9 votes
Accepted

Limitations of 16S rRNA sequencing

There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis. The amount of sequence variation depends on the ...
acvill's user avatar
  • 8,296
8 votes
Accepted

Why does low redox potential mean less oxygen?

You‘re partially correct. Adding reducing agents will cause $O_2$ to be converted to $H_2O_2$, as thiol groups are turning from $SH$ to $S$-$S$ (forming dimers). In a second reaction, further thiols ...
markur's user avatar
  • 1,769
6 votes
Accepted

If we cloned an extinct animal, what would become of its gut biome?

The gut biome would be populated from whatever the environment was of the newly "cloned" animal. Presumably the baby animal would be born by birth from a live host mother, which would be the ...
Maximilian Press's user avatar
5 votes

why don't antibiotics reduce our weight?

First, you present as fact that antibiotics therapy (say AT) does not reduce weight. To show this fact, a study must weigh persons before AT and after. Confounders to this measurement are 1. weight ...
R Stephan's user avatar
  • 3,840
5 votes

Limitations of 16S rRNA sequencing

In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help ...
MikeyC's user avatar
  • 4,714
4 votes
Accepted

Doesn't pasteurization kill gut bacteria such as Akkermansia muciniphila?

This is interesting since Akkermansia muciniphila is a strict anaerobic and does not produces spores (which was my first thought on it). However, digging up the original publication (see reference 1) ...
Chris's user avatar
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4 votes
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Kitchen sponge microbiomes; management versus replacement versus "don't use sponges"?

If your question is, indeed, I'm asking about the nature of sponges, and if it's a good idea to use them to wash dishes and I'd like to stay focused on that. I can answer that. I like the sponge+...
anongoodnurse's user avatar
4 votes

What is the function of E. coli bacteria in the human gut?

Some relevant research has been published in the time since this question was asked and initially answered. The label "commensal E. coli" encompasses a diverse group of strains. Different ...
acvill's user avatar
  • 8,296
4 votes

Neisseria meningitidis transformation into a pathogen

It's not like a strain of E. coli that may cause disease in immunosuppressed individuals yet is a part of normal microbiota for other people. Well, actually, it is kind of like that. The answer is ...
anongoodnurse's user avatar
4 votes
Accepted

What are the considerations for studying population genetics of bacterial pan-genomes?

It is possible to perform gene-level population genetics analyses on microbiome-derived bacterial species.1,2 † However, the biology of bacteria and the nature of metagenomic sequencing data make such ...
acvill's user avatar
  • 8,296
3 votes

What are the considerations for studying population genetics of bacterial pan-genomes?

I will answer this as best as I am able, the updates are helpful for providing context. I'll also note that there are several questions packed in here, which makes it a bit more laborious to answer. I ...
Maximilian Press's user avatar
3 votes
Accepted

Why is it beneficial for bacteria to conjugate? (Horisontal gene transfer)

I am going to try answer it. Bacteria in general has different survival tactics. In general for bacteria the best way how to surviva is as much copies as it cans. So imagine situation, when bacteria ...
L.Diago's user avatar
  • 1,863
3 votes

Standard practice for generating rarefaction curves from Next Generation Sequencing data

I actually work in the same group as Chris (QIIME author), so I hope this helps: An explanation he gave to us a while back about the basis of rarefaction curves is just to give an indication of ...
Joe Healey's user avatar
  • 1,301
3 votes

16s rRNA Sequencing From Gut Microbiome (stool)

In general, you extract DNA, then PCR out the 16rRNA coding regions and finally sequence them. Here some links http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/ http://journals....
alec_djinn's user avatar
  • 3,108
3 votes

identifying OTU interactions / hubs

I am going to assume you have a count table that you are starting with. Every tool you decide to use is going to have its own respective instructions so let me get you pointed in a direction to find ...
jtclaypool's user avatar
3 votes

RNA sequencing and taxonomic analysis of gut microbiome

The article that you link to clarifies in the methods section that there are two different extraction protocols employed, one for 16S information (probably DNA extraction) and one for total RNA. In ...
Maximilian Press's user avatar
2 votes

Limitations of 16S rRNA sequencing

Other answers are excellent by and large. One point that is left out: 16S copy number itself varies among organisms, which leads to significant analytic complexity for trying to really estimate ...
Maximilian Press's user avatar
2 votes

Limitations of 16S rRNA sequencing

In addition to the points raised in the other answers, organisms like bacteria frequently engage in horizontal transfer of genetic material. This means that the relationships between organisms are ...
jakebeal's user avatar
  • 6,977
2 votes
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What is the metagenome like for other classes of animals?

There are multiple parts to an answer for this. 1) There is not only a microbiome in the gut. So microbiomes in general are very diverse. A fish microbiome on the scales will of course be very ...
skymningen's user avatar
  • 1,961
2 votes
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Resource for learning analysis of sequence data via QIIME 2

The QIIME 2 tutorials are the place to get started - see here.
gregcaporaso's user avatar
2 votes

Can you change your gut microbiota by changing your diet? Would that affect calorie uptake?

Firstly, it should be noted that a stable, healthy microbiome is generally thought to be a marker of health; actively disrupting it through diet in an attempt to fight with it over nutrients is ...
Maximilian Press's user avatar
2 votes

Can you increase the microbiota in an insect?

The answer is absolutely yes. There are 3 main ways: Faecal transplant: faecal sample from other insect could be transplanted in order to colonize the gastro-intestinal tract Injection of bacterial ...
Shred's user avatar
  • 406
2 votes

why don't antibiotics reduce our weight?

Antibiotics can cause weight loss, though, especially as they are used in the clinically, they are more likely to cause weight gain than weight loss. This Lancet Infectious Diseases review is not a ...
De Novo's user avatar
  • 8,791
1 vote
Accepted

16S sequencing: pooled or individual samples?

Ultimately, it depends on what insights you are trying to glean from your sequencing data, but from a purely scientific perspective, there's almost never a reason to pool samples in the the way you ...
MikeyC's user avatar
  • 4,714
1 vote
Accepted

Is Klebsiella pneumoniae found in the throat of healthy people?

Klebsiella species, including pneumoniae, are normal members of the healthy human oral microbiome. Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral ...
acvill's user avatar
  • 8,296
1 vote

Microbiome Context for Amino Acid Essentials and Non-Essentials

If your body was filled with highly specialized bacteria living in nutrient-rich conditions, what you suggest could happen*. But in practice, you're not filled with such bacteria, and most of the ...
Victor Chubukov's user avatar
1 vote

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

tl;dr it really might be due mostly to random chance, in terms of intentional mechanisms at least. One thing that is important to remember about the gut tube is that conditions of life for microflora ...
Maximilian Press's user avatar
1 vote

Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome. ...
fanli's user avatar
  • 131

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