@article{rizzo_choudoir_simoes_dayarathne_deangelis_2024, title={High-quality draft genome sequence of <i>Paenibacillus</i> sp. RC80, a candidate for biofuel production}, volume={6}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.01067-23}, DOI={10.1128/mra.01067-23}, abstractNote={ABSTRACT Paenibacillus sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Rizzo, Gabriella and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and Deangelis, Kristen M.}, editor={Thrash, J. CameronEditor}, year={2024}, month={Jun} }
 @article{sullivan_kitzmiller_tran_choudoir_simoes_dayarathne_deangelis_2023, title={Complete genome sequence of <i>Bacillus thuringiensis</i> strain RC340, isolated from a temperate forest soil sample in New England}, volume={10}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00607-23}, DOI={10.1128/MRA.00607-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sullivan, Brendan and Kitzmiller, Claire E. and Tran, Wyatt C. and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and DeAngelis, Kristen M.}, editor={Rasko, DavidEditor}, year={2023}, month={Oct} }
 @article{tran_sullivan_kitzmiller_choudoir_simoes_dayarathne_deangelis_2023, title={Draft genome sequence of <i>Paenibacillus</i> sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts}, volume={10}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00373-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Tran, Wyatt C. and Sullivan, Brendan and Kitzmiller, Claire E. and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and Deangelis, Kristen M.}, year={2023}, month={Oct} }
 @article{kitzmiller_tran_sullivan_cortez_choudoir_simoes_dayarathne_deangelis_2023, title={High-quality genomes of Paenibacillus spp. RC334 and RC343, isolated from a long-term forest soil warming experiment}, volume={8}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00371-23}, DOI={10.1128/MRA.00371-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Kitzmiller, Claire E. and Tran, Wyatt C. and Sullivan, Brendan and Cortez, Florencia and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and Deangelis, Kristen M.}, editor={Baltrus, David A.Editor}, year={2023}, month={Aug} }
 @article{choudoir_narayanan_rodriguez-ramos_simoes_efroni_sondrini_deangelis_2023, title={Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming}, url={https://doi.org/10.1101/2023.03.16.532972}, DOI={10.1101/2023.03.16.532972}, abstractNote={Abstract}, author={Choudoir, Mallory J. and Narayanan, Achala and Rodriguez-Ramos, Damayanti and Simoes, Rachel and Efroni, Alon and Sondrini, Abigail and DeAngelis, Kristen M.}, year={2023}, month={Mar} }
 @article{choudoir_deangelis_2022, title={A framework for integrating microbial dispersal modes into soil ecosystem ecology}, volume={25}, url={http://dx.doi.org/10.1016/j.isci.2022.103887}, DOI={10.1016/j.isci.2022.103887}, abstractNote={Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.}, number={3}, journal={iScience}, publisher={Elsevier BV}, author={Choudoir, Mallory J. and DeAngelis, Kristen M.}, year={2022}, month={Mar}, pages={103887} }
 @article{schaal_choudoir_diwanji_stoffolano_deangelis_2022, title={Chitosan diet alters the microbiome of adult house flies}, url={https://doi.org/10.1101/2022.08.31.502951}, DOI={10.1101/2022.08.31.502951}, abstractNote={Abstract}, author={Schaal, Hila and Choudoir, Mallory J. and Diwanji, Vedang and Stoffolano, John, Jr. and DeAngelis, Kristen M.}, year={2022}, month={Aug} }
 @article{choudoir_eggleston_2022, title={Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges}, volume={7}, url={http://dx.doi.org/10.1128/msystems.01462-21}, DOI={10.1128/msystems.01462-21}, abstractNote={Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations.}, number={3}, journal={mSystems}, publisher={American Society for Microbiology}, author={Choudoir, Mallory J. and Eggleston, Erin M.}, editor={Ishaq, Suzanne LynnEditor}, year={2022}, month={Jun} }
 @article{hariharan_choudoir_diebold_panke-buisse_buckley_2022, title={Streptomyces apricus sp. nov., isolated from soil}, volume={72}, url={https://doi.org/10.1099/ijsem.0.005178}, DOI={10.1099/ijsem.0.005178}, abstractNote={A novel 
                     
                        Streptomyces
                     
                   strain, SUN51T, was isolated from soils sampled in Wisconsin, USA, as part of a 
                     
                        Streptomyces
                     
                   biogeography survey. Genome sequencing revealed that this strain had less than 90 % average nucleotide identity (ANI) to type species of 
                     
                        Streptomyces
                     
                  : SUN51T was most closely related to Streptomyces dioscori A217T (99.5 % 16S rRNA gene identity, 89.4 % ANI). Genome size was estimated at 8.81 Mb, and the genome DNA G+C content was 72 mol%. The strain possessed the cellular fatty acids anteiso-C15 : 0, iso-C16 : 0, 16 : 1 ω7c, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0. The predominant menaquinones were MK-9 H4, MK-9 H6 and MK-9 H8. Strain SUN51T contained the polar lipids phosphatidic acid, phosphatidyl ethanolamine, phosphatidyl glycerol and diphosphatidyl glycerol. The cell wall contained ll-diaminopimelic acid. The strain could grow on a broad range of carbon sources and tolerate temperatures of up to 40 °C. The results of the polyphasic study confirmed that this isolate represents a novel species of the genus 
                     
