2.4 Spatiotemporal factors

The contents of this section have been extracted and modified from the article Disentangling host–microbiota complexity through hologenomics published in Nature Reviews Genetics in 2022 by the authors of the Holo-omics Workbook.

Spatial factors

Spatial resolution. Microbial communities associated with animal and plant hosts vary not only across coarse body parts, but also at the micro-scale, such as between the lumen and the intestinal crypts. Thus, the resolution at which a body site is defined will also determine how a hologenomic system is characterised. For example, the animal gastrointestinal tract can be considered a single sampling unit, 4-5 units or hundreds of micro-units, depending on the sampling and data processing strategies employed. Naturally, each level of resolution will allow different questions to be addressed and will require the use of different technologies and analytical approaches.

Temporal factors

Temporal features to be considered include when, how often, and for how long host-microbiota systems are to be analysed. When a host is first exposed to microbes with regard to temporal benchmarks (number of days or years) must be considered, as should the order in which it is exposed to them. Priority effects relate to how the order of species arrivals in an ecosystem shape the potential for subsequently arriving taxa to establish themselves. Although originally discussed at the macroorganismal level in the context of plant communities, the phenomenon is also relevant for building host-associated microorganism communities, for example as documented in the human gut. In addition, microbial communities are known to vary daily, seasonally and relative to life-stage patterns. Hence, the extent and frequency of sampling determine which of these dynamics will be observed or, conversely, missed. Finally, it is important to consider that the consequences of changes at one time period or life stage may appear only later in time, thus detection of such effects obviously requires that the subsequent period is also studied. For example, interventional animal experiments show that when the immune system develops early in life, there is a window of opportunity where the gut microbiota composition shapes the risk of developing diseases in the future.