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Items: 1 to 50 of 68

1.

Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.

Victoria AJ, Cao E, Salmaso N, Segata N, Donati C.

Microbiol Resour Announc. 2018 Aug 30;7(8). pii: e00876-18. doi: 10.1128/MRA.00876-18. eCollection 2018 Aug.

2.

Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital.

Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N.

Genome Med. 2018 Nov 13;10(1):82. doi: 10.1186/s13073-018-0593-7.

3.

Species-level functional profiling of metagenomes and metatranscriptomes.

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C.

Nat Methods. 2018 Nov;15(11):962-968. doi: 10.1038/s41592-018-0176-y. Epub 2018 Oct 30.

PMID:
30377376
4.

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
5.

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.

6.

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.

7.

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.

8.

The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

Shaaban H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE.

Gates Open Res. 2018 Jan 5;2:3. doi: 10.12688/gatesopenres.12772.1.

9.

On the Road to Strain-Resolved Comparative Metagenomics.

Segata N.

mSystems. 2018 Mar 13;3(2). pii: e00190-17. doi: 10.1128/mSystems.00190-17. eCollection 2018 Mar-Apr.

10.

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.

11.

Selective maternal seeding and environment shape the human gut microbiome.

Korpela K, Costea P, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P.

Genome Res. 2018 Apr;28(4):561-568. doi: 10.1101/gr.233940.117. Epub 2018 Mar 1.

12.

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 ):.

13.

Corrigendum: Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Dec 8;35(12):1211. doi: 10.1038/nbt1217-1211b.

PMID:
29220029
14.

bioBakery: a meta'omic analysis environment.

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.

Bioinformatics. 2018 Apr 1;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

15.

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.

16.

Long-adapter single-strand oligonucleotide probes for the massively multiplexed cloning of kilobase genome regions.

Tosi L, Sridhara V, Yang Y, Guan D, Shpilker P, Segata N, Larman HB, Parekkadan B.

Nat Biomed Eng. 2017;1. pii: 0092. doi: 10.1038/s41551-017-0092. Epub 2017 Jun 26.

17.

Accessible, curated metagenomic data through ExperimentHub.

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L.

Nat Methods. 2017 Oct 31;14(11):1023-1024. doi: 10.1038/nmeth.4468. No abstract available.

18.

The new phylogeny of the genus Mycobacterium: The old and the news.

Tortoli E, Fedrizzi T, Meehan CJ, Trovato A, Grottola A, Giacobazzi E, Serpini GF, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, Frascaro F, De Sanctis V, Pecorari M, Jousson O, Segata N, Cirillo DM.

Infect Genet Evol. 2017 Dec;56:19-25. doi: 10.1016/j.meegid.2017.10.013. Epub 2017 Oct 11.

PMID:
29030295
19.

Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935. Review. Erratum in: Nat Biotechnol. 2017 Dec 8;35(12 ):1211.

PMID:
28898207
20.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E, Segata N, Lebeer S.

mSystems. 2017 Aug 22;2(4). pii: e00061-17. doi: 10.1128/mSystems.00061-17. eCollection 2017 Jul-Aug.

21.

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome.

Beghini F, Pasolli E, Truong TD, Putignani L, Cacciò SM, Segata N.

ISME J. 2017 Dec;11(12):2848-2863. doi: 10.1038/ismej.2017.139. Epub 2017 Aug 22.

22.

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.

Kissling WD, Ahumada JA, Bowser A, Fernandez M, Fernández N, García EA, Guralnick RP, Isaac NJB, Kelling S, Los W, McRae L, Mihoub JB, Obst M, Santamaria M, Skidmore AK, Williams KJ, Agosti D, Amariles D, Arvanitidis C, Bastin L, De Leo F, Egloff W, Elith J, Hobern D, Martin D, Pereira HM, Pesole G, Peterseil J, Saarenmaa H, Schigel D, Schmeller DS, Segata N, Turak E, Uhlir PF, Wee B, Hardisty AR.

Biol Rev Camb Philos Soc. 2018 Feb;93(1):600-625. doi: 10.1111/brv.12359. Epub 2017 Aug 2.

PMID:
28766908
23.

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.

Bacci G, Mengoni A, Fiscarelli E, Segata N, Taccetti G, Dolce D, Paganin P, Morelli P, Tuccio V, De Alessandri A, Lucidi V, Bevivino A.

Int J Mol Sci. 2017 Jul 29;18(8). pii: E1654. doi: 10.3390/ijms18081654.

24.

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.

Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, Mangifesta M, Anzalone R, Zolfo M, Viappiani A, Pasolli E, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Fedi S, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Soffiati M, Tateo S, Pedrotti A, Segata N, van Sinderen D, Ventura M.

