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Using Classic models (Lotka-Volterra) to do microbiome research

Oct

24

What is Lotka-Volterra modeling? It is the simple model of the population dynamics of species competing for common resource, according to Wikipedia. Because there are trillions of microbes in our bodies, it becomes a huge challenge collecting, breaking down, processing, packaging, then accurately making sense of the data in presentable formats. Thanks to computing, high throughput DNA sequencing enables the exploration of dynamics in microbial populations. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities.

Researchers today are able to use an "interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations", according to a February 22, 2019 Frontierso India report (see https://www.frontiersin.org/articles/10.3389/fmicb.2019.00288/full).

"We have developed “Web-gLV” to bridge data delivery gaps to enable biologists to take advantage of the multispecies modeling and simulation without any programming expertise," adds the report. This way, scientists can focus on the Science and rely on the "Web-glv" for the computing and delivery.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #health #healthinnovation #healthtech #machinelearning #mindbody

Prebiotic fiber, short chain fatty acids drive gut and immune health

Oct

22

Downline immune health grid.

Chicory root pictured here is a leading source of Inulin fiber.

Certain foods and herbs support the growth of short chain fatty acids (SCFA). These fiber-rich foods - such as fruit, vegetables, and legumes - contain large amounts of Inulin.

Inulin is a type of soluble fiber found in many plants which gut bacteria convert into SCFA. SCFAs such as butyrate, nourish colon cells, break down glucose and cholesterol, and provide other health benefits. SCFA inhibit histone deacetylases (HDACs) and activate G-protein-coupled receptors (GPCRs). Since HDACs regulate gene expression, inhibition of HDACs has a vast array of downstream consequences. GPCRs, particularly GPR43, GPR41, and GPR109A, have been identified as receptors for SCFAs, but little is known beyond that. Studies have implicated a major role for these GPCRs in the regulation of metabolism, inflammation, and disease. In effect, SCFAs have anti-inflammatory, antitumorigenic, and antimicrobial effects. Butyrate, a four-carbon SCFA, is produced through microbial fermentation of dietary fibers in the lower intestinal tract, enhancing intestinal health and mucosal immunity. They alter and maintain gut and immune system integrity.

Plants naturally produce inulin and use it as an energy source. Today, it’s being added to more and more food products because of its benefits and adaptability. With its creamy consistency, inulin functions as a fat substitute in margarine, salad dressings, and baked goods.

Inulin can be found naturally in foods, such as:

- chicory root
- artichokes
- agave
- asparagus
- bananas
- garlic
- leeks
- wheat
- onions
- wild yams

Again, remember that no body is the same, so get to know your body and it's particular health needs. The key is to maintain a balanced diet, including but not limited to consumption of Inulin intensive food and herbs.

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

"Keystone Species" - Like the Wolves of Yellowstone Park

Oct

17

Isolating Key Bacterial Strains

Thanks in large part to innovative entrepreneurs, microbial influences on our health is reaching new heights. What this means scientifically is that research is showing more than just propensities and patterns. It is able to isolate strains using Ai, specific strains of bacteria that directly affect the neuro-degeneration of MS (multiple sclerosis) patients as one example of many.

Scientists refer to Bacteroides fragilis and Bacteroides stercosis as “keystone species” of the human gut microbiome. Though not abundant, they heavily influence the structure of microbial communities. It may be premature to say, but research points toward these gut microbiome as contributing to one's individuality.

Faecalibacterium prausnitzii might be another keystone species as a gut anti-inflammatory. Rather than “bad” microbes prompting Crohn's disease, for example, a single “good” microbe plays a key role in preventing the disease. Harry Sokol, a gastroenterologist at Saint Antoine Hospital in Paris, found that if he transferred F. prausnitzii in mice, it protected them against experimentally induced intestinal inflammation. "And when he subsequently mixed F. prausnitzii with human immune cells in a test tube, he noted a strong anti-inflammatory response," according to the Scientific American report (see https://www.scientificamerican.com/article/among-trillions-of-microbes-in-the-gut-a-few-are-special/ ).

