270 replies to this topic

[normalizing]

is this your opinion or you read it somewhere?

[RWhigham]

A characteristic of bacteria is that they continually swap genetic material among themselves. While an individual bacterium is too small to host anything but a very small genome, by swapping genes our bacteria in aggregate could have a much larger genome than we do.

 

Bacteria that don't permanently colonize us may contribute to the gene pool of those that do.

So a probiotic strain doesn't necessarily have to colonize us to contribute genes that affect our bionome.

 

 

hazy

is this your opinion or you read it somewhere?

 

 

Something I've known a long long time. I'll find references:

 

Number of bacterial genes in our gut

Microbiology by numbers The number of genes contained within this gut flora outnumbers that contained within our own genome 150-fold, and even in our genome, 8% of the DNA is derived from remnants of viral genomes.

 

Bacterial gene exchange

If you google "bacterial gene exchange" many references will pop up.

For example: Bacterial Gene Exchange and Mobile Genes

 

• Bacteria do not exchange genes by meiosis ....
• Bacteria commonly exchange small pieces of genome, a few genes at a time, through transformation, transduction, or conjugation.
• Transfer between species, even kingdoms, is common, less common  in eukaryotes, though it does occur

    Transformation is the uptake of DNA from outside the cell.

    Phage Transduction is when phages transfer bacterial genes. The article explains 2 ways this occurs

    Conjugation is the process by which a plasmid is transferred from an F+ cell into an F- cell

 

Genomics

 Gene Transfer.jpg   38.51KB   0 downloads

 

HIstorical:  The moratorium on rDNA research

Recombinant DNA Technologies and Researchers' Responsibilities, 1973-1980  The letter appeared in Science on July 26, 1974, and provoked a wide range of commentary, as well as protests from many scientists; nevertheless, the voluntary moratorium--the first in the history of science--was universally observed.  The moratorium was lifted after a set of guidelines were agreed on. As I recall one of the considerations was that bacteria had already been swapping genes for billions of years.

Edited by RWhigham, 13 September 2017 - 08:57 PM.

[albedo]

Hjorth MF, Roager HM, Larsen TM, et al. Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. Int J Obes (Lond). 2017

 

"On the basis of the abundance of specific bacterial genera, the human gut microbiota can be divided into two relatively stable groups that might have a role in personalized nutrition. We studied these simplified enterotypes as prognostic markers for successful body fat loss on two different diets. A total of 62 participants with increased waist circumference were randomly assigned to receive an ad libitum New Nordic Diet (NND) high in fiber/whole grain or an Average Danish Diet for 26 weeks. Participants were grouped into two discrete enterotypes by their relative abundance of Prevotella spp. divided by Bacteroides spp. (P/B ratio) obtained by quantitative PCR analysis. Modifications of dietary effects of pre-treatment P/B group were examined by linear mixed models. Among individuals with high P/B the NND resulted in a 3.15 kg (95% confidence interval (CI): 1.55; 4.76, P<0.001) larger body fat loss compared with ADD, whereas no differences was observed among individuals with low P/B (0.88 kg (95% CI: −0.61; 2.37, P=0.25)). Consequently, a 2.27 kg (95% CI: 0.09; 4.45, P=0.041) difference in responsiveness to the diets were found between the two groups. In summary, subjects with high P/B ratio appeared more susceptible to lose body fat on diets high in fiber and whole grain than subjects with a low P/B ratio."

[APBT]

FULL TEXT LINK:  http://msphere.asm.o...t/2/5/e00327-17

 

 

https://www.scienced...71011123728.htm

 

'Ridiculously healthy' elderly have the same gut microbiome as healthy 30-year-olds

 

Date: October 11, 2017 Source: University of Western Ontario Summary: In one of the largest microbiota studies conducted in humans, researchers have shown a potential link between healthy aging and a healthy gut.

In one of the largest microbiota studies conducted in humans, researchers at Western University, Lawson Health Research Institute and Tianyi Health Science Institute in Zhenjiang, Jiangsu, China have shown a potential link between healthy aging and a healthy gut.

With the establishment of the China-Canada Institute, the researchers studied the gut bacteria in a cohort of more than 1,000 Chinese individuals in a variety of age-ranges from 3 to over 100 years-old who were self-selected to be extremely healthy with no known health issues and no family history of disease. The results showed a direct correlation between health and the microbes in the intestine.

