BI: Fundamental and Applied Microbiomics, Center for (CFAM)

Research Output 2006 2019

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2019
16 Citations (Scopus)

Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018)

Siddell, S. G., Walker, P. J., Lefkowitz, E. J., Mushegian, A. R., Adams, M. J., Dutilh, B. E., Gorbalenya, A. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M., Rubino, L., Sabanadzovic, S., Sanfaçon, H., Simmonds, P., Varsani, A. & 2 others, Zerbini, F. M. & Davison, A. J., Jan 1 2019, (Accepted/In press) In : Archives of Virology.

Research output: Contribution to journalArticle

Viruses

Binomial nomenclature for virus species: a consultation

Siddell, S. G., Walker, P. J., Lefkowitz, E. J., Mushegian, A. R., Dutilh, B. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M. L., Rubino, L., Sabanadzovic, S., Simmonds, P., Varsani, A., Zerbini, F. M. & Davison, A. J., Jan 1 2019, (Accepted/In press) In : Archives of virology.

Research output: Contribution to journalArticle

Open Access
Terminology
Referral and Consultation
Viruses
Names
Virology
1 Citation (Scopus)

Biodiversity and dynamics of cyanobacterial communities during blooms in temperate lake (Harsha Lake, Ohio, USA)

Zhu, B., Cao, H., Li, G., Du, W., Xu, G., Domingo, J. S., Gu, H., Xu, N., Duan, S. & Lu, J., Feb 1 2019, In : Harmful Algae. 82, p. 9-18 10 p.

Research output: Contribution to journalArticle

algal bloom
Cylindrospermopsis
Planktothrix
biodiversity
lakes

Changes in Weight Status and the Intestinal Microbiota Among College Freshman, Aged 18 Y

Journey, E. K., Ortega-Santos, C. P., Bruening, M. & Whisner, C., Jan 1 2019, (Accepted/In press) In : Journal of Adolescent Health.

Research output: Contribution to journalArticle

Waist Circumference
Body Mass Index
Weights and Measures
Weight Gain
Multivariate Analysis
8 Citations (Scopus)

Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Dempsey, D. M., Dutilh, B. E., Harrach, B., Harrison, R. L., Hendrickson, R. C., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M., Rubino, L., Sabanadzovic, S., Simmonds, P., Varsani, A., Zerbini, F. M. & 1 others, Davison, A. J., Jan 1 2019, In : Archives of virology.

Research output: Contribution to journalArticle

Open Access
Terminology
Viruses
RNA Replicase
RNA
8 Citations (Scopus)

Cyanobacterial biocrust diversity in Mediterranean ecosystems along a latitudinal and climatic gradient

Muñoz-Martín, M. Á., Becerra-Absalón, I., Perona, E., Fernández-Valbuena, L., Garcia-Pichel, F. & Mateo, P., Jan 1 2019, In : New Phytologist. 221, 1, p. 123-141 19 p.

Research output: Contribution to journalArticle

Cyanobacteria
Ecosystem
ecosystems
Microcoleus vaginatus
Scytonema
5 Citations (Scopus)

Deamination reaction mechanisms of protonated amines under hydrothermal conditions

Robinson, K. J., Gould, I., Fecteau, K. M., Hartnett, H., Williams, L. & Shock, E., Jan 1 2019, In : Geochimica et Cosmochimica Acta. 244, p. 113-128 16 p.

Research output: Contribution to journalArticle

Amines
Amino Acids
Reaction kinetics
Substitution reactions
Carbon

Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net

Gavelis, G. S., Herranz, M., Wakeman, K. C., Ripken, C., Mitarai, S., Gile, G., Keeling, P. J. & Leander, B. S., Dec 1 2019, In : Scientific Reports. 9, 1, 839.

Research output: Contribution to journalArticle

Dinoflagellida
Nuclear Envelope
Membranes
Freeze Substitution
Kinetochores

Discordant transmission of bacteria and viruses from mothers to babies at birth

Maqsood, R., Rodgers, R., Rodriguez, C., Handley, S. A., Ndao, I. M., Tarr, P. I., Warner, B. B., Lim, E. S. & Holtz, L. R., Dec 10 2019, In : Microbiome. 7, 1, 156.

Research output: Contribution to journalArticle

Open Access
Mothers
Parturition
Microbiota
Viruses
Bacteria
2 Citations (Scopus)

Diverse genomoviruses representing eight new and one known species identified in feces and nests of house finches (Haemorhous mexicanus)

Schmidlin, K., Sepp, T., Khalifeh, A., Smith, K., Fontenele, R. S., McGraw, K. & Varsani, A., Jan 1 2019, In : Archives of virology.