Another “keystone species” microbe worth mentioning that resides in the human gut is the ruminococcus bromii. It is a dominant member of the suite of human gut microbiome that triggers energy and digestion of resistant starches by breaking down and releasing enzymes from these starches that we consume. The ruminococcus bromii primarily reside in the colon.

The function of these "keystone" species enable the proper functioning of other downline microbial activity, much in the same way that the presence of wolves in Yellowstone Park is a keystone species to maintain a balance in the park’s ecosystem.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #health #healthinnovation #healthtech #machinelearning #mindbody

Health Tech Startups Reach Unicorn, Other Milestones; UCSD Funding

Oct

13

$1 billion companies ride the popularity of health care innovations.

Venture funded food app companies such as 23andme started out as a genetics ancestry DNA health kit seller and recently expanded or pivoted to include offering meals based on your gut microbiome. Wired Magazine reported in its March 2019 issue (page 13) about the “Green Giants“, the first unicorn food platforms, SweetGarden and Joe and the Juice.

These companies are a sign that the VC and investment community are taking the emerging health tech market seriously. Livongo and Health Catalyst are two notable health tech companies who had successful IPOs in July 2019. Livongo is a platform that helps people manage their diabetes. Health Catalyst is a health data research company.

While health tech companies have trended toward two key tech related research areas – genomics (e.g., Illumina, Helix, LAM Therapeutics) and microbiome gut research (e.g., Finch Therapeutics, Second Genome, Gingko Bioworks, and Viome) – there remains a high demand for tracking and implementing those and other trends.

Health entrepreneurs can lay the groundwork for successful runs by teaming up with the world’s leading health research institutions to incubate and provide for the ongoing breakthroughs and innovations happening in the industry. Fiscal year ending June 30, 2019, UC San Diego pulled in $1.35 billion in research contracts and grants, breaking funding records according to October 07, 2019 article by the San Diego Tribune (see https://www.sandiegouniontribune.com/news/science/story/2019-10-07/uc-san-diego-shatters-record-for-research-funding-pulling-in-1-35-bi?_amp=true). Microbiome research was key to its success, according to the Tribune article quoting Dr. David Brenner, UCSD’s vice chancellor for health sciences. The hiring of world leading microbiome expert Rob Knight four years ago suggests UCSD aims to become a world leader in microbiome research and appears well on its way.

#datascience #funding #healthinnovation #healthstartups #healthtech #microbiomeresearch #unicorncompany

Japanese Health Care Offers Private Sector Options & Coverage for Herbal Remedies.

Oct

10

Japanese private insurance companies cover eastern medicine.

Author: Chris Kenji Beer

Japanese traditional medicine (Kampo medicine) has a long historical development in Japan that dates back more than 1500 years, and even further back in China. Kampo is similar to India's Ayurveda in its integrative approach that a balance of the human body and mind, mental and physical, are critical to our health. Today, Kampo medicine has been revived accompanied by a scientific reevaluation relevant to modern health care. Kampo medical treatments include chiropractic, aromatherapy, homeopathy, health spa therapy, Ayurveda, hypnosis, flower therapy, thalassotherapy, herb therapy, qigong, yoga, dietary therapy, imagery, meditation, art therapy and prayer (See NIH article, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC516460/). This article references a survey of 1,000 Japanese residents and their percentage use of CAM (alternative medicine), such as Kampo: nutritional and tonic drinks, 43.1%; dietary supplements, 43.1%; health-related appliances, 21.5%; herbs or over-the-counter Kampo, 17.2%; massage or acupressure, 14.8%; ethical Kampo (Kampo prescribed by medical doctors), 10.0%; aromatherapy, 9.3%; chiropractic or osteopathy, 7.1%; acupuncture and moxibustion, 6.7%; homeopathy, 0.3%; other therapies, 6.5%.

