Tag Archives: gut

Gut bacteriophages associated with improved cognitive function and memory in both animals and humans

A growing body of evidence has implicated gut bacteria in regulating neurological processes such as neurodegeneration and cognition. Now, a study from Spanish researchers shows that viruses present in the gut microbiota can also improve mental functions in flies, mice, and humans.

Credit: CDC.

They easily assimilate into their human hosts — 8% of our DNA consists of ancient viruses, with another 40% of our DNA containing genetic code thought to be viral in origin. As it stands, the gut virome (the combined genome of all viruses housed within the intestines) is a crucial but commonly overlooked component of the gut microbiome.

But we’re not entirely sure what it does.

This viral community is comprised chiefly of bacteriophages, viruses that infect bacteria and can transfer genetic code to their bacterial hosts. Remarkably, the integration of bacteriophages or phages into their hosts is so stable that over 80% of all bacterial genomes on earth now contain prophages, permanent phage DNA as part of their own — including the bacteria inside us humans. Now, researchers are inching closer to understanding the effects of this phenomenon.

Gut and brain

In their whitepaper published in the journal Cell Host and Microbe, a multi-institutional team of scientists describes the impact of phages on executive function, a set of cognitive processes and skills that help an individual plan, monitor, and successfully execute their goals. These fundamental skills include adaptable thinking, planning, self-monitoring, self-control, working memory, time management, and organization, the regulation of which is thought, in part, to be controlled by the gut microbiota.

The study focuses on the Caudovirales and Microviridae family of bacteriophages that dominate the human gut virome, containing over 2,800 species of phages between them.

“The complex bacteriophage communities represent one of the biggest gaps in our understanding of the human microbiome. In fact, most studies have focused on the dysbiotic process only in bacterial populations,” write the authors of the new study.

Specifically, the scientists showed that volunteers with increased Caudovirales levels in the gut microbiome performed better in executive processes and verbal memory. In comparison, the data showed that increased Microviridae levels impaired executive abilities. Simply put, there seems to be an association between this type of gut biome and higher cognitive functions.

These two prevalent bacteriophages run parallel to human host cognition, the researchers write, and they may do this by hijacking the bacterial host metabolism.

To reach this conclusion, the researchers first tested fecal samples from 114 volunteers and then validated the results in another 942 participants, measuring levels of both types of bacteriophage. They also gave each volunteer memory and cognitive tests to identify a possible correlation between the levels of each species present in the gut virome and skill levels.

The researchers then studied which foods may transport these two kinds of phage into the human gut -results indicated that the most common route appeared to be through dairy products.

They then transplanted fecal samples from the human volunteers into the guts of fruit flies and mice – after which they compared the animal’s executive function with control groups. As with the human participants, animals transplanted with high levels of Caudovirales tended to do better on the tests – leading to increased scores in object recognition in mice and up-regulated memory-promoting genes in the prefrontal cortex. Improved memory scores and upregulation of memory-involved genes were also observed in fruit flies harboring higher levels of these phages.

Conversely, higher Microviridae levels (correlated with increased fat levels in humans) downregulated these memory-promoting genes in all animals, stunting their performance in the cognition tests. Therefore, the group surmised that bacteriophages warrant consideration as a novel dietary intervention in the microbiome-brain axis.

Regarding this intervention, Arthur C. Ouwehand, Technical Fellow, Health and Nutrition Sciences, DuPont, who was not involved in the study, told Metafact.io:

“Most dietary fibres are one way or another fermentable and provide an energy source for the intestinal microbiota.” Leading “to the formation of beneficial metabolites such as acetic, propionic and butyric acid.”

He goes on to add that “These so-called short-chain fatty acids may also lower the pH of the colonic content, which may contribute to an increased absorption of certain minerals such as calcium and magnesium from the colon. The fibre fermenting members of the colonic microbiota are in general considered beneficial while the protein fermenting members are considered potentially detrimental.”

It would certainly be interesting to identify which foods are acting on bacteriophages contained within our gut bacteria to influence cognition.

Despite this, the researchers acknowledge that their work does not conclusively prove that phages in the gut can impact cognition and explain that the test scores could have resulted from different bacteria levels in the stomach but suggest it does seem likely. They close by stating more work is required to prove the case.

Birds and bats have very weird gut bacteria, and it’s likely linked to flying

Bats and birds don’t seem to need gut bacteria the way other animals do, a new study finds.

Our microbiota or microflora — communities of bacteria making home in our digestive tract — play quite a central role in our health and wellbeing. These tiny helpers aid us in fighting bad bacteria and aid digestion. It’s not just us. Most vertebrates rely on similar bacterial communities for the same tasks.

A phylosymbiosis tree diagram showing a microbiome composition in bats and birds (marked with black bars) compared to other mammalian species.
Image credits Se Jin Song et al., (2020), mBio.

