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.

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Can you increase the microbiota in an insect?

I know you can suppress the microbiota of an insect with antibiotics, but I´m am looking for a way to increase it. For example, can I feed an insect with something that helps boost the bacteria like ...
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2answers
114 views

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 ...
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1answer
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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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totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime

I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME. Here is the situation. ...
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1answer
52 views

Microbiome Context for Amino Acid Essentials and Non-Essentials

Given what we are now learning about the diverse mix and variance of microbiomes (aka bacterias via human gut project), is it possible that synthesis of aminos can be done by specific bacteria and ...
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428 views

Resource for learning analysis of sequence data via QIIME 2

I am trying to study/learn metagenomics through 16s rRNA microbial data and I want to teach myself/review core biology concepts while also learning the QIIME 2 analysis pipeline, as the website ...
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3answers
391 views

Kitchen sponge microbiomes; management versus replacement versus “don't use sponges”? [closed]

I have unfortunately just skimmed through the recent open access paper Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and ...
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1answer
157 views

16s rRNA Sequencing From Gut Microbiome (stool)

Do I extract RNA or DNA from gut microbiome (stool samples) if want to do 16s rRNA sequencing?
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0answers
61 views

How to evaluate broad-sense heritability of microbiome associated plant genotypes in R

I have a data containing 196 accessions of A. thaliana from which I studied leaf bacterial and fungal community and, therefore, sequenced and found several OTUs. Now, I want to evaluate broad-sense ...
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0answers
59 views

Oxygen Uptake Rates in Microbial Cultures

Normally if air is sparged into a fermenter, the oxygen uptake rate is roughly equivalent to the oxygen transfer rate: KLa(C* - CL) = Xμ/YX/O2. How would this equation change if the oxygen ...
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1answer
81 views

What is the metagenome like for other classes of animals?

Lately there's been a lot of discussion around the many non-human cells essential to a healthy human body — called the microbiome, or metagenome. Much of this is in the gut microbiome. See this ...
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Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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Could a prolonged amount of Antibiotics severely affect the digestion Gut Microbiota?

Could taking antibiotics for a prolonged amount of time severely harm or even worse kill off a large proportion of Gut Microbiota responsible entirely for digestion, Resulting in lifelong digestion ...
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1answer
699 views

The effects of auto-brewery syndrome

Why are some people affected so differently by auto-brewery syndrome differently if the syndrome seems to be caused by the single organism saccharomyces cerevisiae? It is known that the syndrome has ...
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1answer
726 views

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 ...
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1answer
6k views

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 ...
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0answers
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Is it worth to experiment with pro-biotics at home?

Let's assume that Joe has done some investigation on Internet and wants to see, if pro-biotics would help him. Now he goes to amazon.com and buys a pro-biotic product with excellent average rating. ...
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2answers
384 views

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 ...
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2answers
663 views

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 ...
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1answer
1k views

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 ...
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1answer
79 views

How many diseases can be linked to disruption in the microbiome of a human?

I was listing to the radio and heard recent research found a link between children and higher cases of asthma when certain bacteria are missing from the microbiome. How many other diseases can be ...
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3answers
24k views

What is the function of E-coli bacteria in our gut?

So, I recently came up with this question. I googled it, but couldn't understand the proper functions of E-coli bacteria. A little definition would be wonderful.
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0answers
52 views

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 ...
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0answers
60 views

How is the appropriately-stratified gut microbiome acquired in organisms performing horizontal transmission?

I am studying horizontal transmission of primary symbionts in insect reproduction. This reminded me of an earlier question I had asked, in which I learned that humans analogously acquired their ...
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1answer
3k views

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,...
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2answers
101 views

Microbiome Data

How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
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2answers
4k views

What is an organism?

The definition of an organism Wikipedia gives is An organism is any contiguous living system. I understand that these are not organisms according to this definition: A bird and a tree it's ...
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1answer
365 views

Are the intestinal microbiota substantially different within a diverticulum of the colon?

From the Wikipedia page for the vermiform appendix: This proposal is based on a new understanding of how the immune system supports the growth of beneficial intestinal bacteria, in combination with ...
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2answers
306 views

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 ...
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2answers
494 views

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?
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457 views

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 ...