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  1. AU="Bazzani, Davide"
  2. AU="Futai, Ryoko"
  3. AU="Ramírez Lasanta, Rafael"
  4. AU="Siannis, F"
  5. AU="Nakamura, M"
  6. AU="Shah, V. P."
  7. AU="Noguerado Asensio, Arturo"
  8. AU="Elías-Rodríguez, Pilar"
  9. AU="Yang, Qing-Yong"
  10. AU="Jonas, Wenke"
  11. AU="Khan, Nawal"
  12. AU="Martini, Lígia A"
  13. AU="Guzzetta, Melissa" AU="Guzzetta, Melissa"
  14. AU="Reiter, Gregor S"
  15. AU="Alberghina, Daniela"
  16. AU=D'Arena Giovanni AU=D'Arena Giovanni
  17. AU="Rutland, Catrin S"
  18. AU="Gocher-Demske, Angela M"
  19. AU="Koide, S S"
  20. AU=Barnbaum Deborah R AU=Barnbaum Deborah R
  21. AU=Xiang Hongfei AU=Xiang Hongfei
  22. AU="Whitehall, Julia"
  23. AU=Silva Severino Jefferson Ribeiro da
  24. AU="Piñero-Pérez, Rocío"
  25. AU="Voss, Stephan"
  26. AU="Jović, Ines"
  27. AU="Pérez-Guerrero, Edsaúl Emilio"
  28. AU="Akiyama, Shoko"
  29. AU="Greene, Wendy R"
  30. AU="Renzetti, Paolo"
  31. AU="Knöpfle, K T"
  32. AU="Peitzsch, Mirko" AU="Peitzsch, Mirko"
  33. AU=Bonet-Sola Daniel
  34. AU="Martín-Alfonso, J.E."
  35. AU=Ramesh BA
  36. AU="Dayanandan, Selvadurai"
  37. AU="Strathmann, Eike A"
  38. AU=Hewitt Stephen M
  39. AU="Meroni, Marco"
  40. AU="Gutierrez Amezcua, Jose Manuel"
  41. AU="Pfeifer, Susanne P"
  42. AU=McGrath Eric J
  43. AU="Wang, Pengyu"
  44. AU="Becker, Joscha Nico"
  45. AU="Chillrud, Steven N"
  46. AU=Werner L P
  47. AU="Tianmin Xu"
  48. AU="Matsagkas, Miltos"
  49. AU="Cosentino, Claudia"
  50. AU="Radbruch, Lukas"
  51. AU=Edwards Justin P.
  52. AU="Morse, Dan J"
  53. AU="Priya, Vansh"
  54. AU="Chen, Eric R"
  55. AU=Behrens Kevin G.
  56. AU=Radtke Heather B
  57. AU="Erdmann, Kati"
  58. AU="Anh, Nguyen P Q"
  59. AU="Arias, Manuel"
  60. AU="Badhrees, I."

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  1. Artikel ; Online: Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases.

    Bazzani, Davide / Heidrich, Vitor / Manghi, Paolo / Blanco-Miguez, Aitor / Asnicar, Francesco / Armanini, Federica / Cavaliere, Sara / Bertelle, Alberto / Dell'Acqua, Federico / Dellasega, Ester / Waldner, Romina / Vicentini, Daniela / Bolzan, Mattia / Tomasi, Cristiano / Segata, Nicola / Pasolli, Edoardo / Ghensi, Paolo

    NPJ biofilms and microbiomes

    2024  Band 10, Heft 1, Seite(n) 12

    Abstract: We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we ... ...