                        Streptomyces
                     
                  , for which the name Streptomyces apricus sp. nov. is proposed. The type strain of this species is SUN51T (=NRRL B-65543T=JCM 33736T).}, number={1}, journal={International Journal of Systematic and Evolutionary Microbiology}, publisher={Microbiology Society}, author={Hariharan, Janani and Choudoir, Mallory J. and Diebold, Peter and Panke-Buisse, Kevin and Buckley, Daniel H.}, year={2022}, month={Jan} }
 @article{choudoir_järvenpää_marttinen_buckley_2021, title={A non-adaptive demographic mechanism for genome expansion in <i>Streptomyces</i>}, volume={1}, url={http://dx.doi.org/10.1101/2021.01.09.426074}, DOI={10.1101/2021.01.09.426074}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Choudoir, Mallory J and Järvenpää, Marko J and Marttinen, Pekka and Buckley, Daniel H}, year={2021}, month={Jan} }
 @article{ishaq_parada_wolf_bonilla_carney_benezra_wissel_friedman_deangelis_robinson_et al._2021, title={Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice}, volume={6}, url={http://dx.doi.org/10.1128/msystems.00471-21}, DOI={10.1128/msystems.00471-21}, abstractNote={Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems.}, number={4}, journal={mSystems}, publisher={American Society for Microbiology}, author={Ishaq, Suzanne L. and Parada, Francisco J. and Wolf, Patricia G. and Bonilla, Carla Y. and Carney, Megan A. and Benezra, Amber and Wissel, Emily and Friedman, Michael and DeAngelis, Kristen M. and Robinson, Jake M. and et al.}, editor={Gilbert, Jack A.Editor}, year={2021}, month={Aug} }
 @article{mcbride_choudoir_fierer_strickland_2020, title={Volatile organic compounds from leaf litter decomposition alter soil microbial communities and carbon dynamics}, url={https://doi.org/10.1002/ecy.3130}, DOI={10.1002/ecy.3130}, abstractNote={Abstract}, journal={Ecology}, author={McBride, Steven G. and Choudoir, Mallory and Fierer, Noah and Strickland, Michael S.}, year={2020}, month={Oct} }
 @article{choudoir_rossabi_gebert_helmig_fierer_2019, title={A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by Actinobacteria}, volume={4}, url={https://doi.org/10.1128/mSystems.00295-18}, DOI={10.1128/mSystems.00295-18}, abstractNote={
            Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling
            Actinobacteria in vitro
            . We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention.
          }, number={2}, journal={mSystems}, publisher={American Society for Microbiology}, author={Choudoir, Mallory and Rossabi, Sam and Gebert, Matthew and Helmig, Detlev and Fierer, Noah}, editor={Whiteson, Katrine L.Editor}, year={2019}, month={Apr} }
 @article{choudoir_pepe-ranney_buckley_2018, title={Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in <em>Streptomyces</em>}, volume={7}, url={http://www.mdpi.com/2079-6382/7/1/12}, DOI={10.3390/antibiotics7010012}, abstractNote={We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence.}, number={1}, journal={Antibiotics}, publisher={MDPI AG}, author={Choudoir, Mallory and Pepe-Ranney, Charles and Buckley, Daniel}, year={2018}, month={Feb}, pages={12} }
 @article{choudoir_buckley_2018, title={Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa}, volume={12}, url={http://dx.doi.org/10.1038/s41396-018-0180-3}, DOI={10.1038/s41396-018-0180-3}, abstractNote={Abstract}, number={9}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Choudoir, Mallory J. and Buckley, Daniel H.}, year={2018}, month={Sep}, pages={2176–2186} }
 @article{choudoir_barberan_menninger_dunn_fierer_2018, title={Variation in range size and dispersal capabilities of microbial taxa}, volume={99}, ISSN={["1939-9170"]}, url={https://doi.org/10.1002/ecy.2094}, DOI={10.1002/ecy.2094}, abstractNote={Abstract}, number={2}, journal={ECOLOGY}, publisher={Wiley}, author={Choudoir, Mallory J. and Barberan, Albert and Menninger, Holly L. and Dunn, Rob R. and Fierer, Noah}, year={2018}, month={Feb}, pages={322–334} }
 @article{rossabi_choudoir_helmig_hueber_fierer_2018, title={Volatile Organic Compound Emissions From Soil Following Wetting Events}, url={https://doi.org/10.1029/2018JG004514}, DOI={10.1029/2018JG004514}, abstractNote={Abstract}, journal={Journal of Geophysical Research: Biogeosciences}, author={Rossabi, Sam and Choudoir, Mallory and Helmig, Detlev and Hueber, Jacques and Fierer, Noah}, year={2018}, month={Jun} }
