That's a bit of a complicated question as far as my take on the setting goes, to be honest.
Taking into account just how incredibly complex ecosystems in the real world are and now much they depend on organisms smaller than the smallest Pokémon (the smallest existing Pokémon are roughly 4 inches or 10 cm - for the sake of comparison, that's about the body length of a large house mouse) for various aspects of their existence – and the fact that similar ecosystems seem to exist in the Pokémon world (alongside things such as filter-feeders and what have you) – one can assume there are absolutely creatures filling these niches and that these creatures are most likely not quite Pokémon. They are, however, closer to Pokémon than they would be to animals - as what we know as "animals" are located not only on a different branch of the tree of life... but in an entirely different frelling forest altogether.
You see, despite some impressive resemblance in geographical terms and the presence of organisms that are extremely similar to our plants and fungi – the Pokémon World is not Earth, and the convergences between these two worlds are nothing short of a coincidence of an astronomical scale. Pokémon represent one of the most successful paradigms of macro-organisms on this world - and note the use of "paradigm", as the sheer amount of endosymbioses that emerged independently along particular lines but not others, sometimes cryptically, the seeming de novo emergence of some Pokemon species from proto-Pokémon or Pokémon-adjacent progenitors that are near-impossible to accurately trace or pinpoint, and the effects of elemental energies and influences both local and alien on these creatures over evolutionary time make Pokémon cladistics so incredibly muddled that they would probably put even the most bloody-minded taxonomist on suicide watch.
So on top of the Pokémon we know and those we don't, there's a whole damn world of microorganisms, small simple creatures, plankton and sometimes far more complicated things that are not quite Pokémon but are most certainly alive (remember the "Tree of Beginning" in the Lucario movie? Bizarre crystalline colonial organism that derives energy from sunlight, with its own immune "zooids" and symbiotic relationships with Pokémon that lived inside it? like that). Most of them, however, do not draw the attention of the average person – certainly not your typical Pokémon trainer – and while their interactions with other forms of life and with Pokémon are certainly a subject of some subsets of biological and ecological research, it is hardly the sort of research that would make for particularly exciting or compelling fic.
There is, however, one known animal, strictly speaking, in the Pokémon world - humans. As you have probably guessed, they are not native to this ecosystem, having arrived and colonized the Pokémon world by means that I have not quite delved too deeply into, at some point in time rather long ago. Due to similarly ill-defined shenanigans most knowledge of the Old World had been lost forcing humans to start anew in their new home, with oral traditions and some preserved knowledge having maintained just enough of what Earth's animals were like to apply the words to loosely similar/analogous creatures. I'm a bit on the fence as for whether some earth plants (common food crops in particular, as those are canonically present in the games – and while it seems that some of them have overlap with what we know as 'berries', some clearly exist alongside their 'berry' equivalents) and microorganism 'hitchhikers' have also found their way to the Pokémon world, escaped into the ecosystem and integrated into it - these things tend to be adaptive as frell after all and we all know how invasive plants can get in particular. And considering how quickly evolutionary processes take root in the Pokémon world due to all the ambient elemental shenanigans, too...
(Which brings us to another point: Humans may be very different from whatever else is going on in the Pokémon world, but as generations pass, they too are changing in subtle ways. The emergence of humans that have minor-grade planar attunements such as psychics, channelers and 'aura guardians' is evidence to this - it may yet be that given enough time, humans too will start taking the weirdass elemental shenanigans into themselves through similar process of endosymbiosis and integrate into the local elemental energy ecology too - who's to say? That's subject for far future speculative fic).