Study: How glyphosate affects gut bacteria

Recently, a study, called "The Effect of Glyphosate on Potential Pathogens and Beneficial Members of Poultry Microbiota In Vitro", was done on the effects gut bacteria and pathological bacteria when exposed to glyphosate. The study is in Curr Microbiol. The abstract is here. The abstract is also on SpringerLink for free. The full study is paywalled (meaning, you have to pay to see the whole study).

1. Highly pathogenic bacteria highly resistant to glyphosate. 
2. Beneficial bacteria are moderate to highly susceptible to glyphosate exposure. That means one doesn't have to ingest much glyphosate to have a problem.

The abstract:

The use of glyphosate modifies the environment which stresses the living microorganisms. The aim of the present study was to determine the real impact of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro. The presented results evidence that the highly pathogenic bacteria as Salmonella Entritidis, Salmonella Gallinarum, Salmonella Typhimurium, Clostridium perfringens and Clostridium botulinum are highly resistant to glyphosate. However, most of beneficial bacteria as Enterococcus faecalis, Enterococcus faecium, Bacillus badius, Bifidobacterium adolescentis and Lactobacillus spp. were found to be moderate to highly susceptible. Also Campylobacter spp. were found to be susceptible to glyphosate. A reduction of beneficial bacteria in the gastrointestinal tract microbiota by ingestion of glyphosate could disturb the normal gut bacterial community.

Below is a partial table of the study results on different bacteria.

Sources
Full study as PDF.
Full study online. PDF available.

Fecal bacteria transplant update

This is a longer post but well-worth reading as the information has effects on many diseases at once.

What is fecal transplant (FT)?

It's when feces from a healthy donor is given to an unhealthy person. FT is non-invasive. No cuts are made, sometimes it is given through a tube in the nose, a capsule form containing freeze-dried bacteria, enema, or other non-invasive ways. Side effects are few.

What are microbiota? 

Microbiota are all the bacteria and microscopic organisms that live in your gut. They help you turn food into vitamins that can be absorbed into the blood stream. There are good bacteria (which help you digest food), and bad bacteria. Under certain conditions, like a chronic lack of fiber, or eating too much sugar or processed foods, the bad bacteria out compete the good bacteria and this syndrome might be linked to diabetes and other illnesses.

Some bullet points:

1. Fecal transplants have been used for at least 1700 years. Source. 
2. 99% of the DNA inside us comes from bacteria. Source. 
3. Limited cases show the treatment is effective in Parkinson's disease, multiple sclerosis, chronic fatigue syndrome and irritable bowel syndrome.
4. FT can be given by nasogastric or nasoduodenal tube, colonoscope, enema, or capsule. 
5. Thinner people have a wider variety of Bacteroidetes, a large tribe of microbes that specialize in breaking down bulky plant starches and fibers into shorter molecules that the body can use as a source of energy. (Source)
6. One bacterium associated with obesity might be a stomach bacterium called Helicobacter pylori. Research by Martin Blaser of New York University suggests that it helps to regulate appetite by modulating levels of ghrelin—a hunger-stimulating hormone, but the use of antibiotics has all but made H. pylori extinct in human stomachs.
7. Since FT is so new, it's probably not covered by any medical insurance in the US.

In China they used to make "poop soup" containing fecal matter and fed it to newborns. This jump started the babies' immune systems and gut bacteria populations. They called it "yellow soup". Initial studies show fecal transplant (FT) works in treating Parkinson's disease, fibromyalgia, chronic fatigue syndrome, myoclonus dystopia, multiple sclerosis, obesity, insulin resistance, metabolic syndrome, and autism.

What are the bad diets like?  What problems might bad diets cause?

At this point scientists have very reasonable theories on how this works, but the truth is they cannot claim they know everything about this issue.

But a bad diet is a diet consistently high in sugar, processed foods and low in fiber. The good bacteria need the fiber to survive. It's their food. So grab those prunes and munch with pride!

When would a person need a fecal transplant? 

Fecal transplants are not yet legal for humans in the US except under limited circumstances, like a persistent C difficile infection, Crohn's disease or ulcerative colitis. But this link says the cure rate is "nearly" 100% out of 200 patients. More studies must be done on how to package, ship and ingest the bacteria so they live and can benefit the person.

A study: "The Impact of Diet and Lifestyle on Gut Microbiota and Human Health".
From NIH. (Lots of good info here!)