HERBAL REMEDIES IN JAPAN.

In Japan, Agaricus blazei Murill is the most popular product. Many cancer patients take this mushroom. This medicinal mushroom contains special types of polysaccharides known as beta glucans which stimulate the activity of natural killer cells that are vital to the immune system. These polysaccharides are believed to be among the most potent polysaccharides for immune health. Beer yeast, Propolis, cereals, banaba, Japanese plum, Chlorella, barley verdure, vegetable juice, collagen, royal jelly and mulberry are also taken. Dong quai is an ingredient covered by Kampo. The ingredients of dong quai are coumarins, essential oils, ferulic acids, psoralens, and vitamin B12 and folinic acid, the active form of folic acid. Shakuyakukanzoto was the most frequently prescribed Kampo drug, known to relieve muscle pain and maintain healthy blood flow. It consists of peony root and licorice extract.

USA dietary supplements which are not covered by American health insurance include Gingko Biloba, Echinacea, Garlic, Ginseng, Soybean, Saw Palmetto, St John's Wort, Valerian, Black Cohosh, Milk Thistle, Evening Primrose, Grape Seed Extract, Bilberry, Green Tea, Pycnogenol, Ginger, Feverfew and Dong quai, amongst others.

JAPANESE HEALTH CARE FOR THE ELDERLY.

Though published so along ago, I was cleaning out the basement storage the other day, and came upon my only printed copy "Japanese Health Care for Elderly" which was published by US-Japan Foundation and National Conference of State Legislatures. I couldn’t find it anywhere. It has been referenced on a number of library websites, but no copy. I realized my co-author Dr. Bill Steslicke and I may have the only copies, along with a few die hard former legislators around the country, so here is a Word doc version. Noteworthy- 1) certain Japanese companies may form their own in-house HMO-style coverage and provisioning. 2) Japanese insurance covers eastern medicine, Kampo medicine described above, including but not limited to herbal remedies and acupuncture.

Here is a downloadable word doc copy of the original publication: https://kotojazz.files.wordpress.com/2016/07/ncsl_japanesehealthcare_forelderly.doc

#acupuncture #ai #artificialintelligence #bacteria #datascience #diet #elderlycare #gutmicrobiome #health #healthinnovation #healthtech #herbs #japanesehealthcare #machinelearning #mindbody #plantnutrition #seniorhealthcare #spices

Herbs that support "the happy chemical", microbiome health

Oct

4

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. 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). 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.

Before getting into the research, what herbs support "healthy happy chemicals"? Herbs that help boost serotonin levels include oatstraw, which is loaded with B vitamins, and the roots of angelica, burdock, dandelion, ginseng, wild yam and black cohosh. There are lots of natural supplements containing these herbs and foods that you can buy online. You can also find supplements that contain L-tryptophan that supports serotonin synthesis, and vitamin B3 (magnesium glycenate) which helps metabolize fats, proteins, and carbohydrates. Basil contains serotonin boosting eugenol and rosmarinic acid.

As mentioned, 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 behavior relevant to many psychiatric and neurological disorders (Microbiome Journal, August 25, 2017). In particular, 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 IFLScience.com’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. 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 miRNA expression in brain regions implicated in anxiety-like behaviours.

"Serotonin is an important neurotransmitter and hormone that is involved in a variety of biological processes. The finding that gut microbes modulate serotonin levels raises the interesting prospect of using them to drive changes in biology," says Hsiao in the Caltech Journal. Hsao is quoted here from the CalTech journal Cell, April 09, 2015 issue.

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

A “Tsunami” of Ai is Coming to Health Care

Oct

1

1. Describe - handcrafted, rule based, symbolic knowledge.
2. Categorize - deep neural network, statistical learning.
3. Explain - contextual adaption, perceived learning and reasoning.

