Beginner question: Should I Mute the Low E?

I'm new to the guitar and have been going through Guitar Fundamentals for the last two weeks with Anders. Today I started going through Lisa's Fundamentals as well, but am not as far through. With that said, it's possible my question is covered in later courses. But thus far, all of the instructions about playing chords that don't include all of the notes teach me to just avoid strumming those notes. The most common examples are the C and D chord. 

Recently I was talking to my nephew who has been playing for a long time, and he told me that when I play those chords, I should be muting the Low E with my thumb. He said to make sure I practice that now in order to develop the habit. When I asked about just skipping those notes when strumming, he said no experienced guitar players do that -- they all Mute with their thumb. It's also worth mentioning that at that point I was actually positioning my middle finger slightly higher on the A string so that it was muting the Low E. He said I definitely should not do that because I should focus on good finger position and not develop bad habits.

So here's my question. What should I be doing??? It seems like it would be really difficult to avoid strumming the Low E and/or A while also keeping a good rhythm, but I also understand that right now a lot of things seem hard. Is that actually a skill I should work on perfecting, or should I be making it "easier" on myself and muting with my thumb?

Your nephew is right. Muting with your thumb will come in time. Right now everything is hard because it’s all new. 

I’m not sure if you will see this in the Fundamentals, but there are song lessons where you will be instructed to mute a string by nudging a finger up against it. 

Take your time with these skills and practice them often, they will come together. 

Best of luck. 

Muting is an essential skill.  But the Fundamentals course is designed to teach (isolate, present & demonstrate) every skill & idea in order.  So, first you learn how to fret properly, then pick or strum properly, then you learn how to mute.   So, it's a slightly more advanced skill in the curriculum.

Some students progress more quickly, some more slowly.  So, in building the courses we try to take all of those different skill levels into account.  Some players are ready to start muting earlier than others.  Some need more time focusing on fretting & picking before they can work on muting.  Learning the guitar is a constant process of refinement, gradually adding skills, layers of complexity.

So in general your nephew is right about learning to mute as soon as you are able to add it in.  But he's also slightly wrong about this:

"When I asked about just skipping those notes when strumming, he said no experienced guitar players do that -- they all Mute with their thumb"

I do both.  I work on picking & strumming very precisely so I don't hit any strings I want to avoid.  And frequently I will add muting in as an added precaution!  But there are some situations in which you simply can't mute with your thumb.  Or you don't want your thumb in the way.  It all depends on the specific musical context.  Sometimes, as you mention, you want to mute with other fingers.

Directly answering your question: yes, if you are able to do so, start adding muting in now.  But know that you should also work on making your picking & strumming as precise as possible.  It's all part of the process!  

If it helps I have a tutorial that covers a deeper dive into muting at various skill levels.  This isn't required material for the Fundamentals.  But when the question of muting comes up we have this tutorial to help explain the topic.

https://www.guitartricks.com/tutorial/2281/

Hope that helps.  Please ask more if necessary.  Keep practicing & best of success!

I have learned as I progress on my guitar journey that there are no hard rights and wrongs. It is what works for you. “Guitar people” especially social media types like to say if you play this song like this, you are doing it wrong, “only do it like this”. I like to reference a couple of pretty accomplished guitarist. Zack Wylde said that every one of the guitarist for Ozzy played the songs differently, from how they fingered the notes and chords to what position of the fretboard they played them in and none of them were wrong because they all played the songs and people knew what they were playing. Alex Lifeson said in an interview that he watches different ways that people play his songs on YouTube and some are actually better than how he plays them. As for muting the low E string, I have found that different situations call for different muting styles. I find that most of the time I will mute an open C chord with the tip of my ring finger and for an open D, I use my thumb. I was doing one of Anders courses years ago and found that it was easier for me to finger a piece differently than he did. I went to the forum and asked him about both ways and if I needed to do it his way for something in the future that I didn’t know that I didn’t know yet. He basically said try both and do what works for you.

Muting the low E string while playing open or barre chords will help maintain the sound crisper and less muddy. The low E string is frequently unnecessary in D or C chords, and ringing it accidently might soccer random distort the sound. In fingerstyle, you may want to mute the bottom E string to eliminate unwanted noise while focusing on the melody on the higher strings.