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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How to Resuspend cells at cell density of 8 log CFU/ml of bacterial culture whose CFU/ml i don't know at 600nm, also it doesn't grow well on MRS agar?
According to procedure after 24 hr growth of Lactobacillus delbruckii subsp lactis in MRS broth, I have to resuspend it at 10 raise to power 8 CFU/ml and then inoculate it further. But it doesn't grow ...
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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 ...
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Doesn't pasteurization kill gut bacteria such as Akkermansia muciniphila?
I've recently watched two presentations on YouTube (this and this) about Akkermansia municiphila, a commensal bacteria that feeds on the mucus of the gut.
What I find confusing is their claim about ...
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If we cloned an extinct animal, what would become of its gut biome?
If we cloned an extinct animal like the mammoth, what would become of its gut biome?
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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 ...
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What are the considerations for studying population genetics of bacterial pan-genomes?
I am beginning to work in the field of human gut microbiome, and wondering how (and if) the concepts of population genetics could be applied there.
Considering the competition between the species ...
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What is the function of E. coli bacteria in the human gut?
What is the function of the bacterium, E. coli, in the human gut?
I have tried to find the answer by searching the Internet (e.g. here), but have been unsuccesful.
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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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RNA sequencing and taxonomic analysis of gut microbiome
I've been searching for methods of RNA sequencing, and I always find that the step of rRNA removal is emphasized. However, in my research, I need to analyze both functional and taxonomic data from the ...
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16S sequencing: pooled or individual samples?
I am planning to run 16S sequencing on a set of individuals to explore microbial diversity. The question I am facing is: should I sequence them individually or I pool them (for example 5 individuals = ...
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Extrapolating rarefaction curves
I am interested in methods for extrapolating rarefaction curves and/or estimating the true species richness. The ecosystem of interest is the gut microbiome and extrapolation is to higher sequencing.
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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 ...
CommunityBot
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Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?
I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed ...
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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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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 ...
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identifying OTU interactions / hubs
I would like to know how can i run a network analysis for identifying major OTUs hubs. I wish to build a network of co-occurring OTUs found in different soils samples.
I've started going through the ...
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Is Klebsiella pneumoniae found in the throat of healthy people? [closed]
Is Klebsiella pneumoniae found in the throat of healthy people?
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Does animal based food contain molecules that behave like dietary fiber for humans?
I have read that dietary fiber is beneficial to human health in many ways, for example that it can help to reduce risk of colorectal cancer. However, when I look at nutrition labels on food it seems ...
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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 ...
CommunityBot
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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 ...
CommunityBot
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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 ...
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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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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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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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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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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?
CommunityBot
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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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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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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 ...
CommunityBot
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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 ...
CommunityBot
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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 ...
CommunityBot
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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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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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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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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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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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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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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 ...
CommunityBot
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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 ...
CommunityBot
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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,...
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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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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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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 ...
CommunityBot
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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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