Serial entrepreneur and Viome CEO Naveen Jain believes there is a big wave of Ai coming to the health sector. “There is a tsunami that's coming," he told CNBC in a TV interview from the Slush technology conference in Helsinki, Finland (December 01, 2017). Jain partly attributes this tsunami to the huge demand for sensors that are driving down the prices, making Ai technology more available to the masses. "The sensors are becoming so cheap. For the first time in our lifetime, we can look deep inside our body (using sensors) to know exactly what is going on," he told CNBC. Jain believes food could become the "next drug," eliminating the need for traditional medicine.

On October 01, 2019, his company Viome was given a highly coveted endorsement in the form of research published about "A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health" in the International Journal of Genomics (Volume 2019, Article ID 171874 about Viome Inc., Los Alamos, NM 87544, USA). The report states that "Humans have co-evolved with the microbiome and have become dependent on its biochemical output, such as certain vitamins and short-chain fatty acids". (see full report, https://doi.org/10.1155/2019/1718741 ).

16S rRNA VS. METATRANSCRIPTOMIC SEQUENCING:

The report explains in detail the chasm of difference between the 16S r RNA and metatranscriptomic sequencing.

16S rRNA gene sequencing tracks a small portion of the prokaryotic 16S ribosomal RNA gen, but does not measure the biochemical functions of the microorganisms or distinguish living from dead organisms. It also excludes some bacteria, most archaea, and all eukaryotic organisms and viruses, resulting in a limited view of the gut microbiome ecosystem, according to the October 1 report.

Metatranscriptomic analysis (metatranscriptomics, RNA sequencing, and RNAseq) offers insights into what the gut microbiome are actually doing and why and how they are doing it. Viomega can make classifications based on a database of 110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of 100 million microbial genes. "The biochemical activities of the gut microbiome by quantifying expression levels of active microbial genes, allowing for the assessment of pathway activities, while also providing strain-level taxonomic resolution for all metabolically active organisms and viruses," says the report. Viome's Viomega now makes this process affordable as well for the first time.

Naveen Jain founded Viome in 2016, a leading personalized microbiome gut sequencing technology company that uses deep machine learning and data science to offer optimal health care solutions for its customers. One of Jain’s “Moonshot” goals is to “truly make illness optional.” To do so, we must “think like the future has already arrived.”

Health care is one of those key global challenges facing this generation. The wholistic approach to wellness that has prevailed for centuries in Asia is being explored in a much broader scale with advanced Ai (artificial intelligence), data science, and other technology by the scientific communities in the U.S. and elsewhere that were not available to previous generations.

What Jain and his team at Viome are using Ai to discover a deeper and more detailed understanding of the mind and body. "Ai is going to play the biggest role because there is so much more data that no humans can ever process," he said.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #healthinnovation #healthtech #machinelearning #mindbody

Ayurveda's "person-centric", non-standardized approach to health

Sep

30

Ayurvedic health is a 3,000 hear old holistic approach to an individual's personal health from India based on the three

Doshas: Vata (air, ether), Pitta (fire), and Kapha (water, earth).

How is Ayurvedic health different from the other approaches to health care? The modern scientific approach has been focused on standardization and applying solutions that work for the majority of people, such as if you get sick, you take this particular medicine and you will be healed of the ailment.

Ayurveda on the other hand, is person-centered vs. pathology-centered. It takes the approach that respects and considers the uniqueness of each individual in applying health care solutions. Ayurveda works with all levels of the person, the physical, mental, and spiritual, and both internal (microcosm) and external factors (macrocosm).

It believes each individual must take responsibility for their own health with a preventive, natural approach to addressing our symptoms and health issues.

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

"Miracle bugs" - Microbial Influences on MS

Sep

19

Research suggests that microbiomes influence brain health in a variety of ways.

Innovative entrepreneurs and researchers are able to isolate, using Ai, specific strains of bacteria that directly affect the neuro-degeneration of MS (multiple sclerosis) patients, as one of many examples.

