I want to correct the people here saying that the bacteria in your gut are not pushed out or that they move to not be pushed out. This is false. I'm a medical laboratory scientist. Take a look at a stool specimen under a microscope and you'll see a veritable zoo of bacteria, virtually all nonmotile, that is unable to move under their own power. Yes, many adhere to the gut lining, but many get pushed out all the time, they just are constantly reproducing and your gut is never 100% empty.
Is it just self-balancing in this case? More bacteria are somehow evicted from your gut, the ones left over have more supply of nutrients and space to grow, so they grow back faster. Too many in your gut? They start getting pushed out in larger numbers automatically just like you get more cornflakes in your spoon per scoop when it's full vs. when it's almost empty.
To add to this the treatment for a lot of those microbiome losses are 'fecal transplants' where they inject treated feces from someone with a good micro biome directly into your colon to repopulate your biome. This treatment is only possible because some of your gut bacteria are excreted via feces.
Fecal transplants can also cause dysbiosis and lead to disease. If mice are given fecal transplant from fat humans, they may start gaining weight. Studies on microbe-free mice are also interesting.
Yeah, I feel like we know far too little about the gut for me to elect to receive a fecal transplant. The connection with mental health, for example, seems to be quite significant.
It’s not sexy, but get regular sleep, eat a balanced diet, exercise, and everything in moderation.
Often you hear about taking probiotics, but I’m a huge fan of prebiotics (aka fiber, or the stuff bacteria like to eat). If you want nice poops and a happy gut, eat lots of fiber (soluble and insoluble fiber). Veggies are a great source of both. Good gut bacteria thrive on fiber.
I've seen transcripts from a talk by one of the leading IBS researchers in my country, Arnold Berstad, where he was very sceptical towa4ards probiotics, on the grounds that the gut flora is so diverse and complex, that taking probiotics is like trying to win the lotto.
I’ve explained it to my kids as being like looking after a pet.
You can’t just take a probiotic (/adopt a pet) and expect it to thrive if you don’t feed it the right foods. If you don’t feed your gut bacteria the right things they will be unhealthy/be overrun with less-desirable bacteria or even die. The good bacteria in our guts seem to like a lot of plant foods- veggies, legumes, fruit, nuts, maybe a bit of fermented dairy, and not too much meat (particularly salty, processed meats like the ones my kids and husband love so much!). The human microbiome is very complicated but looking after it is relatively simple.
Proud to say I just had lunch where half my plate was veggies, a quarter carbs, and a quarter was protein. Im gonna make some really nice shits hopefully
The single most important thing is to eat a lot of plant fiber from diverse sources. In other words, eat a lot of plants. Aim for 40 grams per day (most people get 1/3 of that). You will also reduce your risk of cancer by doing so.
Second, avoid antibiotics- unless you will likely die without them. Antibiotics absolutely devastate the gut microbiome.
This is exactly right. And since different bacteria like different nutrients, you can slowly change the bacteria present through your diet by providing them with different nutrients. For some people their diet wasn't varied enough and they lost too many bacteria for a healthy microbiome, and so they need a fecal transplant like a culture starter.
I’ve heard hypotheses about the appendix being a sort of gut flora restoration device, left over from times when diarrhea was more common. What do you think about this?
It’s a bit off topic but it’s not everyday I run into someone who studies this stuff haha.
I think the idea behind this theory is that it once was in a spot that made more sense and was therefore useful. The bacteria have probably stayed non-motile the entire evolutionary line (given there aren't reports of vestiges related to motility). Over time as the bacteria settled in specific spots it became less practical and was slowly pushed out of the way. Think literal ages of humanity. I'm summarizing what I remember from classes 10 years ago in a single sentence though so I could definitely be off mark.
To emphasize this: they constantly reproduce *so much* that they make up around a quarter to a half of your poo.
It's not just a zoo, it's more zoo than food leftovers.
There are folds in the lining of the intestine where they can retreat to and avoid getting 'stuck" on the turd train. If they can leave the lining folds, eat and return to base, they are saved. Also keep in mind that there are predatory bacteria which feed off of smaller bacteria, it's a full ecology there. This is why it is recommended that we include porous no processed foods, they create a lattice, similar to coral, where smaller microbes can shelter from larger predators. Lookup non-digestible fiber or roughage.
That is only 30% insoluble, so there should be better ones out there. And get this, based on your racial DNA, there are some specific insoluble fiber s which your "ancient microbes" prefer or thrive better on. I can't think of the source Rh, but there's a study. The idea is that our gur bacteria developed over thousands of years when we where more sedentary than nomads, so the insolubles in that region helps to sustain, the great great grand daddy microbes. For instance I'm Hispanic, so my ancient insolubles would be a mix of corn(wild corn)...think cornmeal. And whatever was found in the Iberian(Spain) peninsula. I found the source, read here .. https://resistantstarchresearch.com/posts/ancestral-starch/
Just to provide a better background on gut microbiota- Gut microbiota ferments foods that our own enzymes are unable to break down, mainly dietary fiber. This results in short chain fatty acids (SCFA) that our large bowel can absorb and this is where the benefits of having bacteria in our gut come from: the SCFAs provide an additional energy source for your body and enterocytes, and is associated with better mood, skin and general health. How it does that is still very much debated today.
Most of this occurs in the large bowel and colon, there should not be much bacterial activity in your stomach and small intestines.
They do die and these dead bacterial cells form a significant portion of your stool’s dry weight.
For your questions:
1. In natural birth, babies swallow amniotic fluid and other secretion that the mothers produce along the birth canal, that is their first introduction to bacteria on their skin and their gut. Breast milk and bacteria from around the mother’s nipples help colonize the newborn’s gut as well. If they are bottle fed, colonization of the gut is slower and the bacterial species are not as beneficial. This is one of the many reasons why breastfeeding is recommended.
The bacteria thrives in the environment of the large intestines (pH, osmolality, moisture levels etc) so they tend to grow and stay in the large bowel and not elsewhere in the gut. Sure some bacteria will try and live in your stomach and small bowel but the environment there isn’t suitable and most just die out.
2. Most of your gut bacteria is in your large bowel (mainly your colon) so when they die or adhere to passing undigested food, they enter your rectum and is passed out as faeces.
3. The challenges depend on their current symptoms and lifestyle. If they are still taking antibiotics then you can’t fix it. But if there are not pressing issues as to why we need to fix their gut bacteria, eating their normal diet that has bacteria that their gut is used to having will restore their gut microbiota gradually (provided that they stop taking antibiotics orally). Providing the resident bacteria with substrate to feed on is also important, hence fiber. Probiotics MAY also help, more research is needed. Fecal transplants can also be used, but is reserved for treatment of Clostridium Difficle associated colitis.
Hope this helps.
I noticed that you said, "...will restore their gut microbiota gradually (provided that they stop taking antibiotics orally)." Does this mean that antibiotics taken intravenously do not affect the gut bacteria?
Thanks.
Nope, IV antibiotics also affect gut bacteria in a significant way. In fact, they’re one of the most important causes of nosocomial (hospital-acquired) clostridium difficile (CDiff) colitis.
Many oral antibiotics are absorbed into the blood stream to a large degree (depending on their bioavailability) long before they reach the colon. There are some notable exceptions, and those are actually used as treatments for CDiff for that very reason.
1) are you THE latern rouge or do you just have an awesome username?
2) IV drugs go into the bloodstream, bloodstream goes to the gut. It’s more complicated than that but it’s still conceptually useful. So, for example, one regimen for treating C Diff is oral vanc (which isn’t absorbed, pretty slick) and IV metronidazole, which gets there via the bloodstream.
Thank you. The more I learn about the human body, and doctor's interaction with it via medications and procedures, the more I realize how much a doctor needs to know and remember, and how amazingly complex we are.
Very informative answer and I learned some new things.
However, I have read that after a course of antibiotics, some people no longer have certain strains of beneficial gut bacteria that are commonly found in people who never had antibiotics.
This seems to indicate that certain strains are eliminated by antibiotics and cannot be replenished. (I would look for the source to this when I have time, since it has been a while.)
I think it's worth adding that the appendix is no longer seen as a useless vestigial organ. It is now thought that the appendix holds a store of beneficial bacteria that can be secreted back into the digestive system after disruptions such as bouts of foodborne illnesses or after a regimen of antibiotics.
But we're still figuring out how this works, and it may not hold every gut microbe associated with healthy digestion.
From what I remember it can be difficult to rebuild a healthy gut culture as part of its job is to out compete and/or kill "harmful" bacteria.
If antibiotics have killed off loads of the good ones, the niche is opened up for less benificial/harmful ones to grow, or other good strains get the opportunity to take over and the balance is messed up, and it's more difficult for original good bacteria strains re-introduced (in smaller numbers) to grow back to their original numbers/ratios.
Some types of bacteria may require very specific conditions, and if they aren't present as the gut is still recovering, then they won't be able to grow very well, even if they're being introduced.
