Howard Ochman

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Chimpanzees and humans harbour compositionally similar gut enterotypes
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Nat Commun 3:1179. 2012
  2. pmc Evolutionary relationships of wild hominids recapitulated by gut microbial communities
    Howard Ochman
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
    PLoS Biol 8:e1000546. 2010
  3. pmc SIV-induced instability of the chimpanzee gut microbiome
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    Cell Host Microbe 14:340-5. 2013
  4. pmc Sympatric chimpanzees and gorillas harbor convergent gut microbial communities
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 23:1715-20. 2013
  5. pmc Structural features and the persistence of acquired proteins
    Hema Prasad Narra
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Proteomics 8:4772-81. 2008
  6. pmc The consequences of genetic drift for bacterial genome complexity
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 19:1450-4. 2009
  7. pmc Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 109:13034-9. 2012
  8. pmc Evolutionary origins of genomic repertoires in bacteria
    Emmanuelle Lerat
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
    PLoS Biol 3:e130. 2005
  9. pmc Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 7:e1002252. 2011
  10. ncbi The nature and dynamics of bacterial genomes
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Science 311:1730-3. 2006

Collaborators

Detail Information

Publications45

  1. pmc Chimpanzees and humans harbour compositionally similar gut enterotypes
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Nat Commun 3:1179. 2012
    ..These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees...
  2. pmc Evolutionary relationships of wild hominids recapitulated by gut microbial communities
    Howard Ochman
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
    PLoS Biol 8:e1000546. 2010
    ....
  3. pmc SIV-induced instability of the chimpanzee gut microbiome
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    Cell Host Microbe 14:340-5. 2013
    ..Our results indicate that immune function maintains temporally stable gut communities that are lost when individuals become infected with SIVcpz...
  4. pmc Sympatric chimpanzees and gorillas harbor convergent gut microbial communities
    Andrew H Moeller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 23:1715-20. 2013
    ..These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities. ..
  5. pmc Structural features and the persistence of acquired proteins
    Hema Prasad Narra
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Proteomics 8:4772-81. 2008
    ..coli lineage were more likely to encode soluble and folded proteins, more likely to display environmental modulation of their gene expression, and by extrapolation, are more likely to be functional...
  6. pmc The consequences of genetic drift for bacterial genome complexity
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 19:1450-4. 2009
    ..This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria...
  7. pmc Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 109:13034-9. 2012
    ..This pattern was reinforced in several chimpanzees sampled over long temporal scales, in which the major constituents of the gut microbiota were maintained for nearly a decade...
  8. pmc Evolutionary origins of genomic repertoires in bacteria
    Emmanuelle Lerat
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
    PLoS Biol 3:e130. 2005
    ..Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT...
  9. pmc Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 7:e1002252. 2011
    ..Although pseudogene formation, and thus IGS formation, are ongoing processes in these genomes, a large proportion of intergenic spacers contain functional sequences...
  10. ncbi The nature and dynamics of bacterial genomes
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Science 311:1730-3. 2006
    ..Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell...
  11. pmc Examining bacterial species under the specter of gene transfer and exchange
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, 85721, USA
    Proc Natl Acad Sci U S A 102:6595-9. 2005
    ..Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species...
  12. pmc Genome-wide detection of novel regulatory RNAs in E. coli
    Rahul Raghavan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06516, USA
    Genome Res 21:1487-97. 2011
    ....
  13. ncbi Quartet mapping and the extent of lateral transfer in bacterial genomes
    Vincent Daubin
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, USA
    Mol Biol Evol 21:86-9. 2004
    ..Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa...
  14. pmc Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli
    Vincent Daubin
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 14:1036-42. 2004
    ..Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions...
  15. pmc Origins of flagellar gene operons and secondary flagellar systems
    Renyi Liu
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    J Bacteriol 189:7098-104. 2007
    ..These results demonstrate that the genetic basis of this ancient and structurally conserved organelle has been subject to many lineage-specific modifications...
  16. ncbi Single-cell genomics
    Howard Ochman
    Department of Biochemistry, and Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Environ Microbiol 9:7. 2007
  17. pmc Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Biol Direct 4:35. 2009
    ..In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating...
  18. pmc The effect of chromosome geometry on genetic diversity
    Pradeep Reddy Marri
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Genetics 179:511-6. 2008
    ..Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine...
  19. pmc Extracting single genomes from heterogenous DNA samples: a test case with Carsonella ruddii, the bacterial symbiont of psyllids (Insecta)
    Colin Dale
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
    J Insect Sci 5:3. 2005
    ..The resulting libraries were highly enriched in bacterial sequences. Through the use of alternate enzymes and partial digests, this technique can be adapted to yield virtually pure DNA libraries for individual bacterial species...
  20. pmc The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes
    Nancy A Moran
    Departments of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 87521, USA
    Proc Natl Acad Sci U S A 102:16919-26. 2005