Research output: Contribution to journalArticle

Finches
Feces
Birds
Southwestern United States
DNA Viruses
4 Citations (Scopus)

Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera)

Kraberger, S., Cook, C. N., Schmidlin, K., Fontenele, R. S., Bautista, J., Smith, B. & Varsani, A., Jul 1 2019, In : Infection, Genetics and Evolution. 71, p. 179-188 10 p.

Research output: Contribution to journalArticle

ssDNA viruses
Microviridae
DNA Viruses
Honey
Bees
2 Citations (Scopus)

Energy oversupply to tissues: A single mechanism possibly underlying multiple cancer risk factors

Wu, D. J., Aktipis, C. A. & Pepper, J. W., Jan 21 2019, In : Evolution, Medicine and Public Health. 2019, 1, p. 9-16 8 p.

Research output: Contribution to journalArticle

Open Access
risk factor
cancer
risk factors
somatic cells
neoplasms

Evidence of age-related improvement in the foraging efficiency of Adélie penguins

Lescroël, A., Ballard, G., Massaro, M., Dugger, K., Jennings, S., Pollard, A., Porzig, E., Schmidt, A., Varsani, A., Grémillet, D. & Ainley, D., Dec 1 2019, In : Scientific reports. 9, 1, 3375.

Research output: Contribution to journalArticle

Spheniscidae
Proxy
Breeding
Longitudinal Studies
Demography

Genetic characterization of a recombinant myxoma virus in the iberian hare (Lepus granatensis)

Águeda-Pinto, A., Matos, A. L. D., Abrantes, M., Kraberger, S., Risalde, M. A., Gortázar, C., McFadden, D., Varsani, A. & Esteves, P. J., Jun 1 2019, In : Viruses. 11, 6, 530.

Research output: Contribution to journalArticle

Open Access
Myxoma virus
Hares
Rabbits
Spain
Genes
1 Citation (Scopus)

Geochemical-compositional-functional changes in arctic soil microbiomes post land submergence revealed by metagenomics

Wang, N., Guo, Y., Li, G., Xia, Y., Ma, M., Zang, J., Ma, Y., Yin, X., Han, W., Lv, J. & Cao, H., Jan 1 2019, In : Microbes and Environments. 34, 2, p. 180-190 11 p.

Research output: Contribution to journalArticle

Open Access
functional change
submergence
Arctic region
sediments
Otus

Gut DNA virome diversity and its association with host bacteria regulate inflammatory phenotype and neuronal immunotoxicity in experimental gulf war illness

Seth, R. K., Maqsood, R., Mondal, A., Bose, D., Kimono, D., Holland, L. A., Lloyd, P. J., Klimas, N., Horner, R. D., Sullivan, K., Lim, E. S. & Chatterjee, S., Oct 21 2019, In : Viruses. 11, 10, 968.

Research output: Contribution to journalArticle

Open Access
Dysbiosis
Gulf War
Tight Junction Proteins
Innate Immunity
Claudin-2

Identification of a Novel Adélie Penguin Circovirus at Cape Crozier (Ross Island, Antarctica)

Morandini, V., Dugger, K. M., Ballard, G., Elrod, M., Schmidt, A., Ruoppolo, V., Lescroël, A., Jongsomjit, D., Massaro, M., Pennycook, J., Kooyman, G. L., Schmidlin, K., Kraberger, S., Ainley, D. G. & Varsani, A., Nov 22 2019, In : Viruses. 11, 12

Research output: Contribution to journalArticle

Open Access
Spheniscidae
Circovirus
Islands
Feathers
Genome

Identification of the wild and cultivated hosts of wheat dwarf virus and oat dwarf virus in Iran

Pouramini, N., Heydarnejad, J., Massumi, H. & Varsani, A., Jan 1 2019, (Accepted/In press) In : VirusDisease.

Research output: Contribution to journalArticle

Iran
Triticum
Viruses
Bromus
Geminiviridae
2 Citations (Scopus)

Kin terms and fitness interdependence

Cronk, L., Steklis, D., Steklis, N., van den Akker, O. & Aktipis, C. A., Jan 1 2019, (Accepted/In press) In : Evolution and Human Behavior.

Research output: Contribution to journalArticle

Anthropology
Marriage
Terminology
genetic relationships
fitness

Knowledge and attitudes towards breastfeeding practices: A cross-sectional survey of postnatal mothers in China

Hamze, L., Mao, J. & Reifsnider, E., Jul 1 2019, In : Midwifery. 74, p. 68-75 8 p.