    Abstract We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.
    Mesh-Begriff(e) Humans ; Peri-Implantitis/therapy ; Microbiota
    Sprache Englisch
    Erscheinungsdatum 2024-02-19
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2817021-0
    ISSN 2055-5008 ; 2055-5008
    ISSN (online) 2055-5008
    ISSN 2055-5008
    DOI 10.1038/s41522-024-00482-z
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

    Manara, Serena / Asnicar, Francesco / Beghini, Francesco / Bazzani, Davide / Cumbo, Fabio / Zolfo, Moreno / Nigro, Eleonora / Karcher, Nicolai / Manghi, Paolo / Metzger, Marisa Isabell / Pasolli, Edoardo / Segata, Nicola

    Genome biology. 2019 Dec., v. 20, no. 1

    2019  

    Abstract: BACKGROUND: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human ... ...

    Abstract BACKGROUND: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches. RESULTS: We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories. CONCLUSIONS: The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.
    Schlagwörter Elusimicrobia ; Treponema ; captive animals ; coevolution ; digestive system ; genome ; human population ; humans ; intestinal microorganisms ; lifestyle ; metagenomics ; microbial communities ; microbiome ; monkeys ; phylogeny ; symbiosis
    Sprache Englisch
    Erscheinungsverlauf 2019-12
    Umfang p. 299.
    Erscheinungsort BioMed Central
    Dokumenttyp Artikel
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6906
    ISSN (online) 1474-760X
    ISSN 1465-6906
    DOI 10.1186/s13059-019-1923-9
    Datenquelle NAL Katalog (AGRICOLA)

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  3. Artikel ; Online: Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species.

    Manara, Serena / Asnicar, Francesco / Beghini, Francesco / Bazzani, Davide / Cumbo, Fabio / Zolfo, Moreno / Nigro, Eleonora / Karcher, Nicolai / Manghi, Paolo / Metzger, Marisa Isabell / Pasolli, Edoardo / Segata, Nicola

    Genome biology

    2019  Band 20, Heft 1, Seite(n) 299

    Abstract: Background: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human ... ...

    Abstract Background: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches.
    Results: We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories.
    Conclusions: The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.
    Mesh-Begriff(e) Animals ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Phylogeny ; Primates/microbiology ; Treponema/genetics
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2019-12-28
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-019-1923-9
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

    Asnicar, Francesco / Berry, Sarah E / Valdes, Ana M / Nguyen, Long H / Piccinno, Gianmarco / Drew, David A / Leeming, Emily / Gibson, Rachel / Le Roy, Caroline / Khatib, Haya Al / Francis, Lucy / Mazidi, Mohsen / Mompeo, Olatz / Valles-Colomer, Mireia / Tett, Adrian / Beghini, Francesco / Dubois, Léonard / Bazzani, Davide / Thomas, Andrew Maltez /
    Mirzayi, Chloe / Khleborodova, Asya / Oh, Sehyun / Hine, Rachel / Bonnett, Christopher / Capdevila, Joan / Danzanvilliers, Serge / Giordano, Francesca / Geistlinger, Ludwig / Waldron, Levi / Davies, Richard / Hadjigeorgiou, George / Wolf, Jonathan / Ordovás, José M / Gardner, Christopher / Franks, Paul W / Chan, Andrew T / Huttenhower, Curtis / Spector, Tim D / Segata, Nicola

    Nature medicine

    2021  Band 27, Heft 2, Seite(n) 321–332

    Abstract: The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the ... ...

    Abstract The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.
    Mesh-Begriff(e) Adult ; Biomarkers/metabolism ; Blastocystis/genetics ; Blood Glucose/metabolism ; Child ; Diet/adverse effects ; Fasting/metabolism ; Feeding Behavior ; Female ; Food Microbiology ; Gastrointestinal Microbiome/genetics ; Glucose/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome/genetics ; Microbiota/genetics ; Middle Aged ; Obesity/genetics ; Obesity/metabolism ; Obesity/microbiology ; Postprandial Period/genetics ; Prevotella/genetics ; Prevotella/isolation & purification
    Chemische Substanzen Biomarkers ; Blood Glucose ; Glucose (IY9XDZ35W2)
    Sprache Englisch
    Erscheinungsdatum 2021-01-11
    Erscheinungsland United States
    Dokumenttyp Clinical Trial ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-020-01183-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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