But not birds and bats, a new study found. By drawing on field samples and museum specimens, a team of US researchers has compared the makeup of mammal, bird, reptile, and amphibian microbiota, finding that species which evolved for flight tend not to rely on symbiotic bacteria almost at all.

You can’t fly with us

“If you’re carrying a lot of bacteria in your gut, it can be pretty heavy and may take resources away from you,” says Holly Lutz, a research associate at Chicago’s Field Museum and postdoctoral researcher at the University of California San Diego and co-author of the study.

“So if you’re an animal that has really high energetic demands, say because you’re flying, you may not be able to afford to carry all those bacteria around, and you may not be able to afford to feed them or deal with them.”

The study is the first of its kind and the first to showcase how different the microbiota of flight-capable species are compared to those of other vertebrates. The team believes that the necessities of flight are exactly what caused this difference in gut bacteria.

To the best of our knowledge, animals that are closely related to each other have similar gut microbiomes, because they evolved together — a pattern referred to by scientists as phylosymbiosis. Thus, Se Jin Song, the paper’s co-first author from UC San Diego, says that before the study the team assumed they would “see similar associations between animals and their gut microbes when the animals shared a similar diet.”

“Our pie-in-the-sky idea was that flight could impose a similar type of selection on which microbes animals host,” he explains. “What was shocking was that we didn’t find that birds and bats share a similar microbiome per se, but rather that both lack a specific relationship with microbes.”

For the study, the team analyzed fecal samples from roughly 900 species of vertebrates on a global scale. Researchers, museum collections, and zoo directors from around the world participated in the efforts, which ranged from zoo work to venturing deep into remote Ugandan and Kenyan caves with a flashlight to collect samples from African bats.

An African fruit bat.
Image via Pixabay.

After collecting the needed material, the team used high throughput genetic sequencing to process them. In essence, they extracted all DNA from all the samples, and then used individual genes to sift through the bacterial communities within each sample. For the final step, they pooled all of the data together to form the comparisons between species.

The microbiomes of bats and birds didn’t fit in with the rest of the vertebrates, the team found. While their gut bacteria makeup was quite similar, they had very little in common with other vertebrates. The team believes that it’s their shared lifestyle, not their ancestry (bats and birds are only very distantly related), that shapes their gut flora. In other words, their ability to fly.

Both groups evolved this ability independently, but no matter which way you cut it, flying is very energy-intensive and requires a light body. Bats and birds both have much shorter digestive tracts than comparable land mammals, and they both carry fewer bacteria, which likely helps reduce weight. The authors write that it’s also possible that diet plays a role here; due to the huge energy requirements of active flight, there may simply not be enough food to spare to maintain a symbiotic relationship with the bacteria.

Another important finding is that the few bacteria that do live in the digestive tract of both birds and bats tend to be very varied. Various types of individual bacteria live in the guts of different species of bats or birds, most other groups of amphibians, reptiles, and mammals apart from bats follow specific patterns.

“It’s almost like they’re just picking up whatever’s around them and they don’t really need their microbes to help them in ways that we do,” says Lutz.

“If we ever are putting ourselves in some kind of extreme situation where we’re disrupting our microbiome, there is something that we can learn from animals that don’t need their microbiomes as much.”

Lutz notes that this study wouldn’t have been possible without museum collections from around the world. Specimens of bird and bat kept in cryogenic chambers in the Field Museum’s Collections Resource Center were pulled out to help provide the broad samples needed for a study of this size.

“The scope of this paper —in terms of species that we sampled— is really remarkable. The diversity of collaborators that came together to make this study happen shows how much we can achieve when we reach out and have these big and inter-institutional collaborations,” says Lutz.

The paper “Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats” has been published in the journal mBio.


Over 100 new species of bacteria discovered in your gut

An international research team has created the most comprehensive record of human intestinal flora to date. Over 100 of the species they list are completely new to science.


Image via Pixabay.

Our intestinal microbiome is essential in keeping us healthy, well-fed, and in good spirits. Each one of us carries around 2% of our overall body weight in bacteria. However, we don’t have a very clear idea of what strains call our innards ‘home’. A new study, published by researchers from the Wellcome Sanger Institute, Hudson Institute of Medical Research, Australia, and EMBL’s European Bioinformatics Institute comes to flesh out our understanding of these bugs with the most comprehensive look at human intestinal flora to date.

The resource will allow scientists to better understand our bacterial compadres and make it easier to analyze the particular microbiome of each individual. All in all, the team hopes their work will point the way towards new treatments for diseases such as gastrointestinal disorders, infections, and immune conditions.


“This study has led to the creation of the largest and most comprehensive public database of human health-associated intestinal bacteria,” says first author Dr Samuel Forster from the Wellcome Sanger Institute.

“The gut microbiome plays a major in health and disease. This important resource will fundamentally change the way researchers study the microbiome.”