1. Both short- and long-term dietary change can influence the microbial profiles. I.e. a little "cheating" in the diet can still be bad. 
2. Most of the microbes are bacteria, the gut can also harbor yeasts, single-cell eukaryotes, viruses and small parasitic worms. Not all of these organisms are harmful by themselves, but they can make the populations of good bacteria decrease, which IS harmful. 
3. The most common bacteria in adults are Bifidobacterium, Lactobacillus, Bacteroides, Clostridium, Escherichia, Streptococcus and Ruminococcus. Approximately 60% of the bacteria belong to the Bacteroidetes or Firmicutes phyla.
4. The Human Microbiome Project (Wikipedia page) shows that bacteria populations vary a lot among individuals. 
5. Gut microbes produce a large number of bioactive compounds that can influence health; some like vitamins are beneficial, but some products are toxic.
6. The use of a range of fibers, may be the best way of maintaining a healthy gut microbiota population. (Other studies say avoid sugar, and processed foods.)
7. Bacteria such as Bifidobacterium can generate vitamins (e.g., K, B12, Biotin, Folate, Thiamine). B12 is very important for neurological function, and a lack of B12 can cause some symptoms of depression.  
8. The Bacteroidetes phylum bacteria tend to dominate numerically during youth but numbers decline significantly by old age, whereas the reverse trend occurs for bacteria of the Firmicutes phylum.
9. High fat diets induce increased circulating levels of bacteria-derived LPS in humans, possibly as a consequence of increased intestinal permeability (related to leaky gut syndrome?). LPS is an immune system modulator and potent inflammatory agent linked to the development of common metabolic diseases.

Links

1. "How gut bacteria make us fat and thin." Scientific American. June 1, 2014. READ THIS if nothing else.
2. List of clinics that do FT here. 
3. Wikipedia link to "fecal microbiota transplant".

Monsanto might cause 50% of children to be autistic in the future.

(NOTE: This is speculation and a bit hysterical, but it's an important thing to consider anyway.)

A senior scientist at MIT, Dr. Stephanie Seneff, made these remarks during a panel presentation in Groton, MA last week, specifically cites the Monsanto herbicide, Roundup, as the culprit for the escalating incidence of autism and other neurological disorders. Roundup was originally introduced in the 1970s and could only be used as a weed killer, but is not regularly used on crops such as corn, soy and wheat to kill them right before harvest. Farmers have a problem where all the crop does not ripen at once, so Roundup is used to kill it all at once and then harvested 2 days later. (See the actual Roundup label.)

According to Dr. Seneff, glyphospate interferes with gut bacteria via the Shikimate pathway. Gut bacteria are a critical part of our lives and we are just learning how important they really are. With the gut bacteria depleted, humans are now missing several key amino acids. According to various studies, glyphosate depletes the amino acids tyrosine, tryptophan, and phenylalanine, which can then contribute to obesity, depression, autism, inflammatory bowel disease, Alzheimer’s and Parkinson’s. Monsanto, the seller of glyphospate products, naturally disagrees.


Some critics of Dr. Seneff argue she is confusing correlation with causation, which could very well be true. However, causation is nearly impossible to prove given the human body's complexity, and correlation has often been used in the past to determine the toxicity of a substance. Except when it comes to Monsanto products. And congresscritters that accept "donations" from Monsanto and biotech companies.

There are dozens of studies showing glyphospate danger has correlation with disease and conditions. Yet there are almost no studies saying the same thing about THC, cannabidiol, and pot. Since Congress, the DEA, and the FDA are inconsistent, their judgment cannot be trusted, nor can their decisions be assumed to be for the better of all people. The FDA, especially since they are being sued for covering up facts about glyphospate, appears to make decisions based on hysteria, and donations, rather than actual facts.


Source
Journal Neo.

Disease and microbiota in the gut

Microbiome: all the bacteria, good and bad, that live within and on the surface of the body.

There are some studies that suggest an imbalanced microbiome, either on the skin or in the gut, is the cause of some disease, including autoimmune diseases like diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia. There are also studies that show correlation of an incorrect microbiome to obesity.

This study by Ridaura (2013) shows that mice without certain Bacterioides bacteria tend to be obese. It also has some interesting graphs.This study shows that people who are obese tend to have a higher ratio of Firmicutes:Bacteroidetes bacteria. That is, higher Firmicutes and less Bacteroidetes.

This study tries to find a correlation between diabetes type 1 and gut bacteria.

Scientists even divide people into 3 groups based on their gut bacteria composition.