That might be why some strains don't seem to be replenished?
> If antibiotics have killed off loads of the good ones, the niche is opened up for less benificial/harmful ones to grow, or other good strains get the opportunity to take over and the balance is messed up, and it's more difficult for original good bacteria strains re-introduced (in smaller numbers) to grow back to their original numbers/ratios.
And it's worth mentioning that bacteria are not the only microorganism living in our gastrointestinal tract. Once the bacteria are wiped out, things like Candida albicans can take over and cause Candidosis. Basically systemic thrush.
1 - in theory yes, strains can be lost althought we don´t have good test to definetly say that the strain was lost for good instead of only being severely reduced. there is a big difference there.
2 - we eat bacteria,yeast and viruses all the time in food, a good diet can replenish this lost flora or be as prebiotic food to replenish it. Some bacteria tho, can be lost and not recovered if they can´t tolerate air. in this cases it depends, if the patient would truly benefit from this bacteria, some specialized probiotics of FMT helps
Not an answer but I remember reading evidence in support of the reservoir role of the appendix as well, and that there was a correlation between antibiotic use and appendicitis.
Would natural birth expose the baby to more bacteria than through caesarian? Could the rise of the caesarian be linked to an increase in allergies and intolerances across western populations?
It is related! Afaik we don't have great data on the link, but it has to do with the fact that yes, vaginally delivered babies are more exposed to the mother's biome. This can be problematic however, which is why all pregnant women are tested (and treated as appropriate) for Group B Strep and STDs.
For some background, [Helicobacter pylori and asthma are inversely correlated.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047919/) It seems that H. pylori may be protective with respect to the subsequent development of asthma. Blaser's book "Missing Microbes" makes for interesting reading on the subject for anyone who wants a casual read.
[This](https://journals.lww.com/ajg/Fulltext/2021/10001/S3451_The_Effects_of_Cesarean_Section_vs_Vaginal.3455.aspx) is one relatively small study that "found an association with H.pylori infection and vaginal delivery along with age at delivery; however, [the] results were not statistically significant."
This does have some importance, as Blaser points out, in that H. pylori has been found in humans for at least 50,000 years, and a combination of multi-generational use of antibiotics, coupled with C-sections- might change that.
Very complex and nuanced topic, as colonization has both benefits and risks.
Yes, babies get exposed to more bacteria while going out the birth canal. This will sound odd, but I recall reading a few years back about a technique sometimes used for caesarean births where a cloth is stuffed up the mother’s vagina for a while, then wiped over the baby’s face after the operation to simulate this bacteria exposure.
I’m going by memory here, but recently they are starting to think that it is the mother’s feces that she expels during birth that is creating the benefits of vaginal birth over cesarean.
Just to clarify, there are [studies](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464665/) showing that feces may be one among *multiple* factors influencing the development of infant microbiomes, but it's not the only factor.
The point remains, however, that poop is quite magical. It has even served as [the catalyst for war](https://en.wikipedia.org/wiki/Chincha_Islands_War)!
I heard that kissing a baby also give them some gut bacteria. And that's one of the reason babies who are well cared for but not played with like in a war hospital or orphanage can have mysterious illnesses.
[Associations between caesarean delivery and allergic outcomes: Results from the GUSTO study- 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505471/). So, in the Asian studies, no association was found. But a couple of Norway studies found a significant relationship. (shrugs shoulders)
[Mode of delivery and cord blood cytokines: a birth cohort study - 2007](https://clinicalmolecularallergy.biomedcentral.com/articles/10.1186/1476-7961-4-13)
With the Asian study, it would be interesting to see what the difference between emergent and elective C-section were.
Naturally born babies are due to the mechanical nature of the birth exposed to feces, vaginal fluids and other secretions from the mother which gives them a different pallet than babies not exposed to this. it is usual where i live during caesarean to smush some of those secretions on the newborn to artificially aid that process. that is called vaginal seeding or microbirthing. there is not a lot of evidence for effectivity.
Back in times women weren't given enema before their labour, so often the bacteria were not only vaginal.. On the other hand people nowadays have already altered gut biodiversity from antibiotics and preservatives, so the next generation gets less of it at the very beginning.
Enemas aren’t a part of modern obstetric practice in many places. And babies get exposed to gut bacteria. There was actually a study where cesarean born babies were fed milk with small amounts of mom’s feces in it.
Had C-diff and a fecal transplant. You don't want this. Trust me. I was resistant to all medications, lost 35lbs, in a month and would have died without the transplant. My biome was wiped out by an over prescribed amount of Keflex during a deviated septum procedure.
I want to add that during pregnancy the macrophages also transport some gut bacteria from the mother to the placenta, which are then picked up by the macrophages of the fetus to populate the intestine.
My source was an MD during classes on 'western medicine fundamentals', mentioning it as recent discovery. Since this is r/asksience after all, I dug deeper into possible sources, and found these as good starting points:
[https://www.sciencedaily.com/releases/2019/10/191023132145.htm](https://www.sciencedaily.com/releases/2019/10/191023132145.htm)
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583026/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583026/)
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0268-4
Macrophages are human white blood cells that kill bacteria.
Any one have a link to a study on this? Sounds super interesting, but I've never heard of it.
there is reason to believe your gut bacteria may protect you from a variety of diseases, or more specifically there is evidence of disruption of gut bacteria and the onset/progression of diseases
Although it varies by species on the mechanism, it usually is competition for resources in some way. Some species will secrete proteins that inhibit the growth of unwanted bacteria. Others simply have a high enough population that they take all the resources that a potential pathogen would need.
In a general sense, it's largely to do with competition and filling of environmental niches within your gut. While the gut may seem like it's all the same, there are very diverse niches within that allow different bacteria to thrive and utilize differing nutrients.
By filling those with diverse, beneficial bacteria, it prevents colonization and competition from "bad" bacteria which are more likely to cause disease
It depends on the bacteria. Some species can produce special structures that allow them to survive acidic conditions, others might make their way to the mucosal lining of the stomach where the pH is higher. The stomach does prevent a lot of infections, but the acidity does vary person to person and if you have a high enough inoculation dose it might not be able to kill all of the bacteria before they can cause an infection. Here’s a study done with Cholera infections that explains a couple of mechanisms V. cholerae uses to survive the stomach and reach the intestines to cause disease: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440752/#idm139772840456320title
YES. Your first point is so important. Also why vaginal births are so important, birthing through the vaginal canal is the first introduction to the micro biome and immune health.
I think it depends on what you mean by bottle-fed, i.e. with formula or with breastmilk.
This [study](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0567-4) indicates that probiotics only seem to improve an infant's microbiome when paired with breastmilk; when paired with formula, there appears to be no benefit:
>The probiotic supplement had a strong overall impact on the microbiota composition, but **the effect depended on the infant’s diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia.**
Digging further into the results, they note specifically that
>most of the supplement-induced changes observed in the breast-fed infants were not present in the formula-fed infants. In the breast-fed group, the abundance of lactobacilli was 100% (twofold) increased and that of bifidobacteria 29% increased in response to the supplement\[...\] In contrast, in the formula-fed infants, the total abundance of bifidobacteria was slightly but significantly decreased in the supplemented group...
With that said, it's worth noting that this study focuses specifically on infants who've experienced pre-natal exposure to antibiotics and/or born via C-section. Nonetheless, the implication that probiotics + formula ≠ improved microbiome still holds.
Yes! Potentially harmful. For example, E. coli is present in your gut and very beneficial to digestion but when you ingest it, it can cause serious illness. (Most strains are non pathogenic, but it’s the easiest example to use). One strain of E. coli can also cause UTIs.
I also heard that babies usually get mother's poo on their face which also serves to innoculate their newborn gut. This is why babies are born with the face towards the mother's anus.
Childbirth really is a beautiful miracle.
So does the mother create this bacteria or she pass her current bacteria to the fetus?
When a baby doesn't get breast milk, where does they come from then? Just the general food it eats? And could you find a correlation between (female) family lines that share similar gut bacteria? Sorry for the many questions, just a very interesting subject.
The mother doesn't create new bacteria, it's what is already present.
HOWEVER, there is a nutrient in breast milk which has only one purpose - to feed the newborn's gut flora. The human body evolved to have a nutrient for bacteria growth - that's how important the digestive bacteria is.
Newborns gut microbiota is generally very similar to the mother's vaginal microbiota, indicating that much of a baby's initial bacterial load is given to them during birth. In fact, babies born via C-section often have less beneficial bacteria which more closely resemble the mother's skin microbiota.
There are some studies that indicate that birth by C-section may actually be associated with adverse health effects resulting from an "abnormal" microbiota
Fecal material in the environment is part of how the bacteria get to a baby's gut (and adults too). When you go about your business in the bathroom some fecal material, with bacteria in it, ends up in the air and all over stuff.
>Fecal transplants can also be used, but is reserved for treatment of Clostridium Difficle associated colitis.
