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HerbSprout Microbiome Blog -


Herbsprout is a webblog and podcast dedicated to sharing the health benefits of herbs, food, innovations related to our gut microbiome. Herbsprout seeks to bridge the vast chasm dividing the mainstream medical community and alternative medicine.

16S rRNA VS. Metatranscriptome Sequencing in Microbiome Testing

An International Journal of Genomics report explains in detail the chasm of difference between 16S r RNA and metatranscriptomic sequencing in testing your gut microbiome.

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 2019 report, "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).

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.

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Herbs - God's Pharmacy

Herbs - God's Pharmacy

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How Gut Microbiota Contributes to Depression

How Gut Microbiota Contributes...
The gut microbiota is thought to influence MDD (major depressive disorder) through inflammatory processes, primarily in the gut-brain axis. A December 13, 2019 article by Psychiatry Advisor and the European Journal of Neuroscience, says "mice treated with the probiotic Bifidobacterium adolescentis showed a reversal of neuroinflammation and depressive symptoms." Gut bacteria are essential to communication between the gut and the brain, and helps to regulate brain development and function. See article for more information at .

Experimental evidence links changes in the chemokine network to depressive behavior, and researchers of clinical studies indicated an association between neuroinflammation and MDD, according to the report. This and other similar results of studies have generated increased interest in the use of anti-inflammatory microbiome agents in the treatment of MDD. Another article by Nature Microbiology found two types of bacteria, Coprococcus and Dialister, which are depleted in people with depression. Researchers reported this in a February 4, 2019 in Nature Microbiology article.

Other studies suggest that certain probiotics can serve as effective antidepressants. 34 controlled clinical trials, led by researchers from the Department of Psychiatry and Human Behavior at the Warren Alpert Medical School at Brown University (Rhode Island, USA) came to this conclusion. Of the 34 clinical trials, 27 interventions were probiotic and 7 were prebiotic, including Bifidobacterium longum, Bacillus coagulans, and Lactobacillus alone or in combination with Bifidobacterium. Each demonstrated anti-anxiety and/or anti-depressant effects. See the following article published June 04, 2019 at .

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

Black mondo grass, monkey g...
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,
Contact Qinglong Guo; and Na Lu;
#ai #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #plantnutrition #spices

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First Human Test (of its kind) Confirms Exposure to UVB light improves gut health

First Human Test (of its kind)...
A study published December 05, 2019 by the European Society for Gastroenterology and Motility found that UVB exposures over a one-week period increased the gut microbiota diversity in humans. The study was led by Dr. Bruce A. Vallance from the University of British Columbia and the Women’s Health Research Institute in Vancouver (Canada). Skin exposure to UVB light increased "alpha (within-subject) and beta diversity (between-subjects) in the gut microbiota" in subjects who have not taken vitamin D supplements before the study. The study showed increases in key strains such as Lachnospiraceae, Ruminococcus, and Clostridiaeae.

UVB exposures over a one-week increased the gut microbiota diversity of the group with vitamin D insufficiency to the same level as that of the group that started the study with sufficient serum vitamin D levels. The exposure to UVB positively influenced key gut microbiota such as Lachnospira and Fusicatenibacter.

This is the first study that reports changes in the human gut microbiota in response to UVB light. As decreased exposure to UVB light. Decreased vitamin D production has been associated with the rise in chronic inflammatory diseases. Previous studies relating UVB light to gut microbiota have been conducted on mice. Herbsprout previously reported on UBC's earlier research on the subject. Visit this link to read more,

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What do Kimchi and Sauerkraut have in common?

Both kimchi and sauerkraut are fermented foods. Consuming fermented foods can be healthy for your gut. They help maintain a rich variety of healthy microbiome in your gut.

Fermented foods are naturally rich in probiotics. It is recommended that you consume fermented foods once or twice daily, including foods like kimchi, sauerkraut, cultured yogurt, kefir, pickles, and cultured sour cream. Foods that contain prebiotic fibers are also important for your healthy gut. These include popular vegetables such as onions, garlic, and asparagus.

Get to know your body, because every body is different and our probiotic and prebiotic needs can be very different from one person to another.

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How gut bacteria keeps us healthy

How gut bacteria keeps us hea...
If you've been reading this herbsprout blog, you know that our body's microbiome content can contribute to keeping us healthy and can also create havoc to our body if brought out of balance. Last blog we see that "antibiotics" can save us from these unwanted bacteria. However, since our body needs most microbes to survive, let's take a look at why.

Our gut bacteria helps us stay healthy in a number of ways. These include:

1. they make healthy vitamins for our body by harvesting nutrients from the food we eat;
2. they prevent anxiety and depression;
3. they can prevent neurological diseases such as Multiple Sclerosis, Parkinson's disease, autism, and Alzheimer's;
4. they prevent "leaky gut" which contribute to obesity and diabetes 2;
5. they balance our immune system and control inflammation;
6. they produce serotonin, the "happy chemical"; and
7. they help prevent heart disease.

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"We are running out of antibiotics"

Scientists at Northeastern discovered a new bacteria that is Gram-negative, according to a November 19, 2019 report published by This is significant because gram-negative bacteria, which include E. coli and Salmonella, have an additional, outer membrane that protects them from many antibiotics. "This extra protection is why gram-negative bacteria are at the top of a list of 'priority' pathogens that need to be targeted with new antibiotics, compiled by the World Health Organization", according to the report.

"We are running out of antibiotics," says Kim Lewis, who directs the Antimicrobial Discovery Center at Northeastern, where the discovery of darobactin was made. "We need to be looking for novel compounds with no pre-existing resistance in the clinic or the population."

Yu Imai, a postdoctoral research associate in Lewis' lab, discovered the compound from Photorhabdus bacteria that live inside the gut of a nematode, a tiny parasitic worm found in soil. It's the first time, Lewis says, that the animal microbiome was found to harbor an antibiotic that promises to be useful for humans.

For more information, see

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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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