I've walked into an interesting essay on yeast (not that there's ever a dull moment with yeast) by T.H.Huxley which is dated 1871. I think he raises a good many points. Below, I've gathered some of the text which I think is worth bearing in mind. The site can be found here, thanks to:
"A short time after Cagniard de la Tour discovered the yeast plant, Liebig, struck with the similarity between this and other such processes and the fermentation of sugar, put forward the hypothesis that yeast contains a substance which acts upon sugar, as synaptase acts upon amygdalin. And as the synaptase is certainly neither organized nor alive, but a mere chemical substance, Liebig treated Cagniard de la Tour's discovery with no small contempt, and, from that time to the present, has steadily repudiated the notion that the decomposition of the sugar is, in any sense, the result of the vital activity of the Tortula. But, though the notion that the Tortula is a creature which eats sugar and excretes carbonic acid and alcohol, which is not unjustly ridiculed in the most surprising paper that ever made its appearance in a grave scientific journal, may be untenable, the fact that the Torulæ are alive, and that yeast does not excite fermentation unless it contains living Torulæ, stands fast. Moreover, of late years, the essential participation of living organisms in fermentation other than the alcoholic, has been clearly made out by Pasteur and other chemists.
However, it may be asked, is there any necessary opposition between the so-called "vital" and the strictly physico-chemical views of fermentation? It is quite possible that the living Tortula may excite fermentation in sugar, because it constantly produces, as an essential part of its vital manifestations, some substance which acts upon the sugar, just as the synaptase acts upon the amygdalin. Or it may be, that, without the formation of any such special substance, the physical condition of the living tissue of the yeast plant is sufficient to effect that small disturbance of the equilibrium of the particles of the sugar, which Lavoisier thought sufficient to effect its decomposition.
In his famous "Mikroskopische Untersuchungen" Schwann speaks of Tortula as a "cell"; and, in a remarkable note to the passage in which he refers to the yeast plant, Schwann says:–
"I have been unable to avoid mentioning fermentation, because it is the most fully and exactly known operation of cells, and represents, in the simplest fashion, the process which is repeated by every cell of the living body."
In other words, Schwann conceives that every cell of the living body exerts an influence on the matter which surrounds and permeates it, analogous to that which a Tortula exerts on the saccharine solution by which it is bathed. A wonderfully suggestive thought, opening up views of the nature of the chemical processes of the living body, which have hardly yet received all the development of which they are capable.
As we have seen, the study of yeast has led investigators face to face with problems of immense interest in pure chemistry, and in animal and vegetable morphology. Its physiology is not less rich in subjects for inquiry. Take, for example, the singular fact that yeast will increase indefinitely when grown in the dark, in water containing only tartrate of ammonia, a small percentage of mineral salts, and sugar. Out of these materials the Torulæ will manufacture nitrogenous protoplasm, cellulose, and fatty matters, in any quantity, although they are wholly deprived of those rays of the sun, the influence of which is essential to the growth of ordinary plants. There has been a great deal of speculation lately, as to how the living organisms buried beneath two or three thousand fathoms of water, and therefore in all probability almost deprived of light, live. If any of them possess the same powers as yeast (and the same capacity for living without light is exhibited by some other fungi) there would seem to be no difficulty about the matter.
Of course, it does not follow from this, that all contagious and infectious diseases are caused by organisms of as definite and independent a character as the Tortula; but I think, it does follow that it is prudent and wise to satisfy one's self in each particular case, that the "germ theory" cannot and will not explain the facts, before having recourse to hypotheses which have no equal support from analogy."