"The aim is to bring novel microbiome diagnostic systems to populations, then use food and probiotics to try and improve biomarkers of health," said Gregor Reid, professor at Western's Schulich School of Medicine & Dentistry and Scientist at Lawson Health Research Institute. "It begs the question -- if you can stay active and eat well, will you age better, or is healthy ageing predicated by the bacteria in your gut?"

The study, published this month in the journal mSphere, showed that the overall microbiota composition of the healthy elderly group was similar to that of people decades younger, and that the gut microbiota differed little between individuals from the ages of 30 to over 100.

"The main conclusion is that if you are ridiculously healthy and 90 years old, your gut microbiota is not that different from a healthy 30 year old in the same population," said Greg Gloor, the principal investigator on the study and also a professor at Western's Schulich School of Medicine & Dentistry and Scientist at Lawson Health Research Institute. Whether this is cause or effect is unknown, but the study authors point out that it is the diversity of the gut microbiota that remained the same through their study group.

"This demonstrates that maintaining diversity of your gut as you age is a biomarker of healthy aging, just like low-cholesterol is a biomarker of a healthy circulatory system," Gloor said. The researchers suggest that resetting an elderly microbiota to that of a 30-year-old might help promote health.

"By studying healthy people, we hope to know what we are striving for when people get sick," said Reid.

The study also found a distinct anomaly in the group aged 19 to 24 that has not been observed in large-scale analyses of other populations and they suspect may be unique to this healthy cohort in China. The distinct gut microbiota of this group was a surprising finding and requires further study.

 

[albedo]

 

FULL TEXT LINK:  http://msphere.asm.o...t/2/5/e00327-17

 

 

https://www.scienced...71011123728.htm

 

'Ridiculously healthy' elderly have the same gut microbiome as healthy 30-year-olds

 

....

 

It is a very nice finding APBT. Despite several methodological limitations it is the first time for me to encounter a large-scale study getting a baseline microbiota composition of very healthy individuals of one population spanning from the young to the very old. It can pave the way to conduct similar studies in other populations with possible impact not only to target dysbiosis but also enhance healthspan. Thank you.

 

[normalizing]

i found this interesting article that i would like to share; https://www.nutraing...-damage-in-rats

[albedo]

The ratio of Firmicutes to Bacteroidetes seems evolving with age and being a proxy of a high resistant starch diet which is reported as beneficial. I just wonder if you have measured it (I never did it) and what you make of it. From some of the previous posts, interpreting the results of this and similar tests seem tricky not to mention proactively intervene. Just wonder.

 

Maier TV, Lucio M, Lee LH, et al. Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. MBio. 2017;8(5)

https://www.ncbi.nlm...les/PMC5646248/

 

Mariat D, Firmesse O, Levenez F, et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 2009;9:123.

https://bmcmicrobiol...1471-2180-9-123

[Harkijn]

I never tested this, but these findings neatly tie in with earlier data, also from popular science such as the Blue Zones. In the Blue Zones  old, healthy people eat beans. It may be hard to swallow (pun just a little bit intended  ) for the low carb crowd, but our practical way forward seems clear:

https://www.hsph.har...sistant-starch/

[normalizing]

gut bacteria and cancer; http://www.bbc.com/n...health-41848461

[albedo]

I put the following (paywalled) paper in my to-read list. It looks important as it points to a change in the methodology (called Quantitative Microbiome Profiling) to much better studying the impact of microbiota composition and load to the health and disease phenotype. The bulk of studies seems so far to be limited mainly to assess ratios and percentages:  "...To enable genuine characterization of host–microbiota interactions, microbiome research must exchange ratios for counts^4,8,9..." as quoted from the abstract of the Belgian group.

 

I think we might also watch the space of commercial offerings which I expect to grow in future for our own benefit and testing purposes. Should I find more on this after I go through the paper, I will post here.

 

Vandeputte D, Kathagen G, D'hoe K, et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature. 2017;551(7681):507-511.

 

I spot this interesting study via the Nutra Ingredients site which gives a summary.