The team worked with fecal samples collected from 20 people in the UK and Canada. They isolated, grew, and DNA-sequenced 737 individual strains of bacteria from this material. Further analysis showed these strains make up 273 separate bacterial species — strains are roughly equivalent to a sub-species — including 173 that have never before been sequenced. Of these latter ones, 105 have never been isolated before.

So why is that important? Well, when researchers need to study the effect of microbiomes on human health, they usually sequence the DNA of the whole sample (which is to say, the genomes of all species in a sample), and then try to tease apart its different component species. It works really well if you know what each individual species’ genome looks like — however, we didn’t have reference material for all the inhabitants of our bellies. That’s where the present study comes into the picture.

The data collected by the team will make it cheaper, faster, and easier for researchers to determine which bacteria are present in a certain community, and to research their role in diseases. If researchers need to check a particular hypothesis — that certain bacteria increase in the case of a disease, for example — they can get an isolate from the collection and run it through tests in the lab. Up to now, researchers would have to obtain stool samples from which to isolate particular strains or species — which took a lot of time and incurred costs.

“For researchers trying to find out which species of bacteria are present in a person’s microbiome, the database of reference genomes from pure isolates of gut bacteria is crucial,” says coauthor Dr Rob Finn from EMBL’s European Bioinformatics Institute.

“This culture collection of individual bacteria will be a game-changer for basic and translational microbiome research,” adds senior author Dr Trevor Lawley (also from the Wellcome Sanger Institute). “Ultimately, this will lead us towards developing new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions.”

The paper “Human Gastrointestinal Bacteria Genome and Culture Collection” has been published in the journal Nature Biotechnology.

Wooden Figure belly ache.

Cannabis does reduce intestinal inflammation, and now we know why

New research on mice shows that endocannabinoids help prevent — or control — intestinal inflammation. These findings suggest that such compounds might serve the same function in humans.

Wooden Figure belly ache.

Image credits Wolfgang Claussen.

Cannabis users have long reported that the drug helps reduce the symptoms of inflammatory bowel disease (IBD). New research published by a team from the University of Massachusetts Medical School and the University of Bath explored why. Their findings reveal a novel mechanism that governs inflammation of the gut and may result in a new class of drugs to treat diseases that involve intestinal inflammation.

Pot gut

“There’s been a lot of anecdotal evidence about the benefits of medical marijuana, but there hasn’t been a lot of science to back it up,” said Beth A. McCormick, PhD and paper co-author.

“For the first time, we have an understanding of the molecules involved in the process and how endocannabinoids and cannabinoids control inflammation. This gives clinical researchers a new drug target to explore to treat patients that suffer from inflammatory bowel diseases, and perhaps other diseases, as well.”

While reports of marijuana helping alleviate gut inflammation are quite numerous, evidence to explain why aren’t. This study is the first to identify a biological mechanism that underpins this effect, helping to explain why cannabis reduces intestine inflammation for conditions such as ulcerative colitis and Crohn’s disease.

According to the team, gut inflammation is regulated by two distinct processes that each act in turn depending on the conditions in the intestinal environment.

The first process (which was identified in previous research) kick-starts an aggressive immune response in the intestine. This helps our bodies eliminate pathogens, but overzealous immune cells can also damage the lining of the gut by attacking cells indiscriminately.

The second process turns off this inflammation response. The response is spread by special molecules that move across the epithelial cells in the intestine (i.e. the lining) via the same channels that help flush out toxins from the gut.

The key here is that this second process involves a molecule called an endocannabinoid — which is very similar to the cannabinoids found in cannabis. If there aren’t enough endocannabinoids, inflammation won’t shut down and the body’s immune cells run amok on our guts’ lining.

McCormick and colleagues believe that because cannabis use introduces cannabinoids into the body, these molecules might help relieve gut inflammation as the naturally produced endocannabinoids normally would.

“We need to be clear that while this is a plausible explanation for why marijuana users have reported cannabis relieves symptoms of IBD, we have thus far only evaluated this in mice and have not proven this experimentally in humans,” she adds.

However, the team hopes that these findings will result in new drugs to help treat bowel diseases in humans.

The paper “Intestinal P-glycoprotein exports endocannabinoids to prevent inflammation and maintain homeostasis” has been published in the Journal of Clinical Investigation.

Weight gain is mostly controlled by what you eat — not genetics

If you want to blame someone for those extra pounds, the best place to look is probably in the mirror.

As the world tries to deal with its ever-growing obesity crisis, the main causes of this problem are still under debate. However, more and more studies are indicating that the main culprit is, as expected, food.

Genes decide a lot of things about your body — your eye color, your hair, even how you look like. But, according to a new study, it doesn’t really decide how much you weigh (as an adult, at least). Scientists at King’s College London recently carried out a study on twins to assess how the gut processes and distributes fat.

