## 2 Diversity of Gut Prokaryotes and the Principles of Microbiota Transfer
### Enterotypes of Human and Animal Guts
Notably, the microbial composition exhibited signs of phylosymbiosis, where host evolutionary history correlated with gut bacterial diversity. However, geographic location exerted a stronger influence on microbiota structure than host species, suggesting that environmental factors play a predominant role in structuring gut microbial communities. These findings extend enterotype research to marine teleosts, demonstrating that both intrinsic and extrinsic factors contribute to microbiome differentiation in wild fish populations [47]. Recent studies have demonstrated the influence of habitat preferences on gut microbiota composition in fish. A study on fish from Lake Sanjiao showed that vertical habitat preferences--whether fish inhabit pelagic or benthic zones--play a primary role in shaping gut microbial communities. High-throughput sequencing and stable isotope analysis revealed that gut microbiota of pelagic fish exhibited greater similarity to water microbiota, while benthic fish showed a stronger association with sediment microbiota. Classification models confirmed that habitat preference was a more significant determinant of gut microbiota composition than host taxonomy or trophic level. Additionally, co-occurrence network analysis indicated that the gut microbiota of pelagic fish was more stable than that of benthic fish, likely because of the homogeneity of microbial communities in the water column compared with the higher microbial diversity and variability in sediments. These findings support the idea that environmental factors, rather than host genetics alone, are key determinants of fish gut microbiota composition, contributing to the broader concept of enterotype differentiation across animal species [48]. Although the lack of uniformity in defining enterotypes--both in animals and, as previously noted, in humans--may be confounding, it is vital to consider the methodology behind specific studies. The rapid development of sequencing methods in the last decade causes difficulties in comparing papers published even a few years apart from each other, as the depth of metagenomic analysis can be significantly different. In many cases, a significant share of reads was left unassigned to any known phylum, obfuscating the actual distribution of microorganisms and possibly leading to over- or underrepresentation of some of them. In many studies, operational taxonomic units were also defined in quite a narrow way, which might have led to claims of enterotypes not being detectable in surveyed microbiota, as grouping microorganisms into broader taxa seems to delineate specific enterotypes much more clearly [49]. Apart from these issues, it is once again vital to note that material processing procedures in various studies are far from standardised and often exhibit vast differences in terms of sourcing, collection, storage, and forms of microbial identification. While appropriately describing and modelling gut microbiotas will probably remain a significant challenge, it is equally important to focus on the potential benefits of using these systems of classification as reference points in therapy, disease prevention, and improving overall well-being. Apart from the aforementioned phenotypic changes in animals,certain effects were also observed in humans. One study found a significant correlation between enterotype and stool consistency--a _Prevotella_ enterotype was linked to looser stools, while a different microbial profile, defined by the authors as a _Runinococcaceae-Bacteroides_ enterotype, yielded harder and dryer stools [50]. Different enterotypes may also affect digestion efficiency--the _Bacteroides_-dominated enterotype is characterised by greater alginate breakdown capabilities compared with _Prevotella_-dominated and _Escherichia_-dominated enterotypes [35]. Certain microbiome configurations can also be considered risk factors for diseases, as is the case with type 2 diabetes and the _Bacteroides_ enterotype [36].