Where does our Microbiome come from?

Another thread here reminded of the now common knowledge that something like 90% of the cells in our body are actually ‘foreign’ microbes, germs of one variety or other, that are not part of our body.

Way back my first reaction to the news was how would they fit, but upon reflection I realized they were so much smaller than cells that it’s not an issue.

Then I shut up and accepted the notion and tried learning what it was about.

It didn’t occur to me until this morning to ask, where did they come from originally.

Now, I’ve just spent a fwhile searching the web and skimming information and don’t seem to find the question of origins addressed anywhere. How much of that happens before birth? How many pathways into the body do germs have?

Maybe someone here knows a little about it - please share.

@ Citizenschallenge-v.3


Some use “microbiome” to mean all the microbes in a community. We and others use it to mean the full collection of genes of all the microbes in a community. The human microbiome (all of our microbes’ genes) can be considered a counterpart to the human genome (all of our genes). The genes in our microbiome outnumber the genes in our genome by about 100 to 1.



Oh, you have opened an area of human existence which I just discovered also. I ran across Bonnie Bassler by accident and discovered a whole new world existing underneath our own reality. Do watch the clip.

Without bacteria humans and most likely all other energy consuming organisms could not exist. This is the perfection of bio-chemical symbiosis where two species cooperate to mutual benefit.


It just gets more amazing the more one learns about bacterial communication or “quorum sensing” the earliest language used for information sharing in living things.


I agree that there are some quite interesting possibilities in exploring this subject. I hope to look into it, at some point, enough to have some meaningful input, and get back to this thread, subsequently. Hopefully I will get around to it.

Good videos, thanks W4U.

Here’s a fun read about how your microbiome changes over time - and how it accumulates.

Your Changing Microbiome Before birth, we're all more or less sterile—we have no microbes. Within a few years, we're covered in thousands of different species of microbes, and they colonize every millimeter of the body that's exposed to the outside world. By the time we enter kindergarten, we have vastly different populations living in the different habitats around our bodies. Even as adults and into old age, our microbiota continue to shift.


I had a moment of clarity about the pervasive and indispensable functions of microtubules in the formation of living organisms.

Example: the activation of human cell division which eventually builds an entire 3 dimensional pattern of a living person.

a) a human egg contains DNA, the latent genetic blueprint of a potential 3 dimensional pattern of an entire homo sapiens (sans bacteria).

Microtubules, Cell Division and the Mitotic Spindle
Cell division is not only important to reproduce life, but to make new cells out of old. Microtubules play an important role in cell division by contributing to the formation of the mitotic spindle, which plays a part in the migration of duplicated chromosomes during anaphase. As a “macromolecular machine,” the mitotic spindle separates replicated chromosomes to opposite sides when creating two daughter cells.

The polarity of microtubules, with the attached end being a minus and the floating end being a positive, makes it a critical and dynamic element for bipolar spindle grouping and purpose. The two poles of the spindle, made from microtubule structures, help to segregate and separate duplicated chromosomes reliably.

Two Major Groups of Microtubule Motors

The bead-like construction of microtubules serves as a conveyor belt, track or highway to transport vesicles, organelles and other elements within the cell to the places they need to go. Microtubule motors in eukaryotic cells include kinesins, which move to the plus end of the microtubule – the end that grows – and dyneins that move to the opposite or minus end where the microtubule attaches to the plasma membrane.

As “motor” proteins, kinesins move organelles, mitochondria and vesicles along the microtubule filaments through the power of hydrolysis of the energy currency of the cell, adenosine triphosphate or ATP. The other motor protein, dynein, walks these structures in the opposite direction along microtubule filaments toward the minus end of the cell by converting the chemical energy stored in ATP. Both kinesins and dyneins are the protein motors used during cell division.

Recent studies show that when dynein proteins walk to the end of the minus side of the microtubule, they congregate there instead of falling off. They hop across the span to connect to another microtubule to form what some scientists call “asters,” thought by scientists to be an important process in the formation of the mitotic spindle by morphing the multiple microtubules into a single configuration.


b) a human sperm contains Mitochondria, the processors of DNA instructions which activate the cell duplication process.