Essentially, they analyzed poop samples from over 500 pairs of twins to build up a picture of how the gut microbiome distributes fat. They also analyzed how much of this process is genetic and how much is directed by environmental factors. Overall, they found that only 17.9% of all gut processes could be attributed to hereditary factors, while 67.7% of gut activity was influenced by environmental factors — mainly, the regular diet.

This is an exciting study, not just because it confirms that what we eat governs how our weight is distributed, but because it allows researchers to understand which microbes are associated with which chemical metabolites in the gut. Ultimately, this could help scientists understand how the gut bacteria affects us, and how it can be modified for weight management.

The fecal metabolome largely reflects gut microbial composition, and it is strongly associated with visceral-fat mass, thereby illustrating potential mechanisms underlying the well-established microbial influence on abdominal obesity. Dr. Jonas Zierer, the lead author of the study, believes this could one day be instrumental in dealing with obesity.

‘This study has really accelerated our understanding of the interplay between what we eat, the way it is processed in the gut and the development of fat in the body, but also immunity and inflammation. By analysing the faecal metabolome, we have been able to get a snapshot of both the health of the body and the complex processes taking place in the gut.’

This is also good news because it means that most of the factors associated with extra pounds are modifiable. Zierer adds:

‘This new knowledge means we can alter the gut environment and confront the challenge of obesity from a new angle that is related to modifiable factors such as diet and the microbes in the gut. This is exciting, because unlike our genes and our innate risk to develop fat around the belly, the gut microbes can be modified with probiotics, with drugs or with high fibre diets.’

Head of the Department of Twin Research at King’s, Professor Tim Spector was also excited by the possibility. He emphasizes another advantage of this study — the fact that potential treatments or supplements might be implemented at a large scale through innovative approaches.

‘This exciting work in our twins shows the importance to our health and weight of the thousands of chemicals that gut microbes produce in response to food. Knowing that they are largely controlled by what we eat rather than our genes is great news, and opens up many ways to use food as medicine. In the future these chemicals could even be used in smart toilets or as smart toilet paper.’

Worldwide, over 2 billion people are overweight or obese, and over the past 20 years, obesity rates have more than doubled. The growing trend shows no sign of stopping or slowing down, as childhood obesity also grows at dramatic rates: 1000% in the past 40 years.

Journal Reference: Zierer et al. “The fecal metabolome as a functional readout of the gut microbiome.” Nature Genetics (2018). https://doi.org/10.1038/s41588-018-0135-7

Probiotics and breastfeeding help fight antibiotic resistance in children, study suggests

A targeted probiotic supplementation, in conjunction with breastfeeding, could help reduce the potential for antibiotic resistance, a new study suggests.

Image credits: Andrés Nieto Porras.

Probiotics (live bacteria and yeasts that are allegedly good for your health and digestive system) remain a controversial topic — their benefits are often oversold and rarely backed up by actual science. But in recent years, studies have shown that, in some specific scenarios, probiotics do offer significant advantages.

In a new study, researchers found that breastfed infants who were given a specific probiotic strain of B. infantis had, on average, 87.5% less antibiotic resistance genes in their gut microbiome compared to infants who were breastfed without that probiotics.

Antibiotic resistance is not something many people think about while raising their children, but perhaps we should start paying more attention to it: recently, the World Health Organisation announced antibiotic resistance as one of the biggest threats to global health, and this is definitely a growing concern for the younger generations. Having a simple way to reduce antibiotic resistance could make a big difference in the long run.

[panel style=”panel-default” title=”Antibiotic resistance” footer=””]Because many members of the public take antibiotics when they are not required to, many pathogens have started developing an immunity to common treatments — even the strong treatments. This has become a great concern, especially as some infections have started going beyond the limit of what we can currently treat.

Misuse of antibiotics in both humans and animals is accentuating this problem, and researchers are looking for ways to combat it.[/panel]

Dr. Giorgio Casaburi, lead author of the research, comments:

“These results demonstrate that targeted bacterial supplementation is capable of remodelling the ecology of the infant gut microbiome and therefore reduce antibiotic gene reservoirs in children. We found that supplementation with the infant gut symbiont significantly diminished both the abundance and diversity of antibiotic resistance genes”.

Casaburi and his colleagues administered the probiotic supplement for 21 days. They chose a probiotic uniquely adapted to thrive in the infant’s gastrointestinal system. The probiotic bacteria colonize the infant’s gut. Without it, the gut is colonized by other bacteria which enable the evolution, persistence and dissemination of antibiotic resistance genes.

While this is a fairly small trial, it still showcases an important potential for dealing with antibiotic resistance in a safe way that doesn’t have any unwanted side effects.

“The supplementation offers a novel approach towards providing an alternative, safe and non-invasive method to decrease the number of genes that resist antibiotics in infants” added Dr Casaburi. “This is the first demonstration of significant remodelling of the infant gut microbiome. This modulation could help to reduce the burden and diversity of antibiotic resistance genes in current and future generations”.

