Could you suggest a good source for beginners. - Louis Somers
The interactions between the human body and its microbiome are quite complex. I am going to provide you with an answer that will be based on your comment that you would like an answer from a beginners perspective.
For simplicity sake I will keep the answer to humans as the host organism, though pretty much any multicellular organism can act as a host for microscopic organisms.
Note: A number or the references I use come from Janeway's Immunobiology. The links provided are to the 2001 edition that is on the NCBI bookshelf. The issue, however, is that over the past decade we have learned a great deal more about the immune system since then, and some of the things I refer to were not represented in that edition of the text.
Do intestinal fauna have the same DNA as their host?
The short answer to this question is no. Also, we generally identify microbes of this nature as flora instead of fauna, so you would say intestinal flora.
The human microbiome (microbiota), as it is often referred to, is made up of hundreds of trillions of microorganisms that live in the niche of our digestive tract, airways, urogenital tract, and skin. In fact, the estimate is that there are 10 times as many microbial cells that live on the human body than there are human cells that make up the body itself (1). The difference is that human cells are immense when compared to most of the microbial cells that colonize us (2).
The vast majority of the microorganisms that populate us are single-celled organisms, such as bacteria or fungi (yeasts). Each of these cells is its own entity, in other words is an independent living organism, and they have their own genome (the complete genetic material of an organism) that encodes for their own proteins.
There is a good reference tool, though maybe a little advanced from The University of Utah, The Human Microbiome. This interactive presentation gives a layman's overview. The American Museum of Natural History has also curated an exhibit called The Secret World Inside You.
To add a point for clarification, while the genetic codes of these microbes are different in different species and are different from that of the human host, the molecules that hold the information, namely DNA, are all made of the same nucleic acid building blocks (5). To use an analogy, it is like using the same letters but writing in two different languages. We may use mostly the same characters, but the way we arrange those letters to form words in Spanish or words in English create different meaning.
When these single-celled organisms reproduce, they copy their own DNA and they divide into two new cells, each receiving one copy of that DNA (6).
Since yeast and other fungi are evolutionarily closer ancestors to humans than are bacteria, some of their genes, the sections of DNA that are functional and encode for proteins and RNAs, have a very similar sequence to our own (referred to as having homology) and often perform similar or the same function (7). When this is the case, we say that the genes are evolutionarily conserved, but for the most part evolutionarily conserved genes will vary in sequence from organism to organism, and the variation will usually increase the farther back you go in order to find a common ancestor between the organisms.
The human body is made up of about 37.2 trillion cells, on average (8). Almost all of these cells, with the exception of Red Blood Cells, have a copy of the hosts genome (9). All of these cells arose from a single egg produced by the mother and fertilized by the father's sperm (10). The egg and the sperm contained half the genome necessary for the embryo to develop. The DNA from the mother and the DNA from the father come together when the nuclei fuse. So we have our own genome that came from our mother and father, and the microbes have their own genome which they inherited from the ancestral cells that gave rise to them.
That is a slightly simplified answer as there can be different ways that the DNA can be passed between the organisms, but for the most part, we have our own DNA and, even though they live on us and in us, the microbes have their own DNA.
Your first paragraph.
I cannot tell you necessarily why seed that we swallow and digest do not germinate inside of us. It is likely that the seeds are not receiving the proper signals from the environment of our digestive track to initiate the genetic program to begin germination and development into a plant.
I also heard that the immune system uses the same technique to detect intruders (and subsequently attack donor-organs).
The vertebrate immune system is a diverse, highly-tuned system of surveillance that monitors for pathogens or foreign bodies that are introduced into the body that may be dangerous to the survival of the organism (11).
For humans, the first set of defense are barrier defenses (12). The surface of our skin consists of several layers of dead, keratinized cells that form an impermeable barrier. As long as this layer is not breached, it does an excellent job of keeping yeast and bacteria outside, away from tissue that they could damage.
On the interior surfaces, our airways, gastrointestinal tract, and genitourinary tracts contain specialized cells that produce large amounts of mucus that will coat the surfaces of these tissue. Mucus serves multiple roles. First it keeps the tissue moist, so that it does not dehydrate. Next it keeps the microbes at a distance from our cells, so that they do not come in direct contact with our epithelial cells (The cells that make up the linings of our digestive tract, genitourinary tract, and airways). Third, it can trap microbes in it. The epithelium is able to "sweep" the mucus along and as a result it is able to clear bacteria out of the body (13).
Included in the barrier defenses are actually the microbial organisms themselves. The interaction between the host and an organism which is neither detrimental or actively beneficial is known as commensalism (13). Basically, all of these trillions of microorganisms that life on us do not hurt us. In return, they get an environment in which they can live. As a result of this, commensal organisms will grow on these surfaces, will take up all of the space, and will use up the nutrients that could be used by pathogenic organisms (organisms that are actively able to cause an infection) to establish an infection.
The next level of defense comes from the cells of the innate immune system (14). In innate immunity, specialized cells monitor the area they are in for Pathogen-Associated Molecular Patterns (PAMPs). PAMPs can be sugars that make up the cell walls of the microbe or proteins that get expressed on the surface of the organism, such as Flagellin, a protein only found in the flagella of certain pathogen. The innate immune cells have pattern recognition receptors (PRR) that have a general specificity for recognizing and responding to the PAMPs. Our cells even have PRRs for DNA and Double Stranded RNA's, however those are usually found in vesicles on the inside of the cell. These interactions are very general, however once PRRs bind to the PAMP, they are able to signal into the cytoplasm, which can lead to the production of proteins, among other possible responses.
