So, a lot of theories have been flying around about how the Sage could have 'spread' chakra to other people. Frankly, I think this is a waste of time. As it stands it's now a fact that the Sage is the ultimate ancestor of all shinobi.
First, as of Chapter 646, it has been established that there are only two known ways of attaining chakra; either an individual must eat the Fruit of the Shinju, or they must be a descendant of someone who has.
Second, in Chapter 642, Obito states explicitly that he had attained the 'Power of the Ancestor of All Shinobi'. The term 'Ancestor' implies a biological, familial relationship. If Kishimoto had meant otherwise, he could have used the term Progenitor or another word with similar meaning.
So, unless Kishimoto reveals information to the contrary, there is absolutely no reason to believe that the Sage is not the biological ancestor of all living chakra-users.
Now, to answer some possible objections.
1. "But everyone has chakra, it's not possible that everyone in the Narutoverse is a descendant of the Sage." This is wrong. This point has been raised numerous times in many threads, but no one has been able to provide a single reference to where the manga actually states this.
2. "But if everyone was a descendant of the Sage, they'd all be OP or running around with Sharingan, Mokuton, etc." Simply being a descendant of the Sage does not mean that they will inherit his traits. For example, none of Hashirama's direct descendants inherited his Mokuton, his massive level of chakra, or his control. Given that the Sage and his immediate family would have had to marry individuals who lacked chakra, it would have rapidly watered down his power.
3. "But it would undermine the importance of the Senju and the Uchiha." Not really. The Uchiha and the Senju/Uzumaki are the sole remaining clans who retained knowledge of their heritage and carried the respective ideologies of their ancestors.
Also, I'd like to point out another problem that these theories have. Simply 'infusing' chakra into someone's body would not give them the ability to generate their own or manipulate it. That's dependent on the existence of the Keirakukei or the Chakra Pathway System, of which the Tenketsu and the Eight Gates are apart. Without the Chakra Pathway System, even if someone had chakra within their body, it would eventually run out and they would still be unable to mold their own chakra or use jutsu.
First, as of Chapter 646, it has been established that there are only two known ways of attaining chakra; either an individual must eat the Fruit of the Shinju, or they must be a descendant of someone who has.
Second, in Chapter 642, Obito states explicitly that he had attained the 'Power of the Ancestor of All Shinobi'. The term 'Ancestor' implies a biological, familial relationship. If Kishimoto had meant otherwise, he could have used the term Progenitor or another word with similar meaning.
So, unless Kishimoto reveals information to the contrary, there is absolutely no reason to believe that the Sage is not the biological ancestor of all living chakra-users.
Now, to answer some possible objections.
1. "But everyone has chakra, it's not possible that everyone in the Narutoverse is a descendant of the Sage." This is wrong. This point has been raised numerous times in many threads, but no one has been able to provide a single reference to where the manga actually states this.
2. "But if everyone was a descendant of the Sage, they'd all be OP or running around with Sharingan, Mokuton, etc." Simply being a descendant of the Sage does not mean that they will inherit his traits. For example, none of Hashirama's direct descendants inherited his Mokuton, his massive level of chakra, or his control. Given that the Sage and his immediate family would have had to marry individuals who lacked chakra, it would have rapidly watered down his power.
3. "But it would undermine the importance of the Senju and the Uchiha." Not really. The Uchiha and the Senju/Uzumaki are the sole remaining clans who retained knowledge of their heritage and carried the respective ideologies of their ancestors.
Also, I'd like to point out another problem that these theories have. Simply 'infusing' chakra into someone's body would not give them the ability to generate their own or manipulate it. That's dependent on the existence of the Keirakukei or the Chakra Pathway System, of which the Tenketsu and the Eight Gates are apart. Without the Chakra Pathway System, even if someone had chakra within their body, it would eventually run out and they would still be unable to mold their own chakra or use jutsu.