The results have not yet been peer-reviewed and will be presented at European Society for Paediatric Gastroenterology Hepatology and Nutrition.

stressed frog

Stress could be as harmful to your gut’s health as junk food

A study on mice performed by researchers at Brigham Young University (BYU) found stress can be as bad for digestion as a diet of low-nutrient fast food.

stressed frog

Credit: Pixabay.


The team studied the gut microbiota of these mice. These bacteria live in a relationship that is vital to normal health, although some species are also opportunistic pathogens that can invade the host gut and cause disease. The human body is host to around 100 trillion microbes, meaning they outnumber somatic cells by about 10 to 1.  

Microorganisms start colonizing the gut immediately after birth in mammalian hosts and are followed by a succession of populations until a stable adult microbiota has been established.

Studies on the microbiota, though numerous, can be extremely challenging. Because there are so many different species of microorganisms colonizing the gut, it can be very difficult if not impossible to identify which organisms are beneficial and which are bad for our health, especially since the effects are rooted in an interplay of various bacteria. Most gut bacteria can’t be cultured in a dish, making these types of studies even harder. What we do know for sure is that the microbiota is essential to the health of all mammals.

Sometimes, the intestine-wandering bacteria can affect us in unexpected ways. For instance, when a team at BYU sampled the gut microbiome from female mice subjected to a stress test, the microbiota resembled that of an obese mouse. This surprising finding seems to suggest that stress can have as much of an impact on our metabolism as poor diet. Interestingly enough, male mice didn’t exhibit the same microbiome shift, but they became more anxious and less physically active.

“Stress can be harmful in a lot of ways but this research is novel in that it ties stress to female-specific changes in the gut microbiota,” BYU professor of microbiology and molecular biology Laura Bridgewater said in a statement. “We sometimes think of stress as a purely psychological phenomenon but it causes distinct physical changes.”

These findings, which were reported in a paper in Scientific Reports, logically follow previous findings. For instance, scientists previously found that high levels of the stress hormone cortisol are linked to a higher body mass index (BMI). The higher the BMI, the more likely an individual is overweight or obese.

This sort of metabolic response to stress, though a nuisance to our modern lifestyle, may have provided evolutionary advantages. When faced with a threat, like a predator, glucose levels rise so we have more energy for our ‘flight or fight’ response. However, when glucose rises, so does insulin, which causes fat storage.

As such, these findings suggest that any diet or weight loss routine should also be paired with stress management. Obese people looking to lose weight are advised to relax more often by engaging in calming and pleasurable activities.

“In society, women tend to have higher rates of depression and anxiety, which are linked to stress,” Bridgewater said. “This study suggests that a possible source of the gender discrepancy may be the different ways gut microbiota responds to stress in males versus females.”

Researchers develop probiotic beer that “boosts your immunity and improves gut health”

If you needed yet another reason to drink beer, science just gave it to you. Researchers from the National University of Singapore (NUS) just developed a new type of probiotic beer which could improve your immune system and neutralize pathogens and toxins.

Cheers! Associate Professor Liu Shao Quan (left) and Miss Chan Mei Zhi Alcine (right), showcasing their newly-developed probiotic beer. Image credits: NUS.

The idea of developing a healthy, probiotic beer, came from Miss Chan Mei Zhi Alcine, a fourth-year student from the Food Science and Technology Programme at the NUS Faculty of Science. Chan realized that while the market abounds with dairy-based probiotics, there’s another huge untapped market for probiotics: beer. Due to its nature, beer is a fertile ground for probiotics, and the craft beer phenomenon has been growing at a staggering rate in many parts of the world — so why not blend the two?

“The health benefits of probiotics are well known. While good bacteria are often present in food that have been fermented, there are currently no beers in the market that contain probiotics. Developing sufficient counts of live probiotics in beer is a challenging feat as beers contain hop acids that prevent the growth and survival of probiotics. As a believer of achieving a healthy diet through consuming probiotics, this is a natural choice for me when I picked a topic for my final-year project,” said Miss Chan, who will be graduating in July 2017.

Working with Associate Professor Liu Shao Quan, she used a strain of Lactobacillus paracasei called L26, which seems to be particularly promising. The probiotic gives a strong taste with pleasant aromas, and the beer itself is quite light — with only 3.5% alcohol.

“For this beer, we used a lactic acid bacterium as a probiotic microorganism,” explains Chan Mei Zhi Alcine, who developed the beer, in a statement. “It will utilise sugars present in the wort to produce sour-tasting lactic acid, resulting in a beer with sharp and tart flavors. The final product, which takes around a month to brew, has an alcohol content of about 3.5 percent.”

