It would be great if we could “program” antibiotics to only go after bacteria that we want to kill. Unfortunately, we can’t.

We can screen antibiotics to see if they’ll kill the type of bacteria we want to kill, but we usually just have to put up with them killing “friendly” bacteria and hope that we can repopulate our systems with good bacteria from the environment. Our friendly bacteria can actually help to fight off the invaders, so killing them can cause digestive problems, yeast infections (particularly in women), and other problems.. It’s like using a powerful bug spray in a house that has some bugs that are pests. You also kill the little predators (like spiders) that help to kill the pests.

In a way, a bacteria community recovering after antibiotics is like a plant community re-establishing itself after all of the vegetation has been bulldozed away. Ecologists call this process “succession.” The community may go through a few stages before getting back to what it was like before the disturbance. It may not even come back exactly like it was before the disturbance.

There are more bacterial cells in our bodies than our own cells. This is possible because bacterial cells are so much smaller. The study of all the ecological relationships on the microscopic level is getting a lot more attention. Various medical issues may be due to changes in our micro-communities in our gut, skin, and elsewhere.

We caused the evolution of antibiotic-resistant bacteria without meaning to. It used to be common to prescribe antibiotics for almost any infection, even viral infections (which can’t be cured with antibiotics). The result was that antibiotics killed off the bacteria that were vulnerable to the particular antibiotic and only left behind individual bacteria that were resistant to the antibiotic. These bacteria reproduced. When the new generations were exposed to the antibiotic, only the most resistant of these survived. This is an example of how selection can lead to evolution. Now some bacteria that we want to kill are resistant to all antibiotics, or we can only kill them with antibiotics that are very harsh for the patient.

Medical professionals are starting to use antibiotics only when they are needed. How would this help us in the battle against” bad” microbes?

You may want to study microbial ecology. It’s a field that will probably get more and more attention.

This is a great question! Some antibiotics target very specific processes that are involved in various aspects of the bacterium's ability to cause disease. These include the ability of the bacterium to be able to cause disease - one of the key steps is being able to bind to a human cell - for example, bacteria that cause urinary tract infections need to be able to bind to specific regions on human cells, an antibiotic can be targeted to specifically prevent this interaction from occurring. It may also affect processes going on inside of the bacterium; for example, the ability to produce key nutrients, molecules such as fatty acids, nucleic acids, proteins.

Targeted antibiotics are super important in medicine. They allow us to specifically target the bacteria that we are interested in getting rid of. It helps to slow the rise of bacteria that are resistant to antibiotics as well. Additionally, it can help prevent wiping out the good bacteria in your body. Unfortunately, it can be hard to know when to use a very targeted antibiotic - a lot of testing needs to be done to figure out what exactly the bacteria is and a lot of times that cannot be done in a timely manner. Also sometimes it's hard to have an exact target on just the bad guys. Often the bad bacteria will use processes and proteins that are used by (or very similar to) the good bacteria as well.

Antibiotics are an important arsenal in our tool box. They should not be abused! If you ever have to take antibiotics make sure to take them as directed and always supplement with some good probiotics!!!

Well, they kinda don't. Antibiotics are poisons. Some life-forms are more vulnerable to certain poisons than others. Different antibiotics are poisonous to different bacteria. We choose some antibiotics over others because they are deadly to bacteria that we don't like, but are less harmful to us. Which antibiotic you need depends on what bacterium is making you sick.

Giving somebody the wrong antibiotic may kill off the good bacteria but not the bad ones, and make the patient even sicker.

They don't!

Actually, bacteria change in response to antibiotics so the antibiotics won't kill the bacteria - that's 'antibiotic resistance.' The antibiotics kill good and bad bacteria, but they don't kill the antibiotic resistant bacteria, even if they're bad bacteria. Sometimes people eat yogurt after taking antibiotics, to get some good bacteria back into their bodies.

Here's an article about antibiotic resistance: Antibiotic resistance: delaying the inevitable - Understanding Evolution
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Scientific American magazine has an article about how antibiotics kill bacterial cells and not human cells, but that wasn't your question: How do antibiotics kill bacterial cells but not human cells? You can read it in Scientific American:
how-do-antibiotics-kill

A big issue with antibiotics is that they aren’t that selective! Often useful bacteria are targeted by antibiotics also. Antibiotics generally target a family of bacteria, not a specific species of bacteria. This is why some people get nauseous when taking antibiotics.

That being said, you do take specific antibiotics for specific bacteria. This is because the antibiotic’s target is more important or at a greater concentration in the target bacteria. In general, antibiotics stop a cell from growing or kill the cell by targeting crucial cellular machinery, such as enzymes used in cell wall synthesis.

Since bacteria play a fairly important role in our bodies, you should only use them when you really need to.

Antibiotics are interesting and very diverse in terms of how they kill bacteria, but the underlying principle is the same - they stop a vital process from happening such that bacteria cannot go through normal life cycles.

For instance, when we drink water, our bodies use the tiny water particles to fuel biochemical processes in order for use to live. Bacteria need water, too, and all kind of other nutrients, just like we do, so imagine that an antibiotic is now stopping the bacteria from taking up water! That would certain slow, stop or altogether kill the bacteria. In reality, antibiotics generally work by "sticking" to and blocking bacterial proteins that help replicate DNA, help make bacterial cell walls (important for structure and protection of bacteria), help construct cell envelopes, or help make other proteins that bacteria need. We call this process of "sticking" the binding of a small molecule (the antibiotic) to a protein, which is just the antibiotic fitting into a particular place on the protein and interacting with that protein. The reason that many antibiotics are so good at blocking bacterial proteins is that these antibiotics look and act very similarly to whatever particles the proteins already bind to and use in the bacterial cell, but are different enough that the bacteria cannot use these antibiotics as resources like they can use their preferred particles.

For a more relatable example, think about this:
We know that square pegs will fit into square holes of the same size, but round pegs won't. If we imagine that the things binding to bacterial proteins naturally (ones that bacteria actually need to survive) are square pegs, fitting into the square holes of the proteins, then we can think of antibiotics are squares that are slightly larger or smaller than hole, or maybe even roughly the same size but a little more rectangular. They would still kind of fit, enough to stop the natural stuff from binding. So how can antibiotics distinguish between our proteins and bacteria proteins? By having chemical properties that are inherent in their structures, such that they will preferentially penetrate bacterial cells bind to those proteins, rather than penetrate our cells and bind to our proteins. Antibiotics are designed to have very particular structures such that they only bind to specific proteins from specific bacteria , and that's why we are told to take certain antibiotics for certain infections and different antibiotics for other infections. This is akin to round pegs in round holes for antibiotics against some bacteria, and square pegs in square holes for other antibiotics against other bacteria.