Evidence map›Paper›PMID 30902854›Full record

ArticleApplied and environmental microbiology2019

Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities.

Noha H Youssef, Ibrahim F Farag, C Ryan Hahn, Jessica Jarett, Eric Becraft, Emiley Eloe-Fadrosh, Jorge Lightfoot, Austin Bourgeois, Tanner Cole, Stephanie Ferrante and 12 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Applied and environmental microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
1.7field-weighted citation impact, top 16% of its field
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

9 citing papers in PubMed, 21 citations in OpenAlex.

  1. Article
  2. The dynamic history of prokaryotic phyla: discovery, diversity and division.International journal of systematic and evolutionary microbiology · 2024
    Review
  3. Article
  4. Article
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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

22 authors at 6 institutions in 2 countries.

Noha H YoussefDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA noha@okstate.edu.
Ibrahim F FaragDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
C Ryan HahnDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Jessica JarettUS DOE Joint Genome Institute, Walnut Creek, California, USA.
Eric BecraftUniversity of North Alabama, Florence, Alabama, USA.
Emiley Eloe-FadroshUS DOE Joint Genome Institute, Walnut Creek, California, USA.
Jorge LightfootDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Austin BourgeoisDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Tanner ColeDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Stephanie FerranteDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Mandy TruelockDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
William MarshDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Michael JamaleddineDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Samantha RickettsDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Ronald SimpsonDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Allyson McFaddenDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Wouter HoffDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Nikolai V RavinInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
Stefan SievertWoods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA.
Ramunas StepanauskasBigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA.
Tanja WoykeUS DOE Joint Genome Institute, Walnut Creek, California, USA.
Mostafa ElshahedDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA.
Oklahoma State University · USJoint Genome Institute · USBigelow Laboratory for Ocean Sciences · USRussian Academy of Sciences · RUUniversity of North Alabama · USWoods Hole Oceanographic Institution · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (

Indexed as

FermentationGenome, BacterialBacteriaCell WallOklahomaRNA, BacterialRNA, Ribosomal, 16SRNA, BacterialRNA, Ribosomal, 16Scandidate phylaenvironmental genomicsmetagenomic binssingle-cell genomics

Identifiers

PMID30902854
PMCPMC6498177
OpenAlexW2924452349

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.