Now, we’ll be the first to breathe in a healthy dose of skepticism when it comes to probiotics. Studies have often been contradictory or inconclusive when it comes to probiotics, and they’re certainly given much more credit than they deserve on the market. However, Lactobacillus paracasei L26 was documented as having immune-boosting properties in mice — though this has yet to be confirmed in humans. They’ve already taken out a patent for the recipe to sell it commercially, which means we won’t be seeing a peer-reviewed study on the beer and a decisive verdict on its positive properties. Still, Liu is confident that the bacterium strain, which was isolated from the human gut, will make for a delicious and healthy beer, which he expects people to enjoy.

“The general health benefits associated with consuming food and beverages with probiotic strains have driven demand dramatically. In recent years, consumption of craft or specialty beers has gained popularity too. Alcine’s invention is placed in a unique position that caters to these two trends. I am confident that the probiotic gut-friendly beer will be well-received by beer drinkers, as they can now enjoy their beers and be healthy.”

It’s not the first attempt to create a beer with secondary healthy effects. In 2008, Rice University researchers brewed an “anti-cancer beer” though we haven’t heard much of it since. While not really the same approach, another cool project was delivered by a small brewery in Scandinavia — PangPang Brewery developed what they call the perfect shower beer. People have brewed beer for millennia, I’m really happy to see this type of innovations finally kicking in.

The appendix keeps you healthy and your gut bacteria happy, study finds

A new international study found that the appendix plays a part in your immune system and helps preserve the integrity of gut flora.

Image credits Tom Woodward / Flickr.

We humans have a pretty casual relationship with our appendixes. We hang around, sure, but they don’t seem to do much and we’re not very committed. When it hurts, we’ll take it out. Sometimes it seems like it’s going to hurt, so we take it out just to be sure — we’re too busy with our other, steady organs to go through all the drama.

A new study, however, found that we should take this little pouchy thing more seriously. An international team led by Heather F. Smith, Ph.D. and Associate Professor at Midwestern University Arizona’s College of Osteopathic Medicine studied the evolution and function of the appendix in several mammal species and found that it plays an important purpose in the body — particularly as a safe haven for intestinal flora.

Appendixes — what do they even do?

Dr Smith’s team wanted to understand why some species have one, and others don’t. They gathered data on the presence or absence of the appendix in 533 mammal species, and its relation to other gastrointestinal and environmental traits. By correlating this data with the species’ genetic tree, they were able to track the evolution of appendixes in mammalian species.

The first surprise they had was that several lineages have independently evolved the organ, and they almost never get rid of it afterwards. This comes as an argument against the common belief that appendixes don’t serve any purpose in the body. By cross-checking for other factors such as diet, climate, or social factors, the team has refuted several previous hypotheses linking the appendix to diet or environmental factors.

So there’s a lot of things it doesn’t do — but what does it do? The team believes it acts as a secondary immune organ. They found that species which have an appendix also show higher average levels of lymphoid tissue in the cecum (the first bit of the large intestine). This tissue is also known to foster several strains of gut flora, suggesting that the appendix acts as a kind of safe house from which bacteria can repopulate the gastrointestinal tract if needed — after you take strong oral antibiotics, for example.

Animals with certain shapes of ceca, such as the tapering and spiral-shaped ones, were more likely to have an appendix than species with round or cylindrical ones. This led the researchers to believe that the appendix evolves as part of a larger “cecoappendicular complex”.

Seven cecal character states included in this study.
Image credits Brent Adrian et. al / Midwestern University.

The full paper “Morphological evolution of the mammalian cecum and cecal appendix” has been published in the journal Comptes Rendus Palevol.

Scientist gives himself Fecal Transplant from Hunter-Gatherer from Tanzania… to See how it Goes

A field researcher from America has transplanted fecal microbiome from a Tanzanian tribesman to his own gut. Why? Well… to see what happens, basically.

Fecal bacteria, magnified 10,000x Fecal transplant is increasingly accepted as a medical treatment for some diseases. Eric Erbe, digital colorization by Christopher Pooley

Fecal bacteria, magnified 10,000x Fecal transplant is increasingly accepted as a medical treatment for some diseases. Eric Erbe, digital colorization by Christopher Pooley

“AS THE SUN set over Lake Eyasi in Tanzania, nearly thirty minutes had passed since I had inserted a turkey baster into my bum and injected the feces of a Hadza man – a member of one of the last remaining hunter-gatherers tribes in the world – into the nether regions of my distal colon.”

It’s not every day you get the chance to read an essay which starts like this, isn’t it? Yet that’s exactly how Jeff Leach, the man behind this research, starts his story. He has been part of a team working in Tanzania and living side by side with the Hadza, a group of hunter gatherer people. The Hadza live now the same way their ancestors have for thousands or even tens of thousands of years; they are the last full-time hunter-gatherers in Africa. What’s interesting is that the Hadza are not genetically related to any other people, and their language is unique.

