JBPC Publications 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.

Gurdebeke, P. R., Mertens, K. N., Pospelova, V., Matsuoka, K., Li, Z., Gribble, K. E., Gu, H., Bogus, K., Vrielinck, H., & Louwye, S. (2019). “Taxonomic revision, phylogeny, and cyst wall composition of the dinoflagellate cyst genus Votadinium Reid (Dinophyceae, Peridiniales, Protoperidiniaceae).” Palynology, 1-26. doi:10.1080/01916122.2019.158062.

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

Bhatnagar, S., Cowley, E. S., Kopf, S. H., Castro, S. P., Kearney, S., Dawson, S. C., Hanselmann, K., & Ruff, S. E. (2019). “Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.” bioRxiv, 604504. doi:10.1101/60450.

Bono, L. M., Orton, R. J., Peredo, E. L., Morrison, H. G., Sistrom, M., Simmons, S., & Turner, P. E. (2019). “Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community.” bioRxiv, 772475. doi:10.1101/77247.

Coker, M. O., Hoen, A. G., Dade, E., Lundgren, S., Li, Z., Wong, A. D., Zens, M. S., Palys, T. J., Morrison, H. G., Sogin, M. L., Baker, E. R., Karagas, M. R., & Madan, J. C. (2019). “Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.” BJOG, 0(0), 0. doi:10.1111/1471-0528.1579.

Cramm, M. A., Chakraborty, A., Li, C., Ruff, S. E., Jorgensen, B. B., & Hubert, C. R. J. (2019). “Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.” Front Microbiol, 10, 945. doi:10.3389/fmicb.2019.0094.

Delmont, T. O., Kiefl, E., Kilinc, O., Esen, O. C., Uysal, I., Rappe, M. S., Giovannoni, S., & Eren, A. M. (2019). “Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade.” Elife, 8(ARTN e46497). doi:10.7554/eLife.4649.

Edsinger, E., Pnini, R., Ono, N., Yanagisawa, R., Dever, K., & Miller, J. (2019). “Social tolerance in Octopus laqueus – a maximal entropy model.” bioRxiv, 526905. doi:10.1101/52690.

Fiore-Donno, A. M., Richter-Heitmann, T., Degrune, F., Dumack, K., Regan, K., Mahran, S., Boeddinghaus, R., Rillig, M., Friedrich, M. W., Kandeler, E., & Bonkowski, M. (2019). “Environmental selection and spatiotemporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland.” bioRxiv, 531970. doi:10.1101/53197.

Funikov, S. Y., Rezvykh, A. P., Kulikova, D. A., Zelentsova, E. S., Chuvakova, L. N., Tyukmaeva, V. I., Arkhipova, I. R., & Evgen’ev, M. B. (2019). “Insulator proteins contribute to expression of gene loci repositioned into heterochromatin in the course of Drosophila evolution.” bioRxiv, 802371. doi:10.1101/80237.

Goldmann, K., Boeddinghaus, R. S., Klemmer, S., Regan, K. M., Heintz-Buschart, A., Fischer, M., Prati, D., Piepho, H. P., Berner, D., Marhan, S., Kandeler, E., Buscot, F., & Wubet, T. (2019). “Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot.” Environ Microbiol, 0(0). doi:10.1111/1462-2920.1465.

Han, M., Dsouza, M., Zhou, C., Li, H., Zhang, J., Chen, C., Yao, Q., Zhong, C., Zhou, H., Gilbert, J. A., Wang, Z., & Ning, K. (2019). “Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake.” Genomics Proteomics Bioinformatics, 17(1), 76-90. doi:10.1016/j.gpb.2018.04.00.

McKay, L. J., Dlakic, M., Fields, M. W., Delmont, T. O., Eren, A. M., Jay, Z. J., Klingelsmith, K. B., Rusch, D. B., & Inskeep, W. P. (2019). “Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.” Nat Microbiol, 4(4), 614-622. doi:10.1038/s41564-019-0362-.

Mincer, T. J., Zettler, E. R., & Amaral-Zettler, L. A. (2019). “Biofilms on Plastic Debris and Their Influence on Marine Nutrient Cycling, Productivity, and Hazardous Chemical Mobility.” In H. Takada & H. K. Karapanagioti (Ed.), Hazardous Chemicals Associated with Plastics in the Marine Environment (pp. 221-233): Cham: Springer International Publishing.

Nedoluzhko, A. V., Sharko, F. S., Lê, B. M., Tsygankova, S. V., Boulygina, E. S., Rastorguev, S. M., Sokolov, A. S., Rodriguez, F., Mazur, A. M., Polilov, A. A., Benton, R., Evgen’ev, M. B., Arkhipova, I. R., Prokhortchouk, E. B., & Skryabin, K. G. (2019). “A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum.” bioRxiv, 579052. doi:10.1101/57905.