Here you can think of PRRs like a motion detector in a security system; the dog, or your two year old, or an intruder are going to set off the alarm just the same. It is not specific. The motion sensor "knows" that something that it is supposed to recognize, i.e. a moving object larger than a mouse passed by and it triggered the response, but it cannot tell you which moving object triggered it, only that it was triggered.
The innate immune cells are also able to respond by "eating" the pathogen in a process called phagocytosis. Here, they break up the bacteria, yeast, or the remnants of other dead host cells or large pathogens, things like worms, and put the broken up pieces on protein molecules on their surface.
When innate immune cells do this, they are presenting molecules to specialized immune cells (adaptive immune cells (14)), B-Cells and T-Cells, that are highly specific as to what they will react to. These cells can also cause a lot of damage to the host, so they are tightly regulated. Think of the interactions as keys and locks. A protein from a bacteria should turn a few of these cells on, but a protein from the host should not fit the lock.
All of these immune cells also respond to diffused chemical signals called cytokines. These molecules are secreted by some cells and are received by receptors on the host cells. Sometimes the secretion is by another immune cell, sometimes it is from a non-immune system host cell, and sometimes these molecules can be secreted by the bacteria, fungi, or worms themselves.
Depending on the chemical signals that are secreted, and how the cells are interacting at the time of the message, and which cells are receiving the message, will determine the response to the message. It is contextual. Think of the phrase "You're killing me." If someone says it, while laughing, to a good friend who is telling jokes, it means one thing. If it is screamed as someone is being choked by an attacker, it means something very different.
To summarize, the immune cells are surveilling the environment and trying to pick up what is friend and what is foe and they try to respond accordingly.
Over time and coevolution, our microbiomes have developed ways of communicating with our immune system to let it know that these microbes do not mean any harm. They are able to "train" the immune cells using chemical signaling to temper the immune systems response to them (15), and this is how they are able to coexist within our body and with an immune system that is constantly on seek an destroy missions. Also because of the mucus, our microbiome usually isn't in direct contact with our cells, so it is a different kind of interaction than if an infecting pathogen were to breech the barriers and gain access to sterile areas where no bacteria or fungi should be found, and as a result, the immune system reacts differently.
As for organ and tissue rejections (16), the issue here is that each of our cells, except for Red Blood Cells, present molecules on their surface that identify it as being a cell that was made by the body itself. You can almost think of it as a sport's teams jersey. The immune cells can survey the proteins displayed on the surface of our cells and tell that they are ours instead of from a pathogen. The problem is that each person makes a different array of these proteins, so if I were to give you a kidney, the proteins that the cells from my kidney make and put on their surface for immune cells to look at will be different from yours. In this case, because the keys do not fit the locks, the immune system reacts to the donated organ as an intruder and begins to attack it. Immune cells are extremely lethal and will kill the donated organ if they are not suppressed. That is why transplant recipients need to have their immune systems suppressed in order to survive with the donated organ. You might ask "well what if we just took all these proteins off of the surface so that they don't get recognized?" Well, the problem is that we have another class of immune cells known as Natural Killer Cells that patrol the body looking for cells that are not presenting these proteins, so the immune system is pretty adept and finding and killing things that it does not recognize specifically as self.
I was wondering, when a baby gets weaned (starts eating regular food), where do these fauna come from? Does the baby produce them, or are they provided in the food and survive the defense system?
To be honest, the majority of the microbiome is laid down during vaginal birth and breast feeding. Passing through the birth canal, microbes from the mother's vagina and feces are ingested by the newborn and this is their first real dose of microbiome, though some research is suggesting that the microbiome begins to form in the fetus before birth and is transferred through the placenta from the mother to the fetus.
Assuming we do not kill these bacteria with antibiotics, have other pathogenic bacteria take over the territory (yes, bacteria and fungi, like gangs, have turf wars; that is why we often find our antibiotics as compounds secreted by these organisms), or have a disease that wipes out the microbiome, and provide it with a health diet, then the microbiome pretty much is maintained by the microbial cells reproducing by cell division.
Also we will pick up these bacteria from the environment. We are constantly shedding enormous amounts of these cells into our environment. Babies touch things and put their hands in their mouths. This transfers good microbes as well as bad ones, and it is really just a natural part of the process. That is why the overuse of antibiotics and antibacterial soaps can cause unintended consequences. We are killing the good as well as the bad.
This reference, Your Changing Microbiome, again from The University of Utah is a good resource.
So to summarize, babies get the microbiome at birth through vaginal flora and maternal feces. They are also getting daily doses from the microbes that colonize the mother's skin when she nurses the child. Then these bacteria are also in the environment, so babies touch things, then they put their hands (or feet, the little contortionists) in their mouths and they get doses this way. Raw fruits and vegetables will also have microbes on them that will be taken in. As for the microbes, they have cell walls that allow them to live in environments that would be hostile if they did not have the cell walls. They also communicate with our immune system and "train" it not to kill them, and as long as nothing that we do, such as take antibiotics or get a disease, the microbiome will pretty much maintain itself through replication.