Year: 2026
Type: preprint
Abstract: Temporal changes in wastewater microbiomes can reflect shifts in microbial abundance, detectable membership, and genome recovery. We paired genome-resolved and read-based metagenomics to distinguish these signals in 25 spatially pooled university wastewater samples collected during wet and dry periods. The workflow recovered 203 wet-period and 230 dry-period metagenome-assembled genomes (MAGs). Community composition differed between periods in both MAG-derived presence/absence profiles (Jaccard PERMANOVA, R 2 = 0.548, p = 0.001) and read-based relative-abundance profiles (Bray–Curtis PERMANOVA, R 2 = 0.167, p = 0.001). Greater dry-period read-based richness persisted after rarefaction but disappeared under more stringent abundance thresholds, indicating a substantial contribution from low-abundance detections. Of 57 period-associated core species in the MAG-derived profiles, 14 had exact species-level matches in the read-based dataset. All 14 remained detectable at ≥90% prevalence in the opposite period, and 13 had higher relative abundance in the period corresponding to their MAG-based association. Continued species detection therefore accompanied changes in community composition and MAG-based representation. Perfect/Strict CARD/RGI resistance-associated annotations occurred in 94.1% of wet-period and 92.2% of dry-period MAGs and were distributed across shared-core and period-associated taxa. These findings reveal repeated detection of a matched subset of microbial taxa beneath temporal community restructuring, together with widespread resistance-associated genetic potential among recovered genomes. Combining read-based and genome-resolved profiles helps distinguish changes in detectable membership from changes in the genomic characterization available for wastewater surveillance. Importance A changing wastewater microbial profile can suggest that organisms have disappeared or been replaced. In this university wastewater time series, community composition differed between sampling periods, yet all 14 species that could be matched between the period-associated MAG core and read-based profiles remained highly prevalent in the opposite period. Most also shifted in relative abundance in the direction of their MAG-based association. Thus, continued species detection can coexist with changes in community composition and genome representation. Resistance-associated annotations were widespread among the recovered genomes, providing complementary information about their genetic potential. Paired analyses can help wastewater surveillance distinguish organisms that remain detectable from those for which genomic context is available.
Authors: Gabriela Franco, Archana Anand
Institution: San Francisco State University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7221796893