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  • 1. Edwards, Robert A.
    et al.
    Vega, Alejandro A.
    Norman, Holly M.
    Ohaeri, Maria
    Levi, Kyle
    Dinsdale, Elizabeth A.
    Cinek, Ondrej
    Aziz, Ramy K.
    McNair, Katelyn
    Barr, Jeremy J.
    Bibby, Kyle
    Brouns, Stan J. J.
    Cazares, Adrian
    de Jonge, Patrick A.
    Desnues, Christelle
    Diaz Munoz, Samuel L.
    Fineran, Peter C.
    Kurilshikov, Alexander
    Lavigne, Rob
    Mazankova, Karla
    McCarthy, David T.
    Nobrega, Franklin L.
    Reyes Munoz, Alejandro
    Tapia, German
    Trefault, Nicole
    Tyakht, Alexander
    Vinuesa, Pablo
    Wagemans, Jeroen
    Zhernakova, Alexandra
    Aarestrup, Frank M.
    Ahmadov, Gunduz
    Alassaf, Abeer
    Anton, Josefa
    Asangba, Abigail
    Billings, Emma K.
    Cantu, Vito Adrian
    Carlton, Jane M.
    Cazares, Daniel
    Cho, Gyu-Sung
    Condeff, Tess
    Cortes, Pilar
    Cranfield, Mike
    Cuevas, Daniel A.
    De la Iglesia, Rodrigo
    Decewicz, Przemyslaw
    Doane, Michael P.
    Dominy, Nathaniel J.
    Dziewit, Lukasz
    Elwasila, Bashir Mukhtar
    Murat Eren, A.
    Franz, Charles
    Fu, Jingyuan
    Garcia-Aljaro, Cristina
    Ghedin, Elodie
    Gulino, Kristen M.
    Haggerty, John M.
    Head, Steven R.
    Hendriksen, Rene S.
    Hill, Colin
    Hyoty, Heikki
    Ilina, Elena N.
    Irwin, Mitchell T.
    Jeffries, Thomas C.
    Jofre, Juan
    Junge, Randall E.
    Kelley, Scott T.
    Mirzaei, Mohammadali Khan
    Kowalewski, Martin
    Kumaresan, Deepak
    Leigh, Steven R.
    Lipson, David
    Lisitsyna, Eugenia S.
    Llagostera, Montserrat
    Maritz, Julia M.
    Marr, Linsey C.
    McCann, Angela
    Molshanski-Mor, Shahar
    Monteiro, Silvia
    Moreira-Grez, Benjamin
    Morris, Megan
    Mugisha, Lawrence
    Muniesa, Maite
    Neve, Horst
    Nam-phuong, Nguyen
    Nigro, Olivia D.
    Nilsson, Anders S.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    O'Connell, Taylor
    Odeh, Rasha
    Oliver, Andrew
    Piuri, Mariana
    Prussin, Aaron J.
    Qimron, Udi
    Quan, Zhe-Xue
    Rainetova, Petra
    Ramirez-Rojas, Adan
    Raya, Raul
    Reasor, Kim
    Rice, Gillian A. O.
    Rossi, Alessandro
    Santos, Ricardo
    Shimashita, John
    Stachler, Elyse N.
    Stene, Lars C.
    Strain, Ronan
    Stumpf, Rebecca
    Torres, Pedro J.
    Twaddle, Alan
    Ibekwe, MaryAnn Ugochi
    Villagra, Nicolas
    Wandro, Stephen
    White, Bryan
    Whiteley, Andy
    Whiteson, Katrine L.
    Wijmenga, Cisca
    Zambrano, Maria M.
    Zschach, Henrike
    Dutilh, Bas E.
    Global phylogeography and ancient evolution of the widespread human gut virus crAssphage2019In: Nature Microbiology, E-ISSN 2058-5276, Vol. 4, no 10, p. 1727-1736Article in journal (Refereed)
    Abstract [en]

    Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

  • 2. Emerson, Joanne B.
    et al.
    Roux, Simon
    Brum, Jennifer R.
    Bolduc, Benjamin
    Woodcroft, Ben J.
    Jang, Ho Bin
    Singleton, Caitlin M.
    Soden, Lindsey M.
    Naas, Adrian E.
    Boyd, Joel A.
    Hodgkins, Suzanne B.
    Wilson, Rachel M.
    Trubl, Gareth
    Li, Changsheng
    Frokings, Steve
    Pope, Phillip B.
    Wrighton, Kelly C.
    Crill, Patrick M.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Chanton, Jeffrey P.
    Saleska, Scott R.
    Tyson, Gene W.
    Rich, Virginia
    Sullivan, Matthew B.
    Host-linked soil viral ecology along a permafrost thaw gradient2018In: Nature Microbiology, E-ISSN 2058-5276, Vol. 3, no 8, p. 870-880Article in journal (Refereed)
    Abstract [en]

    Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood(1-7). The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans(8-10), remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

  • 3.
    Wang, Hao
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dou, Dan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Östbye, Henrik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Revol, Rebecca
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Daniels, Robert
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Structural restrictions for influenza neuraminidase activity promote adaptation and diversification2019In: Nature Microbiology, E-ISSN 2058-5276, Vol. 4, no 12, p. 2565-2577Article in journal (Refereed)
    Abstract [en]

    Influenza neuraminidase (NA) is a sialidase that contributes to viral mobility by removing the extracellular receptors for the haemagglutinin (HA) glycoprotein. However, it remains unclear why influenza NAs evolved to function as Ca2+-dependent tetramers that display variable stability. Here, we show that the Ca2+ ion located at the centre of the NA tetramer is a major stability determinant, as this Ca2+ ion is required for catalysis and its binding affinity varies between NAs. By examining NAs from 2009 pandemic-like H1N1 viruses, we traced the affinity variation to local substitutions that cause residues in the central Ca2+-binding pocket to reposition. A temporal analysis revealed that these local substitutions predictably alter the stability of the 2009 pandemic-like NAs and contribute to the tendency for the stability to vary up and down over time. In addition to the changes in stability, the structural plasticity of NA was also shown to support the formation of heterotetramers, which creates a mechanism for NA to obtain hybrid properties and propagate suboptimal mutants. Together, these results demonstrate how the structural restrictions for activity provide influenza NA with several mechanisms for adaptation and diversification.

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