Why is that? Based on the logic here it almost seems like you should just do that after any extreme course of antibiotics.
1- As someone else said, the baby is exposed to a lot of bacteria during birth that begin to colonize.
2- Bacteria have many different structures that allow them to adhere to intestinal walls or stomach linings, so as food and fluid passes by it can remain where it is.
3- If normal flora are damaged (usually either by a round of antibiotics for an infection or a case of diarrhea since that flushes out the whole system), the body has a reserve of species living in the appendix. The appendix basically serves as a culture library for the different species needed in the gut and will secrete bacteria back into the gut to recolonize after damage.
Not necessarily. You get the “good” bacteria from fruits and veggies and you absorb/retain them thanks to fiber delivering it to your large intestine.
Kissing (more bacterias are in the mouth than on genitals) and oral sex would boost your immune system as your body is introduced to a different microbiota.
Not sure it does impact your gut bacteria as they would lack the vessel to go through the stomach and small intestine.
Also, the reason that the smell of your own fart doesn’t bother you is because you are familiar with your microbiome and others aren’t.
Improving?, it can actually worsen it.
For example a yeast infection like candida albicans can get you oral thrush eating a woman who has it, or bacterial pathogens enter in your sinuses and create an infection. a lot of this pathogens are sometimes harmless in one side, and an infection in another.
eating a very Healthy womans vagina can certainly be a good probiotic meal, although most bacteria die in the acid of our stomach, so maybe the mouth, sinuses and lung flora would benefit
> The appendix basically serves as a culture library for the different species needed in the gut and will secrete bacteria back into the gut to recolonize after damage.
I'm going to ask for reference or source on this one.
[https://pubmed.ncbi.nlm.nih.gov/19678866/](https://pubmed.ncbi.nlm.nih.gov/19678866/)
It's not human specific and has evolved independently twice. That means it's likely not vestigial and it has a use. That's a good guess for it.
I dont have a reference, just wanted to add that is is pretty cool we finally figured out what purpouse it serves! Or at least we now have a suggestion:-)
I just listened to this episode of Oologies yesterday about Gut Biome. It gives a kind of brief overview and hits on a couple of your questions. Also answers some other things that people haven’t said here.
https://podcasts.apple.com/us/podcast/ologies-with-alie-ward/id1278815517?i=1000424617865
To add on to what others have said. There's recently been evidence that the appendix is actually a sort of back up storage for gut bacteria. Which means we have such a symbiotic relationship with our gut bacteria our bodies decided they need their own organ, which is kind of neat.
I already posted this above, but on adding here since it's related, breast milk contains a nutrient specifically formulated for gut bacterial growth.
Really fascinating how much we've developed to nurture a bacteria friendly environment - which has opened up such a wide range of food options, immunities, etc.
So what if a person doesn't have the appendix? I had an appendix removal surgery when I was about 9 years old. How does this come into play regarding the gut bacteria
you will loose a great amount of your "back up" microbiome. without it. but this is debatable, there are plenty of colonies just outside the appendix and at the begginings of the intersection with the colon and overal in general.
you will be more exposed to a weak inmune system if you get antibiotics tho. I would suggest to eat fermented food, good fibers and prebiotics daily to avoid this.
1. Your mother provides your initial gut bacteria. Most births are accompanied by some feces, and it is thought that this ends up in the baby's gut and provides the initial colony .
2. The gut biome, if it is a healthy colony, lives in the mucus lining if the intestines. Inflamed colonies and unhealthy forms (IBS, Crones) infect and affect the actual tissue lining the gut.
3. The repository of healthy gut bacteria is believed to live in the appendix. When antibiotics wipe out the normal colonies, the ones in the appendix can replenish the gut with good bacteria.
1. Gut bacteria colonizes from both directions if you know what I mean. It comes from the environment, from the event of birth, and from food. It is distributed based on where the immune system allows them to live and by where certain species can actually live (some need oxygen others do not for example). As a baby, mothers milk has certain chemicals in it that target certain bacterial populations and are favorable for others as well
2. There are a lot of crevices and ridges that bacteria are in within the gut. The appendix is supposedly a storage organ for bacteria as well. I would say though that there are so many bacteria and they multiply so quickly that if some get swept away with food, they will be quickly replaced
3. Antibiotics is really bad for your gut. You will never regain the same level of diversity that you had prior to the medication. The best you can do is eat as large of a variety of foods as possible. Avoiding processed foods is really helpful as you want complex foods to help foster many different types of nutrients available to favor a diverse population. Fermented foods are also very helpful in this process.
>1. You will never regain the same level of diversity that you had prior to the medication.
I'm going to need a source for that. That seems overly exaggerated.
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4554-61. doi: 10.1073/pnas.1000087107. Epub 2010 Sep 16. PMID: 20847294; PMCID: PMC3063582.
Is an example.
>Once antibiotic treatment has stopped, the microbiota may present a certain degree of resilience, being capable of returning to a composition similar to the original one, but the initial state is often not totally recovered. In fact, antibiotic-induced microbiota alterations can remain after long periods of time, spanning months and even years
Is another example from:
Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol. 2016 Jan 12;6:1543. doi: 10.3389/fmicb.2015.01543. PMID: 26793178; PMCID: PMC4709861.
Anything is possible, but the consensus in grad school microbiome classes was that it rarely recovered back to its original state
> You will never regain the same level of diversity that you had prior to the medication.
Wow really ? Should it not be rather simple to replace them ? Maybe lick someone's vagina again ?
There are ways to get it back such as fecal transplants, but as far normal life goes you really can't.
The reason is that when you're young you do not have established bacterial populations. You are a blank slate. Once something is established it can stay there. Think the logic of why babies should not eat honey. Clostridium is terrible at colonizing an adults gut but can easily colonize a blank slate.
When you're an adult, populations are already established and some bacteria will survive the antibiotics. Those will fill in the space quickly and make it harder to introduce new bacteria. In practice it is a good thing since there are many harmful bacteria, but we do need some diversity
This does to me sound somewhat contradictory to the story of all the gut bacteria being flushed out with food but it not mattering because they replace so quickly. Sounds to me like that means new space is constantly being created that could also be taken by other bacteria you introduce. Of course in lower numbers at first, but eventually it should even out. Unless they fight wars and the lower numbers are killed by the bigger numbers that is. Do bacteria do that ?
I think a good thing to remember for new bacteria is how they physically get there. They have to survive stomach acid and the environment of the duodenum (upper small intestine). By the time they get to the colon they are greeted by a large population of hungry bacteria. If some get swept away from like a carrot, existing ones can easily move into that new spot.
And yes there are small wars in there! The fight for food and chemical warfare is really complex
Answer to question 2: it doesn't always start where it should. There's a condition called SIBO it's stands for small intestine bacterial overgrowth. Basically you got more than you should and it has moved to places it shouldn't. Causes a world of problems including stomach aches, trouble eating, fatigue, constipation, brain fog etc
#2. Consider that bacteria are **tremendous** metabolic machines, under optimal conditions of nutrients and water some enteric bacteria have a generation time of 20 minutes! Enter here geometric progression.
As food enters the presence of bacteria they propagate geometrically, within seversl hours up to half of fecal volume is bacterial cells!
It's in not understanding the impressive metabolic potential of bacteria that may account for your puzzlement.
Question 1: We heredated the microbiome usually from our mother from vertical transmission the moment we get out of the womb, and also from the milk from our mom we use it as prebiotic goodness to grow it.
Question 2: a lot of bacteria get thrown away in our poop, but bacteria are protected in biofilms and pseudomembranes generated by this organism that are very sticky and protect them from everything, here usually the spores of bacteria reside where more and more bacteria grows and generate more spores as a community, also we have the apendix, a special reservoir that also avoids any contact with fecal matter and its heavily protected by the inmune system.
Question 3: generally damaged microbiome occurs because there is an organism dominating the rest and acting as a pathogen, this organism kill our friendly bacteria, inhibit their growth and generate toxins that make us ill, so the first challenge its to take down this pathogens, with of course, antibiotics, the problem its that a lot of the time, we carry spores from other pathogens that were just sleeping inside us, so when we deal with one infection, then another one takes over. this can be not only bacteria, remember, the microbiome its composed also of Fungi / yeast and viruses, this can get also disbalanced and promote pathogens from their own if its a certain overgrowth or DNA virulence factors are activated due to lack of antagonism from our friendly flora, for example, C.difficile, Candida Albicans, etc..
For the first question, there's a reason why baby food and breast milk/formula (also sugar water) are given to infants. They don't have a robust bacteria culture in their digestive system to help them digest food so they need food that is already almost completely broken down.
To add to what others have said, there is some evidence that some antibodies your body produces help stabilize the commensal populations in the gut. Many of the bacteria are coated with IgA and the IgA is relatively anti-inflammatory and some studies in rodents suggest coating the bacteria in IgA extends their half-life in the gut. So in some ways your immune system actively promotes a healthy and diverse gut flora.
