Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. (Q34247218)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

title

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

1 reference

Manuel Martínez-García

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

David M Brazel

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Brandon K. Swan

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Patrick S Chain

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Gary Xie

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Nicole J Poulton

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Chien-Chi Lo

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Ramunas Stepanauskas

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

13

Kai Ziervogel

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

4

Carol Arnosti

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

author name string

Krista G Reitenga

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Monica Lluesma Gomez

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Dashiell E D Masland

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Brian Thompson

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Wendy K Bellows

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Sanaa Ahmed

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Cheryl D Gleasner

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Chris J Detter

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

language of work or name

English

0 references

publication date

20 April 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

page(s)

e35314

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons CC0 License

30 January 2020

copyright license

start time

20 April 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

describes a project that uses

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Global distribution and diversity of marine Verrucomicrobia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Decontamination of MDA reagents for single cell whole genome amplification

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Single-cell genomics reveals organismal interactions in uncultivated marine protists.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Microbial extracellular enzymes and the marine carbon cycle

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

CDD: a Conserved Domain Database for the functional annotation of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Capturing diversity of marine heterotrophic protists: one cell at a time

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

The integrated microbial genomes system: an expanding comparative analysis resource

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

PROSITE, a protein domain database for functional characterization and annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Shifting the genomic gold standard for the prokaryotic species definition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Assembling the marine metagenome, one cell at a time

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

The SWISS-MODEL Repository and associated resources

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Bacteria associated with benthic diatoms from Lake Constance: phylogeny and influences on diatom growth and secretion of extracellular polymeric substances

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Genomics of cellulosic biofuels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum 'Verrucomicrobia', isolated from a sponge (Porifera).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Sequencing genomes from single cells by polymerase cloning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Toxic effects on bacterial metabolism of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Genomic DNA amplification from a single bacterium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Application of tetranucleotide frequencies for the assignment of genomic fragments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

ARB: a software environment for sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Versatile and open software for comparing large genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

The Uncultured Microbial Majority

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Complete genome sequence of the marine planctomycete Pirellula sp. strain 1

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Comprehensive human genome amplification using multiple displacement amplification

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Defensive extrusive ectosymbionts of Euplotidium (Ciliophora) that contain microtubule-like structures are bacteria related to Verrucomicrobia

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Flow cytometric analysis of 5-cyano-2,3-ditolyl tetrazolium chloride activity of marine bacterioplankton in dilution cultures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Basic local alignment search tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Molecular Architecture and Electrostatic Properties of a Bacterial Porin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3335022

Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute

6 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

Fluorescent derivatization of polysaccharides and carbohydrate-containing biopolymers for measurement of enzyme activities in complex media

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

A comparative study of carboxyfluorescein diacetate and carboxyfluorescein diacetate succinimidyl ester as indicators of bacterial activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035314

MEROPS: the peptidase database

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22536372

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22536372

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0035314

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22536372%20AND%20SRC:MED&resulttype=core&format=json