Cheryl P. Andam

Cheryl P. Andam

Assistant Professor

Educational background:

Postdoc, Harvard University
Postdoc, Cornell University
Ph.D., University of Connecticut
M.S., Binghamton University, State University of New York
B.S., University of the Philippines Los Banos

General area of interest:

Microbial ecology, evolution and genomics; horizontal gene transfer and recombination; ancient evolution and the Tree/Net of Life; microbial biogeography

Courses taught:

GEN 713 Microbial Ecology and Evolution


My lab aims to elucidate the evolutionary processes and ecological factors that drive the diversification and adaptation of microorganisms in various ecosystems, transcending different time scales ranging from disease outbreaks to the origins of life. Using an inter-disciplinary approach combining next-generation sequencing (genomics), population genetics, phylogenetics and lab-based assays, I aim to identify the underlying mechanisms that govern population-level structure and dynamics of microbes in response to environmental perturbations and selective pressures.

Streptomyces diversity and evolution:

With more than 650 recognized species, the bacterial genus Streptomyces (phylum Actinobacteria) constitutes one of the largest and most diverse genera in the bacterial domain. They are ubiquitous in soil and decaying vegetation, where they play an important role in organic matter degradation, as well as in association with diverse eukaryotes. They widely known for being the major producers of majority of antibiotics used in clinical settings. I am establishing a culture collection of diverse Streptomyces species from soil, compost material, soil invertebrates (e.g., earthworms), vertebrates, animal feces and other habitats. My goal is to understand the forces that have shape their diversity. I am also interested in identifying super-killer Streptomyces strains, or those that are able to inhibit the growth of many other bacteria in the population. These have tremendous impact on enhancing antibiotic discovery approaches and alleviating multidrug resistance.

Horizontal gene transfer (HGT) and recombination:

HGT, 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. Hence, phylogenetic uncertainties due to multiple origins of DNA, crossing even species barriers, make it challenging to study their evolution. I am particularly interested in the process, mechanisms and impacts of horizontal gene transfer on the ecology, evolution and genome structure of bacteria and archaea. My interests lie in understanding HGT (1) that have occurred in ancient evolution and the Tree of Life, and (2) HGT in recent bacterial populations. We have previously shown that HGT plays a major role in the evolutionary history and genetic diversity of Streptomyces, but the extent of HGT varies considerably between species. DNA horizontally acquired by ancestral lineages and passed on to descendants through vertical inheritance has also contributed to Streptomyces speciation. I aim to answer the following questions: (1) What is the origin of microbial species, and what evolutionary and ecological mechanisms keep them separate once they begin to diverge? (2) To what extent are these mechanisms universal across diverse types of microbes, and more broadly across the entire the tree of life?

Population structure and within-species diversity of bacteria:

Extensive fine-scale genetic diversity is found in many microbial species across varied environments (clinic, agriculture, soil, marine, freshwater), but for most, the evolutionary and ecological processes and mechanisms that generate the observed variation remain unclear. While neutral drift can account for this within-species diversity, it is more likely that many microbial species contain numerous populations occupying discrete ecological niches, including cryptic niches that are not readily observable or measured. This is particularly important in ecosystems disturbed by anthropogenic activities, which can greatly affect the genomic variation and adaptive capacity of microbes. Using bacterial samples from farms, livestock and compost, I aim to address the following: (1) What are the genomic differences among members of a single species? (2) How did they arise and to which extent are they neutral or have an ecological relevance? (3) How do environmental perturbations, such as pollution, rising global temperatures and land use change, alter the genomic diversity and population structure of microbes? (4) What generates the diversity of antibiotics and antibiotic producing bacteria in nature?


Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall B, Hanage WP. 2017. Genomic epidemiology of penicillin non-susceptible pneumococci with non-vaccine serotypes causing invasive disease in the USA. J Clin Microbiol (Epub ahead of print).

Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ. 2016. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Nat Acad Sci USA 113(52):15066-15071.

Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Plessis MD, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD, PAGe Consortium . 2016. Understanding pneumococcal serotype serotype 1 biology through population genomic analysis. BMC Infect Dis 16:649.

Chaguza C, Andam CP, Harris SK, Cornick JE, Yang M, Bricio-Moreno L, Kamng’ona AW, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WP. 2016. Recombination in Streptococcus pneumoniae lineages increases with carriage duration and size of the polysaccharide capsule. mBio 7: e01053-16.

Andam CP, Worby CJ, Chang Q, Campana MG. 2016. Microbial genomics of ancient plagues and outbreaks. Trends in Microbiol 24:978-990.

Andam CP, Doroghazi JR, Campbell AN, Kelly PJ, Choudoir MJ, Buckley DH. 2016. A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces. mBio 7:e02200-15.  Featured in Cornell Chronicle, May 25, 2016 ( Commentary by Dr. Jennifer BH Martiny (UC Irvine), June 7, 2016. (

Andam CP, Choudoir MJ, Nguyen VA, Park HS, Buckley DH. 2016. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages. ISME Journal 10: 1731-1741.

Pepe-Ranney C, Koechli C, Potrafka R, Andam C, Eggleston E, Garcia-Pichel F, Buckley DH. 2016. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. ISME Journal 10:287-298.

Andam CP, Carver SM, Berthrong ST. 2015. Horizontal gene flow in managed ecosystems. Ann Rev Ecol Evol Syst 46:121-143.

Fournier GP, Andam CP, Gogarten JP. 2015. Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol 15:70.  Rated as highly accessed.

Andam CP, Hanage WP. 2015. Mechanisms of genome evolution in Streptococcus. Infect Genet Evol 33:334–342.

Andam CP, Harlow TJ, Papke RT, Gogarten JP. 2012. Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. BMC Evol Biol 12:85.

Andrus A, Andam C, Parker MA. 2012. American origin of Cupriavidus bacteria associated with invasive Mimosa legumes in the Philippines. FEMS Microbiol Ecol 80:747–750.

Fournier GP, Andam CP, Alm EJ, Gogarten JP. 2012.  Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig Life Evol Biosph 41:621–632.

Andam CP, Driscoll JR, Enke TN, Macula AJ, Gal S. 2012. Comparison of different polymerase chain reaction methods to analyze a DNA computing library. Nat Computing 11:339–349.

Andam CP, Gogarten JP. 2011. Biased gene transfer and its implications for the concept of lineage. Biol Direct 6:47.

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP. 2011.  A rooted net of life. Biol Direct 6:45. Rated as highly accessed.

Andam CP, Gogarten JP. 2011. Biased gene transfer in microbial evolution. Nature Rev Microbiol 9:543–555.

Andam CP, Fournier GP, Gogarten JP. 2011. Multi-level populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev 35:756–767.

Andam CP, Williams D, Gogarten JP. 2010. Biased gene transfer mimics patterns created through shared ancestry. Proc Nat Acad Sci USA 107:10679–10684.

Andam CP, Williams D, Gogarten JP. 2010. Natural taxonomy in light of horizontal gene transfer. Special issue on the Tree of Life. Biol & Philo 25:589–602.

Macula AJ, Gal S, Andam C, Renz TE, Bishop MA. 2009. PCR non-adaptive group testing of DNA libraries for biomolecular computing and taggant applications. Discrete Math Algorithms Appl 1:59–69.

Andam CP, Parker MA. 2008. Origins of Bradyrhizobium nodule symbionts from two legume trees in the Philippines. J Biogeog 35: 1030–1039.

Andam CP, Parker MA. 2007.  Novel Alphaproteobacterial root nodule symbiont associated with Lupinus texensis. Appl Environ Microbiol 73: 5687–5691.       

Andam CP, Mondo SJ, Parker MA. 2007. Monophyly of nodA and nifH genes across Texas and Costa Rican populations of Cupriavidus nodule symbionts.  Appl Environ Microbiol 73: 4686–4690.


Rudman Hall, Room 206
Durham, NH 03824
(603) 862-1881