Positions

Research Areas research areas

Overview

  • My research focuses on microbial population genomics and evolution. I was trained at the University of the Philippines (B.S.), Binghamton University (M.S.), University of Connecticut (Ph.D.), Cornell University (Postdoc) and the Harvard School of Public Health (Postdoc).

    Current work in my lab aims to elucidate the evolutionary processes and ecological factors that drive the diversification and adaptation of microorganisms in different environments. Specifically, we study the genomic differences between strains and species, with implications to the evolution of antibiotic resistance, emergence of virulent lineages, host adaptation, gene flow, geographical distribution and spread. Using an inter-disciplinary approach combining next-generation sequencing (genomics), population genetics, phylogenetics and lab-based assays, we ask the questions:

    (1) How extensive are the genomic differences within a species? How did they arise and to which extent are they neutral or adaptive?
    (2) How do perturbations, such as antibiotic use or environmental change, alter the genomic diversity and population structure of microbes? 
    (3) What is the genetic basis of host adaptation and host switching?
    (4) How is resistance maintained and distributed in bacterial populations, and what are the mechanisms that promote the emergence and dissemination of super-fit multidrug resistant clones?
    (5) How can we use genomic data to identify co-circulating, independent transmission chains and unsuspected “cryptic” transmission events?

    We study different species of bacterial pathogens. My lab works closely with the New Hampshire Veterinary Diagnostic Laboratory (NHVDL) to study the emergence of antibiotic resistance in multiple Staphylococcus species and enteric bacteria from pets, livestock and wildlife. We also work with NH state health and agriculture agencies to study the genome dynamics and evolution of bacterial pathogens such as Salmonella enterica, Campylobacter jejuni and Staphylococcus aureus infecting humans and animals. We also use publicly available genomes to further explore the nature of microbial species and the different evolutionary processes that contribute to their diversification and adaptation.

    Within-species variation: Bacterial and archaeal populations are remarkably heterogeneous. They may be clonal, but microbial populations are often composed of multiple co-circulating lineages distinguished by phenotypic and genetic differences, the latter originating from both allelic variation and gene content variation. While puzzling, within-species heterogeneity in microbes is not uncommon, but the underlying factors that drive this variation remain unclear. We are interested in understanding the processes that contribute to the generation and maintenance of this variation within a species. To address this, we study "populations of genomes" that represent clusters of close relatives within and between environments or hosts.

    Horizontal gene transfer (HGT) and recombination: The acquisition of genetic material between two organisms that do not share a direct ancestor-descendant relationship is an important mechanism that contributes to the rapid creation of biological novelty that otherwise might have taken millions of years to occur. This is particularly pervasive across microbial lineages, creating phenotypic and genetic variation that can take bewilderingly complex forms even between closely related lineages. HGT enables organisms to acquire pre-existing adaptive characters from other organisms, regardless of phylogenetic distance. Thus, instead of genetic traits within lineages always emerging gradually through successive mutations and selection, evolution is accelerated as a parallel process, where inventions made in different lineages can come together in a single cell through HGT. In microbial populations, HGT and recombination (the acquisition of genetic material through genetic exchange of similar DNA sequences) are important processes that can lead to extensive genetic diversity in terms of gene content and allelic variation within a species. We are interested in identifying HGT and recombination events, and understand its contributions to the evolution of diverse microbial species.
  • Publications