    ..defensa life cycle. We propose that, in these mutualistic symbionts, phage-borne toxin genes provide defense to the aphid host and are a basis for the observed protection against eukaryotic parasites...
  21. pmc Stepwise formation of the bacterial flagellar system
    Renyi Liu
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 104:7116-21. 2007
    ..These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene...
  22. pmc A selective force favoring increased G+C content in bacterial genes
    Rahul Raghavan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 109:14504-7. 2012
    ....
  23. pmc Pea aphid as both host and vector for the phytopathogenic bacterium Pseudomonas syringae
    John Stavrinides
    Department of Ecology and Evolutionary Biology, University of Arizona, 1007 E Lowell Street, Tucson, Arizona 85721, USA
    Appl Environ Microbiol 75:2230-5. 2009
    ..These interactions illustrate that aphids can also vector bacterial pathogens and that even seemingly host-restricted pathogens can have alternative host specificities and lifestyles...
  24. doi The fate of new bacterial genes
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    FEMS Microbiol Rev 33:38-43. 2009
    ..This review summarizes the methods for identifying new genes in bacterial genomes and examines the features that promote the retention and elimination of these evolutionary novelties...
  25. pmc Psi-Phi: exploring the outer limits of bacterial pseudogenes
    Emmanuelle Lerat
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 87521, USA
    Genome Res 14:2273-8. 2004
    ..Almost all (>95%) pseudogenes are restricted to only one of the genomes and are of relatively recent origin, suggesting that these bacteria possess active mechanisms to eliminate nonfunctional genes...
  26. ncbi A bunch of fun-guys: the whole-genome view of yeast evolution
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 87521, USA
    Trends Genet 21:1-3. 2005
    ..The pattern of genome evolution in yeast differs from that in bacteria apparently as a result of stronger selective constraints on bacterial chromosomes...
  27. ncbi Exploring microbial microevolution with microarrays
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Infect Genet Evol 5:103-8. 2005
    ..In this review, we evaluate some of the evolutionary patterns and processes affecting bacterial genomes as detected with microarrays, and also delineate the limitations and conclusions stemming from such studies...
  28. pmc Illumina-based analysis of microbial community diversity
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
    ISME J 6:183-94. 2012
    ..By considering each source of error, we delineate ways to make biologically relevant and robust conclusions from the millions of sequencing reads that can be readily generated by this technology...
  29. ncbi Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
    Scott R Santos
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Environ Microbiol 6:754-9. 2004
    ..We foresee the analysis of these protein-coding regions as being complementary to ribosomal DNA for answering questions pertaining to bacterial identification, classification, phylogenetics and evolution...
  30. pmc The emergence and fate of horizontally acquired genes in Escherichia coli
    Mark W J van Passel
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona, United States of America
    PLoS Comput Biol 4:e1000059. 2008
    ..With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates...
  31. ncbi Start-up entities in the origin of new genes
    Vincent Daubin
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Curr Opin Genet Dev 14:616-9. 2004
    ..This invention of such novel functions seems to be founded on a strategy that secures the short-term survival of parasitic elements and thereby contributes to the renovation of gene repertoires in their host...
  32. pmc Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes
    David Williams
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    BMC Genomics 14:537. 2013
    ..We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads...
  33. doi Disentangling associated genomes
    Daniel B Sloan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    Methods Enzymol 531:445-64. 2013
    ....
  34. pmc Genome reduction promotes increase in protein functional complexity in bacteria
    Yogeshwar D Kelkar
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Genetics 193:303-7. 2013
    ..This suggests that surviving proteins form increasingly complex functional relationships to compensate for genes that are lost...
  35. pmc Recognizing the pseudogenes in bacterial genomes
    Emmanuelle Lerat
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 87521, USA
    Nucleic Acids Res 33:3125-32. 2005
    ....
  36. pmc Genomes on the shrink
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 102:11959-60. 2005
  37. ncbi Of what use is sex to bacteria?
    Hema Prasad Narra
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
    Curr Biol 16:R705-10. 2006
    ....
  38. pmc Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome
    Tyler Jarvik
    Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85718, USA
    J Bacteriol 192:560-7. 2010
    ....
  39. ncbi Erosion of interaction networks in reduced and degraded genomes
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    J Exp Zool B Mol Dev Evol 308:97-103. 2007
    ....
  40. pmc Causes and consequences of genome expansion in fungi
    Yogeshwar D Kelkar
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:13-23. 2012
    ....
  41. pmc Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli
    Rahul Raghavan
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 27388, West Haven, CT 06516 7388, USA
    J Bacteriol 193:2871-4. 2011
    ....
  42. ncbi Neutral mutations and neutral substitutions in bacterial genomes
    Howard Ochman
    Department of Biochemistry and Molecular Biophysics, University of Arizona, USA
    Mol Biol Evol 20:2091-6. 2003
    ..These differences have resulted in conflicting interpretations of the nonselective forces that affect mutation rates...
  43. pmc Deletional Bias across the Three Domains of Life
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona
    Genome Biol Evol 2009:145-52. 2009
    ..Furthermore, deletional bias, rather than natural selection, is the primary mechanism by which the compact gene packing within most prokaryotic genomes is maintained...
  44. ncbi Phylogenetics and the cohesion of bacterial genomes
    Vincent Daubin
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ, 85721, USA
    Science 301:829-32. 2003
    ..Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree...