Evidence map›Paper›PMID 39231974›Full record

ArticleScientific data2024

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

Tiffany Oliver, Neha Varghese, Simon Roux, Frederik Schulz, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Robert Riley, Kurt LaButti and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
  2. Article
  3. A genomic view of Earth's biomes.Nature reviews. Genetics · 2026
    Review
  4. Article
  5. An organotrophicApplied and environmental microbiology · 2025
    Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

34 authors.

Tiffany OliverDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. toliver4@spelman.edu.
Neha VargheseDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Simon RouxDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Frederik SchulzDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Marcel HuntemannDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-1284-3748
Alicia ClumEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Brian FosterDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Bryce FosterDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Robert RileyDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Kurt LaButtiDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Robert EganDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Patrick HajekDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Supratim MukherjeeDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-6322-2271
Galina OvchinnikovaDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
T B K ReddyDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-0871-5567
Sara CalhounDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Richard D HayesDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-5236-7918
Robin R RohwerDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-2664-6489
Zhichao ZhouDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.ORCID 0000-0002-9120-6762
Chris DaumDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0003-3895-5892
Alex CopelandDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-3971-5439
I-Min A ChenDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Natalia N IvanovaDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-5802-9485
Nikos C KyrpidesDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-6131-0462
Nigel J MounceyDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Tijana Glavina Del RioDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Igor V GrigorievDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-3136-8903
Steven HofmeyrApplied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Leonid OlikerApplied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Katherine YelickApplied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Karthik AnantharamanDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.ORCID 0000-0002-9584-2491
Katherine D McMahonDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Tanja WoykeDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID 0000-0002-9485-5637
Emiley A Eloe-FadroshDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. eaeloefadrosh@lbl.gov.ORCID 0000-0002-8162-1276

Funding

NSF | BIO | Division of Biological Infrastructure (DBI) DBI-2011002NSF | BIO | Division of Environmental Biology (DEB) DEB-1344254NSF | BIO | Division of Environmental Biology (DEB) DEB-2025982NSF | BIO | Division of Molecular and Cellular Biosciences (MCB) MCB-0702395United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) WIS01516, WIS01789, WIS03004U.S. Department of Energy (DOE) 17-SC-20-SCU.S. Department of Energy (DOE) 89233218CNA000001U.S. Department of Energy (DOE) DE-AC02-05CH11231U.S. Department of Energy (DOE) DE-AC05-00OR22725U.S. Department of Energy (DOE) DE-AC05-76RL01830
6 · The paper itself

Abstract

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Indexed as

LakesMetagenomeBacteriaMetagenomicsPhylogeny

Identifiers

PMID39231974
PMCPMC11374980

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.