Systemic antibiotics can have a negative impact on these gut bacteria. Some people recover their healthy ratio of bacteria, others never do. And it is suspected that imbalanced bacteria cause other autoimmune problems. So avoid antiobiotics, especially systemic ones.

For more fun sites try these:

• What germs are on your cellphones and shoes? Link. 

Sources

1. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944. Epub 2011 Apr 20. Erratum in: Nature. 2011 Jun 30;474(7353):666. Nature. 2014 Feb 27;506(7489):516. PubMed PMID: 21508958; PubMed Central PMCID: PMC3728647. NIH abstract. NIH full study.
2. Human Microbiome Project. Studying microbiomes to understand their role in human health. They also have the genomes of reference strains of bacteria. Link here.
3. Giongo, A., Gano, K. A., Crabb, D. B., Mukherjee, N., Novelo, L. L., Casella, G., … Triplett, E. W. (2011). Toward defining the autoimmune microbiome for type 1 diabetes. The ISME Journal, 5(1), 82–91. http://doi.org/10.1038/ismej.2010.92.  
4. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA; Kong; Conlan; Deming; Davis; Young; Bouffard; Blakesley; Murray; Green; Turner; Segre (2009). "Topographical and Temporal Diversity of the Human Skin Microbiome". Science 324 (5931): 1190–2. Bibcode:2009Sci...324.1190G. doi:10.1126/science.1171700. PMC 2805064. PMID 19478181. NIH full study.
5. Home Microbiome site. Link. "The Home Microbiome Study is lead by PI Jack Gilbert, postdoc Daniel Smith, and technician Jarrad Hampton-Marcell at Argonne National Laboratories, and funded by the Alfred P. Sloan Foundation. This study is working in collaboration with MicroBE.net and the Earth Microbiome Project to bring together microbial samples from as many environments as possible in order to understand how microbial community structure is shaped by environmental factors."
6. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013 Sep 6;341(6150):1241214. doi: 10.1126/science.1241214. PubMed PMID: 24009397; PubMed Central PMCID: PMC3829625. NIH abstract. This one has fascinating charts.
7. Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. http://doi.org/10.1038/nature07540. Full study at NIH. 
8. Wikipedia page for "microbiota". Many studies here.
9. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006 Dec 21;444(7122):1027-31. PubMed PMID: 17183312 NIH abstract. "Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes."
10. Wolf, K. J., & Lorenz, R. G. (2012). Gut Microbiota and Obesity. Current Obesity Reports, 1(1), 1–8. http://doi.org/10.1007/s13679-011-0001-8. Link to NIH full study. 
11. Zimmer, Carl. Gut Bacteria Divide People into 3 Groups. New York Times, Apr 20, 2011. Link to article.  Link to Nature article.

High-sugar diet alters gut microbiota for the worse

Another way sugar is bad for you.

From LA Times:

A report published in the new journal Science Translational Medicine has made an interesting discovery concerning the relationship between sugar intake and the balance of intestinal flora. Researchers have discovered that a diet high in sugar and fat substantially alters the bacterial composition in the gut, making it difficult to maintain a healthy weight.

From NIH 2014 "Obesity as a Consequence of Gut Bacteria and Diet Interactions":

At the experimental level, analysis of fecal samples revealed a potential link between obesity and alterations in the gut flora (drop in Bacteroidetes and increase in Firmicutes), the specific gut microbiome being associated with the obese phenotype. The sparse data in humans supports the fact that fat storage is favoured by the presence of the gut microbiota, through a multifaceted mechanism.

It results from a long-term disbalance between energy intake and expenditure, that is, increased consumption of more energy-dense, nutrient-poor foods containing high levels of sugar and saturated fats in combination with reduced physical activity. Obesity is now characterized by a cluster of important chronic metabolic disorders, including insulin resistance, type 2 diabetes, fatty liver disease, atherosclerosis, hypertension, and hypercholesterolemia, and by a low grade of systemic inflammation [3], being the cause of exacerbation of all the above and leading to increased morbidity and mortality.

There's a lot of good studies referenced there, you might want to read the NIH study.

Sugar substitutes can promote glucose intolerance, imbalance gut flora

From The Scientist:

Non-caloric sweeteners can spur glucose intolerance in mice and some people, according to a study published today (September 17) in Nature. Researchers from the Weizmann Institute of Science in Israel and their colleagues have uncovered “the unexpected effect that artificial sweeteners drive changes in the [gut] microbiota, which promote glucose intolerance,” said University of Chicago pathologist Cathryn Nagler, who studies how the microbiota regulate allergic responses to food and penned an editorial accompanying the study.