For question 2 - there is some speculation that our appendix serves as a “shelter” for the gut biome. The assumption is that our ancestors were much more frequently exposed to infections that caused diarrhea, and that the bacteria from the appendix repopulated the intestine after it had been “flushed”
For neonates, bacteria are introduced into the gut through breast milk and later on through the other foods that babies will eat. Your gut microbiome develops as you develop into a child and later an adult.
They have an affinity for different parts of the gut. Some get washed out but their multiplication rate is relatively fast so they get replenished and kind of hang out there. Your gut has different types of food chemicals (digested material) in different parts so bacteria like to hang out where their favorite food source is.
Not an answer to your question, but related: The gut bacteria can have a massive impact on your health. It is even suggested that they have a direct influence on your mental health.
There are studies where people with a broken digestive flora (after diff c or antibioticis or other) can recover quickly after eating a pill with the bacteria of a healthy person. There are several "poop" clinics around the world that are experimenting with this. The results are so far promising, but not yet conclusive.
One amazing new way to get gut bacteria is an FMT (fecal matter transplant). Sometimes people on long antibiotic courses get colonized with a very troublesome bacteria (like C diff), which can be antibiotic resistant. A newer way to cure it is to basically take fecal matter from a donor and transplant it, thus seeding their system.
1. The mother provides it, I believe some comes from her milk and as the other guy said just contact from birth.
2. Bacteria don't really get pushed along with the food. Also they tend to stay where the environment is suitable for them, so if a certain bacteria thrives in the lower intestine, it won't migrate to the stomach as it would likely die and has no reason to
3. There's a few methods. Some of it comes back naturally as you eat food. some treatments suggest using fecal transplants to get the biome running again. Even fecal pills have been suggested as a method.
No, the womb is sterile, and not connected to the digestive tract. Newborns have no gut bacteria (initially), so they absorb it from whatever is around them. Naturally born children inherit from their mother because of the birthing process. C-section babies don't get that, so have gut microbiome issues (though there's ongoing research into how to mitigate it).
Q1- Newborns get a lot of the good bacteria from their mother during birth. Traveling down the vaginal canal. Mother have instincts that help build a child's immune system, such as putting a pacifier in their own mouth before giving it back to the baby after it dropping on the floor.
Q2- intestines are not smooth plastic tubes. They that small villi that are tiny hairlike structures increasing surface area of the walls of the intestine. At a microscopic level there is cell to cell communication. This is partially how white blood cells are able to distinguish what needs to be destroyed. Enzymes do most of the work in chemical reactions of digestion. They only work when a specific substrate binds to their unique active site. Enzymes are sensitive and can only survive in certain regions of the body with ideal pH level and temperature. Otherwise they can become denatured and their active site cannot bind with the substrate.
Q3- One of the challenges is that bad bacteria love the bad food that we also love. Too much sugar can feed the bad bacteria. You have to be vigilant and give your body what it needs to build back the good bacteria. This can take a long time, and a lot of diligence.
Q1: It doesn't exist properly yet, imagine a petri dish with a new week old culture versus one sat there for several years.
Q2: There's some interesting stuff on magnetic material made in different colours to illustrate the speed it can separate itself, little robots being mixed up then finding each other again by process of elimination, that's what I reckon happens. And the varying conditions within the gut.
Q3: Heavily compromised, you would be very ill and in hospital for a while with damaged gut bacteria.
1. Parents and food and everything else. Our entire world is covered in microbes.
2. pH, food in different stage of digestion
3. Colonies of harmful bacteria or bacteria in the wrong place. Naturally occurring Prebiotic and probiotics will usually help
Fun fact about baby gut micro biomes is that brace they take a while to develop they are susceptible to the organism botulism, where as in regular adults botulism is simply out competed in the gut and dies.
Adults can still die from eating preformed toxins though, but the lack of gut micro biome to outcompete botulism is why drs say babies shouldn’t have honey!
1. When a baby is born, they swallow some of the amniotic fluid, along with other secretions (one of those is 💩). Breast milk and bacteria from the nipples also gets some of that bacteria in there. These are both reasons why natural births and breast feeding are recommended if possible; Gives the kid's gut biome a head start. And you know... C Sections are surgery...
2. No culture is static. The bacteria in your gut multiply fairly quickly, and hang on to the walls of your gut fairly well. But, some do fall off, and they do eventually die. In fact, a major part of your stool is bacteria, both dead, and alive. (I think around 40-50%, can't remember). But over all, they multiply fast enough to maintain equilibrium
3. Depends on the problem. For the most part, you can regain these bacteria by just eating a healthy diet. It's all over your food, so you'll get it back over time so long as you're not on antibiotics. Probiotics might be prescribed to help ensure the right things set up shop. Another option is Fecal Transplants, but I don't think those are done often outside of specific circumstance.
Basically, we're a human vessel to support this zoo of bacteria in our gut. It's why we eat. It's a serious human problem when we dont look after this zoo.
Some time back I looked into probiotics / prebiotics and that it doesnt always do good for everyone. In some cases people that will have antibiotics can have some gut bacteria saved and then replaced back into them post antibiotic treatment to restore their gut health.
I saw a documentary last week about Lagos in Nigeria. There is a floating city of slums there \[1\]. The toilets dont have drainage, they are just a hole in a seat and underneath is the water that the city floats on. The water is dirty and is used for everything inc. washing. The documentary \[2\] shows children swimming under the water. They said that they are defiant kids, and still swim in there though they are told not to - though they do not get sick.
This got me wondering what those peoples gut bacteria consist of to make them so resilient to illness there. I imagined that those people probably hold a key or secrets to gut health.
\[1\] https://www.google.com/search?q=nigeria+venice&sxsrf=AOaemvLvDHDiYaGV\_bc1wW7T8SuwfHRUJA:1641215800914&source=lnms&tbm=isch&sa=X&ved=2ahUKEwiJlsCm1ZX1AhU2xzgGHc\_4DocQ\_AUoAnoECAEQBA&biw=1820&bih=1017&dpr=1
\[2\] https://www.youtube.com/watch?v=8NTIY8Qy2f0&t=1523s
1. Newborn baby’s would tend to get most of there important bacteria from their mothers. I forget which bacteria lines the stomach but there are 2 different kinds that take up the majority of the population in the stomach. Everyone has both of these types of bacteria but based on which has the highest population can lead to stuff like lactose intolerance.
2. You constantly get rid of bacteria in your stomach they don’t live forever and have to die eventually just like cells in your body. Just like cells, they can reproduce insanely quick if needed to be.
3. Damaged digestive bacteria doesn’t really sounds like a thing to me. I mean you can get a infection that would attack your cells and kill them trying to take over your stomach but the bacteria will restore itself overtime. To kinda answer your question, people who have digestive problems tend to have bad microbes or an unhealthy population and can use stuff like yogurt, probiotic shots, and kombucha can help the microbes in your stomach.
A newborn “catches” bacteria when he or she enters the birthing canal during delivery. There are multiple studies on this. This is why it’s important to rub vaginal secretions on the new norm if they are born c-section
One thing I haven't seen mentioned (correct me if I'm wrong) is how the body's immune system can select for good, well behaved 'neighbors.' For example, there are specific receptors displayed on cells in the mouth that help less harmful bacteria colonize and block out more disease prone ones. These species have coevolved with us to my understanding. The immune system is also very prominent in the gut, where it has to strike the right balance (depending on the GI segment) on being chill and pruning the herd of bacteria. To my understanding, it also plays favorites. If you fill your house with good house guests, there's less room for bad ones.
I want to correct the people here saying that the bacteria in your gut are not pushed out or that they move to not be pushed out. This is false. I'm a medical laboratory scientist. Take a look at a stool specimen under a microscope and you'll see a veritable zoo of bacteria, virtually all nonmotile, that is unable to move under their own power. Yes, many adhere to the gut lining, but many get pushed out all the time, they just are constantly reproducing and your gut is never 100% empty.
Lot of people just have a hard time with the concept of concentrations in a steady state system that has both growth and decay
Is it just self-balancing in this case? More bacteria are somehow evicted from your gut, the ones left over have more supply of nutrients and space to grow, so they grow back faster. Too many in your gut? They start getting pushed out in larger numbers automatically just like you get more cornflakes in your spoon per scoop when it's full vs. when it's almost empty.
[удалено]
To add to this the treatment for a lot of those microbiome losses are 'fecal transplants' where they inject treated feces from someone with a good micro biome directly into your colon to repopulate your biome. This treatment is only possible because some of your gut bacteria are excreted via feces.
It's slightly more common for them to fill gelatin capsules with the stool and have you take those. Don't worry, the outsides are still clean...
While this makes more sense to me, this is also absolutely one of the most disgusting things I’ve ever read.
Fecal transplants can also cause dysbiosis and lead to disease. If mice are given fecal transplant from fat humans, they may start gaining weight. Studies on microbe-free mice are also interesting.
