JBPC Publications – 2019 to current

2021:

Coker MO, Laue HE, Hoen AG, Hilliard M, Dade E, Li Z, Palys T, Morrison HG, Baker E, Karagas MR and Madan JC. Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life. Front. Microbiol. 07 April 2021; 12:642197. doi: 10.3389/fmicb.2021.642197PMID: 33897650; PMCID: PMC8059768

Klasek SA, Brock MT, Morrison HG, Weinig C and Maignien L. Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure. Front. Microbiol. 07 April 2021; 12:645784. doi: 10.3389/fmicb.2021.645784PMID: 33897658; PMCID: PMC8058099

Pieper C, Magalhães Loureiro C, Law KL, Amaral-Zettler LA, Quintino V, Rodrigues AM, Ventura MA, Martins A. Marine litter footprint in the Azores Islands: A climatological perspective. Sci Total Environ. 2021 Mar 20;761:143310. doi: 10.1016/j.scitotenv.2020.143310. Epub 2020 Nov 4. PMID: 33183812.

Schön I, Rodriguez F, Dunn M, Martens K, Shribak M, Arkhipova IR. A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes (Basel). 2021 Mar 11;12(3):401. doi: 10.3390/genes12030401. PMID: 33799706; PMCID: PMC7998251.

Nowell RW, Wilson CG, Almeida P, Schiffer PH, Fontaneto D, Becks L, Rodriguez F, Arkhipova IR, Barraclough TG. Evolutionary dynamics of transposable elements in bdelloid rotifers. Elife. 2021 Feb 5;10:e63194. doi: 10.7554/eLife.63194. PMID: 33543711; PMCID: PMC7943196.

Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA. Structural and developmental principles of neuropil assembly in C. elegans. Nature. 2021 Mar;591(7848):99-104. doi: 10.1038/s41586-020-03169-5. Epub 2021 Feb 24. PubMed PMID: 33627875.

Wang, Y, Wegener, G, Ruff, SE, & Wang, F. Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea. Environ Microbioliogy. 2021 Feb; 23(2):530-541. doi: 10.1111/1462-2920.15057. PMID: 32367670

Gribble KE. Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging. Nutr Healthy Aging. 2021 Jan 20;6(1):1-15. doi: 10.3233/NHA-200104. PMID: 33709041; PMCID: PMC7903245.

Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol. 2021 Jan;6(1):3-6. doi: 10.1038/s41564-020-00834-3. PMID: 33349678.

Vogel FA, Schlundt C, Stote RE, Ratto JA, Amaral-Zettler LA. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms. 2021 Jan 16;9(1):186. doi: 10.3390/microorganisms9010186. PMID: 33467086; PMCID: PMC7830162.

Zhao S, Zettler ER, Amaral-Zettler LA, Mincer TJ. Microbial carrying capacity and carbon biomass of plastic marine debris. ISME J. 2021 Jan;15(1):67-77. doi: 10.1038/s41396-020-00756-2. Epub 2020 Sep 2. PMID: 32879460; PMCID: PMC7852875.

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.

2019:

Lundgren SN, Madan JC, Karagas MR, Morrison HG, Hoen AG, Christensen BC. Microbial Communities in Human Milk Relate to Measures of Maternal Weight. Front Microbiol. 2019 Dec 20;10:2886. doi: 10.3389/fmicb.2019.02886. PMID: 31921063; PMCID: PMC6933483.

Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen’ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLoS One. 2019 Dec 23;14(12):e0226485. doi: 10.1371/journal.pone.0226485. PMID: 31869362; PMCID: PMC6927652.

Antosca KM, Chernikova DA, Price CE, Ruoff KL, Li K, Guill MF, Sontag NR, Morrison HG, Hao S, Drumm ML, MacKenzie TA, Dorman DB, Feenan LM, Williams MA, Dessaint J, Yuan IH, Aldrich BJ, Moulton LA, Ting L, Martinez-Del Campo A, Stewart EJ, Karagas MR, O’Toole GA, Madan JC. Altered Stool Microbiota of Infants with Cystic Fibrosis Shows a Reduction in Genera Associated with Immune Programming from Birth. J Bacteriol. 2019 Jul 24;201(16):e00274-19. doi: 10.1128/JB.00274-19. PMID: 31209076; PMCID: PMC6657602.

