Questions tagged [microbiome]

Tag for questions related to the collection of all the microorganisms living in association with the body of a multicellular organism, such as the human microbiome, or the full collection of genes of all the microbes in a community, such as all of the organisms that form the human microbiome.

The Human Microbiome

The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses. Bacteria in an average human body number ten times more than human cells, for a total of about 1000 more genes than are present in the human genome. Because of their small size, however, microorganisms make up only about 1 to 3 percent of our body mass (that's 2 to 6 pounds of bacteria in a 200-pound adult). These microbes are generally not harmful to us, in fact they are essential for maintaining health. For example, they produce some vitamins that we do not have the genes to make, break down our food to extract nutrients we need to survive, teach our immune systems how to recognize dangerous invaders and even produce helpful anti-inflammatory compounds that fight off other disease-causing microbes. An ever-growing number of studies have demonstrated that changes in the composition of our microbiomes correlate with numerous disease states, raising the possibility that manipulation of these communities could be used to treat disease.

-- from the Human Microbiome Project

Microbiota

A collection or community of microbes.

-- from the University of Utah

Microbiome

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.

-- from the University of Utah

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How does the microbial environment in your gut initiate?

Clearly, a zygote does not harbor any microbes. As it develops, and the alimentary canal tissue is differentiated, I logically assume that there is still no microbial activity in the fetus's gut. I'm thus also assuming that the commencement of…
LanceLafontaine
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Relationship between our microbiome and personalized nutrition

Recently, it has been asked whether there are 'metabolic types' between humans that can benefit from a sort of personalized nutrition. One answer suggested that one discerning factor could be the human microbiome. It is known that host–microbial…
Gianpaolo R
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How heavy are all foreign microorganisms in and on the human body?

I define "foreign microorganism" as a microorganism which is not produced by the human body (not antibodies or leukocytes) including bacteria, viruses, fungi, biofilm aggregates or small lifeforms independent if they are benign or hostile. Let's say…
user10094
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Standard practice for generating rarefaction curves from Next Generation Sequencing data

We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database. To generate a rarefaction curve, my understanding is that one…
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What is the effect of garlic on intestinal flora?

Now that we can compare whole microbiomes, has there been investigations on the effect of garlic (or diallyl disulfide, its main ingredient) on intestinal flora? From the proven antimicrobial activity, it should work like antibiotics. But does it…
R Stephan
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Where do the bacteria within the vagina originate from?

I understand that it's feasible the bacteria within the gastrointestinal tract originate from the food we eat and air we breath, but where does this population of microbes originate from?
user560
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Can an argument be made that humans are 90% bacterial?

On the blog, All about Scientist in Microword: Microbiology, I read the post We are 90% bacteria, actually, which says that humans are 90% bacterial cells. If this is the case, then why don't we behave like them and why isn't the bacteria genetic…
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Limitations of 16S rRNA sequencing

Looking at the microbiome analysis literature there seems to have been a shift away from 16S rRNA sequencing analysis toward shotgun sequencing of the whole genome. While the motivation given is typically that there is more information obtained by…
gcorso
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Is honey in hot green tea unsafe?

I used Google to try to figure out what kind of mixture honey has with hot water, and I found several Ayurvedic sources claiming that honey in hot water is toxic. For example: Honey – NEVER Put It in Hot Water/Teas 5 Reasons You Should NEVER Cook…
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why don't antibiotics reduce our weight?

I know that a significant weight of the human body (in Kgs) is contributed by microbiota. I also know that antibiotics can often be broad spectrum and kill all the bacterias regardless of them being good or bad for us. So why doesn't antibiotic…
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Do intestinal flora have the same DNA as their host?

Please bear with me, this is not my professional field and I might be mixing things up. In an explanation why seeds won't start growing in one's intestines, the explanation given was that foreign bodies are detected by the DNA they carry and get…
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Can you change your gut microbiota by changing your diet? Would that affect calorie uptake?

I have seen peer-reviewed papers mentioning the daily changes in gut microbiota composition according to dietary changes. See for example this paper: http://genomebiology.com/2014/15/7/R89 My question is related to this one: Relationship between our…
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Why does low redox potential mean less oxygen?

I often see statements about adding reducing agents like cysteine to anaerobic medium to decrease the amount of the dissolved oxygen. However, I am not sure why. I am wondering if it is because under the low redox potential conditions, dissolved…
Beginner
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Neisseria meningitidis transformation into a pathogen

I read the wikipedia article about Neisseria meningitidis, and it says that N. meningitidis is a part of the normal nonpathogenic flora in the nasopharynx of up to 5–15% of adults In some cases however, it infects the bloodstream, creating a…
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Why is it beneficial for bacteria to conjugate? (Horisontal gene transfer)

Why is it beneficial for bacteria to conjugate? I would think it's more beneficial to take a plasmid from another cell, than to give yours away or "share". Not homework, I'm just curious.
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