JBPC Publications 2020

Utter DR, Borisy GG, Eren AM, Cavanaugh CM, Mark Welch JL. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biol. 2020 Dec 16;21(1):293. doi: 10.1186/s13059-020-02200-2. PMID: 33323129; PMCID: PMC7739467.

Shaiber A, Willis AD, Delmont TO, Roux S, Chen LX, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol. 2020 Dec 16;21(1):292. doi: 10.1186/s13059-020-02195-w. PMID: 33323122; PMCID: PMC7739484.

Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun. 2020 Dec 18;11(1):6421. doi: 10.1038/s41467-020-19614-y. PMID: 33339818; PMCID: PMC7749112.

Arkhipova IR. Metagenome Proteins and Database Contamination. mSphere. 2020 Nov 4;5(6):e00854-20. doi: 10.1128/mSphere.00854-20. PMID: 33148820; PMCID: PMC7643828.

Sieber CMK, Paul BG, Castelle CJ, Hu P, Tringe SG, Valentine DL, Andersen GL, Banfield JF. Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. mBio. 2019 Nov 12;10(6):e02128-19. doi: 10.1128/mBio.02128-19. PMID: 31719174; PMCID: PMC6851277.

Vallota-Eastman A, Arrington EC, Meeken S, Roux S, Dasari K, Rosen S, Miller JF, Valentine DL, Paul BG. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics. 2020 Sep 25;21(1):664. doi: 10.1186/s12864-020-07052-5. PMID: 32977771; PMCID: PMC7517822.

Mark Welch JL, Ramírez-Puebla ST, Borisy GG. Oral Microbiome Geography: Micron-Scale Habitat and Niche. Cell Host Microbe. 2020 Aug 12;28(2):160-168. doi: 10.1016/j.chom.2020.07.009. PMID: 32791109; PMCID: PMC7604680.

Quigley CTC, Capistrant-Fossa KA, Morrison HG, Johnson LE, Morozov A, Hertzberg VS, Brawley SH. Bacterial Communities Show Algal Host (Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone. Front Microbiol. 2020 Sep 24;11:563118. doi: 10.3389/fmicb.2020.563118. PMID: 33072025; PMCID: PMC7541829.

Funikov SY, Rezvykh AP, Kulikova DA, Zelentsova ES, Protsenko LA, Chuvakova LN, Tyukmaeva VI, Arkhipova IR, Evgen’ev MB. Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. Sci Rep. 2020 Jul 17;10(1):11893. doi: 10.1038/s41598-020-68879-2. PMID: 32681087; PMCID: PMC7368049.

Fowler BL, Neubert MG, Hunter-Cevera KR, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Dynamics and functional diversity of the smallest phytoplankton on the Northeast US Shelf. Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12215-12221. doi: 10.1073/pnas.1918439117. Epub 2020 May 15. PMID: 32414929; PMCID: PMC7275697.

Hernández CM, van Daalen SF, Caswell H, Neubert MG, Gribble KE. A demographic and evolutionary analysis of maternal effect senescence. Proc Natl Acad Sci U S A. 2020 Jul 14;117(28):16431-16437. doi: 10.1073/pnas.1919988117. PMID: 32601237; PMCID: PMC7368264.

Lemonnier, C., Perennou, M., Eveillard, D., Fernandez-Guerra, A., Leynaert, A., Marie, L., Morrison H. G., Memery L., Paillard C.,  Maignien, L. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. FRONTIERS IN MARINE SCIENCE. 2020 Jun 09; 7, 13 pages. doi:10.3389/fmars.2020.00376

Schlundt C, Mark Welch JL, Knochel AM, Zettler ER, Amaral-Zettler LA. Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris. Mol Ecol Resour. 2020 May;20(3):620-634. doi: 10.1111/1755-0998.13119. PMID: 31782619; PMCID: PMC7318237.

Hunter-Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. Limnol Oceanogr. 2020 May;65(5):1085-1102. doi: 10.1002/lno.11374. Epub 2019 Nov 19. PMID: 32612307; PMCID: PMC7319482.