Ivashkin E, Melnikova V, Kurtova A, Brun NR, Obukhova A, Khabarova MY, Yakusheff A, Adameyko I, Gribble KE, Voronezhskaya EE. Transglutaminase Activity Determines Nuclear Localization of Serotonin Immunoreactivity in the Early Embryos of Invertebrates and Vertebrates. ACS Chem Neurosci. 2019 Aug 21;10(8):3888-3899. doi: 10.1021/acschemneuro.9b00346. Epub 2019 Jul 23. PMID: 31291540.

Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis. Annu Rev Microbiol. 2019 Sep 8;73:335-358. doi: 10.1146/annurev-micro-090817-062503. Epub 2019 Jun 10. PMID: 31180804; PMCID: PMC7153577.

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol. 2019 Sep;17(9):569-586. doi: 10.1038/s41579-019-0222-5. Epub 2019 Jun 18. PMID: 31213707; PMCID: PMC7136171.

Blommaert J, Riss S, Hecox-Lea B, Mark Welch DB, Stelzer CP. Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex. BMC Genomics. 2019 Jun 7;20(1):466. doi: 10.1186/s12864-019-5859-y. PMID: 31174483; PMCID: PMC6555955.

Kivenson V, Lemkau KL, Pizarro O, Yoerger DR, Kaiser C, Nelson RK, Carmichael C, Paul BG, Reddy CM, Valentine DL. Ocean Dumping of Containerized DDT Waste Was a Sloppy Process. Environ Sci Technol. 2019 Mar 19;53(6):2971-2980. doi: 10.1021/acs.est.8b05859. Epub 2019 Mar 4. PMID: 30829032.

Dobay A, Haas C, Fucile G, Downey N, Morrison HG, Kratzer A, Arora N. Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Sci Int Genet. 2019 May;40:105-113. doi: 10.1016/j.fsigen.2019.02.010. Epub 2019 Feb 11. PMID: 30785061.

Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems. 2019 May 14;4(4):e00177-19. doi: 10.1128/mSystems.00177-19. PMID: 31098396; PMCID:
PMC6517690.

Arkhipova IR, Yushenova IA. Giant Transposons in Eukaryotes: Is Bigger Better? Genome Biol Evol. 2019 Mar 1;11(3):906-918. doi: 10.1093/gbe/evz041. PMID: 30796812; PMCID: PMC6431247.

Hubbard CJ, Li B, McMinn R, Brock MT, Maignien L, Ewers BE, Kliebenstein D, Weinig C. The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory. Mol Ecol. 2019 Apr;28(7):1801-1811. doi: 10.1111/mec.14989. Epub 2019 Feb 6. PMID: 30582660.

Bock MJ, Jarvis GC, Corey EL, Stone EE, Gribble KE. Maternal age alters offspring lifespan, fitness, and lifespan extension under caloric restriction. Sci Rep. 2019 Feb 28;9(1):3138. doi: 10.1038/s41598-019-40011-z. PMID: 30816287; PMCID: PMC6395700.

Trigodet F, Larché N, Morrison HG, Jebbar M, Thierry D, Maignien L. Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater. Front Microbiol. 2019 Feb 7;10:170. doi: 10.3389/fmicb.2019.00170. PMID: 30792705; PMCID: PMC6374330.

Ecklu-Mensah, G., Sackey, S. T., Morrison, H. G., Sogin, M. L., Murphy, L. G., & Reznikoff, W. S. (2019). Assessment of bacterial diversity in western Accra, Ghana, drinking water samples. JOURNAL OF WATER SANITATION AND HYGIENE FOR DEVELOPMENT, 9(4), 644-661. doi:10.2166/washdev.2019.123

Print Friendly, PDF & Email