I think the true answer lies in whether human involvement is an outcome of its animality or their civilized being:
It is evident that modern civilized man disrupts "natural" ecosystems
or "biotic communities" on a vast scale. However, it would be
challenging, if not impossible, to draw a clear line between the
activities of early human tribes that presumably integrated into and
formed parts of "biotic communities" and the destructive activities of
the modern world. Is man part of "nature" or not? Can his existence be
reconciled with the concept of the "complex organism"? Seen as an
exceptionally powerful biotic factor that increasingly disturbs the
equilibrium of preexisting ecosystems, eventually destroying them
while simultaneously creating new ones of a very different nature,
human activity finds its rightful place in ecology. Tansley, A. G. (1935). The Use and Abuse of Vegetational Concepts and Terms. Ecology, 16(3), 284–307. https://doi.org/10.2307/1930070
For sewage, activated sludge, and wastewater, there is a chance that the necessary factors that would lead to such bacteria would be there without the interference of civilized man. It would be in the form of, for example, Stagnant Water Bodies, Animal Dung Accumulations, and Decaying Organic Matter:
As an ecological factor acting on vegetation the effect of grazing
heavy enough to prevent the development of woody plants is essentially
the same effect wherever it occurs. If such grazing exists the grazing
animals are an important factor in the biome actually present whether
they came by themselves or were introduced by man. The dynamic
equilibrium maintained is primarily an equilibrium between the grazing
animals and the grasses and other hemicryptophytes which can exist and
flourish although they are continually eaten back.
Tansley, A. G.(1935). The Use and Abuse of Vegetational Concepts and Terms.
Ecology, 16(3), 284–307. https://doi.org/10.2307/1930070
So it's a matter of possibility not conclusive knowledge that these habitats are native.
For food, it would probably be a matter of the type of processing and refinement that a certain kind of food goes through.