From the USDA via a 2014 Colorado State University study:

Obesity rates among children in the United States have tripled in the past three decades and approximately one third of all children or adolescents are currently overweight or obese (CDC). Obese children are more likely to be pre-diabetics and have one or more risk factors associated with cardiovascular disease, problems that become exacerbated as they enter adulthood. To combat weight gain and obesity related disease a number of low energy foods, usually containing non-nutritive sweeteners (NNS) such as saccharine, sucralose, and aspartame have become increasingly prevalent and are recommended sugar substitutes for individuals with Type 2 diabetes. However, two recent human observational studies found positive correlations between consumption of artificial sweeteners, particularly diet sodas, with increased obesity and metabolic syndrome.Weight gain is thought to occur when energy intake surpasses energy expenditure; and foods sweetened with NNS's are designed to reduce caloric consumption while enhancing the flavor of many foods. However, new insights into the role of intestinal flora in harvesting energy from the diet and in contributing to both increased appetite and insulin resistance suggest that the "energy in/energy out" equation may be oversimplified. In particular, several studies support that the relative proportion of the two major intestinal bacterial phyla, Firmicutes and Bacteriodetes, affect the harvest of calories from the diet. Therefore, if NNS alter the intestinal flora such that there are proportionately higher levels of Firmicutes, foods that would normally have passed undigested from the body are metabolized and absorbed through the intestines, increasing the total calories available to the host. We hypothesize that consumption of NNS may later the intestinal microflora to favor greater dietary energy harvest and/or increased inflammation associated with obesity and this study is designed to explore this hypothesis.  

Be careful of artificial sweeteners. Try stevia instead. The Japanese have been using it since the 1970s and the Guarani indians from South America used it long before that.

The good bacteria in your gut

It wasn't until recently that doctors and scientists knew how important the good bacteria in your gut are.  Gut microbiota live in the digestive tract of animals, and help them digest food as well as absorb vitamins. One study from UCLA shows that eating probiotics via yogurt can change how a person's brain works. There are many sources of probiotics in pill form but they are useless, the bacteria simply don't survive the drying out process.

From Wikipedia:

Gut microorganisms benefit the host by collecting the energy from the fermentation of undigested carbohydrates and the subsequent absorption of short-chain fatty acids. The most important of these fatty acids are butyrates, metabolised by the colonic epithelium; propionates by the liver; and acetates by the muscle tissue. Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols and xenobiotics. 99% of the bacteria in the gut come from 30-40 species. Bacteria make up 60% of the dry weight of feces. The currently known genera of fungi of the gut flora include Candida, Saccharomyces, Aspergillus, and Penicillium.

70% of Upper Respiratory Infections are from viruses, not bacteria, so antibiotics will not help you most of the time. Overuse of antibiotics can lead to an imbalance of the gut bacteria, allowing bad bacteria to take over. More about gut flora and antibiotics:

Altering the numbers of gut bacteria, for example by taking broad-spectrum antibiotics, may affect the host's health and ability to digest food.^[52] Antibiotics can cause antibiotic-associated diarrhea (AAD) by irritating the bowel directly, changing the levels of gut flora, or allowing pathogenic bacteria to grow.

Fiber is said to encourage the growth of helpful gut microbiota, but you must eat it every day in enough quantity to be helpful.

Bacteria and cancer:

Some genera of bacteria, such as Bacteroides and Clostridium, have been associated with an increase in tumor growth rate, while other genera, such as Lactobacillus and Bifidobacteria, are known to prevent tumor formation.

Gut bacteria and obesity:

The mutual influence of gut flora composition and weight condition is connected to differences in the energy-reabsorbing potential of different ratios of Firmicutes and Bacteroidetes, especially in the digestion of fatty acids and dietary polysaccharides, as shown by experiments^[63] wherein the (caecum) gut flora of obese mice were transplanted into germ-free recipient mice, leading to an increase in weight despite a decrease in food consumption. The experimentation and results suggest bacteria specific to lean and obese genes can be a weapon in the fight against the obesity epidemic.

Fecal bacteriotherapy (or "poop pill") is an attempt to give a person with the wrong ratio of bacteria, a healthy set of bacteria. But so far the bacteria do not survive drying out, and a "fresh" pill is not so appetizing.

So be kind to your bacteria, do not take antibiotics unless you really have to, and eat more fiber to encourage the growth of good bacteria.