Mitchell L. Sogin

Marine Biological Laboratory

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Hilary G. Morrison

Marine Biological Laboratory

A. Murat Eren

Helmholtz Institute for Functional Marine Biodiversity

Susan M. Huse

Zoetis (United States)

Joseph H. Vineis

Marine Biological Laboratory

Sandra L. McLellan

University of Wisconsin–Milwaukee

David B. Mark Welch

Marine Biological Laboratory

Eugene B. Chang

University of Chicago

Julie A. Huber

Woods Hole Oceanographic Institution

Carl R. Woese

University of Illinois Urbana-Champaign

Andrew G. McArthur

McMaster University

Cooperative Institutions

Marine Biological Laboratory

126

University of Chicago

Woods Hole Oceanographic Institution

University of California, San Diego

University of Illinois Urbana-Champaign

Harvard University

Dartmouth College

University of Washington

University of Arizona

National Institutes of Health

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A Molecular Reassessment of the Leptomyxid Amoebae

Protist (2000)

Linda A. Amaral Zettler Thomas A. Nerad Charles J. O’Kelly Michael T. Peglar Michael T. Peglar

Monophyly

10.1078/1434-4610-00025

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Citations (102)

Primary structure of theChlorella vulgarissmall subunit ribosomal RNA coding region

Nucleic Acids Research (1989)

Volker A. R. Huss Mitchell L. Sogin

Journal Article Primary structure of the Chlorella vulgaris small subunit ribosomal RNA coding region Get access Volker A.R. Huss, Volker A.R. Huss National Jewish Center for Immunology and Respiratory Medicine1400 Jackson Street, Denver, CO 80206, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Mitchell L. Sogin Mitchell L. Sogin National Jewish Center for Immunology and Respiratory Medicine1400 Jackson Street, Denver, CO 80206, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 3, 11 February 1989, Page 1255, https://doi.org/10.1093/nar/17.3.1255 Published: 11 February 1989 Article history Received: 20 December 1988 Published: 11 February 1989

10.1093/nar/17.3.1255

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Citations (35)

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

JAMA Pediatrics (2016)

Juliette C. Madan Anne G. Hoen Sara Lundgren Shohreh F. Farzan Kathryn L. Cottingham

The intestinal microbiome plays a critical role in infant development, and delivery mode and feeding method (breast milk vs formula) are determinants of its composition. However, the importance of delivery mode beyond the first days of life is unknown, and studies of associations between infant feeding and microbiome composition have been generally limited to comparisons between exclusively breastfed and formula-fed infants, with little consideration given to combination feeding of both breast milk and formula.To examine the associations of delivery mode and feeding method with infant intestinal microbiome composition at approximately 6 weeks of life.Prospective observational study of 102 infants followed up as part of a US pregnancy cohort study.Delivery mode was abstracted from delivery medical records, and feeding method prior to the time of stool collection was ascertained through detailed questionnaires.Stool microbiome composition was characterized using next-generation sequencing of the 16S rRNA gene.There were 102 infants (mean gestational age, 39.7 weeks; range, 37.1-41.9 weeks) included in this study, of whom 70 were delivered vaginally and 32 by cesarean delivery. In the first 6 weeks of life, 70 were exclusively breastfed, 26 received combination feeding, and 6 were exclusively formula fed. We identified independent associations between microbial community composition and both delivery mode (P< .001; Q < .001) and feeding method (P = .01; Q < .001). Differences in microbial community composition between vaginally delivered infants and infants delivered by cesarean birth were equivalent to or significantly larger than those between feeding groups (P = .003). Bacterial communities associated with combination feeding were more similar to those associated with exclusive formula feeding than exclusive breastfeeding (P = .002). We identified 6 individual bacterial genera that were differentially abundant between delivery mode and feeding groups.The infant intestinal microbiome at approximately 6 weeks of age is significantly associated with both delivery mode and feeding method, and the supplementation of breast milk feeding with formula is associated with a microbiome composition that resembles that of infants who are exclusively formula fed. These results may inform feeding choices and shed light on the mechanisms behind the lifelong health consequences of delivery and infant feeding modalities.

Formula feeding

Infant feeding

Gut microbiome

10.1001/jamapediatrics.2015.3732

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Citations (259)

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

Molecular Ecology (2010)

Hélène Agogué Dominique Lamy Phillip R. Neal Mitchell L. Sogin Gerhard J. Herndl

Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to 5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830,000 pyrotags, we identified 10,780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.

Bacterioplankton

Bathyal zone

Alphaproteobacteria

10.1111/j.1365-294x.2010.04932.x

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Citations (243)

Partial purification and properties of a ribosomal RNA maturation endonuclease from Bacillus subtilis.

Journal of Biological Chemistry (1977)

Mitchell L. Sogin B Pace Norman R. Pace

Data are presented on the partial purification and properties of a 5 S ribosomal RNA maturation nuclease, termed RNase M5, from Bacillus subtillis 168. RNase M5 specifically cleaves 21 and 42 nucleotides, respectively, from the 5' and 3' termini of a 5 S rRNA precursor to yield the mature (116 nucleotides) 5 S rRNA. The cleavage is endonucleolytic with the formation of 5'-phosphoryl and 3'-hydroxyl groups. Enzyme action requires divalent cations, which may be furnished by either certain metals or by polyamines. The activity is separable into two components both of which are required for activity. It appears that the same nuclease excises the 5'- and 3'-terminal segments since preparations lose the capacity to modify the two termini with an identical first order thermal decay rate. Certain features of the rRNA precursor which may be involved in cognitive interaction with RNase M5 are discussed.

