9

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 region of the 16S rRNA gene amplified, and the choice of region depends on the desired universality of your primers as well as the read length constraints of ...


4

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 elucidate causal mechanisms. 16s is mostly limited to providing information about the taxonomy of a community. While there are ways of "predicting" the ...


3

The reason they look like that is because they have very small genomes so they have to build themselves out of multiple copies of a few building blocks. This leads to a high degree of symmetry in the component pieces; in particular icosahedral symmetry in the genome storage capsid (made of 235 copies in the smallest phage, 3115 copies in G-phage, as ...


3

Many things on nanoscale look like small crystals or several small crystals put together - i.e., they adopt a limited number of symmetric shapes allowed for packing identical objects in three dimensions (see, e.g., the shapes given here). Viral capsids, composed of many identical proteins (capsomers) is an example of such crystal structures.


2

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 more complex than the relationships between the stable core elements like ribosomal RNA (see, for example the mosaic genome of Rickettsia felis). Focusing on only ...


1

If the cells are growing at all, then they are actively expressing a whole bunch of different proteins. Ribosomal RNA, however, makes up the vast majority of all RNA in a typical cell, however. There are also far fewer different rRNAs than there are mRNAs, so the relative concentration per rRNA is even greater. As such, unless rRNA is excluded (e.g., using ...


1

From my experience, bacterial RNA-seq libraries derived from exponentially growing cells that have not been prepared using an rRNA depletion kit will result in >80% of reads mapping to 16S and 23S rRNA genes. Ask your colleague if they used a bacterial rRNA depletion kit prior to RNA library preparation. It is also my understanding that rRNA tends to be ...


1

Skirting the Question's fringe, and too long for a comment: On symbiosis with viruses, from some science magazine: Most viruses are harmful, but some viruses have a mutually beneficial relationship with their hosts. A lot of viruses help their hosts by attacking their competition. For example, the hepatitis G virus slows down the growth of HIV, the virus ...


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