The Hadza are also at the mercy of the local weather and climate. Leach’s team has collected numerous (over 2000) samples from humans, animals, and the environment in order to observe how the microbial communities in and around the Hadza change as a result of the weather patterns – especially the six month variation (dry season – wet season).

A Hadza hunting party. Image via The Telegraph

“[The question is] what a normal or healthy microbiome might have looked like before the niceties and medications of late whacked the crap out of our gut bugs in the so-called modern world,” Leach writes.

For this purpose, the Hadza are indeed ideal subjects. They are not stone-age or isolated people – they’ve had plenty of contact with other humans, but they still have the same diet and lifestyle they’ve had for millennia, and almost never use modern medication.

The microbiome in the colon is starting to receive more and more attention – and rightfully so. The health impact it has on our bodies is huge, and has been widely ignored in Western medicine, until recently. Eating “probiotics” and similar foods is a good step, but this just “scratches the surface”. Meanwhile, fecal transplant has been used more and more to treat various afflictions.

“Recent research suggests that use of antibiotics may be fundamentally altering our gut biomes for the worse, increasing rates of allergies, asthma and weight gain. In one recent lab study, introduction of genetically altered gut bacteria prevented mice from getting fat. In another, artificial sweetners altered gut microbes and contributed to obesity and other metabolic disorders in mice, and some correlation to the same effect was found in people”, Popular Science writes.

So understanding how our biome changed as a result of a modern lifestyle could have huge implications for future medicine… but is a fecal transplant really necessary? Leach and his team believe it will greatly accelerate the study. Their results are already interesting, but they want to find out as soon as possible if modern humans can survive with ancient fecal biome.

“On the original question of whether or not the gut microbiome composition of the Hadza changes between wet and dry seasons, our initial – though unpublished data – suggest yes. To our knowledge this is the first study in the world to document this pattern among rural and remote populations. Ecologically speaking, this suggests there may not be one steady state – or equilibrium – for the human gut. It’s moving target with multiple steady states.”, Leach writes further.

Another reason why he is doing this is to test his theory: that we have conducted a biome genocide, basically wiping out most of the bacteria that inhabits our gut. He wants to see what will happen when you get that biome back.

“Microbial extinction [is] something I believe we all suffer from in the western world and may be at the root of what’s making us sick.”

Is there truth to his theories? The fact that he would risk inserting a hunter-gatherer’s feces inside of him seems to indicate that at the very least, he’s very confident in his ideas. Personally, I think what he says makes a lot of sense. Most of what we are is actually bacteria or other foreign bodies – it seems extremely unlikely for those elements to not have any particular impact; wiping them out (as we are doing today, with modern drugs and the modern diet) likely has serious consequences. We’ll keep you posted on how the situation develops.

Source: (Re)Becoming Human: what happened the day I replaced 99% of the genes in my body with that of a hunter-gatherer, by Jeff Leach.

Hadza women roasting tubers. © Alyssa Crittenden

The ‘good’ and ‘bad’ bacteria in your gut are subjective to lifestyle, hunter-gatherer study shows

 Hadza women roasting tubers. © Alyssa Crittenden

Hadza women roasting tubers.
© Alyssa Crittenden

You could be sitting alone and still be completely outnumbered for your body is home to trillions upon trillions of tiny passengers – bacteria. In fact, there as ten times more bacteria living inside you then cells in the body. Don’t get scared, though. The vast majority of these co-redident organisms are our friends. They help us digest food, provide energy and break down nasty stuff that ocassionaly wind up in our stomachs. As our diet has diversified, however, so has our gut microbiome configuration.

A recent study which looked at what kind of bacteria dwell in the guts of people belonging to a hunter-gatherer community in Tanzania demonstrates this idea, after researchers found a unique microbial profile with features yet unseen in any other human group. The findings could have important consequences in how physicians and scientists alike look at so called “good” and “bad” bacteria.

Humans trapped in time

An international team of reserachers , composed of anthropologists, microbial ecologists, molecular biologists, and analytical chemists, traveled to Tanzania where they sampled individuals from the Hadza hunter-gatherer community. The Hadza are one of the few people left on Earth who have remained isolated and continue to live as their forefathers did since in the Paleolithic. As such, they provide an invaluable window into history, both from an anthropological perspective and a biological one.

The Hadza people’s gut configuration was compared against that belong to that of urban living Italians, representative of a “westernized” population. The results show that the Hadza possess a much more diverse microbiom. Explicitely, there are much more bacteria species living in their guts than in those belonging to westerners.

“This is extremely relevant for human health”, says Stephanie Schnorr of the Max Planck Institute for Evolutionary Anthropology. “Several diseases emerging in industrialized countries, like IBS, colorectal cancer, obesity, type II diabetes, Crohn’s disease and others, are significantly associated with a reduction in gut microbial diversity.”