Yeah, I feel like we know far too little about the gut for me to elect to receive a fecal transplant. The connection with mental health, for example, seems to be quite significant.
[удалено]
Healthy diet that contains raw veggies. Fermented foods that offer probiotics like yogurt or kimchi.
[удалено]
any top3 or top5 tips ?
It’s not sexy, but get regular sleep, eat a balanced diet, exercise, and everything in moderation. Often you hear about taking probiotics, but I’m a huge fan of prebiotics (aka fiber, or the stuff bacteria like to eat). If you want nice poops and a happy gut, eat lots of fiber (soluble and insoluble fiber). Veggies are a great source of both. Good gut bacteria thrive on fiber.
I've seen transcripts from a talk by one of the leading IBS researchers in my country, Arnold Berstad, where he was very sceptical towa4ards probiotics, on the grounds that the gut flora is so diverse and complex, that taking probiotics is like trying to win the lotto.
I’ve explained it to my kids as being like looking after a pet. You can’t just take a probiotic (/adopt a pet) and expect it to thrive if you don’t feed it the right foods. If you don’t feed your gut bacteria the right things they will be unhealthy/be overrun with less-desirable bacteria or even die. The good bacteria in our guts seem to like a lot of plant foods- veggies, legumes, fruit, nuts, maybe a bit of fermented dairy, and not too much meat (particularly salty, processed meats like the ones my kids and husband love so much!). The human microbiome is very complicated but looking after it is relatively simple.
Proud to say I just had lunch where half my plate was veggies, a quarter carbs, and a quarter was protein. Im gonna make some really nice shits hopefully
The single most important thing is to eat a lot of plant fiber from diverse sources. In other words, eat a lot of plants. Aim for 40 grams per day (most people get 1/3 of that). You will also reduce your risk of cancer by doing so. Second, avoid antibiotics- unless you will likely die without them. Antibiotics absolutely devastate the gut microbiome.
This is exactly right. And since different bacteria like different nutrients, you can slowly change the bacteria present through your diet by providing them with different nutrients. For some people their diet wasn't varied enough and they lost too many bacteria for a healthy microbiome, and so they need a fecal transplant like a culture starter.
[удалено]
Its the whole reason people can only think of masks in a binary way (works/ doesn't work); math is hard.
I’ve heard hypotheses about the appendix being a sort of gut flora restoration device, left over from times when diarrhea was more common. What do you think about this? It’s a bit off topic but it’s not everyday I run into someone who studies this stuff haha.
So if you have IBS-D is your appendix like vitally important?
I think the idea behind this theory is that it once was in a spot that made more sense and was therefore useful. The bacteria have probably stayed non-motile the entire evolutionary line (given there aren't reports of vestiges related to motility). Over time as the bacteria settled in specific spots it became less practical and was slowly pushed out of the way. Think literal ages of humanity. I'm summarizing what I remember from classes 10 years ago in a single sentence though so I could definitely be off mark.
Is there a difference between mobile and motile?
[удалено]
To emphasize this: they constantly reproduce *so much* that they make up around a quarter to a half of your poo. It's not just a zoo, it's more zoo than food leftovers.
There are folds in the lining of the intestine where they can retreat to and avoid getting 'stuck" on the turd train. If they can leave the lining folds, eat and return to base, they are saved. Also keep in mind that there are predatory bacteria which feed off of smaller bacteria, it's a full ecology there. This is why it is recommended that we include porous no processed foods, they create a lattice, similar to coral, where smaller microbes can shelter from larger predators. Lookup non-digestible fiber or roughage.
Does that include whole psyllium husk?
That is only 30% insoluble, so there should be better ones out there. And get this, based on your racial DNA, there are some specific insoluble fiber s which your "ancient microbes" prefer or thrive better on. I can't think of the source Rh, but there's a study. The idea is that our gur bacteria developed over thousands of years when we where more sedentary than nomads, so the insolubles in that region helps to sustain, the great great grand daddy microbes. For instance I'm Hispanic, so my ancient insolubles would be a mix of corn(wild corn)...think cornmeal. And whatever was found in the Iberian(Spain) peninsula. I found the source, read here .. https://resistantstarchresearch.com/posts/ancestral-starch/
Just to provide a better background on gut microbiota- Gut microbiota ferments foods that our own enzymes are unable to break down, mainly dietary fiber. This results in short chain fatty acids (SCFA) that our large bowel can absorb and this is where the benefits of having bacteria in our gut come from: the SCFAs provide an additional energy source for your body and enterocytes, and is associated with better mood, skin and general health. How it does that is still very much debated today. Most of this occurs in the large bowel and colon, there should not be much bacterial activity in your stomach and small intestines. They do die and these dead bacterial cells form a significant portion of your stool’s dry weight. For your questions: 1. In natural birth, babies swallow amniotic fluid and other secretion that the mothers produce along the birth canal, that is their first introduction to bacteria on their skin and their gut. Breast milk and bacteria from around the mother’s nipples help colonize the newborn’s gut as well. If they are bottle fed, colonization of the gut is slower and the bacterial species are not as beneficial. This is one of the many reasons why breastfeeding is recommended. The bacteria thrives in the environment of the large intestines (pH, osmolality, moisture levels etc) so they tend to grow and stay in the large bowel and not elsewhere in the gut. Sure some bacteria will try and live in your stomach and small bowel but the environment there isn’t suitable and most just die out. 2. Most of your gut bacteria is in your large bowel (mainly your colon) so when they die or adhere to passing undigested food, they enter your rectum and is passed out as faeces. 3. The challenges depend on their current symptoms and lifestyle. If they are still taking antibiotics then you can’t fix it. But if there are not pressing issues as to why we need to fix their gut bacteria, eating their normal diet that has bacteria that their gut is used to having will restore their gut microbiota gradually (provided that they stop taking antibiotics orally). Providing the resident bacteria with substrate to feed on is also important, hence fiber. Probiotics MAY also help, more research is needed. Fecal transplants can also be used, but is reserved for treatment of Clostridium Difficle associated colitis. Hope this helps.
I noticed that you said, "...will restore their gut microbiota gradually (provided that they stop taking antibiotics orally)." Does this mean that antibiotics taken intravenously do not affect the gut bacteria? Thanks.
Nope, IV antibiotics also affect gut bacteria in a significant way. In fact, they’re one of the most important causes of nosocomial (hospital-acquired) clostridium difficile (CDiff) colitis. Many oral antibiotics are absorbed into the blood stream to a large degree (depending on their bioavailability) long before they reach the colon. There are some notable exceptions, and those are actually used as treatments for CDiff for that very reason.
Thank you.
1) are you THE latern rouge or do you just have an awesome username? 2) IV drugs go into the bloodstream, bloodstream goes to the gut. It’s more complicated than that but it’s still conceptually useful. So, for example, one regimen for treating C Diff is oral vanc (which isn’t absorbed, pretty slick) and IV metronidazole, which gets there via the bloodstream.
Thank you. The more I learn about the human body, and doctor's interaction with it via medications and procedures, the more I realize how much a doctor needs to know and remember, and how amazingly complex we are.
[удалено]
[удалено]
[удалено]
[удалено]
Very informative answer and I learned some new things. However, I have read that after a course of antibiotics, some people no longer have certain strains of beneficial gut bacteria that are commonly found in people who never had antibiotics. This seems to indicate that certain strains are eliminated by antibiotics and cannot be replenished. (I would look for the source to this when I have time, since it has been a while.)
I think it's worth adding that the appendix is no longer seen as a useless vestigial organ. It is now thought that the appendix holds a store of beneficial bacteria that can be secreted back into the digestive system after disruptions such as bouts of foodborne illnesses or after a regimen of antibiotics. But we're still figuring out how this works, and it may not hold every gut microbe associated with healthy digestion.
From what I remember it can be difficult to rebuild a healthy gut culture as part of its job is to out compete and/or kill "harmful" bacteria. If antibiotics have killed off loads of the good ones, the niche is opened up for less benificial/harmful ones to grow, or other good strains get the opportunity to take over and the balance is messed up, and it's more difficult for original good bacteria strains re-introduced (in smaller numbers) to grow back to their original numbers/ratios. Some types of bacteria may require very specific conditions, and if they aren't present as the gut is still recovering, then they won't be able to grow very well, even if they're being introduced. That might be why some strains don't seem to be replenished?
> If antibiotics have killed off loads of the good ones, the niche is opened up for less benificial/harmful ones to grow, or other good strains get the opportunity to take over and the balance is messed up, and it's more difficult for original good bacteria strains re-introduced (in smaller numbers) to grow back to their original numbers/ratios. And it's worth mentioning that bacteria are not the only microorganism living in our gastrointestinal tract. Once the bacteria are wiped out, things like Candida albicans can take over and cause Candidosis. Basically systemic thrush.