    Academic Article

    Year Title
    2018 Utilization of Low Grade Wood for Use as Animal Bedding: A Case Study of Eastern HemlockJournal of Forestry.  116:520-528. 2018
    2018 Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009Eurosurveillance.  23:15-23. 2018
    2018 Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009.Eurosurveillance.  23:1700592. 2018
    2018 Therapeutic effect of Northern Labrador tea extracts for acute myeloid leukemia.Phytotherapy Research.  32:1636-1641. 2018
    2017 Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi.Vaccine.  35:4594-4602. 2017
    2017 Genome Surfing As Driver of Microbial Genomic Diversity.Trends in Microbiology.  25:624-636. 2017
    2017 Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States.Emerging Infectious Diseases.  23:1012-1015. 2017
    2017 Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.Molecular Biology and Evolution.  34:1167-1182. 2017
    2017 Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.Journal of Clinical Microbiology.  55:1104-1115. 2017
    2016 Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.Proceedings of the National Academy of Sciences of the United States of America.  113:15066-15071. 2016
    2016 Microbial Genomics of Ancient Plagues and Outbreaks.Trends in Microbiology.  24:978-990. 2016
    2016 Understanding pneumococcal serotype 1 biology through population genomic analysis.BMC Infectious Diseases.  16:649. 2016
    2016 Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.mBio.  7:e01053-e01016. 2016
    2016 Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages.ISME Journal.  10:1731-1741. 2016
    2016 A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces.mBio.  7:e02200-e02215. 2016
    2016 Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation.ISME Journal.  10:287-298. 2016
    2015 Mechanisms of genome evolution of Streptococcus.Infection, Genetics and Evolution.  33:334-342. 2015
    2015 Ancient horizontal gene transfer and the last common ancestors.BMC Evolutionary Biology.  15:70. 2015
    2012 Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life (vol 41, pg 621, 2011)Origins of Life and Evolution of Biospheres Origins of Life.  42:377-377. 2012
    2012 Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.BMC Evolutionary Biology.  12:85. 2012
    2012 American origin of Cupriavidus bacteria associated with invasive Mimosa legumes in the Philippines.FEMS Microbiology Ecology.  80:747-750. 2012
    2012 Comparison of different methods to analyze a DNA computing library using the polymerase chain reactionNatural Computing.  11:339-349. 2012
    2011 Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life.Origins of Life and Evolution of Biospheres Origins of Life.  41:621-632. 2011
    2011 Biased gene transfer and its implications for the concept of lineage.Biology Direct.  6:47. 2011
    2011 A rooted net of life.Biology Direct.  6:45. 2011
    2011 Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.FEMS Microbiology Reviews.  35:756-767. 2011
    2011 Biased gene transfer in microbial evolution.Nature Reviews Microbiology.  9:543-555. 2011
    2010 Natural taxonomy in light of horizontal gene transferBiology and Philosophy.  25:589-602. 2010
    2010 Biased gene transfer mimics patterns created through shared ancestry.Proceedings of the National Academy of Sciences of the United States of America.  107:10679-10684. 2010
    2009 PCR NONADAPTIVE GROUP TESTING OF DNA LIBRARIES FOR BIOMOLECULAR COMPUTING AND TAGGANT APPLICATIONSDiscrete Mathematics, Algorithms and Applications.  01:59-69. 2009
    2008 Origins of Bradyrhizobium nodule symbionts from two legume trees in the PhilippinesJournal of Biogeography.  35:1030-1039. 2008
    2007 Novel alphaproteobacterial root nodule symbiont associated with Lupinus texensis.Applied and Environmental Microbiology.  73:5687-5691. 2007
    2007 Monophyly of nodA and nifH genes across Texan and Costa Rican populations of Cupriavidus nodule symbionts.Applied and Environmental Microbiology.  73:4686-4690. 2007

    Chapter

    Year Title
    2017 Population Structure of Pathogenic Bacteria.  51-70. 2017
    2015 Horizontal Gene Flow in Managed EcosystemsAnnual Review of Ecology and Systematics Annual Review of Ecology, Evolution, and Systematics. 121-143. 2015
    2010 Horizontal Gene Transfer and the Formation of Groups of Microorganisms.  167-184. 2010

    Conference Proceeding

    Year Title
    2018 A Novel Approach for Increasing Taxonomic Resolution in Protein-Based Alignments.BCB. 538-538. 2018

    Teaching Activities

  • Adv Rsrch Exp/MCBS Taught course 2019
  • General Microbiology Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • General Microbiology Lab Taught course 2019
  • Microbial Ecology & Evolution Taught course 2019
  • Adv Rsrch Exp/MCBS Taught course 2018
  • Doctoral Research Taught course 2018
  • Microbial Ecology & Evolution Taught course 2018
  • Infectious Disease and Health Taught course 2017
  • Infectious Disease and Health Taught course 2017
  • Microbial Ecology & Evolution Taught course 2017
  • Education And Training

  • B.S. Forestry, University of The Phillipines
  • M.S. Biology/Biological Sciences, State University of New York at Binghamton
  • Ph.D. Microbiology, University of Connecticut
  • Full Name

  • Cheryl Marie Andam