Research output: Contribution to journalArticle

Breast Feeding
China
Cross-Sectional Studies
Mothers
Postpartum Period

Kombucha: A novel model system for cooperation and conflict in a complex multi-species microbial ecosystem

May, A., Narayanan, S., Alcock, J., Varsani, A., Maley, C. & Aktipis, A., Jan 1 2019, In : PeerJ. 2019, 9, e7565.

Research output: Contribution to journalArticle

Open Access
microbial ecology
Tea
Yeast
Ecosystems
Ecosystem

Long-term warming in Alaska enlarges the diazotrophic community in deep soils

Feng, J., Penton, C., He, Z., Van Nostrand, J. D., Yuan, M. M., Wu, L., Wang, C., Qin, Y., Shi, Z. J., Guo, X., Schuur, E. A. G., Luo, Y., Bracho, R., Konstantinidis, K. T., Cole, J. R., Tiedje, J. M., Yang, Y. & Zhou, J., Jan 1 2019, In : mBio. 10, 1, e02521-18.

Research output: Contribution to journalArticle

Open Access
Soil
Biomass
Ecosystem
Climate
Nitrogenase
18 Citations (Scopus)

Minimum information about an uncultivated virus genome (MIUVIG)

Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., Amid, C., Aziz, R. K., Bordenstein, S. R., Bork, P., Breitbart, M., Cochrane, G. R., Daly, R. A., Desnues, C., Duhaime, M. B., Emerson, J. B. & 41 others, Enault, F., Fuhrman, J. A., Hingamp, P., Hugenholtz, P., Hurwitz, B. L., Ivanova, N. N., Labonté, J. M., Lee, K. B., Malmstrom, R. R., Martinez-Garcia, M., Mizrachi, I. K., Ogata, H., Páez-Espino, D., Petit, M. A., Putonti, C., Rattei, T., Reyes, A., Rodriguez-Valera, F., Rosario, K., Schriml, L., Schulz, F., Steward, G. F., Sullivan, M. B., Sunagawa, S., Suttle, C. A., Temperton, B., Tringe, S. G., Thurber, R. V., Webster, N. S., Whiteson, K. L., Wilhelm, S. W., Wommack, K. E., Woyke, T., Wrighton, K. C., Yilmaz, P., Yoshida, T., Young, M. J., Yutin, N., Allen, L. Z., Kyrpides, N. C. & Eloe-Fadrosh, E. A., Jan 1 2019, In : Nature biotechnology. 37, 1, p. 29-37 9 p.

Research output: Contribution to journalArticle

Open Access
Viruses
Genes
Genome
Metagenome
Archaea

Molecular and partial biological characterization of the coat protein sequences of Iranian alfalfa mosaic virus isolates

Mangeli, F., Massumi, H., Alipour, F., Maddahian, M., Heydarnejad, J., Hosseinipour, A., Amid-Motlagh, M. H., Azizizadeh, M. & Varsani, A., Aug 15 2019, In : Journal of Plant Pathology. 101, 3, p. 735-742 8 p.

Research output: Contribution to journalArticle

Alfalfa mosaic virus
coat proteins
amino acid sequences
signs and symptoms (plants)
alfalfa
1 Citation (Scopus)

Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

Kazlauskas, D., Varsani, A., Koonin, E. V. & Krupovic, M., Jul 31 2019, In : Nature communications. 10, 1, 1 p.

Research output: Contribution to journalArticle

Open Access
plasmids
DNA Viruses
Single-Stranded DNA
viruses
Viruses

Novel smacoviruses identified in the faeces of two wild felids: North American bobcat and African lion

Kraberger, S., Serieys, L., Fountain-Jones, N., Packer, C., Riley, S. & Varsani, A., Jan 1 2019, In : Archives of virology.

Research output: Contribution to journalArticle

Lynx
Lions
Feces
African Americans
Felidae
8 Citations (Scopus)

Nursing biocrusts: isolation, cultivation, and fitness test of indigenous cyanobacteria

Giraldo-Silva, A., Nelson, C., Barger, N. N. & Garcia-Pichel, F., Jan 1 2019, In : Restoration Ecology.

Research output: Contribution to journalArticle

soil crusts
soil crust
breast feeding
Cyanobacteria
cyanobacterium
4 Citations (Scopus)

Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes

Dorrell, R. G., Azuma, T., Nomura, M., de Kerdrel, G. A., Paoli, L., Yang, S., Bowler, C., Ishii, K. I., Miyashita, H., Gile, G. & Kamikawa, R., Apr 2 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 14, p. 6914-6923 10 p.