[albedo]

In case you have overlooked sometime ago this study by a team in Germany (MPI): in a vertebrate animal model (turquoise killifish) a sort of fecal transplant induced increased longevity (I understand ~37% in median life span) not very dissimilarly to what obtained with blood in mice:

 

"Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota during host aging is largely unexplored. Here, using the African turquoise killifish (Nothobranchius furzeri), a naturally short-lived vertebrate, we show that the gut microbiota plays a key role in modulating vertebrate life span. Recolonizing the gut of middle-age individuals with bacteria from young donors resulted in life span extension and delayed behavioral decline. This intervention prevented the decrease in microbial diversity associated with host aging and maintained a young-like gut bacterial community, characterized by overrepresentation of the key genera Exiguobacterium, Planococcus, Propionigenium and Psychrobacter. Our findings demonstrate that the natural microbial gut community of young individuals can causally induce long-lasting beneficial systemic effects that lead to life span extension in a vertebrate model." (bold mine)

 

 killfish.PNG   67.24KB   3 downloads

 

Smith P, Willemsen D, Popkes M, et al. Regulation of life span by the gut microbiota in the short-lived African turquoise killifish. Elife. 2017;6

 

[normalizing]

i found this few days ago; https://www.superfoo...s-side-effects/

 

anyway, for me the biggest side effect of probiotics is huge apetite and weight gain. this is very logical because you introduce more and more hungry bacteria in you and force your body to feed them more which ends up with overeating and constant hunger. i really think its good idea to take probiotics once a week instead of regularly, honestly it causes me a lot of problems with hunger

[albedo]

i found this few days ago; https://www.superfoo...s-side-effects/

 

anyway, for me the biggest side effect of probiotics is huge apetite and weight gain. this is very logical because you introduce more and more hungry bacteria in you and force your body to feed them more which ends up with overeating and constant hunger. i really think its good idea to take probiotics once a week instead of regularly, honestly it causes me a lot of problems with hunger

 

On different strains effects on weight gain and weight loss, you might check this:

 

Million M, Angelakis E, Paul M, Armougom F, Leibovici L, Raoult D. Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals. Microb Pathog. 2012;53(2):100-8.

 

I have been off the probiotics for a while now and simply experimenting increasing my daily fiber intake, feeling great.
 

(edit: spelling)

Edited by albedo, 23 January 2018 - 10:38 PM.

[normalizing]

i was on antibiotics recently though, so i have been dosing quite high on probiotics and i gained weight. also i get allergic reactions, must be something to do with  bacteria not quite fitting in yet

[albedo]

In case you have overlooked sometime ago this study by a team in Germany (MPI): in a vertebrate animal model (turquoise killifish) a sort of fecal transplant induced increased longevity (I understand ~37% in median life span) not very dissimilarly to what obtained with blood in mice:

 

"Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota during host aging is largely unexplored. Here, using the African turquoise killifish (Nothobranchius furzeri), a naturally short-lived vertebrate, we show that the gut microbiota plays a key role in modulating vertebrate life span. Recolonizing the gut of middle-age individuals with bacteria from young donors resulted in life span extension and delayed behavioral decline. This intervention prevented the decrease in microbial diversity associated with host aging and maintained a young-like gut bacterial community, characterized by overrepresentation of the key genera Exiguobacterium, Planococcus, Propionigenium and Psychrobacter. Our findings demonstrate that the natural microbial gut community of young individuals can causally induce long-lasting beneficial systemic effects that lead to life span extension in a vertebrate model." (bold mine)

 

killfish.PNG

 

Smith P, Willemsen D, Popkes M, et al. Regulation of life span by the gut microbiota in the short-lived African turquoise killifish. Elife. 2017;6

 

Josh Mitteldorf reviews the result in his blog here "...This single study raises the possibility that understanding the microbiome as a system could be a powerful new avenue toward health and longevity..."

https://joshmitteldo...al-transplants/
 

[normalizing]

*sigh*

[albedo]

I found this a very good review on the role of the microbiome in disease and the changes due to aging up to the centenarians. It is not open though.

 

Kundu P, Blacher E, Elinav E, Pettersson S. Our Gut Microbiome: The Evolving Inner Self. Cell. 2017;171(7):1481-1493.

 gut innerself.PNG   291.47KB   0 downloads

[albedo]

We normally think about *gut* microbiome but an equally fascinating though relatively new area is the "lung microbiome". Given the rising rate of infections and antibiotic use (and resistance) in the elderly, without mentioning the hugely debilitating conditions such as COPD and CF, I expect this be given more and more attention.

 

Have you studied it? Any experience? Please ....

 

O'dwyer DN, Dickson RP, Moore BB. The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease. J Immunol. 2016;196(12):4839-47.

https://www.ncbi.nlm...les/PMC4894335/

 

[normalizing]

how do you introduce probiotics into the lungs? i have had so many lung infections and i smoke and inhale crap all the time, definitely need probiotics for the lungs, how is that possible??

[albedo]

how do you introduce probiotics into the lungs? i have had so many lung infections and i smoke and inhale crap all the time, definitely need probiotics for the lungs, how is that possible??