Miracle “bugs”

Getting down to specifics, one study identified a connection between bacterial strains Akkermansia muciniphila and Acinetobacter calcoaceticus, and multiple sclerosis. A study conducted by the University of California San Francisco (UCSF) found a connection between gut microbiomes and neuron-degeneration characterized by MS (September 11, 2017 Online Edition of Proceedings of the National Academy of Sciences (PNAS). In the study, postdoctoral UCSF researcher Egle Cekanaviciute, PhD, and collaborators found specific species of bacteria in the gut among 71 MS patients they analyzed that were not present in 71 healthy control subjects. The study found that Akkermansia muciniphila and Acinetobacter calcoaceticus—triggered human immune cells to become pro-inflammatory, while another found at lower than usual levels in MS patients — Parabacteroides distasonis—triggered immune-regulatory responses. Sergio Baranzini, PhD, a professor of neurology at UCSF explains in the article that “twins only share an MS diagnosis about 35 percent of the time.” Baranzini and Cekanaviciute’s studies took the research a step further, to identify the effects of specific microbiomes – the increased presence of ones that cause harmful effects versus the decreased presence of ones that are helpful – how they actually impact human health.

This demonstrates concrete evidence associating the role of microbiomes and MS. Baranzini and Cekanaviciute’s research took the research a step to the next level. It identified the effects of specific microbiomes - the increased presence of ones that cause harmful effects versus the decreased presence of ones that are helpful - how they actually impact human health. With this knowledge, scientists have the tools now to potentially cure degenerative diseases like MS for the first time!

The brain – microbial body connections seem endless, as the engine of microbial research redefines the health care industry.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #healthinnovation #healthtech #machinelearning #mindbody

Chinese herbal impacts on gut health

Sep

17

Radix Scutellariae also known as baical skullcap seed/ root is the root of Scutellaria baicalensis, the source of the 2,000 year old Chinese medicine Huang Qin.

In addition to animal studies, several studies of natural products have been performed on human gut microbiota. Gegen Qinlian Decoction (GQD), a traditional Chinese herbal formula, reshaped the gut microbiota in a clinical study by China Pharmaceutical University (see reference below) in which 187 T2D (type 2 diabetes) patients participated. The data showed that the symptoms of T2D, such as fasting blood glucose levels and hemoglobin A1c (HbA1c) levels, were ameliorated in GQD-treated patients, with increased amounts of beneficial bacteria, including Faecalibacterium, Gemmiger, Bifidobacterium, and Escherichia. Radix Scutellariae (baical skullcap seed/ root) in GQT is the main herbal component that facilitated the potent inhibition of MMP-2. MMP-2 (matrix metalloproteinase-2) contributes to cancer cells migration and the progression of breast cancer, among others. GQT is also widely used to treat diarrhea and inflammation symptoms in various gastrointestinal disorders. (see https://www.sciencedirect.com/science/article/pii/S0753332218369075).

Another clinical study involving ten obese Korean women was conducted to investigate the antiobesity activity of the water extract of Ephedra sinica Stapf. This study revealed that, in seven of the ten obese women, BW and body mass index (BMI) were decreased after administration of this herb. (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. Contact Qinglong Guo; qinglongguo@hotmail.com and Na Lu; nalu@cpu.edu.cn). ).

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

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Using Classic models (Lotka-Volterra) to do microbiome research

Prebiotic fiber, short chain fatty acids drive gut and immune health

"Keystone Species" - Like the Wolves of Yellowstone Park

Health Tech Startups Reach Unicorn, Other Milestones; UCSD Funding

Japanese Health Care Offers Private Sector Options & Coverage for Herbal Remedies.

Herbs that support "the happy chemical", microbiome health

A “Tsunami” of Ai is Coming to Health Care

Ayurveda's "person-centric", non-standardized approach to health

"Miracle bugs" - Microbial Influences on MS

Chinese herbal impacts on gut health

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