A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus

Fierer, Noah; Holland‐Moritz, Hannah; Alexiev, Alexandra; Batther, Harpreet; Dragone, Nicholas B.; Friar, Liam; Gebert, Matthew J.; Gering, Sarah; Henley, Jessica B.; Jech, Sierra; Kibby, Emily; Melie, Tina; Patterson, William B.; Peterson, Eric D.; Schutz, Kyle; Stallard-Olivera, Elias; Sterrett, John D.; Walsh, Corinne M.; Mansfeldt, Cresten

doi:10.1128/msystems.00651-22

Cited by 10 publications

(9 citation statements)

References 55 publications

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“…This study has shown that bacteria such as Proteobacteria, Campylobacterota, Bacteroidota and Firmicutes are relatively highly abundant in WWTP. These findings are consistent with several previous result [ 38 , 39 , 40 ]. In this study, up to 41% of the bacterial sequences were potential animal pathogens, with the most abundant pathogen being the genus Arcobacter in the phylum Campylobacterota, accounting for 6.79% of the total number of sequences.…”

Section: Discussionsupporting

confidence: 94%

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Zhao,

Yang,

Fan

et al. 2024

Viruses

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The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.

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Section: Discussionsupporting

confidence: 94%

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Zhao,

Yang,

Fan

et al. 2024

Viruses

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“…The many new taxa recovered here by reference-free metagenomics improve the public collections and will potentiate future reference-based metagenomics and sewage monitoring. We found that sewage microbiomes drift apart over time so samples that are temporally close, also have lower beta-diversity confirming expectations and previous findings 13,26 . Surprisingly though, we found striking differences in the impact of seasonality on the surveyed cities.…”

Section: Discussionsupporting

confidence: 91%

“…Since environmental bacteria inherently possess numerous AMR genes, distinguishing the origins of these genes is vital for the focused monitoring of AMR genes associated with human activity. Previous studies have shown that the microbial composition within sewage can exhibit significant variability both temporally and spatially within the same sewage system 13 . In addition, there may be differences in composition and seasonality of microbes across different geographic regions 2 .…”

Section: Introductionmentioning

confidence: 99%

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

Becsei,

Fuschi,

Otani

et al. 2024

Preprint

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Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we designed this study to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We used longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recovered 2,332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1,334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) showed strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) had occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.

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“…Extrapolating this ratio to 100%, their estimation suggests that only 15% of amplicons in a typical sewage sample originate from human stool. However, Fierer et al (2022) found that bacteria derived from fecal material constitute a relatively small fraction of the taxa in collected samples, underscoring the significance of environmental sources in shaping the sewage microbiome. It is still unclear if raw sewage truly reflects the microbial composition of the human gut.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 virus in Raw Wastewater from Student Residence Halls with concomitant 16S rRNA Bacterial Community Structure changes

Li,

Ash,

Joyner

et al. 2024

Preprint

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The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in sewage is well-established, but the concomitant changes in microbial compositions during the pandemic remain insufficiently explored. This study investigates the impact of the SARS-CoV-2 virus on microbial compositions in raw sewage, utilizing 16S rRNA sequencing to analyze wastewater samples collected from six dormitories over a one-year field trial at the University of Tennessee, Knoxville. The concentration of SARS-CoV-2 RNA was assessed using a reverse transcription-quantitative polymerase chain reaction. Significant variations in bacterial composition were evident across the six dormitories, highlighting the importance of independently considering spatial differences when evaluating the raw wastewater microbiome. Positive samples for SARS-CoV-2 exhibited a prominent representation of exclusive species across all dormitories, coupled with significantly reduced bacterial diversity compared to negative samples. The correlation observed between the relative abundance of enteric pathogens and potential pathogens at sampling sites introduces a significant dimension to our understanding of COVID-19, especially the notable correlation observed in positive SARS-CoV-2 samples. Furthermore, the significant correlation in the relative abundance of potential pathogens between positive and negative SARS-CoV-2 raw sewage samples may be linked to the enduring effects of microbial dysbiosis observed during COVID-19 recovery. These findings provide valuable insights into the microbial dynamics in raw sewage during the COVID-19 pandemic.

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A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus

Cited by 10 publications

References 55 publications

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

SARS-CoV-2 virus in Raw Wastewater from Student Residence Halls with concomitant 16S rRNA Bacterial Community Structure changes

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