberation from the limits of the other goals; infinite possibilities

Source: Dr. Vivek Shanbhag, Bastyr University, Ayurvedic Health Advisor Program, Kenmore, WA.

#India #ai #artificialintelligence #ayurveda #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

Indian Ayurvedic Health defined

Dec

30

Ayurveda is an over 3,000 year old health program originating in India. Ayurveda begins with fundamental principles centered around maintaining good health. These are described in the three doshas - Vata, Pitta, Kapha and the 4 goals of Ayurveda. I will explain the 4 goals in the next blog entry to be published in a few days.

Veda means acquired knowledge and data research, which accumulated over thousands of years in India from general meetings called Ashrams, according to Bastyr University's Professor of Ayurvedic Health Dr. Vivek Shanbhag.

Possibly the most effective way to accurately and clearly explain the three doshas of Ayurveda are Dr. Shanbhag's association of Ayurveda to computing. Ayurveda is your tools and means to achieve your four goals of life. He describes the three doshas as follows:

VATA is like data entry.
PITTA is the processing of that data.
KAPHA is the storing and recall of the data.

VATA is the sensory intake, communications and transport of data and the elements, air and ether.
PITTA is the transformation, digesting, processing and metabolizing of the data and the elements, fire and water.
KAPHA is the storing, growth, and memorizing of the data and the elements; water and earth.

Everyone wants to increase happiness and comfort.
Everyone wants to decrease their pain and suffering. The status of our health is a key contributor to these basic life goals.

#India #ai #artificialintelligence #ayurveda #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #neurotransmitters #plantnutrition #sertonin #spices #thehappychemical

Black mondo grass, monkey grass support microbiome gut health and antiobesity

Dec

17

Ophiopogon is an ornamental grass native to China, India, Japan, and Vietnam.
Ophiopogon japonicus is better known as dwarf lilyturf, mondograss, fountainplant, and monkeygrass; or in Japanese: リュウノヒゲ ryu-no-hige ("dragon's beard") or ジャノヒゲ ja-no-hige ("snake's beard") (source: see Wikipedia).

In traditional Chinese medicine Ophiopogon japonicus' tuber root, is the key herb for yin deficiency. According to the "Chinese Herbal Medicine Materia Medica," the tuber part of the root of Ophiopogon japonicus enters the heart, lung, and stomach channels and nourishes the yin of the stomach, spleen, heart, and lungs and eases irritability. The herb is sweet, slightly bitter and slightly cold. The herb in Chinese medicine is known as mai men dong (Chinese: 麥門冬).

Now there is science to back up these claims, according to a February 2019 Chinese Pharmaceuticals University report. MDG-1, a water-soluble polysaccharide extracted from the root of Ophiopogon japonicus Ker Gawl has been reported to regulate body metabolism, including weight loss, antiobesity, and antidiabetes. Professor L. Shi demonstrated that, in HFD-induced obese mice that were treated with "MDG-1 at a high dose of 300 mg/kg for 12 weeks, the ratio of Firmicutes/Bacteroidetes (F/B) decreased to normal levels." In addition, it was found that in HFD-induced diabetic mice, MDG-1 decreased the number of pathogenic bacteria (Escherichia coli and Streptococcus) (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).

See full report, https://www.hindawi.com/journals/ecam/2019/2682748/
Contact Qinglong Guo; qinglongguo@hotmail.com and Na Lu; nalu@cpu.edu.cn

#ai #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #plantnutrition #spices

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

Nov

21

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 https://www.businessinsider.com/microbiome-startup-ubiome-files-for-bankruptcy-2019-9 ). 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.

#datascience #disruptors #funding #healthinnovation #healthstartups #healthtech #unicorncompany

Institutional Innovations - DNA sequencing issues

Nov

18

A November 15, 2019 report published by Nature.com 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 https://www.nature.com/articles/s41576-019-0180-9 ). 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 #ai #artificialintelligence #bacteria #datascience #genomics #gutmicrobiome #healthinnovation #healthtech #machinelearning #mindbody #structuralvariance

Impact of Cooked vs. Raw Food on Gut Microbiota

Nov

7

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, https://www.gutmicrobiotaforhealth.com/en/beyond-nutrients-and-bioactive-compounds-in-food-cooking-also-matters-for-the-gut-microbiome/

#ai #artificialintelligence #bacteria #datascience #diet #food #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