Antosca K, Hoen AG, Palys T, Hilliard M, Morrison HG, Coker M, Madan J, Karagas MR. Reliability of stool microbiome methods for DNA yields and sequencing among infants and young children. Microbiologyopen. 2020 May;9(5):e1018. doi: 10.1002/mbo3.1018. Epub 2020 Mar 12. PMID: 32166902; PMCID: PMC7221451.

Chakraborty, A, Ruff, SE, Dong, X, Ellefson, ED, Li, C, Brooks, JM, McBee, J, Bernard, BB, & Hubert, CRJ. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proc Natl Acad Sci U S A.  2020 May; 117(20), 11029-11037. doi: 10.1073/pnas.2002289117 PMID: 32354993; PMCID: PMC7245137

Grettenberger, CL, McCauley Rench, RL, Gruen, DS, Mills, DB, Carney, C, Brainard, J, Hamasaki, H, Ramirez, R, Watanabe, Y, Amaral-Zettler, LA, Ohmoto, H, & Macalady, JL. Microbial population structure in a stratified, acidic pit lake in the Iberian Pyrite Belt. GEOMICROBIOLOGY JOURNAL. 2020 Apr11; 37(7), 623-634. doi: 10.1080/01490451.2020.1751748.

Chen, LX, Anantharaman, K, Shaiber, A, Eren, AM, & Banfield, JF. Accurate and complete genomes from metagenomes. Genome Research. 2020 March 30(3), 315-333. doi: 10.1101/gr.258640.119  PMID: 32188701; PMCID: PMC7111523

Dai, Z, Sevillano-Rivera, MC, Calus, ST, Bautista-de Los Santos, QM, Eren, AM, van der Wielen, P, Ijaz, UZ, & Pinto, AJ. Disinfection exhibits systematic impacts on the drinking water microbiome. Microbiome. 2020 March20; 8(1), 42. doi: 10.1186/s40168-020-00813-0. PMID: 32197656; PMCID: PMC7085177

Wilbert SA, Mark Welch JL, Borisy GG. Spatial Ecology of the Human Tongue Dorsum Microbiome. Cell Rep. 2020 Mar 24;30(12):4003-4015.e3. doi: 10.1016/j.celrep.2020.02.097. PMID: 32209464; PMCID: PMC7179516.

Amaral-Zettler LA, Zettler ER, Mincer TJ. Ecology of the plastisphere. Nat Rev Microbiol. 2020 Mar;18(3):139-151. doi: 10.1038/s41579-019-0308-0. PMID: 31937947.

Rossetti BJ, Wilbert SA, Mark Welch JL, Borisy GG, Nagy JG. Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs. Bioinformatics. 2020 Feb 1;36(3):910-917. doi: 10.1093/bioinformatics/btz674. PMID: 31504202; PMCID: PMC7523684.

Kuloyo, O, Ruff, SE, Cahill, A, Connors, L, Zorz, JK, Hrabe de Angelis, I, Nightingale, M, Mayer, B, & Strous, M. Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environ Microbiology. 2020 Feb03; 22(4), 1222-1237. doi: 10.1111/1462-2920.14929 PMID: 32017377; PMCID: PMC7187433

Bhatnagar, S, Cowley, ES, Kopf, SH, Castro, SP, Kearney, S, Dawson, SC, Hanselmann, K, & Ruff, SE. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome. 2020 Jan; 15(1). doi: 10.1186/s40793-019-0348-0 

Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR, Madan JC. Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study. BJOG. 2020 Jan;127(2):217-227. doi: 10.1111/1471-0528.15799. PMID: 31006170; PMCID: PMC6803026.

Gurdebeke PR,  Mertens KN, Pospelova V, Matsuoka K, Li Z, Gribble KE, Gu H, Bogus K, Vrielinck H & Louwye S. Taxonomic revision, phylogeny, and cyst wall composition of the dinoflagellate cyst genus Votadinium Reid (Dinophyceae, Peridiniales, Protoperidiniaceae), Palynology. 2020; 44:2,310-335, doi: 10.1080/01916122.2019.1580627

Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol. 2020 Jan;5(1):2-3. doi: 10.1038/s41564-019-0644-x. PMID: 31857734.