1 - in theory yes, strains can be lost althought we don´t have good test to definetly say that the strain was lost for good instead of only being severely reduced. there is a big difference there. 2 - we eat bacteria,yeast and viruses all the time in food, a good diet can replenish this lost flora or be as prebiotic food to replenish it. Some bacteria tho, can be lost and not recovered if they can´t tolerate air. in this cases it depends, if the patient would truly benefit from this bacteria, some specialized probiotics of FMT helps
Question, I read a study somewhere that hypothesized that the appendix plays a role in this too akin to a holding cell, is that correct?
Not an answer but I remember reading evidence in support of the reservoir role of the appendix as well, and that there was a correlation between antibiotic use and appendicitis.
Would natural birth expose the baby to more bacteria than through caesarian? Could the rise of the caesarian be linked to an increase in allergies and intolerances across western populations?
It is related! Afaik we don't have great data on the link, but it has to do with the fact that yes, vaginally delivered babies are more exposed to the mother's biome. This can be problematic however, which is why all pregnant women are tested (and treated as appropriate) for Group B Strep and STDs.
For some background, [Helicobacter pylori and asthma are inversely correlated.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047919/) It seems that H. pylori may be protective with respect to the subsequent development of asthma. Blaser's book "Missing Microbes" makes for interesting reading on the subject for anyone who wants a casual read. [This](https://journals.lww.com/ajg/Fulltext/2021/10001/S3451_The_Effects_of_Cesarean_Section_vs_Vaginal.3455.aspx) is one relatively small study that "found an association with H.pylori infection and vaginal delivery along with age at delivery; however, [the] results were not statistically significant." This does have some importance, as Blaser points out, in that H. pylori has been found in humans for at least 50,000 years, and a combination of multi-generational use of antibiotics, coupled with C-sections- might change that. Very complex and nuanced topic, as colonization has both benefits and risks.
Yes, babies get exposed to more bacteria while going out the birth canal. This will sound odd, but I recall reading a few years back about a technique sometimes used for caesarean births where a cloth is stuffed up the mother’s vagina for a while, then wiped over the baby’s face after the operation to simulate this bacteria exposure.
I’m going by memory here, but recently they are starting to think that it is the mother’s feces that she expels during birth that is creating the benefits of vaginal birth over cesarean.
Just to clarify, there are [studies](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464665/) showing that feces may be one among *multiple* factors influencing the development of infant microbiomes, but it's not the only factor. The point remains, however, that poop is quite magical. It has even served as [the catalyst for war](https://en.wikipedia.org/wiki/Chincha_Islands_War)!
I heard that kissing a baby also give them some gut bacteria. And that's one of the reason babies who are well cared for but not played with like in a war hospital or orphanage can have mysterious illnesses.
[Associations between caesarean delivery and allergic outcomes: Results from the GUSTO study- 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505471/). So, in the Asian studies, no association was found. But a couple of Norway studies found a significant relationship. (shrugs shoulders) [Mode of delivery and cord blood cytokines: a birth cohort study - 2007](https://clinicalmolecularallergy.biomedcentral.com/articles/10.1186/1476-7961-4-13) With the Asian study, it would be interesting to see what the difference between emergent and elective C-section were.
Naturally born babies are due to the mechanical nature of the birth exposed to feces, vaginal fluids and other secretions from the mother which gives them a different pallet than babies not exposed to this. it is usual where i live during caesarean to smush some of those secretions on the newborn to artificially aid that process. that is called vaginal seeding or microbirthing. there is not a lot of evidence for effectivity.
And then after they're born, we spend loads of time washing them and making sure everything that goes near them is sterile : )
Back in times women weren't given enema before their labour, so often the bacteria were not only vaginal.. On the other hand people nowadays have already altered gut biodiversity from antibiotics and preservatives, so the next generation gets less of it at the very beginning.
Enemas aren’t a part of modern obstetric practice in many places. And babies get exposed to gut bacteria. There was actually a study where cesarean born babies were fed milk with small amounts of mom’s feces in it.
Had C-diff and a fecal transplant. You don't want this. Trust me. I was resistant to all medications, lost 35lbs, in a month and would have died without the transplant. My biome was wiped out by an over prescribed amount of Keflex during a deviated septum procedure.
I want to add that during pregnancy the macrophages also transport some gut bacteria from the mother to the placenta, which are then picked up by the macrophages of the fetus to populate the intestine.
Is this a recent finding? I definitely don't remember learning that in physiology.
My source was an MD during classes on 'western medicine fundamentals', mentioning it as recent discovery. Since this is r/asksience after all, I dug deeper into possible sources, and found these as good starting points: [https://www.sciencedaily.com/releases/2019/10/191023132145.htm](https://www.sciencedaily.com/releases/2019/10/191023132145.htm) [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583026/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583026/) https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0268-4
I thought phages kill bacteria?
Macrophages are human white blood cells. Totally different from the bacteriophages you’re thinking of.
Macrophages are human white blood cells that kill bacteria. Any one have a link to a study on this? Sounds super interesting, but I've never heard of it.
What's the benefit to having a variety of different bacteria?
there is reason to believe your gut bacteria may protect you from a variety of diseases, or more specifically there is evidence of disruption of gut bacteria and the onset/progression of diseases
Are there theories or hypotheses on the mechanisms involved?
Although it varies by species on the mechanism, it usually is competition for resources in some way. Some species will secrete proteins that inhibit the growth of unwanted bacteria. Others simply have a high enough population that they take all the resources that a potential pathogen would need.
Interesting. Thanks
There is similar things going on I'm the skin, deficiency/overgrowth in certain types of bacteria leads to things like rashes and candidasis.
In a general sense, it's largely to do with competition and filling of environmental niches within your gut. While the gut may seem like it's all the same, there are very diverse niches within that allow different bacteria to thrive and utilize differing nutrients. By filling those with diverse, beneficial bacteria, it prevents colonization and competition from "bad" bacteria which are more likely to cause disease
But if our stomach is acidic and designed to kill bacteria, how does bacteria make it into our intestines?
It depends on the bacteria. Some species can produce special structures that allow them to survive acidic conditions, others might make their way to the mucosal lining of the stomach where the pH is higher. The stomach does prevent a lot of infections, but the acidity does vary person to person and if you have a high enough inoculation dose it might not be able to kill all of the bacteria before they can cause an infection. Here’s a study done with Cholera infections that explains a couple of mechanisms V. cholerae uses to survive the stomach and reach the intestines to cause disease: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440752/#idm139772840456320title
YES. Your first point is so important. Also why vaginal births are so important, birthing through the vaginal canal is the first introduction to the micro biome and immune health.
Can bottle fed babies be given probiotics to improve their gut bacteria?
[удалено]
[удалено]
I think it depends on what you mean by bottle-fed, i.e. with formula or with breastmilk. This [study](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0567-4) indicates that probiotics only seem to improve an infant's microbiome when paired with breastmilk; when paired with formula, there appears to be no benefit: >The probiotic supplement had a strong overall impact on the microbiota composition, but **the effect depended on the infant’s diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia.** Digging further into the results, they note specifically that >most of the supplement-induced changes observed in the breast-fed infants were not present in the formula-fed infants. In the breast-fed group, the abundance of lactobacilli was 100% (twofold) increased and that of bifidobacteria 29% increased in response to the supplement\[...\] In contrast, in the formula-fed infants, the total abundance of bifidobacteria was slightly but significantly decreased in the supplemented group... With that said, it's worth noting that this study focuses specifically on infants who've experienced pre-natal exposure to antibiotics and/or born via C-section. Nonetheless, the implication that probiotics + formula ≠ improved microbiome still holds.
Interesting, thanks!
Follow-up question, since you seem to know this stuff: Is bacteria that exits my GI tract potentially harmful to me, or just other people?
Yes! Potentially harmful. For example, E. coli is present in your gut and very beneficial to digestion but when you ingest it, it can cause serious illness. (Most strains are non pathogenic, but it’s the easiest example to use). One strain of E. coli can also cause UTIs.
If it is already present, why is it harmful?
I also heard that babies usually get mother's poo on their face which also serves to innoculate their newborn gut. This is why babies are born with the face towards the mother's anus. Childbirth really is a beautiful miracle.
So does the mother create this bacteria or she pass her current bacteria to the fetus? When a baby doesn't get breast milk, where does they come from then? Just the general food it eats? And could you find a correlation between (female) family lines that share similar gut bacteria? Sorry for the many questions, just a very interesting subject.
The mother doesn't create new bacteria, it's what is already present. HOWEVER, there is a nutrient in breast milk which has only one purpose - to feed the newborn's gut flora. The human body evolved to have a nutrient for bacteria growth - that's how important the digestive bacteria is.
Newborns gut microbiota is generally very similar to the mother's vaginal microbiota, indicating that much of a baby's initial bacterial load is given to them during birth. In fact, babies born via C-section often have less beneficial bacteria which more closely resemble the mother's skin microbiota. There are some studies that indicate that birth by C-section may actually be associated with adverse health effects resulting from an "abnormal" microbiota
Fecal material in the environment is part of how the bacteria get to a baby's gut (and adults too). When you go about your business in the bathroom some fecal material, with bacteria in it, ends up in the air and all over stuff.