The bacteria in your gut adapt to the environment

Gut bacteria in Hadza vs italian community. (c) Nature Communications

Gut bacteria in Hadza vs italian community. (c) Nature Communications

The Hadza microbiota is well adapted for processing indigestible fibres from a plant-rich diet and likely helps the Hadza get more energy from the fibrous foods that they consume.What’s particularly interesting is that the men and women different considerably in the bacteria species they posses, because of their habits and lifestyle. While both men and women share the food they gather (men hunt game and collect honey; women collect tubers and other plants), each sex eats more of the food their target, since they’re around it more on a day to day basis. The researchers call this proof of sexual divison of labor, demonstrated by bacteria diversity which is quite remarkably by itself.

The most striking finding, however, was that the Hadza microbiome, both men and women, contains high levels of bacteria, like Treponema, that in western populations are often considered signs of disease, and low levels of other bacteria, like Bifidobacterium, that in western populations are considered “healthy”. This without the Hadza experiencing any of the negative effects found in the western populace. Therefore, we must redefine our notions of “healthy” and “unhealthy” bacteria, since these distinctions are clearly dependent on the environment we live in.

“Co-resident microbes are our ‘old friends’ that help us adapt to different lifestyles and environments”, says Amanda Henry, leader of the Max Planck Research Group on Plant Foods in Hominin Dietary Ecology. “Through this analysis of the Hadza gut microbiota, we have increased our knowledge of human-microbiome adaptations to life in a savanna environment and improved our understanding of how gut microbiota may have helped our ancestors adapt and survive during the Paleolithic.”

The results were published in the journal Nature Communications.

Microscale electric field gradients can tell the difference between good and bad bacteria in minutes from extremely small samples. Photo: Paul V. Jones

Device identifies and sorts bad germs from the good ones in minutes, instead of days

Your gut is home to some 100 trillion bacteria – more than the entire number of cells in the whole human body. Clearly, bacteria are fond of human intestines, as we humans, unknowingly or not, are fond of them. After all, without bacteria our organisms would be deprived of extremely vital vitamin sources and digestion aids. However, not all bacteria are beneficial – some, of course, are detrimental to human health and can cause death. Diagnosing bad bacteria infection is currently a laborious, lengthy and expensive process. A new device developed by scientists at Arizona State University’s Department of Chemistry and Biochemistry seeks to address this issue by significantly speeding up harmful bacteria identification.  Hopefully, in the next phase the researchers will turn the device portable, so that doctors as well as anyone else for that matter may run a quick check for bad bacteria effortlessly.

Microscale electric field gradients   can tell the difference between good and bad bacteria in minutes from extremely small samples. Photo: Paul V. Jones

Microscale electric field gradients can tell the difference between good and bad bacteria in minutes from extremely small samples. Photo: Paul V. Jones

One of the most common gut bacteria is the E. coli, which for the most part is beneficial for the organism producing K2 vitamins and preventing the establishment of pathogenic bacteria. Some E. coli strains, however, are harmful like the O157:H7 E. coli strain which is responsible every year for  2,000 hospitalizations and 60 deaths in the U.S. alone. Bacterial diagnosis typically involves collecting a culture sample either from food or infected patients, after which lab analysis is performed. Usually this takes a few days to make and is costly.

[ALSO READ] How bacteria colonize the human gut – study reveals important insights

Researchers at Arizona State University believe they have found a solution that could be used to easily and cheaply diagnose bad bacteria in a matter of minutes, instead of days. Inside a polymer chip, a saw-toothed microchannel concentrates and sorts microorganisms inserted inside based on their electrical properties. All forms of matter, including bacteria, have their unique electrical properties and simply by studying their electrical response researchers can tell what kind of bacteria they’re dealing with.

Sorting out germs

For their device, the Arizona researchers  used an ordinary strain of E. coli along with two pathogenic varieties. They injected the cells into each channel and simply applied voltage to drive the cells downstream. The geometric features of the channel shape the electric field, creating regions of different intensity.  This field creates what’s called a dielectrophoretic force which traps certain kinds of bacteria around the channel based on their molecular and electrical properties. During their demonstration, the team led by Professor Mark Hayes, separated extremely similar bacteria—pathogenic and nonpathogenic strains within the single species, E. coli.

“The fact that we can distinguish such similar bacteria has significant implications for doctors and health officials,” says Hayes. He explains, “that scientists have struggled to find ways to rapidly identify bacteria. E. coli O157:H7 is very similar in size and shape to other subtypes of the bacteria. But unlike many of the others it has the ability to produce shiga-like toxin, a protein that breaks down blood vessel walls in the digestive tract.”

It’s important to mention that the device worked with pure cultures. Obviously, in the real world when you carry out a sample it will be filled with all kinds of impurities. The researchers plan to tackle this with their next version which should be able to accurately detect bacteria in a complex mixture. Also, making the device portable is a big goal.

The device was described in a paper published in the journal Analytical and Bioanalytical Chemistry.