Marilen Benner

MICROBIOTA AND ENDOMETRIAL HEALTH 185 6 Supplementary Table 1. Commonly used microbial detection methods Strengths Limitations Culture-based techniques Allows detection of live bacteria Hard to detect slow-growing or fastidious species; some species are non-culturable No costly apparatus for read-out needed No indication of relative species representation within a sample Labor and time-consuming Safety concern for involved staff qPCR Less labor intensive and time-consuming compared to culture-based methods Biased approach as species-specific primers are needed High throughput possible Sensitive 16S amplicon sequencing Possible to study fastidious or cultivation resistant organisms Sensitive to contamination, from reagents and environment of the sample acquisition/processing. Thorough controls needed. Phyla / genus (to lesser extent) level distinction also possible Little accuracy on species level Allows assessment of community diversity Relative abundance of species detected can be affected by biomass of sample Unclassified microorganisms detectable Detection of bacterial DNA does not necessarily mean presence of live bacteria; additional assay needed for live/dead discrimination Complex data analysis Whole genome shotgun sequencing Enhanced species detection (debated, see Tessler et al., 2017) Probability of lower taxon count, likely resulting from limitations in mapping reads to databases Increased information on diversity Expensive Details on species’ genome Information on viruses, fungi and protozoa additional to bacteria