ArticleMicrobial ecology2011
High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.
Article in Microbial ecology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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.
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.
Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
- Long-Read Metagenomics and CAZyme Discovery.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Effects of Chemical and Mechanical Lysis on Microbial DNA Yield, Integrity, and Downstream Amplicon Sequencing of Rumen Bacteria and Protozoa.Frontiers in microbiology · 2020Article
- Fiber Supplements Derived From Sugarcane Stem, Wheat Dextrin and Psyllium Husk Have DifferentFrontiers in microbiology · 2018Article
- Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.BMC research notes · 2017Article
- Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.Applied and environmental microbiology · 2017Article
- The effect of temperature and retention time on methane production and microbial community composition in staged anaerobic digesters fed with food waste.Biotechnology for biofuels · 2017Article
- Article
- Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations.Microbiome · 2015Article
- Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.Genome research · 2014Article
- Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.Journal of industrial microbiology & biotechnology · 2014Article
- Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.Microbial ecology · 2013Article
- Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima.3 Biotech · 2013Article
- Draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from the bovine rumen.Journal of bacteriology · 2012Article
- Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.PloS one · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.