Sperm swim by means of a prominent flagellum, composed of a core of microtubules, whose sliding is powered by flagellar dynein. This array of microtubules and associated motor and linker proteins is known as an axoneme. The midpiece of the sperm contains a prominent array of mitochondria, which are required to produce huge amounts of ATP, whose hydrolysis powers the conformational changes in flagellar dynein that mediate microtubule sliding.


So what we have here is a single celled dormand egg and a single celled dynamic processor of chromosomal (DNA) instructions…

This simple interactive combination of a fundamental building block and a little machine that makes copies of the building blocks and placement in accordance to the inherent blueprint contained in the DNA.

These two single celled organelles produce an entire living organism and continue to build new and and refresh old cells in the organisms.

We speak of “hard problems” in the questions of life and consciousness, but rather than ask the hard problem , we can begin to address some “hard answers” which apparently are all that is neessary for organizing a living thing.

All that is required to build an entire fully formed organism is an egg and a sperm. That’s it folks, nothing else required except a little love.


Watching TNG last night made me think of the title of this thread.

Dr. Polaski was dying from a genetic disease where her DNA was slightly modified, causing her and the others on the outpost she was at to age super fast.

The only possible way to cure them all was to use the transporter to beam them onboard but use a copy of their healthy DNA to reconstitute them.

I wonder what would really happen if you did that. Would it be possible to reinoculate a person, or are there too many different microbes doing too many different things to get them all in place before you suffer in some way?


3p14rat said,

I wonder what would really happen if you did that. Would it be possible to reinoculate a person, or are there too many different microbes doing too many different things to get them all in place before you suffer in some way?

Have a look at CRISPR which allows us to cut and paste DNA .

CRISPR gene editing is a method by which the genomes of living organisms may be edited. It is based on a simplified version of the bacterial CRISPR/Cas (CRISPR-Cas9) antiviral defense system. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added.[1]

However, at the microbial level, we are working on “communicating” with bacteria via “quorum sensing” which is the language used by bacteria to communicate with each other. This remarkable ability of single celled organisms is chemically based where specific chemicals are “words” which trigger chemical responses such a “virulence”.

Bonnie Bassler has an excellent and entertaining video describing the research into “quorum sensing” and the possible therapeutic uses by facilitating or preventing intra-species communication.

She even describes how a ‘cuttlefish’ uses bio-luminescent bacteria as a “cloaking device”

The uses of bioluminescence by animals include counter-illumination camouflage, mimicry of other animals, for example to lure prey, and signalling to other individuals of the same species, such as to attract mates. In the laboratory, luciferase-based systems are used in genetic engineering and for biomedical research. Other researchers are investigating the possibility of using bioluminescent systems for street and decorative lighting, and a bioluminescent plant has been created.[1]

Here is a short but very informative presentation of the newest area of research into bacterial behaviors and possible control mechanisms.


CC-v.3 said,

Now, I’ve just spent a while searching the web and skimming information and don’t seem to find the question of origins addressed anywhere. How much of that happens before birth? How many pathways into the body do germs have?

Maybe someone here knows a little about it – please share.

Actually, some bacteria are so closely related to human functions that some of their RNA is contained in human DNA

Bonnie Bassler explains that bacteria are some of the oldest living things on earth. They are the RNA based Prokyarotes which came befor the Cambrian age which allowed for the evolutin of the DNA based Eukaryotic organisms.

IOW, there were the first organisms able to communicate via chemical information hundreds of millions of years ago and may well be the original proto-template for communication languages.

Bacteria and Humans Have Been Swapping DNA for Millennia

Bacteria inhabit most tissues in the human body, and genes from some of these microbes have made their way to the human genome. Could this genetic transfer contribute to diseases such as cancer?

But LGT (lateral gene transfer) is not limited to bacteria. Scientists now recognize that microbes transfer DNA to the plants, fungi, and animals they infect or reside in, and conversely, human long interspersed elements (LINEs) have been found in bacterial genomes. Moreover, researchers have documented LGT from fungi to insects and from algae to sea slugs. There is reason to believe that any two major groups of organisms—including humans—can share their genetic codes.


For interested persons,

This links to a a comprehensive set of articles about cellular behaviors.