 

The only I know is the same question asked in a patient conf call with Dr. Kevin Winthrop (min 21:50 on at ): he acknowledges the theoretical interested but was not sure if and who is working on the idea. Moreover he said you might have a higher differentiation of individual responses.
 

[normalizing]

also add some probiotics to the skin as they prevent cancer; https://www.medicaln...cles/321085.php

[albedo]

I am not sure this nice review has been posted in this thread: it discusses the impact of microbiome not only on health & disease but on aging itself. There are very interesting comments on metformin, folate and methionine reduction and species-specific signaling.

 

Heintz C, Mair W. You are what you host: microbiome modulation of the aging process. Cell. 2014;156(3):408-11.

"The critical impact that microbiota have on health and disease makes the interaction between host and microbiome increasingly important as we evaluate therapeutics. Here, we highlight growing evidence that, beyond disease, microbes also affect the most fundamental of host physiological phenotypes, the rate of aging itself"

 

 microbiome and aging.PNG   484.19KB   0 downloads

 

 

[normalizing]

i have been following this thread for a very very long time and i enjoy it and contribute to it once a while but im afraid i figured after many attempts at using probiotics for better health ive come to the conclusion those greedy little bastards make me super hungry all the time and i eat extra more than usual and i have actually gained quite the weight since using probiotics so im reconsidering this and im going to stop for a while and see how it goes. i UNDERSTAND if people get upset that i claim probiotics are weight gainers, maybe its my personal makeup dealing with them, but I WILL state they did that after a long experiment for a definitive fact! ive tried both, probiotic foods like yogurt AND supplements. same effect always!

 

i will update after  i quit them, thanks

 

edit: i did start losing weight on antibiotics not sure if thats just their toxicity on the body or the massacre of those hungry little probiotic bastards

Edited by hazy, 03 April 2018 - 03:49 AM.

[albedo]

i have been following this thread for a very very long time and i enjoy it and contribute to it once a while but im afraid i figured after many attempts at using probiotics for better health ive come to the conclusion those greedy little bastards make me super hungry all the time and i eat extra more than usual and i have actually gained quite the weight since using probiotics so im reconsidering this and im going to stop for a while and see how it goes. i UNDERSTAND if people get upset that i claim probiotics are weight gainers, maybe its my personal makeup dealing with them, but I WILL state they did that after a long experiment for a definitive fact! ive tried both, probiotic foods like yogurt AND supplements. same effect always!

 

i will update after  i quit them, thanks

 

edit: i did start losing weight on antibiotics not sure if thats just their toxicity on the body or the massacre of those hungry little probiotic bastards

 

Hazy, I am very, very far to be able to provide a competent advice and of course your experimentation and monitoring is the best approach. Btw, nobody is upset to you claims because everyone is different but it is true generally probiotics and high fiber foods are associated to weight loss.

 

Maybe something you cal also research is the hormonal link where microbiota composition impacts ghrelin concentration which is known to modulate hunger. The majority of circulating ghrelin is produced in the gastric mucosa and stimulates the appetite. There are also links to gastric infection with H. pylori and antibiotics therapy.

 

Maybe you can look at:

 

Alcock J, Maley CC, Aktipis CA. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays. 2014;36(10):940-9.

https://www.ncbi.nlm...les/PMC4270213/

 

Yanagi H, Tsuda A, Matsushima M, et al. Changes in the gut microbiota composition and the plasma ghrelin level in patients withinfected patients with eradication therapy. BMJ Open Gastroenterol. 2017;4(1):e000182.

http://bmjopengastro...ent/4/1/e000182

 

Good luck and let us know.

 

 

 

[normalizing]

high fiber, low carbs MIGHT help with weight loss WITH or WITHOUT using probiotics, from lots of studies i have seen. But, i have been taking probiotics with high carbs and lots of fat and protein contrary to that, but why? the problem is each time i take probiotics they make me so hungry and high fiber only foods do not satisfy me enough! that honestly i need sugars and carbs too! that is ONLY when i take probiotics, otherwise carbs and sugars do not attract me in general. but it could also be my alcohol consumption fueling this lust? yes everyone is different, could just be me, or maybe it has to do with complex dynamics between probiotics and alcohol consumption, maybe? or just something completely different that i cannot tell...

Edited by hazy, 04 April 2018 - 03:26 AM.

