I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type of human has the same DNA, since every human has a different DNA. What am I missing here?
All humans have some differences in their DNA, but there's far more that is shared. On average the difference between humans is only about one thousandth of their full DNA, which means we're about 99.9% the same. These differences aren't distributed fully randomly, but are often because of specific gene alternatives. (Random mutations do occur, but they are also often fatal, so the random mutations we see of living adults are much more restrictive than all the random mutations that occur.)
To identify the human genome is to study many people's DNA and to label the parts that are shared between everyone, the parts with two or three variations, and the parts with even more variations. Even though every person has different DNA, we can still say they fit the pattern, just like every T-shirt may be unique but they all fit the T-shirt pattern and not the trousers pattern.
DNA is only the substance that makes up the genome.
DNA can come with many forms. For example, the fragments you get by PCR in the lab are DNA. A bacterium also has DNA molecules in it. You may also find DNA fragments in many other places, like in our blood, or at a crime scene.
Genome, however, is a very specific term. It means all the heritable substances in an individual or an organism. Most times, when we talk about the genome in eukaryotes, we refer to the nucleus genome, that is, the DNA in the nucleus.
Note that genomes do not have to be made of DNA. RNA viruses, for example, only have RNA as their genomes. Yet we still refer to that as a genome, because that is the heritable substances for those viruses.
DNA is the product you get if you paste the nucleotides A, T, C and G together. This is DNA and all genomes consist of these basic building blocks like a book consists of letters. Still, the genome, or the content of the book is the specific combination of these letters plus the proteins that bind to the chromosomes, the folding of the DNA and all the epigenetic modifications that can happen. So yes, we all have the same DNA in terms of the same building blocks, but the content is different.
Might have misunderstood you - but "we" have sampled and "decoded" the DNA of a few humans (often volunteers who surrendered their body to science after their death) - but this gives of course only the genetic code of those few individuals.
When scientists say we decoded the genome they mean they deciphered which parts of the DNA "do" specific things - the actual "genes" or gene-sequences - usually done when looking at the DNA molecule packed up into the chromosomes to give easier "orientation".
And by my understanding the first task was accomplished - supported by use of supercomputers, but the deciphering of the gene-sequences still has a long way to go for scientists to state "complete." But there is growing success - And as usual scientists will not stop until complete.
"To have the genome done" means that we have sequenced all the DNA in particular reference individuals. You are correct that every human has different DNA, so there is no such thing as a single "human genome", as (almost) everyone's is unique. But the vast majority of everyone's DNA is identical - that's what makes us human. Having the full sequence of a few "normal" individuals who don't have glaring genetic defects is extremely useful for learning about the genome of all individuals, since so much of it is the same from person to person.
I've used the term "reference" a few times, since we use a few individuals' genomes as an expectation of what a human genome looks like. The process of sequencing DNA involves breaking it into many bits, and then recombining them using a computer. You can put the pieces together without the reference, but it is much more difficult and time consuming. Even if there are differences from the reference, having an expectation of what >99% of the genome should be makes the problem much simpler. In a way, it's like the difference between doing a jigsaw puzzle without knowing what it's supposed to look like, and using the picture on the box as a reference. Even if your exact jigsaw puzzle has a few different pieces, the box reference is mostly the same and immensely useful.
Think of it as a special book. Everyone's book is different, but they all have the same number of chapters and each chapter covers the same topic in each individual book (sorta). The problem is we can only read a few words at a time.
When the genome is "done", it means that someone has read a bunch of these sentence fragments from one person's book and then assembled all the words in the correct order to make a complete book. Then we can get a good idea of how many chapters it has and what those chapters are about.
However, the human genome wouldn't be a novel, it would be more like a set of encyclopedias.
When people say "the genome" for a species, they mean a reference genome. To quote wikipedia,
A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species' set of genes. As they are often assembled from the sequencing of DNA from a number of donors, reference genomes do not accurately represent the set of genes of any single person.
The genome is updated over time as more is learned, the most recent human reference is hg38.
For individualized results, the patient is sequenced and the data is compared to the reference genome. Then, the differences are presented as a list of genetic variants. This is more efficient than looking at the entire genome for each patient, because on average greater than 99.9% of sites match the reference.
Yes you are right. 99.9% of our genome remains same, it is only the 0.1% which makes each individual unique from the rest of us. Single nucleotide polymorphisms (SNPs) contributes to the 0.1% variation in our genome. SNPs explain the variation in eye color, susceptibility towards disease conditions etc