Nuclease

Cleavage (geology)

Divalent

RNase MRP

10.1016/s0021-9258(17)40663-6

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Citations (48)

Phylogenetic Analysis of Olfactory Receptor Genes from Mudpuppy (Necturus maculosus)

Biological Bulletin (1997)

Qiao Zhou G. Hinkle Mitchell L. Sogin Vincent E. Dionne

Necturus

10.1086/bblv193n2p248

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Citations (10)

Microbial Population Structures in the Deep Marine Biosphere

Science (2007)

Julie A. Huber David B. Mark Welch Hilary G. Morrison Susan M. Huse Phillip R. Neal

The analytical power of environmental DNA sequences for modeling microbial ecosystems depends on accurate assessments of population structure, including diversity (richness) and relative abundance (evenness). We investigated both aspects of population structure for microbial communities at two neighboring hydrothermal vents by examining the sequences of more than 900,000 microbial small-subunit ribosomal RNA amplicons. The two vent communities have different population structures that reflect local geochemical regimes. Descriptions of archaeal diversity were nearly exhaustive, but despite collecting an unparalleled number of sequences, statistical analyses indicated additional bacterial diversity at every taxonomic level. We predict that hundreds of thousands of sequences will be necessary to capture the vast diversity of microbial communities, and that different patterns of evenness for both high- and low-abundance taxa may be important in defining microbial ecosystem dynamics.

Rank abundance curve

10.1126/science.1146689

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Citations (876)

Phylogeny of the genera Entamoeba and Endolimax as deduced from small- subunit ribosomal RNA sequences

Molecular Biology and Evolution (1999)

Jeffrey D. Silberman C Graham Clark Louis S. Diamond Mitchell L. Sogin

We sequenced small-subunit ribosomal RNA genes (16S-like rDNAs) of 10 species belonging to the genera Entamoeba and Endolimax. This study was undertaken to (1) resolve the relationships among the major lineages of Entamoeba previously identified by riboprinting; (2) examine the validity of grouping the genera Entamoeba and Endolimax in the same family, the Entamoebidae; and (3) examine how different models of nucleotide evolution influence the position of Entamoeba in eukaryotic phylogenetic reconstructions. The results obtained with distance, parsimony, and maximum-likelihood analyses support monophyly of the genus Entamoeba and are largely in accord with riboprinting results. Species of Entamoeba producing cysts with the same number of nuclei from monophyletic groups. The most basal Entamoeba species are those that produce cysts with eight nuclei, while the group producing four-nucleated cysts is most derived. Most phylogenetic reconstructions support monophyly of the Entamoebidae. In maximum-likelihood and parsimony analyses, Endolimax is a sister taxon to Entamoeba, while in some distance analyses, it represents a separate lineage. The secondary loss of mitochondria and other organelles from these genera is confirmed by their relatively late divergence in eukaryotic 16S-like rDNA phylogenies. Finally, we show that the positions of some (fast-evolving) eukaryotic lineages are uncertain in trees constructed with models that make corrections for among-site rate variation.

Monophyly

Entamoeba

Maximum parsimony

10.1093/oxfordjournals.molbev.a026086

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Citations (118)

16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis, and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group

European Journal of Protistology (1996)

Detlef D. Leipe Susan M. Tong C. Louise Goggin Susan B. Slemenda Norman J. Pieniążek

Protist

Monophyly

10.1016/s0932-4739(96)80004-6

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Citations (116)

Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A ( mcrA ) Genes in Hydrothermal Sediments of the Guaymas Basin

Applied and Environmental Microbiology (2005)

A. S. Dhillon Mark A. Lever Karen G. Lloyd Daniel B. Albert Mitchell L. Sogin

ABSTRACT The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase ( mcrA ) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H 2 /CO 2 - and formate-utilizing family Methanomicrobiales , two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum . The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile family Methanosarcinales , one 16S rRNA amplicon and most of the mcrA PCR amplicons were affiliated with the obligately acetate utilizing species Methanosaeta concilii . The mcrA clone libraries also included phylotypes related to the methyl-disproportionating genus Methanococcoides . However, two mcrA and two 16S rRNA lineages within the Methanosarcinales were unrelated to any cultured genus. Overall, the clone libraries indicate a diversified methanogen community that uses H 2 /CO 2 , formate, acetate, and methylated substrates. Phylogenetic affiliations of mcrA and 16S rRNA clones with thermophilic and nonthermophilic cultured isolates indicate a mixed mesophilic and thermophilic methanogen community in the surficial Guaymas sediments.

Methanogen

Methanomicrobiales

Candidatus

Crenarchaeota

Library

Methanococcus

10.1128/aem.71.8.4592-4601.2005

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Citations (154)