Microbiome. 2017 Jun 26;5(1):66. doi: 10.1186/s40168-017-0282-6.

25.

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.

26.

Genomic characterization of Nontuberculous Mycobacteria.

Fedrizzi T, Meehan CJ, Grottola A, Giacobazzi E, Fregni Serpini G, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, De Sanctis V, Rumpianesi F, Pecorari M, Jousson O, Tortoli E, Segata N.

Sci Rep. 2017 Mar 27;7:45258. doi: 10.1038/srep45258.

27.

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.

28.

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.

29.

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.

30.

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
31.

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N.

Nat Microbiol. 2016 May 27;1(7):16070. doi: 10.1038/nmicrobiol.2016.70.

PMID:
27572971
32.

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

Pasolli E, Truong DT, Malik F, Waldron L, Segata N.

PLoS Comput Biol. 2016 Jul 11;12(7):e1004977. doi: 10.1371/journal.pcbi.1004977. eCollection 2016 Jul.

33.

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers.

Segata N, Baldini F, Pompon J, Garrett WS, Truong DT, Dabiré RK, Diabaté A, Levashina EA, Catteruccia F.

Sci Rep. 2016 Apr 18;6:24207. doi: 10.1038/srep24207.

34.

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
35.

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.

36.

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C.

PLoS Comput Biol. 2015 Dec 18;11(12):e1004557. doi: 10.1371/journal.pcbi.1004557. eCollection 2015 Dec.

37.

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut.

Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L, Ferrario C, Mangifesta M, Hevia A, Viappiani A, Scholz M, Arioli S, Sanchez B, Lane J, Ward DV, Hickey R, Mora D, Segata N, Margolles A, van Sinderen D, Ventura M.

Sci Rep. 2015 Oct 28;5:15782. doi: 10.1038/srep15782.

38.

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
39.

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.

40.

Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity.

Segata N.

Curr Biol. 2015 Jul 20;25(14):R611-3. doi: 10.1016/j.cub.2015.05.040.

41.

Compact graphical representation of phylogenetic data and metadata with GraPhlAn.

Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N.

PeerJ. 2015 Jun 18;3:e1029. doi: 10.7717/peerj.1029. eCollection 2015.

42.

Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.

Fusco da Costa AR, Fedrizzi T, Lopes ML, Pecorari M, Oliveira da Costa WL, Giacobazzi E, da Costa Bahia JR, De Sanctis V, Batista Lima KV, Bertorelli R, Grottola A, Fabio A, Mariottini A, Ferretti P, Di Leva F, Fregni Serpini G, Tagliazucchi S, Rumpianesi F, Jousson O, Segata N, Tortoli E.

Int J Syst Evol Microbiol. 2015 Feb;65(Pt 2):656-62. doi: 10.1099/ijs.0.068395-0. Epub 2014 Dec 8.

PMID:
25487637
43.

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol.

Milani C, Lugli GA, Turroni F, Mancabelli L, Duranti S, Viappiani A, Mangifesta M, Segata N, van Sinderen D, Ventura M.

FEMS Microbiol Ecol. 2014 Nov;90(2):493-503. doi: 10.1111/1574-6941.12410. Epub 2014 Sep 8.

44.

Evidence of natural Wolbachia infections in field populations of Anopheles gambiae.

Baldini F, Segata N, Pompon J, Marcenac P, Shaw WR, Dabiré RK, Diabaté A, Levashina EA, Catteruccia F.

Nat Commun. 2014 Jun 6;5:3985. doi: 10.1038/ncomms4985.

45.

Relating the metatranscriptome and metagenome of the human gut.

Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19.

46.

Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform.

Dassi E, Ballarini A, Covello G; HTM-CMB2013, Quattrone A, Jousson O, De Sanctis V, Bertorelli R, Denti MA, Segata N.

J Biotechnol. 2014 Nov 20;190:30-9. doi: 10.1016/j.jbiotec.2014.03.024. Epub 2014 Mar 23.

PMID:
24670254
47.

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission.

Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS.

ISME J. 2014 Jul;8(7):1403-17. doi: 10.1038/ismej.2014.3. Epub 2014 Feb 6.

48.

MetaRef: a pan-genomic database for comparative and community microbial genomics.

Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N.

Nucleic Acids Res. 2014 Jan;42(Database issue):D617-24. doi: 10.1093/nar/gkt1078. Epub 2013 Nov 6.

49.

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis.

Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR.

Elife. 2013 Nov 5;2:e01202. doi: 10.7554/eLife.01202.

50.

Two-stage microbial community experimental design.

Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C.

ISME J. 2013 Dec;7(12):2330-9. doi: 10.1038/ismej.2013.139. Epub 2013 Aug 15.

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