The fact is that our internal biomes differ greatly - to some extent, at least (and many would say to a large extent), according to our diet. The bacterial content of any animal's digestive system plays a large part in - well - digesting their food. Naturally my gut flora will be vastly different to that of, say, a spider or a mole - but it will also change over time, when my diet changes, and as my overall health changes. So my gut flora as a vegetarian in my mid 70s will be very different to that of my neighbour who is a frequent meat-eater in his 30s. However, his gut flora will also be different to those of his peers who eat a highly-processed diet of Greggs pies, ready meals and fizzy drinks, as N does most of his own cooking and enjoys nothing more than game from the estate on which he works as head gardener together with home (or rather estate) produced veggies, and big pint mugs of tea!
Although there is no such thing as 'thin' bacteria or 'fat' microbes, gut flora definitely helps to regulate metabolism and nutrient absorption - and hence, will have an effect on weight management. How significant that effect is in different individuals, clinical condition , and why, is still part of ongoing and active research, but it is known that a person eating a largely industrially-processed diet will have a different gut flora to the person eating a less-processed diet. The greater difference in their diet, the greater difference in their gut flora. There are links - correlations, if you like - between a highly-processed diet and the incidence of obesity in a society. Correlation is, we can all agree, not causation.
However, it is clear that it is not merely the energy (ie calorie) content of the diet vs the calories of physical activity expended that is the deciding factor in weight gain, loss or maintenance. Ignoring clinical conditions and disorders which may affect such, and looking only at 'well' individuals, gut flora - which I will remind you is different in every individual - helps to determine how much energy your body absorbs, and also how hungry or full you feel.
How much energy your body absorbs from its diet, and how hungry or full you feel, is surely a large part of weight gain, loss, or maintenance?
So even if the industrially-made cottage pie contains exactly the same *ingredients* as the home-made one, they will most likely not be entering similar environments in which to be digested, and the calories thus absorbed in different digestive systems will vary ...
There's a lot of research going on wrt gut flora and the microbiome - naturally much of it is concentrated on illness (such as the concept of faecal transfer of healthy gut flora to the sufferer of C dfficile infection) rather than on the 'well-but-obese', but spin-offs are already happening to a small extent and there will undoubtedly be further developments in the future.