John A. Raven

Plastids evolved after a cell entered a genetically different cell, followed by integration of the two genomes. Many photosynthetic cells can ingest organic particles as food, as now demonstrated in an ancestral green alga.

Some eukaryotic photosynthetic organisms are capable of ingesting organic particles into their cells — when the particles are digested, this combination is termed mixotrophy. Photosynthetic eukaryotes originated by ingestion of pre-existing photosynthetic cells by (typically) non-photosynthetic cells, followed by genetic integration

Figure 1. Cymbomonas. Light micrograph of Cymbomonas. The feeding duct opens to the exterior at the anterior end of the cell, i.e. the end at which the four flagella are inserted. The cells do not always swim with the anterior end forward. Scale bar represents 5 μm. Photo courtesy of Eunsoo Kim.


What intrigues me most is what biological “processor” inside the cells is able to translate any foreign genetic information and process it as if it were part the original.

The single suitor that presents itself as functional is the microtubule, that remarkably versatile biological processor which is a “common denominator” to all eukaryotic organisms and is responsible for cell division.


And this link may be of interest for visual representations of several micro organizations and functions.

The microtubule. A remarkably versatile self-assembling micro-processor and functional motor.


How deep in the earth’s biome would you expect life to exist? How about 2 miles deep into the earth’s crust?

check this out.


The more I discover about microtubules, the more intrigued I become. For an evolved fundamental dynamic machine capable of affecting cell duplication and information processing the microtubule must rank as supremely important in the networking of fundamental functional neural networks.

Optical trap provides new insights into motor molecules – nature’s ultimate nanomachines


When it comes to nanotechnology, many researchers turn to nature for inspiration. Of particular interest to nanoengineers is the naturally occurring protein kinesin -- one of several "motor molecules" that facilitate movement in living cells.

A mere ten-millionth of an inch long, kinesin is the workhorse of the cell, hauling chromosomes, neurotransmitters and other vital cargo along tiny tracks called “microtubules.” While one end of a kinesin molecule holds onto its cargo, the other end uses a strange two-headed structure to grab the microtubule and pull the cargo forward.

A two-headed kinesin molecule (green) hauls a glass bead (blue) along a microtubule (red). Using an optical trap (pink) to apply force, Steven Block and colleagues were able to control the movement of individual kinesin molecules. The wireframe schematic on the right depicts the energy barriers that kinesin has to overcome to complete a single step. Courtesy of : Joshua W. Shaevitz/Stanford University

“This is one of the most efficient engines anyone has ever seen,” Shaevitz noted. “Some estimates put it at near 100 percent efficiency. It’s an amazing little thing.”

Asbury agreed: “Kinesin is an example of where Mother Nature kicks our butt. For me, I’m motivated just by understanding how this fascinating thing works.”


Mind boggling, fantastic.

Keep them coming Write4U :slight_smile:

CC-v.3 said,

Keep them coming Write4U

As you desire,

Emergence of the Macroscopic Quantum Superposition State in Microtubules*

ABSTRACT Many researchers conceive communication in Microtubules (MTs), and established theoretical models to show both classical and quantum information processing. In this paper, we studied the usually neglected interactions between the electronic dipole of water molecules in microtubules and the quantized electromagnetic radiation field. We find that the emergence collective coherent radiation, and it can turn into macroscopic quantum superposition state when passing through MTs. This could have a fundamental role in the quantum information processing.

I was just advised that the above link is to a unreliable site, which will post any proposition as long as you pay for it.

That does not necessarily mean that all offerings are bunko, some are copied from reliable sites. It’s just difficult to determine unless you actually start tracing the original source.

Scientific Research Publishing (SCIRP) is an academic publisher of presumably peer-reviewed open-access electronic journals, conference proceedings, and scientific anthologies of questionable quality.[1][2][3] Although it has an address in southern California, in reality it is a "Chinese operation".[4]

The company has been accused of being a predatory open access publisher[6] and of using email spam to solicit papers for submission.[4] In 2014 there was a mass resignation of the editorial board of one of the company’s journals, Advances in Anthropology, with the outgoing Editor-in-Chief saying of the publisher “For them it was only about making money. We were simply their ‘front’.”[7]