In reference to the patent: WO2013050792A1
How can bacteria be patented? It is not an "invention" whatsoever.
No, bacteria as such can't be patented.
It is true that this application (you mention the appl. no.) is now patented e. g. in Europe and the patent specification will be published there under the publication no.: EP2763685 B1
The last action was:20.01.2016 ANNOUNCEMENT OF INTENTION TO GRANT
You find the text proposed for grant here: https://register.epo.org/application?number=EP12775538&lng=en&tab=doclist
The patent will however cover only products with the bacteria and methods using it or for producing the products. The bacteria as such are not claimed.
Pure discoveries are not seen as inventions and are therefore not patentable subject-matter, bacteria will be seen as a discovery. E. g. in Europe regulated by Article 52 (2)(a):
"(2) The following in particular shall not be regarded as inventions within the meaning of paragraph 1:
(a) discoveries, scientific theories and mathematical methods"
However this is valid only for the mentioned things, like discoveries, as such. See therefore Article 52 (3):
"(3) Paragraph 2 shall exclude the patentability of the subject-matter or activities referred to therein only to the extent to which a European patent application or European patent relates to such subject-matter or activities as such"
For more details for other countries or regions and their patent law see here:
Another related question can be found here:
Yes, at least in the U.S., a bacterium can be, and has been, patented. In 1980 the SCOTUS, in Diamond v. Chakrabarty, famously ruled that the fact that it was a living thing did not make it unpatentable. It was an oil eating organism not found in nature.