Nissimov, J. I., Talmy, D., Haramaty, L., Fredricks, H. F., Zelzion, E., Knowles, B., Eren, A. M., Vandzura, R., Laber, C. P., Schieler, B. M., Johns, C. T., More, K. D., Coolen, M. J. L., Follows, M. J., Bhattacharya, D., Van Mooy, B. A. S., & Bidle, K. D. (2019). “Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology.” Environ Microbiol, 21(6), 2182-2197. doi:10.1111/1462-2920.1463.

Peramba, K. B., & Edsinger, E. (2019). “Imaging the neuromuscular systems of cephalopod arms and suckers.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Peramba, K. B., Nash, C., Walters, D., Hackworth, L., Schumm, M., Pineda, O., & Edsinger, E. (2019). “Squid Monday: Characterizing population structure in Doryteuthis pealeii.” Paper presented at the Annual Meeting of the Society for Integrative and Comparative Biology, Tampa, FL.

Perez Castro, S., Cleland, E. E., Wagner, R., Sawad, R. A., & Lipson, D. A. (2019). “Soil microbial responses to drought and exotic plants shift carbon metabolism.” ISME J, 13(7), 1776-1787. doi:10.1038/s41396-019-0389-.

Puritty, C. E., Esch, E. H., Castro, S. P., Ryan, E. M., Lipson, D. A., & Cleland, E. E. (2019). “Drought in Southern California coastal sage scrub reduces herbaceous biomass of exotic species more than native species, but exotic growth recovers quickly when drought ends.” Plant Ecology, 220(2), 151-169. doi:10.1007/s11258-019-00912-.

Reveillaud, J., Bordenstein, S. R., Cruaud, C., Shaiber, A., Esen, O. C., Weill, M., Makoundou, P., Lolans, K., Watson, A. R., Rakotoarivony, I., Bordenstein, S. R., & Eren, A. M. (2019). “The Wolbachia mobilome in Culex pipiens includes a putative plasmid.” Nat Commun, 10(1), 1051. doi:10.1038/s41467-019-08973-.

Richter, N., Longo, W. M., George, S., Shipunova, A., Huang, Y., & Amaral-Zettler, L. (2019). “Phylogenetic diversity in freshwater-dwelling Isochrysidales haptophytes with implications for alkenone production.” Geobiology, 17(3), 272-280. doi:10.1111/gbi.1233.

Rossetti, B. J., Wilbert, S. A., Mark Welch, J. L., Borisy, G. G., & Nagy, J. G. (2019). “Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs.” bioRxiv, 674. doi:10.1093/bioinformatics/btz67.

Ruff, S. E. (2019). “Microbial communities and metabolisms at hydrocarbon seeps.” In A. Teske & V. Carvalho (Ed.), Marine Hydrocarbon Seeps – Microbiology and Biogeochemistry of a Global Marine Habitat (pp. 280): Springer.

Ruff, S. E., Felden, J., Gruber-Vodicka, H. R., Marcon, Y., Knittel, K., Ramette, A., & Boetius, A. (2019). “In situ development of a methanotrophic microbiome in deep-sea sediments.” ISME J, 13(1), 197-213. doi:10.1038/s41396-018-0263-.

Sevillano, M., Dai, Z., Calus, S., Bautista-de los Santos, Q. M., Eren, A. M., van der Wielen, P. W. J. J., Ijaz, U. Z., & Pinto, A. J. (2019). “Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance.” bioRxiv, 675561. doi:10.1101/67556.

Shaiber, A., & Eren, A. M. (2019). “Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories.” MBio, 10(3), e00725-00719. doi:10.1128/mBio.00725-1.

Theroux, S., Huang, Y. S., Toney, J. L., Andersen, R., Nyren, P., Bohn, R., Salacup, J., Murphy, L., & Amaral-Zettler, L. (2019). “Successional blooms of alkenone-producing haptophytes in Lake George, North Dakota: Implications for continental paleoclimate reconstructions.” Limnology and Oceanography, 0(0), 11311. doi:10.1002/lno.1131.

Trigodet, F., Larché, N., Morrison, H. G., Maignien, L., & Thierry, D. (2019). “Influence of dissolved oxygen content on the bacteria‐induced ennoblement of stainless steels in seawater and its consequence on the localized corrosion risk.” Materials and Corrosion, 0(0). doi:10.1002/maco.20191122.

Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2019). “High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies.” bioRxiv, 759969. doi:10.1101/75996.

Yeoman, C. J., Brutscher, L. M., Esen, O. C., Ibaoglu, F., Fowler, C., Eren, A. M., Wanner, K., & Weaver, D. K. (2019). “Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus).” PeerJ, 7, e7548. doi:10.7717/peerj.754.