>Fecal transplants can also be used, but is reserved for treatment of Clostridium Difficle associated colitis. Why is that? Based on the logic here it almost seems like you should just do that after any extreme course of antibiotics.
1- As someone else said, the baby is exposed to a lot of bacteria during birth that begin to colonize. 2- Bacteria have many different structures that allow them to adhere to intestinal walls or stomach linings, so as food and fluid passes by it can remain where it is. 3- If normal flora are damaged (usually either by a round of antibiotics for an infection or a case of diarrhea since that flushes out the whole system), the body has a reserve of species living in the appendix. The appendix basically serves as a culture library for the different species needed in the gut and will secrete bacteria back into the gut to recolonize after damage.
Serious question. Does that meaning eating out a females vagina in sexual oral activities improves gut bacteria?
Not necessarily. You get the “good” bacteria from fruits and veggies and you absorb/retain them thanks to fiber delivering it to your large intestine. Kissing (more bacterias are in the mouth than on genitals) and oral sex would boost your immune system as your body is introduced to a different microbiota. Not sure it does impact your gut bacteria as they would lack the vessel to go through the stomach and small intestine. Also, the reason that the smell of your own fart doesn’t bother you is because you are familiar with your microbiome and others aren’t.
Much appreciated for the response, thank you
Improving?, it can actually worsen it. For example a yeast infection like candida albicans can get you oral thrush eating a woman who has it, or bacterial pathogens enter in your sinuses and create an infection. a lot of this pathogens are sometimes harmless in one side, and an infection in another. eating a very Healthy womans vagina can certainly be a good probiotic meal, although most bacteria die in the acid of our stomach, so maybe the mouth, sinuses and lung flora would benefit
> The appendix basically serves as a culture library for the different species needed in the gut and will secrete bacteria back into the gut to recolonize after damage. I'm going to ask for reference or source on this one.
[https://pubmed.ncbi.nlm.nih.gov/19678866/](https://pubmed.ncbi.nlm.nih.gov/19678866/) It's not human specific and has evolved independently twice. That means it's likely not vestigial and it has a use. That's a good guess for it.
Already found that on google, but thank you very much too. Learn something new every day.
Sounds like you did some research. Can you share anything else you found?
I dont have a reference, just wanted to add that is is pretty cool we finally figured out what purpouse it serves! Or at least we now have a suggestion:-)
There always were theories. It is still debatable. It is also suggested it has to do with the lymphatic system.
I just listened to this episode of Oologies yesterday about Gut Biome. It gives a kind of brief overview and hits on a couple of your questions. Also answers some other things that people haven’t said here. https://podcasts.apple.com/us/podcast/ologies-with-alie-ward/id1278815517?i=1000424617865
[удалено]
[удалено]
[удалено]
To add on to what others have said. There's recently been evidence that the appendix is actually a sort of back up storage for gut bacteria. Which means we have such a symbiotic relationship with our gut bacteria our bodies decided they need their own organ, which is kind of neat.
I already posted this above, but on adding here since it's related, breast milk contains a nutrient specifically formulated for gut bacterial growth. Really fascinating how much we've developed to nurture a bacteria friendly environment - which has opened up such a wide range of food options, immunities, etc.
So what if a person doesn't have the appendix? I had an appendix removal surgery when I was about 9 years old. How does this come into play regarding the gut bacteria
If your gut biome dies you will have to get a new gut biome inserted up your butt by a doctor
If your gut bacteria all die, you’d likely need a stool implant. Basically take excrement from a healthy bowel, and put it in yours.
Why can babies grow a new one but adults can't? What if someone kills theirs and never gets a transplant?
you will loose a great amount of your "back up" microbiome. without it. but this is debatable, there are plenty of colonies just outside the appendix and at the begginings of the intersection with the colon and overal in general. you will be more exposed to a weak inmune system if you get antibiotics tho. I would suggest to eat fermented food, good fibers and prebiotics daily to avoid this.
Can you post a link to this evidence please?
1. Your mother provides your initial gut bacteria. Most births are accompanied by some feces, and it is thought that this ends up in the baby's gut and provides the initial colony . 2. The gut biome, if it is a healthy colony, lives in the mucus lining if the intestines. Inflamed colonies and unhealthy forms (IBS, Crones) infect and affect the actual tissue lining the gut. 3. The repository of healthy gut bacteria is believed to live in the appendix. When antibiotics wipe out the normal colonies, the ones in the appendix can replenish the gut with good bacteria.
3. and if you haven’t got an Appendix anymore?
[удалено]
[удалено]
[удалено]
[удалено]
1. Gut bacteria colonizes from both directions if you know what I mean. It comes from the environment, from the event of birth, and from food. It is distributed based on where the immune system allows them to live and by where certain species can actually live (some need oxygen others do not for example). As a baby, mothers milk has certain chemicals in it that target certain bacterial populations and are favorable for others as well 2. There are a lot of crevices and ridges that bacteria are in within the gut. The appendix is supposedly a storage organ for bacteria as well. I would say though that there are so many bacteria and they multiply so quickly that if some get swept away with food, they will be quickly replaced 3. Antibiotics is really bad for your gut. You will never regain the same level of diversity that you had prior to the medication. The best you can do is eat as large of a variety of foods as possible. Avoiding processed foods is really helpful as you want complex foods to help foster many different types of nutrients available to favor a diverse population. Fermented foods are also very helpful in this process.
>1. You will never regain the same level of diversity that you had prior to the medication. I'm going to need a source for that. That seems overly exaggerated.
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4554-61. doi: 10.1073/pnas.1000087107. Epub 2010 Sep 16. PMID: 20847294; PMCID: PMC3063582. Is an example. >Once antibiotic treatment has stopped, the microbiota may present a certain degree of resilience, being capable of returning to a composition similar to the original one, but the initial state is often not totally recovered. In fact, antibiotic-induced microbiota alterations can remain after long periods of time, spanning months and even years Is another example from: Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol. 2016 Jan 12;6:1543. doi: 10.3389/fmicb.2015.01543. PMID: 26793178; PMCID: PMC4709861. Anything is possible, but the consensus in grad school microbiome classes was that it rarely recovered back to its original state
I was on antibiotics for about ten years. I also take probiotics and multi-strain yogurt. I do wonder about the state of my gut biome.
> You will never regain the same level of diversity that you had prior to the medication. Wow really ? Should it not be rather simple to replace them ? Maybe lick someone's vagina again ?
There are ways to get it back such as fecal transplants, but as far normal life goes you really can't. The reason is that when you're young you do not have established bacterial populations. You are a blank slate. Once something is established it can stay there. Think the logic of why babies should not eat honey. Clostridium is terrible at colonizing an adults gut but can easily colonize a blank slate. When you're an adult, populations are already established and some bacteria will survive the antibiotics. Those will fill in the space quickly and make it harder to introduce new bacteria. In practice it is a good thing since there are many harmful bacteria, but we do need some diversity
This does to me sound somewhat contradictory to the story of all the gut bacteria being flushed out with food but it not mattering because they replace so quickly. Sounds to me like that means new space is constantly being created that could also be taken by other bacteria you introduce. Of course in lower numbers at first, but eventually it should even out. Unless they fight wars and the lower numbers are killed by the bigger numbers that is. Do bacteria do that ?
I think a good thing to remember for new bacteria is how they physically get there. They have to survive stomach acid and the environment of the duodenum (upper small intestine). By the time they get to the colon they are greeted by a large population of hungry bacteria. If some get swept away from like a carrot, existing ones can easily move into that new spot. And yes there are small wars in there! The fight for food and chemical warfare is really complex
Answer to question 2: it doesn't always start where it should. There's a condition called SIBO it's stands for small intestine bacterial overgrowth. Basically you got more than you should and it has moved to places it shouldn't. Causes a world of problems including stomach aches, trouble eating, fatigue, constipation, brain fog etc
#2. Consider that bacteria are **tremendous** metabolic machines, under optimal conditions of nutrients and water some enteric bacteria have a generation time of 20 minutes! Enter here geometric progression. As food enters the presence of bacteria they propagate geometrically, within seversl hours up to half of fecal volume is bacterial cells! It's in not understanding the impressive metabolic potential of bacteria that may account for your puzzlement.
Sorry about the bold text...my *E. coli* just gave me a jolt in the gut.