 @article{choudoir_panke-buisse_andam_buckley_2017, title={Genome Surfing As Driver of Microbial Genomic Diversity}, volume={25}, url={http://dx.doi.org/10.1016/j.tim.2017.02.006}, DOI={10.1016/j.tim.2017.02.006}, abstractNote={Microbial genomic diversity is often explained by invoking selection acting on large populations at demographic equilibrium. However, historical fluctuations in population size can produce nonadaptive changes in genomic diversity due to drift. Gene surfing can explain patterns of genomic diversity in diverse species of plants and animals as a consequence of postglacial range expansion driven by historical climate change during the Pleistocene. We propose that genome surfing can result when the demographic mechanisms which produce gene surfing act on microbial populations capable of horizontal gene transfer (HGT). Patterns of genetic diversity and gene flow within Streptomyces are indicative of postglacial demographic range expansion. Genome surfing provides a mechanism to explain ancestral patterns of horizontal gene exchange and current patterns of genomic diversity observed within Streptomyces. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. a severe reduction in a population size. the number of individuals of an idealized population needed to capture the genetic diversity of the actual population. the moving boundary of a range expansion. a reduction in genetic diversity caused when a small number of individuals founds a population. a genetic consequence of range expansion driven by neutral variations in gene frequencies that occur at an expansion edge. an evolutionary mechanism whereby allele or gene frequencies change as a result of random sampling effects. contemporaneous introgression of many horizontally acquired genes into a pan-genome as a consequence of gene surfing. the permanent incorporation of genes from one pan-genome into a second pan-genome of a divergent lineage. a mechanism that causes spatial gradients of genetic diversity when dispersal limitation allows the local accumulation of genetic variation. a radial pattern of genetic discontinuity produced during range expansions. a population characterized by unlimited gene flow. the physical co-occurrence of items in space and time. an event that occurs when a population colonizes a geographic region which it did not previously occupy, and which may or may not already be occupied by other populations, as facilitated by dispersal. an evolutionary mechanism whereby allele or gene frequencies change in response to fitness effects. a loss of genetic variation resulting from a rapid fixation of a beneficial allele or gene.}, number={8}, journal={Trends in Microbiology}, publisher={Elsevier BV}, author={Choudoir, Mallory J. and Panke-Buisse, Kevin and Andam, Cheryl P. and Buckley, Daniel H.}, year={2017}, month={Aug}, pages={624–636} }
 @article{andam_doroghazi_campbell_kelly_choudoir_buckley_2016, title={A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces}, volume={7}, number={2}, journal={mBio}, publisher={Am Soc Microbiol}, author={Andam, Cheryl P and Doroghazi, James R and Campbell, Ashley N and Kelly, Peter J and Choudoir, Mallory J and Buckley, Daniel H}, year={2016}, pages={e02200–15} }
 @article{andam_choudoir_nguyen_park_buckley_2016, title={Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages}, journal={The ISME journal}, publisher={Nature Publishing Group}, author={Andam, Cheryl P and Choudoir, Mallory J and Nguyen, Anh Vinh and Park, Han Sol and Buckley, Daniel H}, year={2016} }
 @article{choudoir_doroghazi_d.h._2016, title={Latitude delineates patterns of biogeography in terrestrial Streptomyces}, volume={18}, DOI={10.1111/1462-2920.13420}, abstractNote={Summary}, journal={Environmental Microbiology}, author={Choudoir, M.J. and Doroghazi, Buckley, JR and D.H.}, year={2016}, pages={4931–4945} }
 @article{choudoir_campbell_buckley_2012, title={Grappling with Proteus: population level approaches to understanding microbial diversity}, volume={3}, journal={Frontiers in microbiology}, publisher={Frontiers}, author={Choudoir, Mallory J and Campbell, Ashley N and Buckley, Daniel H}, year={2012}, pages={336} }
 @article{raphael_choudoir_lúquez_fernández_maslanka_2010, title={Sequence diversity of genes encoding botulinum neurotoxin type F}, volume={76}, number={14}, journal={Applied and environmental microbiology}, publisher={Am Soc Microbiol}, author={Raphael, Brian H and Choudoir, Mallory J and Lúquez, Carolina and Fernández, Rafael and Maslanka, Susan E}, year={2010}, pages={4805–4812} }
 @article{kramer_choudoir_wielgus_bhaskar_jiang_2009, title={Correlation between transcript abundance of the RB gene and the level of the RB-mediated late blight resistance in potato}, volume={22}, number={4}, journal={Molecular Plant-Microbe Interactions}, publisher={Am Phytopath Society}, author={Kramer, Lara C and Choudoir, Mallory J and Wielgus, Susan M and Bhaskar, Pudota B and Jiang, Jiming}, year={2009}, pages={447–455} }