Chinese herbal remedy & "bugs in the belly" aid weight loss / diabetes

Oct

31

It is becoming more accepted that Chinese herbs such as ginseng, berberine, and curcumin, have wide ranging biological impacts on our gut microbiome. On April 15, 2019, Chinese scientists published test results of the microbial effects of a popular Chinese herb called Coptis chinensis. Berberine, the main active ingredient of Coptis chinensis, is known as an antidiabetes drug and can regulate blood glucose. Berberine is beneficial for HFD-induced (high fat diet) insulin resistance, as it improves insulin sensitivity and reduces the homeostasis caused by insulin. They found that administration of berberine reduced the ratio of F/B (Firmicutes/Bacteroidetes) and partly recovered the composition of gut microbiota changed by HFD feeding. The report was published by China's 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; see https://www.hindawi.com/journals/ecam/2019/2682748/ ).

A July 2019 paper published in the journal Nature, demonstrated ways to apply specific strains of microbiota to positively influence weight and diabetes. They found that a molecule produced by certain bacteria can interact with protein receptors in mice and improve the rodent's glucose regulation. These same receptors are also found in humans. It was a key step toward understanding how bacteria keeps us healthy, and what changes in bacteria occur when we fall prey to disease, empowering us to harness naturally occurring microbes to treat illness. Scientists found that microbiome differences can relate to our weight and diabetes. For example, studies of the microbe Akkermansia muciniphila has shown influence in obesity among humans. The July 2019 study by Nature Medicine showed "evidence for a negative correlation between Akkermansia muciniphila abundance and overweight, obesity, untreated type 2 diabetes mellitus or hypertension". 40 volunteers were enrolled and 32 completed the three month trial resulting in improved insulin sensitivity, reduced cholesterol, and slightly decreased body weight. A. muciniphila reduced the levels of liver dysfunction and inflammation. (See article, https://www.nature.com/articles/s41591-019-0495-2 ).

Other microbial species may also impact diabetes. Researchers at Rockefeller University were able to isolate N-acil amides with GPR119, which helps control blood sugar in mice. “Mice that received N-acil amides had significantly better glucose metabolism that those that didn’t. Over the past couple of years, Rockefeller biologist's Sean Brady and his team analyzed stool samples for microbial DNA. In essence, they found that N-acil amides help the body regulate itself.

A person with diabetes is more likely to have this certain suite of microbes than a person without diabetes, for example. But the mechanisms of this bacterial influence are still pretty mysterious.” (Source: “Scientists want to Turn our Gut Bacteria into Medicine,” Popular Science, Claire Maldarelli, Aug. 31, 2017; http://www.popsci.com/gut-bacteria-medicine?zLzbIvdKfbdGTwyp.03 ).

#ai #artificialintelligence #bacteria #chinesemedicine #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

How Does Ultraviolet Light Influence Our Gut Microbiome?

Oct

27

According to an October 24, 2019 report by various departments of the University of British Columbia Hospital and medical centers in Vancouver, BC., the recent worldwide rise in immune and inflammatory diseases such as multiple sclerosis (MS) and inflammatory bowel diseases (IBD) has been linked to decreased exposure to sunlight/UVB light and production of vitamin D, as well as changes in gut microbiome.

Their research found that Vitamin D deficiency has shown to promote an inflammatory environment which leads to dysbiosis, an imbalance in the gut microbiome. By exposing the skin to Narrow Band Ultraviolet B (NB-UVB) light to increase vitamin D levels, the makeup of the human intestinal microbiota improves. Studies support the concept that UVB light is beneficial to health, beyond its ability to promote cutaneous vitamin D production. This report found significant effect on the microbiota composition after repeated exposures, specifically for subjects that were not taking vitamin D supplements. Keystone species such as Lachnospiraceae, Ruminococcus, and Clostridiaeae strains were notably affected. (See UBC report, https://www.frontiersin.org/articles/10.3389/fmicb.2019.02410/full )

#UVlight #datascience #healthinnovation #healthstartups #healthtech #microbiomeresearch #unicorncompany #vitaminD

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Microbial strain gives Japanese Sushi-eating advantage

Honeysuckle - Chinese remedy for common cold and more

A little history on the origins of Ayurveda

Indian Ayurvedic Health defined

Black mondo grass, monkey grass support microbiome gut health and antiobesity

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

Institutional Innovations - DNA sequencing issues

Impact of Cooked vs. Raw Food on Gut Microbiota

Chinese herbal remedy & "bugs in the belly" aid weight loss / diabetes

How Does Ultraviolet Light Influence Our Gut Microbiome?

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