Research output: Contribution to journalArticle

Plastids
Plastid Genomes
Photosynthesis
Mitochondria
Chloroplast Proteins
2 Citations (Scopus)

Production of Carboxylic Acids from Aldehydes under Hydrothermal Conditions: A Kinetics Study of Benzaldehyde

Fecteau, K. M., Gould, I., Glein, C. R., Williams, L., Hartnett, H. & Shock, E., Jan 1 2019, (Accepted/In press) In : ACS Earth and Space Chemistry.

Research output: Contribution to journalArticle

carboxylic acid
aldehyde
Carboxylic Acids
aldehydes
Aldehydes

Reshaping the rhizosphere microbiome by bio-organic amendment to enhance crop yield in a maize-cabbage rotation system

Qiao, C., Penton, C., Xiong, W., Liu, C., Wang, R., Liu, Z., Xu, X., Li, R. & Shen, Q., Jan 1 2019, In : Applied Soil Ecology.

Research output: Contribution to journalArticle

Rhizosphere
Brassica
Microbiota
Fertilizers
cabbage

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

Sommers, P., Fontenele, R. S., Kringen, T., Kraberger, S., Porazinska, D. L., Darcy, J. L., Schmidt, S. K. & Varsani, A., Nov 4 2019, In : Viruses. 11, 11

Research output: Contribution to journalArticle

Open Access
DNA Viruses
Single-Stranded DNA
Viruses
Genome
Fresh Water
1 Citation (Scopus)

Six-Week High-Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats

Crawford, M., Whisner, C., Al-Nakkash, L. & Sweazea, K., Feb 1 2019, In : Lipids. 54, 2-3, p. 119-131 13 p.

Research output: Contribution to journalArticle

High Fat Diet
Nutrition
Endotoxins
Rats
Obesity
4 Citations (Scopus)
Open Access
Microbiota
Cyanobacteria
Nitrogen
Soil
Carbon Monoxide
3 Citations (Scopus)

Suppression of banana Panama disease induced by soil microbiome reconstruction through an integrated agricultural strategy

Shen, Z., Xue, C., Penton, C., Thomashow, L. S., Zhang, N., Wang, B., Ruan, Y., Li, R. & Shen, Q., Jan 1 2019, In : Soil Biology and Biochemistry. 128, p. 164-174 11 p.

Research output: Contribution to journalArticle

Fumigation
Panama
Musa
Microbiota
fumigation
Adiposity
Sleep
Diet
Feeding Behavior
Breast Feeding
3 Citations (Scopus)

Timing the evolutionary advent of cyanobacteria and the later great oxidation event using gene phylogenies of a sunscreen

Garcia-Pichel, F., Lombard, J., Soule, T., Dunaj, S., Wu, S. H. & Wojciechowski, M., May 1 2019, In : mBio. 10, 3, e00561-19.

Research output: Contribution to journalArticle

Open Access
Sunscreening Agents
Cyanobacteria
Phylogeny
Operon
Photosynthesis
3 Citations (Scopus)

Unravelling the single-stranded DNA virome of the New Zealand blackfly

Kraberger, S., Schmidlin, K., Fontenele, R. S., Walters, M. & Varsani, A., Jun 1 2019, In : Viruses. 11, 6, 532.

Research output: Contribution to journalArticle

Open Access
Simuliidae
Viral Structures
Single-Stranded DNA
New Zealand
Metagenomics
2018
1 Citation (Scopus)

Acculturation, Cultural Values, and Breastfeeding in Overweight or Obese, Low-Income, Hispanic Women at 1 Month Postpartum

Shin, C., Reifsnider, E., McClain, D., Jeong, M., McCormick, D. P. & Moramarco, M., Mar 1 2018, (Accepted/In press) In : Journal of Human Lactation.

Research output: Contribution to journalArticle

Acculturation
Breast Feeding
Hispanic Americans
Postpartum Period
Randomized Controlled Trials
4 Citations (Scopus)

A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales

Driscoll, C. B., Meyer, K. A., Šulčius, S., Brown, N. M., Dick, G. J., Cao, H., Gasiūnas, G., Timinskas, A., Yin, Y., Landry, Z. C., Otten, T. G., Davis, T. W., Watson, S. B. & Dreher, T. W., Jul 1 2018, In : Harmful Algae. 77, p. 93-107 15 p.

Research output: Contribution to journalArticle

Nostocales
Cyanobacteria
cyanobacterium
algal bloom
genome
16 Citations (Scopus)

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

Briddon, R. W., Martin, D. P., Roumagnac, P., Navas-Castillo, J., Fiallo-Olivé, E., Moriones, E., Lett, J. M., Zerbini, F. M. & Varsani, A., May 9 2018, (Accepted/In press) In : Archives of Virology. p. 1-14 14 p.

