List of works - Mitchell Sogin

A Global Census of Marine Microbes

article

A filtering method to generate high quality short reads using illumina paired-end technology

scientific article

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

scientific article

A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan

scientific article

A single genus in the gut microbiome reflects host preference and specificity

scientific article

A spliceosomal intron in Giardia lamblia

scientific article

Accuracy and quality of massively parallel DNA pyrosequencing

scientific article

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

scientific article

Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia

scientific article

Anvi'o: an advanced analysis and visualization platform for 'omics data

scientific article

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants

scientific article published on 11 January 2016

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis

scientific article published on 26 March 2015

Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.

scientific article

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

scientific article

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis

scientific article

Cloning and analysis of the CYP1A promoter from the atlantic killifish (Fundulus heteroclitus).

scientific article

Community structures of fecal bacteria in cattle from different animal feeding operations

scientific article

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

scientific article published on 31 July 2015

Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations

scientific article

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

scientific article published on 14 February 2014

Comparison of the microbial community structures of untreated wastewaters from different geographic locales

scientific article

Correction: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.

scientific article

DRISEE overestimates errors in metagenomic sequencing data.

scientific article

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

scientific article

Domain evolution and functional diversification of sulfite reductases

scientific article published on 01 February 2005

Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.

scientific article published on 24 August 2016

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

scientific article

Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica

scientific article published on April 2002

Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia

scientific article (publication date: August 2004)

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

scientific article

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

scientific article

Fetal exposures and perinatal influences on the stool microbiota of premature infants

scientific article

From Genes to Genomes: Beyond Biodiversity in Spain’s Rio Tinto ⬇️

scientific article published on April 1, 2003

Genetic code supports targeted insertion of two amino acids by one codon

scientific article

Genetic exchange within and between assemblages of Giardia duodenalis

scientific article

Genomic Markers of Ancient Anaerobic Microbial Pathways: Sulfate Reduction, Methanogenesis, and Methane Oxidation ⬇️

scientific article published on April 1, 2003

Giardia lamblia RNA polymerase II: amanitin-resistant transcription.

scientific article published on 6 May 2003

Giardia lamblia: identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system.

scientific article published in May 2002

Global distribution and diversity of marine Verrucomicrobia

scientific article

Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems

scientific article published in 2011

Gut microbial colonisation in premature neonates predicts neonatal sepsis

scientific article published on 06 May 2012

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

scientific article (publication date: 7 March 2006)

Host-specificity among abundant and rare taxa in the sponge microbiome

scientific article (publication date: June 2014)

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

scientific article

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii

scientific article published on 28 December 2015

Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR.

scientific article published in December 2002

Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis

scientific article

Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer

scientific article published in February 2003

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

scientific article

Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts

scientific article published on 14 May 2010

Macroecological patterns of marine bacteria on a global scale

article by Anthony S. Amend et al published 7 November 2012 in Journal of Biogeography

Marine bacteria exhibit a bipolar distribution

scientific article (publication date: 5 February 2013)

Metagenomic analysis of the medicinal leech gut microbiota

scientific article

Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin

scientific article published in August 2005

Microbial community composition in sediments resists perturbation by nutrient enrichment

scientific article

Microbial diversity in the deep sea and the underexplored "rare biosphere"

scientific article

Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities

scientific article

Microbial population structures in the deep marine biosphere

scientific article

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy)

scientific article published on 01 December 2018

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

scientific article

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

scientific article

Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin ⬇️

scientific article published on May 1, 2003

Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential

scientific article

Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis

scientific article

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea).

scientific article published in December 2002

Monopylocystis visvesvarai n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments

scientific article

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

scientific article published on 04 March 2013

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

scientific article

Patient-Specific Bacteroides Genome Variants in Pouchitis

scientific article

Pelobionts are degenerate protists: insights from molecules and morphology.

scientific article

Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

scientific article (publication date: 2003)

Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa

article

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA

scholarly article by Nora Grahl et al published 8 August 2018 in mSphere

Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation

scientific article

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

scientific article

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping

scientific article published on 9 August 2017

Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition.

scientific article published in March 2005

Sewage reflects the distribution of human faecal Lachnospiraceae.

scientific article

Sewage reflects the microbiomes of human populations.

scientific article

Sex-specific associations of infants' gut microbiome with arsenic exposure in a US population

scientific article published in Scientific Reports

Shifts in the microbial community composition of Gulf Coast beaches following beach oiling

scientific article

The identification of a new Giardia duodenalis assemblage in marine vertebrates and a preliminary analysis of G. duodenalis population biology in marine systems

scientific article

The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention

scientific article

The microbiota regulates susceptibility to Fas-mediated acute hepatic injury

scientific article

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

scientific article (publication date: 18 November 2008)

The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth

scientific article published on 23 May 2018

The rare biosphere: sorting out fact from fiction

scientific article published on 11 October 2010

Two new small-subunit ribosomal RNA gene lineages within the subclass gymnamoebia

scientific article

Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation

scientific article

VAMPS: a website for visualization and analysis of microbial population structures

scientific article (publication date: 5 February 2014)

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing.

scientific article

List of works by Mitchell Sogin

A Global Census of Marine Microbes

A filtering method to generate high quality short reads using illumina paired-end technology

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan

A single genus in the gut microbiome reflects host preference and specificity

A spliceosomal intron in Giardia lamblia

Accuracy and quality of massively parallel DNA pyrosequencing

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia

Anvi'o: an advanced analysis and visualization platform for 'omics data

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis

Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis

Cloning and analysis of the CYP1A promoter from the atlantic killifish (Fundulus heteroclitus).

Community structures of fecal bacteria in cattle from different animal feeding operations

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

Comparison of the microbial community structures of untreated wastewaters from different geographic locales

Correction: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.

DRISEE overestimates errors in metagenomic sequencing data.

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

Domain evolution and functional diversification of sulfite reductases

Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica

Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

Fetal exposures and perinatal influences on the stool microbiota of premature infants

From Genes to Genomes: Beyond Biodiversity in Spain’s Rio Tinto ⬇️

Genetic code supports targeted insertion of two amino acids by one codon

Genetic exchange within and between assemblages of Giardia duodenalis

Genomic Markers of Ancient Anaerobic Microbial Pathways: Sulfate Reduction, Methanogenesis, and Methane Oxidation ⬇️

Giardia lamblia RNA polymerase II: amanitin-resistant transcription.

Giardia lamblia: identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system.

Global distribution and diversity of marine Verrucomicrobia

Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems

Gut microbial colonisation in premature neonates predicts neonatal sepsis

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

Host-specificity among abundant and rare taxa in the sponge microbiome

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii

Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR.

Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis

Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts

Macroecological patterns of marine bacteria on a global scale

Marine bacteria exhibit a bipolar distribution

Metagenomic analysis of the medicinal leech gut microbiota

Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin

Microbial community composition in sediments resists perturbation by nutrient enrichment

Microbial diversity in the deep sea and the underexplored "rare biosphere"

Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities

Microbial population structures in the deep marine biosphere

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy)

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin ⬇️

Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential

Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea).

Monopylocystis visvesvarai n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

Patient-Specific Bacteroides Genome Variants in Pouchitis

Pelobionts are degenerate protists: insights from molecules and morphology.

Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA

Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping

Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition.

Sewage reflects the distribution of human faecal Lachnospiraceae.

Sewage reflects the microbiomes of human populations.