[albedo]

I just learned about the crosstalk between DNA methylation (a known and accurate possible biomarker of aging and even possibly having a causative role, see Steve Hovarth's work) and the microbiome epigenetic regulation. Finally it is not that surprising a strong link must exists. I think it is important as possibly impacting on the panel of what we can proactively do to fight aging:

 

"The core human gut microbiota contributes to the developmental origin of diseases by modifying metabolic pathways. To evaluate the predominant microbiota as an epigenetic modifier, we classified 8 pregnant women into two groups based on their dominant microbiota, i.e., Bacteroidetes, Firmicutes, and Proteobacteria. Deep sequencing of DNA methylomes revealed a clear association between bacterial predominance and epigenetic profiles. The genes with differentially methylated promoters in the group in which Firmicutes was dominant were linked to risk of disease, predominantly to cardiovascular disease and specifically to lipid metabolism, obesity, and the inflammatory response. This is one of the first studies that highlights the association of the predominant bacterial phyla in the gut with methylation patterns. Further longitudinal and in-depth studies targeting individual microbial species or metabolites are recommended to give us a deeper insight into the molecular mechanism of such epigenetic modifications."

 

Kumar H, Lund R, Laiho A, et al. Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. MBio. 2014;5(6)

 

Qin Y, Wade PA. Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018;163(2):105-112.

[albedo]

I was looking at interaction between gut microbiota and metformin and pop into this short review:

 

Gut Microbiota and Metabolic Disorders

http://www.ncbi.nlm....les/PMC4483604/

 

We know of the beneficial effects via the AMPK path and was wondering if benefits via the modulation of gut microbiota, which look do exist (e.g. via the increase of Akkermansia also mentioned above in this thread), are happening at much lower doses that those typically required to reduce hepatic release of glucose.....

 

"...In addition, a specific protective action in relation to T2D was observed in the case of a specific bacterium, Akkermansia muciniphila, which was shown to both reduce chronic subclinical inflammation and improve insulin sensitivity [82]. Interestingly, metformin seems to induce modifications in the microbiota by promoting the increase of GLP-1, specific types of SCFAs, mainly butyrate and propionate, as well as of glycine levels, an amino acid associated with improved insulin sensitivity [83]. Moreover, recent evidence indicates the gut microbiota as a site of metformin action [66]. In a double-blind study, with treatment-naive T2D individuals randomized to placebo or metformin showed that metformin had remarkable effects on the intestinal microbiome. These results were verified in a subgroup of the placebo cluster that switched to metformin 6 months after the start of the trial. Transfer of fecal samples from metformin-treated donors to germ-free mice showed an improvement in  glucose tolerance in mice that received metformin-altered microbiota. By investigating metformin–microbiota interactions, Wu and colleagues revealed that metformin affects pathways with common biological functions in species from two different phyla, Proteobacteria and Firmicutes, and many of the metformin regulated genes in these species encoded metalloproteins or metal transporters. These findings support the idea that the altered gut microbiota mediates some of metformin’s antidiabetic effects. Although metformin is currently the firstline medication for the treatment of T2D [84], particularly in overweight and obese people [85], its mechanism of action is still poorly defined. When, in 2005, Levri and colleagues set out to determine whether metformin was an effective medication for treatment of overweight or obese adults without diabetes mellitus or polycystic ovary syndrome, they found out that there were no sufficient evidence for the use of metformin as treatment of overweight or obese adults, and that additional studies were needed to answer this clinical question [86]. However, a 2016 randomized placebo-controlled, double-blind trial on 62 adolescents aged 10–16 years with obesity and IR conducted by Van der Aa and colleagues [87] shows that an 18-month treatment with metformin plus physical activity twice a week results in a stabilization of the body mass index. According to these results, metformin may be, therefore, used as an additional therapy in combination with lifestyle intervention in adolescents with obesity and IR [87]. Overall, these data confirm the pivotal role of the microbiota in the genesis of T2D..." (bolding is mine)

 

Pascale A, Marchesi N, Marelli C, et al. Microbiota and metabolic diseases. Endocrine. 2018

[albedo]

Also from Darryl: "...Whereas metformin increases Akkermansia in mice by 12%, oligofructose (onions, leeks, garlic etc) increases Akkermansia 100-fold and beans 20-fold..."

https://www.longecit...ndpost&p=790036

https://www.longecit...ndpost&p=793779

Edited by albedo, 11 May 2018 - 09:46 PM.

[albedo]

Tim Spector’s Top Ten List of Gut-Friendly Foods

http://www.cbc.ca/na...-friendly-foods

[albedo]

Qin Y, Wade PA. Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018;163(2):105-112.

https://www.ncbi.nlm...pubmed/29161429