Research output: Contribution to journalArticle

Nanovirus
Geminiviridae
Single-Stranded DNA
Begomovirus
Cocos
21 Citations (Scopus)

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community

Lim, E., Rodriguez, C. & Holtz, L. R., May 11 2018, In : Microbiome. 6, 1, 1 p.

Research output: Contribution to journalArticle

Microbiota
Amniotic Fluid
Pregnancy
Fetus
Viruses
2 Citations (Scopus)

A new niche for anoxygenic phototrophs as endoliths

Roush, D., Couradeau, E., Guida, B., Neuer, S. & Garcia-Pichel, F., Feb 1 2018, In : Applied and Environmental Microbiology. 84, 4, e02055-17.

Research output: Contribution to journalArticle

photosynthetic bacteria
autotrophs
niche
niches
Bacteria

Associations of Diabetes-Related Distress and Depressive Symptoms With Glycemic Control in Korean Americans With Type 2 Diabetes

Jeong, M. & Reifsnider, E., Dec 1 2018, In : Diabetes Educator. 44, 6, p. 531-540 10 p.

Research output: Contribution to journalArticle

Asian Americans
Type 2 Diabetes Mellitus
Depression
Self Care
Psychology
10 Citations (Scopus)

Biochar application influences microbial assemblage complexity and composition due to soil and bioenergy crop type interactions

Yu, J., Deem, L. M., Crow, S. E., Deenik, J. L. & Penton, C., Feb 1 2018, In : Soil Biology and Biochemistry. 117, p. 97-107 11 p.

Research output: Contribution to journalArticle

biochar
energy crops
bioenergy
Oxisol
fertility
4 Citations (Scopus)

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra

Liang, J., Xia, J., Shi, Z., Jiang, L., Ma, S., Lu, X., Mauritz, M., Natali, S. M., Pegoraro, E., Penton, C., Plaza, C., Salmon, V. G., Celis, G., Cole, J. R., Konstantinidis, K. T., Tiedje, J. M., Zhou, J., Schuur, E. A. G. & Luo, Y., Oct 1 2018, In : Global Change Biology. 24, 10, p. 4946-4959 14 p.

Research output: Contribution to journalArticle

Organic carbon
tundra
Buffers
warming
organic carbon
4 Citations (Scopus)

Cancer initiation and progression within the cancer microenvironment

Leong, S. P., Aktipis, C. A. & Maley, C., Jul 11 2018, (Accepted/In press) In : Clinical and Experimental Metastasis. p. 1-7 7 p.

Research output: Contribution to journalArticle

Tumor Microenvironment
Neoplasms
Growth
Biological Phenomena
Melanoma
65 Citations (Scopus)

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

King, A. M. Q., Lefkowitz, E. J., Mushegian, A. R., Adams, M. J., Dutilh, B. E., Gorbalenya, A. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M. L., Rubino, L., Sabanadzovic, S., Sanfaçon, H., Siddell, S. G., Simmonds, P., Varsani, A. & 2 others, Zerbini, F. M. & Davison, A. J., May 12 2018, (Accepted/In press) In : Archives of Virology. p. 1-31 31 p.

Research output: Contribution to journalArticle

Terminology
Viruses
Names
3 Citations (Scopus)

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea

De Martini, F., Neuer, S., Hamill, D., Robidart, J. & Lomas, M. W., Jan 1 2018, (Accepted/In press) In : Limnology and Oceanography.

Research output: Contribution to journalArticle

Sargasso Sea
Prochlorococcus
Synechococcus
particulate organic carbon
carbon flux
1 Citation (Scopus)
Virology
DNA Viruses
Single-Stranded DNA
11 Citations (Scopus)

Cross-cultural invariances in the architecture of shame

Sznycer, D., Xygalatas, D., Agey, E., Alami, S., An, X. F., Ananyeva, K. I., Atkinson, Q. D., Broitman, B. R., Conte, T. J., Flores, C., Fukushima, S., Hitokoto, H., Kharitonov, A. N., Onyishi, C. N., Onyishi, I. E., Romero, P. P., Schrock, J. M., Snodgrass, J. J., Sugiyama, L. S., Takemura, K. & 6 others, Townsend, C., Zhuang, J. Y., Aktipis, C. A., Cronk, L., Cosmides, L. & Tooby, J., Sep 25 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 39, p. 9702-9707 6 p.

Research output: Contribution to journalArticle

Shame
Cultural Evolution
Theft
Action Potentials
Language