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Items: 26

1.

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls.

Le Gall G, Guttula K, Kellingray L, Tett AJ, Ten Hoopen R, Kemsley KE, Savva GM, Ibrahim A, Narbad A.

Oncotarget. 2018 Sep 7;9(70):33278-33289. doi: 10.18632/oncotarget.26022. eCollection 2018 Sep 7.

2.

Complementary intestinal mucosa and microbiota responses to caloric restriction.

Duszka K, Ellero-Simatos S, Ow GS, Defernez M, Paramalingam E, Tett A, Ying S, König J, Narbad A, Kuznetsov VA, Guillou H, Wahli W.

Sci Rep. 2018 Jul 27;8(1):11338. doi: 10.1038/s41598-018-29815-7.

3.

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ.

Cell Host Microbe. 2018 Jul 11;24(1):146-154.e4. doi: 10.1016/j.chom.2018.06.007.

PMID:
30001517
4.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N.

Cell Host Microbe. 2018 Jul 11;24(1):133-145.e5. doi: 10.1016/j.chom.2018.06.005.

5.

The short-term impact of probiotic consumption on the oral cavity microbiome.

Dassi E, Ferretti P, Covello G; HTM-CMB-2015, Bertorelli R, Denti MA, De Sanctis V, Tett A, Segata N.

Sci Rep. 2018 Jul 11;8(1):10476. doi: 10.1038/s41598-018-28491-x.

6.

Profiling microbial strains in urban environments using metagenomic sequencing data.

Zolfo M, Asnicar F, Manghi P, Pasolli E, Tett A, Segata N.

Biol Direct. 2018 May 9;13(1):9. doi: 10.1186/s13062-018-0211-z.

7.

Correction for Pinto et al., "Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Strains from a Freshwater Ecosystem".

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2018 Mar 8;6(10). pii: e00169-18. doi: 10.1128/genomeA.00169-18. No abstract available.

8.

Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem.

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2018 Feb 1;6(5). pii: e00009-18. doi: 10.1128/genomeA.00009-18. Erratum in: Genome Announc. 2018 Mar 8;6(10 ):.

9.

Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater.

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2017 Nov 22;5(47). pii: e01294-17. doi: 10.1128/genomeA.01294-17.

10.

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism.

Korecka A, Dona A, Lahiri S, Tett AJ, Al-Asmakh M, Braniste V, D'Arienzo R, Abbaspour A, Reichardt N, Fujii-Kuriyama Y, Rafter J, Narbad A, Holmes E, Nicholson J, Arulampalam V, Pettersson S.

NPJ Biofilms Microbiomes. 2016 Aug 24;2:16014. doi: 10.1038/npjbiofilms.2016.14. eCollection 2016.

11.

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis.

Tett A, Pasolli E, Farina S, Truong DT, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, Bertorelli R, Girolomoni G, Cristofolini M, Segata N.

NPJ Biofilms Microbiomes. 2017 Jun 22;3:14. doi: 10.1038/s41522-017-0022-5. eCollection 2017.

12.

Microbial strain-level population structure and genetic diversity from metagenomes.

Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N.

Genome Res. 2017 Apr;27(4):626-638. doi: 10.1101/gr.216242.116. Epub 2017 Feb 6.

13.

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.

Asnicar F, Manara S, Zolfo M, Truong DT, Scholz M, Armanini F, Ferretti P, Gorfer V, Pedrotti A, Tett A, Segata N.

mSystems. 2017 Jan 17;2(1). pii: e00164-16. doi: 10.1128/mSystems.00164-16. eCollection 2017 Jan-Feb.

14.

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.

Zolfo M, Tett A, Jousson O, Donati C, Segata N.

Nucleic Acids Res. 2017 Jan 25;45(2):e7. doi: 10.1093/nar/gkw837. Epub 2016 Sep 19.

15.

Experimental metagenomics and ribosomal profiling of the human skin microbiome.

Ferretti P, Farina S, Cristofolini M, Girolomoni G, Tett A, Segata N.

Exp Dermatol. 2017 Mar;26(3):211-219. doi: 10.1111/exd.13210. Epub 2017 Jan 20. Review.

PMID:
27623553
16.

Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N.

Nat Methods. 2016 May;13(5):435-8. doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.

PMID:
26999001
17.

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants.

Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, Segata N, Morrow AL.

Cell Rep. 2016 Mar 29;14(12):2912-24. doi: 10.1016/j.celrep.2016.03.015. Epub 2016 Mar 17.

18.

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.

Nat Methods. 2015 Oct;12(10):902-3. doi: 10.1038/nmeth.3589. No abstract available. Erratum in: Nat Methods. 2016 Jan;13(1):101.

PMID:
26418763
19.

Exploring Vertical Transmission of Bifidobacteria from Mother to Child.

Milani C, Mancabelli L, Lugli GA, Duranti S, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Ferretti P, Gorfer V, Tett A, Segata N, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2015 Oct;81(20):7078-87. doi: 10.1128/AEM.02037-15. Epub 2015 Jul 31.

20.

The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: a randomized crossover intervention trial.

Foerster J, Maskarinec G, Reichardt N, Tett A, Narbad A, Blaut M, Boeing H.

PLoS One. 2014 Oct 9;9(10):e109606. doi: 10.1371/journal.pone.0109606. eCollection 2014.

21.

Characterisation of SalRAB a salicylic acid inducible positively regulated efflux system of Rhizobium leguminosarum bv viciae 3841.

Tett AJ, Karunakaran R, Poole PS.

PLoS One. 2014 Aug 18;9(8):e103647. doi: 10.1371/journal.pone.0103647. eCollection 2014.

22.

Regulatable vectors for environmental gene expression in Alphaproteobacteria.

Tett AJ, Rudder SJ, Bourdès A, Karunakaran R, Poole PS.

Appl Environ Microbiol. 2012 Oct;78(19):7137-40. doi: 10.1128/AEM.01188-12. Epub 2012 Jul 20.

23.

Progress towards understanding the fate of plasmids in bacterial communities.

Slater FR, Bailey MJ, Tett AJ, Turner SL.

FEMS Microbiol Ecol. 2008 Oct;66(1):3-13. doi: 10.1111/j.1574-6941.2008.00505.x. Epub 2008 May 28. Review.

24.

The minimum information about a genome sequence (MIGS) specification.

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360.

25.

Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet.

Tett A, Spiers AJ, Crossman LC, Ager D, Ciric L, Dow JM, Fry JC, Harris D, Lilley A, Oliver A, Parkhill J, Quail MA, Rainey PB, Saunders NJ, Seeger K, Snyder LA, Squares R, Thomas CM, Turner SL, Zhang XX, Field D, Bailey MJ.

ISME J. 2007 Aug;1(4):331-40. Epub 2007 Jul 5.

26.

The plasmid genome database.

Mølbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D.

Microbiology. 2003 Nov;149(Pt 11):3043-5. No abstract available.

PMID:
14600215

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