A case for global standardisation of genomics and wastewater-based epidemiology

The Lancet Microbe, Journal Year: 2025, Volume and Issue: unknown, P. 101092 - 101092

Published: March 1, 2025

Language: Английский

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Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing

ISME Communications, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 1, 2025

Abstract Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes enrichment cultures, no single technique render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor incorporation non-canonical bases genome-resolved metagenomic datasets elucidate replication patterns bacteria phages. This technology enables reconstruction prokaryotic viral genomes (alongside genomics downstream analyses like predictions), addition providing information regarding cultures. By spiking base analog 5-bromo-2′-deoxyuridine (BrdU) into activated sludge microcosms, determined that 114 118 high-quality recovered were actively replicating cultures from identified slow (low BrdU change abundance) rapidly organisms (high abundance). Some detected exhibited regions rich predicted represent prophages lytic cycle. Ultimately, this novel means monitoring responses microbes, deciphering active elements will advance empower strategies aimed at isolating previously uncultivated pure culture.

Language: Английский

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Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 14, 2024

Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes enrichment cultures, no single technique render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor incorporation non-canonical bases genome-resolved metagenomic datasets elucidate replication patterns bacteria phages. This technology enables reconstruction prokaryotic viral genomes (alongside genomics downstream analyses like predictions), addition providing information regarding cultures. By spiking base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, determined that 114 118 high-quality recovered were actively replicating cultures from identified slow (low BrdU change abundance) rapidly organisms (high abundance). Some detected exhibited regions rich predicted represent prophages lytic cycle. Ultimately, this novel means monitoring responses microbes, deciphering active elements will advance empower strategies aimed at isolating previously uncultivated pure culture.

Language: Английский

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Oxford Nanopore long read-based shotgun metagenomic data sets of simulated bacterial communities originating from fresh spinach and surface water

Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: 13(9)

Published: Aug. 20, 2024

ABSTRACT Oxford Nanopore long reads of simulated bacterial communities from fresh spinach and surface water were generated (R9.4.1+SQK-LSK109 R10.4+SQK-LSK112; 0.5, one, two million reads). Salmonella enterica serotype Heidelberg, Montevideo, or Typhimurium was included alone in combination the community, while community harbored Pseudomonas aeruginosa .

Language: Английский

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