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Article
Open AccessPrevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, im...
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Article
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
The human genome encodes only a small number of digestive glycoside hydrolases for the breakdown of sucrose, lactose and starch. Instead, the large diversity o...
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Article
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.
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Article
Going viral: next-generation sequencing applied to phage populations in the human gut
Methods for purifying virus-like particles (VLPs) from microbial communities, procedures for amplifying the small quantities of DNA that are recovered from VLP...
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Article
Unlocking the potential of metagenomics through replicated experimental design
Metagenomics holds enormous promise for discovering novel enzymes and organisms that are biomarkers or drivers of processes relevant to disease, industry and the environment. In the past two years, we have see...
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Article
Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries
Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial spec...
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Article
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for...
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Article
QIIME allows analysis of high-throughput community sequencing data
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Article
Worlds within worlds: evolution of the vertebrate gut microbiota
Comparative analyses between microbial communities in the human gut versus diverse other environments can help elucidate the environmental and evolutionary par...
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Article
DNA microarrays and beyond: completing the journey from tissue to cell
For the cell biologist, identifying changes in gene expression using DNA microarrays is just the start of a long journey from tissue to cell. We discuss how chip users can first filter noise (false-positives) ...
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Article
Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs
N-myristoyltransferase (Nmt) attaches myristate to the N-terminal glycine of many important eukaryotic and viral proteins. It is a target for anti-fungal and anti-viral therapy. We have determined the structur...