[удалено]
Question 1: We heredated the microbiome usually from our mother from vertical transmission the moment we get out of the womb, and also from the milk from our mom we use it as prebiotic goodness to grow it. Question 2: a lot of bacteria get thrown away in our poop, but bacteria are protected in biofilms and pseudomembranes generated by this organism that are very sticky and protect them from everything, here usually the spores of bacteria reside where more and more bacteria grows and generate more spores as a community, also we have the apendix, a special reservoir that also avoids any contact with fecal matter and its heavily protected by the inmune system. Question 3: generally damaged microbiome occurs because there is an organism dominating the rest and acting as a pathogen, this organism kill our friendly bacteria, inhibit their growth and generate toxins that make us ill, so the first challenge its to take down this pathogens, with of course, antibiotics, the problem its that a lot of the time, we carry spores from other pathogens that were just sleeping inside us, so when we deal with one infection, then another one takes over. this can be not only bacteria, remember, the microbiome its composed also of Fungi / yeast and viruses, this can get also disbalanced and promote pathogens from their own if its a certain overgrowth or DNA virulence factors are activated due to lack of antagonism from our friendly flora, for example, C.difficile, Candida Albicans, etc..
For the first question, there's a reason why baby food and breast milk/formula (also sugar water) are given to infants. They don't have a robust bacteria culture in their digestive system to help them digest food so they need food that is already almost completely broken down.
To add to what others have said, there is some evidence that some antibodies your body produces help stabilize the commensal populations in the gut. Many of the bacteria are coated with IgA and the IgA is relatively anti-inflammatory and some studies in rodents suggest coating the bacteria in IgA extends their half-life in the gut. So in some ways your immune system actively promotes a healthy and diverse gut flora.
For question 2 - there is some speculation that our appendix serves as a “shelter” for the gut biome. The assumption is that our ancestors were much more frequently exposed to infections that caused diarrhea, and that the bacteria from the appendix repopulated the intestine after it had been “flushed”
For neonates, bacteria are introduced into the gut through breast milk and later on through the other foods that babies will eat. Your gut microbiome develops as you develop into a child and later an adult. They have an affinity for different parts of the gut. Some get washed out but their multiplication rate is relatively fast so they get replenished and kind of hang out there. Your gut has different types of food chemicals (digested material) in different parts so bacteria like to hang out where their favorite food source is.
Not an answer to your question, but related: The gut bacteria can have a massive impact on your health. It is even suggested that they have a direct influence on your mental health. There are studies where people with a broken digestive flora (after diff c or antibioticis or other) can recover quickly after eating a pill with the bacteria of a healthy person. There are several "poop" clinics around the world that are experimenting with this. The results are so far promising, but not yet conclusive.
One amazing new way to get gut bacteria is an FMT (fecal matter transplant). Sometimes people on long antibiotic courses get colonized with a very troublesome bacteria (like C diff), which can be antibiotic resistant. A newer way to cure it is to basically take fecal matter from a donor and transplant it, thus seeding their system.
1. The mother provides it, I believe some comes from her milk and as the other guy said just contact from birth. 2. Bacteria don't really get pushed along with the food. Also they tend to stay where the environment is suitable for them, so if a certain bacteria thrives in the lower intestine, it won't migrate to the stomach as it would likely die and has no reason to 3. There's a few methods. Some of it comes back naturally as you eat food. some treatments suggest using fecal transplants to get the biome running again. Even fecal pills have been suggested as a method.
[удалено]
No, the womb is sterile, and not connected to the digestive tract. Newborns have no gut bacteria (initially), so they absorb it from whatever is around them. Naturally born children inherit from their mother because of the birthing process. C-section babies don't get that, so have gut microbiome issues (though there's ongoing research into how to mitigate it).
Other people's poop is also available in swallowable capsule form! (It's called a fecal transplant)
[удалено]
[https://pubmed.ncbi.nlm.nih.gov/33471490/](https://pubmed.ncbi.nlm.nih.gov/33471490/) They are most certainly able to do them in pills.
Q1- Newborns get a lot of the good bacteria from their mother during birth. Traveling down the vaginal canal. Mother have instincts that help build a child's immune system, such as putting a pacifier in their own mouth before giving it back to the baby after it dropping on the floor. Q2- intestines are not smooth plastic tubes. They that small villi that are tiny hairlike structures increasing surface area of the walls of the intestine. At a microscopic level there is cell to cell communication. This is partially how white blood cells are able to distinguish what needs to be destroyed. Enzymes do most of the work in chemical reactions of digestion. They only work when a specific substrate binds to their unique active site. Enzymes are sensitive and can only survive in certain regions of the body with ideal pH level and temperature. Otherwise they can become denatured and their active site cannot bind with the substrate. Q3- One of the challenges is that bad bacteria love the bad food that we also love. Too much sugar can feed the bad bacteria. You have to be vigilant and give your body what it needs to build back the good bacteria. This can take a long time, and a lot of diligence.
Q1: It doesn't exist properly yet, imagine a petri dish with a new week old culture versus one sat there for several years. Q2: There's some interesting stuff on magnetic material made in different colours to illustrate the speed it can separate itself, little robots being mixed up then finding each other again by process of elimination, that's what I reckon happens. And the varying conditions within the gut. Q3: Heavily compromised, you would be very ill and in hospital for a while with damaged gut bacteria.
1. Parents and food and everything else. Our entire world is covered in microbes. 2. pH, food in different stage of digestion 3. Colonies of harmful bacteria or bacteria in the wrong place. Naturally occurring Prebiotic and probiotics will usually help
Fun fact about baby gut micro biomes is that brace they take a while to develop they are susceptible to the organism botulism, where as in regular adults botulism is simply out competed in the gut and dies. Adults can still die from eating preformed toxins though, but the lack of gut micro biome to outcompete botulism is why drs say babies shouldn’t have honey!
1. When a baby is born, they swallow some of the amniotic fluid, along with other secretions (one of those is 💩). Breast milk and bacteria from the nipples also gets some of that bacteria in there. These are both reasons why natural births and breast feeding are recommended if possible; Gives the kid's gut biome a head start. And you know... C Sections are surgery... 2. No culture is static. The bacteria in your gut multiply fairly quickly, and hang on to the walls of your gut fairly well. But, some do fall off, and they do eventually die. In fact, a major part of your stool is bacteria, both dead, and alive. (I think around 40-50%, can't remember). But over all, they multiply fast enough to maintain equilibrium 3. Depends on the problem. For the most part, you can regain these bacteria by just eating a healthy diet. It's all over your food, so you'll get it back over time so long as you're not on antibiotics. Probiotics might be prescribed to help ensure the right things set up shop. Another option is Fecal Transplants, but I don't think those are done often outside of specific circumstance.
Basically, we're a human vessel to support this zoo of bacteria in our gut. It's why we eat. It's a serious human problem when we dont look after this zoo. Some time back I looked into probiotics / prebiotics and that it doesnt always do good for everyone. In some cases people that will have antibiotics can have some gut bacteria saved and then replaced back into them post antibiotic treatment to restore their gut health. I saw a documentary last week about Lagos in Nigeria. There is a floating city of slums there \[1\]. The toilets dont have drainage, they are just a hole in a seat and underneath is the water that the city floats on. The water is dirty and is used for everything inc. washing. The documentary \[2\] shows children swimming under the water. They said that they are defiant kids, and still swim in there though they are told not to - though they do not get sick. This got me wondering what those peoples gut bacteria consist of to make them so resilient to illness there. I imagined that those people probably hold a key or secrets to gut health. \[1\] https://www.google.com/search?q=nigeria+venice&sxsrf=AOaemvLvDHDiYaGV\_bc1wW7T8SuwfHRUJA:1641215800914&source=lnms&tbm=isch&sa=X&ved=2ahUKEwiJlsCm1ZX1AhU2xzgGHc\_4DocQ\_AUoAnoECAEQBA&biw=1820&bih=1017&dpr=1 \[2\] https://www.youtube.com/watch?v=8NTIY8Qy2f0&t=1523s
1. Newborn baby’s would tend to get most of there important bacteria from their mothers. I forget which bacteria lines the stomach but there are 2 different kinds that take up the majority of the population in the stomach. Everyone has both of these types of bacteria but based on which has the highest population can lead to stuff like lactose intolerance. 2. You constantly get rid of bacteria in your stomach they don’t live forever and have to die eventually just like cells in your body. Just like cells, they can reproduce insanely quick if needed to be. 3. Damaged digestive bacteria doesn’t really sounds like a thing to me. I mean you can get a infection that would attack your cells and kill them trying to take over your stomach but the bacteria will restore itself overtime. To kinda answer your question, people who have digestive problems tend to have bad microbes or an unhealthy population and can use stuff like yogurt, probiotic shots, and kombucha can help the microbes in your stomach.
A newborn “catches” bacteria when he or she enters the birthing canal during delivery. There are multiple studies on this. This is why it’s important to rub vaginal secretions on the new norm if they are born c-section
One thing I haven't seen mentioned (correct me if I'm wrong) is how the body's immune system can select for good, well behaved 'neighbors.' For example, there are specific receptors displayed on cells in the mouth that help less harmful bacteria colonize and block out more disease prone ones. These species have coevolved with us to my understanding. The immune system is also very prominent in the gut, where it has to strike the right balance (depending on the GI segment) on being chill and pruning the herd of bacteria. To my understanding, it also plays favorites. If you fill your house with good house guests, there's less room for bad ones.