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1. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Author

Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, and Segata, Nicola

Published
2023
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2. Closely related Lak megaphages replicate in the microbiomes of diverse animals

Author

Crisci, Marco A, Chen, Lin-Xing, Devoto, Audra E, Borges, Adair L, Bordin, Nicola, Sachdeva, Rohan, Tett, Adrian, Sharrar, Allison M, Segata, Nicola, Debenedetti, Francesco, Bailey, Mick, Burt, Rachel, Wood, Rhiannon M, Rowden, Lewis J, Corsini, Paula M, van Winden, Steven, Holmes, Mark A, Lei, Shufei, Banfield, Jillian F, and Santini, Joanne M

Subjects
Genetics, Human Genome, Microbiome, Omics, Virology
Abstract

Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.

Published
2021

3. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions

Author

Blanco-Míguez, Aitor, Gálvez, Eric J.C., Pasolli, Edoardo, De Filippis, Francesca, Amend, Lena, Huang, Kun D., Manghi, Paolo, Lesker, Till-Robin, Riedel, Thomas, Cova, Linda, Punčochář, Michal, Thomas, Andrew Maltez, Valles-Colomer, Mireia, Schober, Isabel, Hitch, Thomas C.A., Clavel, Thomas, Berry, Sarah E., Davies, Richard, Wolf, Jonathan, Spector, Tim D., Overmann, Jörg, Tett, Adrian, Ercolini, Danilo, Segata, Nicola, and Strowig, Till

Published
2023
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4. The person-to-person transmission landscape of the gut and oral microbiomes

Author

Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, Maria Carmen, and Segata, Nicola

Published
2023
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6. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Author

Asnicar, Francesco, Berry, Sarah E., Valdes, Ana M., Nguyen, Long H., Piccinno, Gianmarco, Drew, David A., Leeming, Emily, Gibson, Rachel, Le Roy, Caroline, Al Khatib, Haya, Francis, Lucy, Mazidi, Mohsen, Mompeo, Olatz, Valles-Colomer, Mireia, Tett, Adrian, Beghini, Francesco, and Dubois, Leonard

Subjects
Digestive organs -- Physiological aspects, Metabolism -- Research, Medical research, Medicine, Experimental, Microbiota (Symbiotic organisms) -- Physiological aspects, Host-bacteria relationships -- Physiological aspects, Diet -- Physiological aspects, Biological sciences, Health
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. Analyses from the gut microbiome of over 1,000 individuals from the PREDICT 1 study, for which detailed long-term diet information as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements are available, unveil new associations between specific gut microbes, dietary habits and cardiometabolic health., Author(s): Francesco Asnicar [sup.1] , Sarah E. Berry [sup.2] , Ana M. Valdes [sup.3] [sup.4] , Long H. Nguyen [sup.5] , Gianmarco Piccinno [sup.1] , David A. Drew [sup.5] , [...]

Published
2021
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9. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Author

Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, and Segata, Nicola

Published
2019
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10. Plasmid genomic studies of the large phytosphere associated plasmid pQBR103

Author

Tett, Adrian James

Subjects
572.8
Abstract

pQBR103 is a representative of the large pQBR collection of ecologically well characterised self-transmissible and mercury resistant plasmids. These plasmids constitute five genetically distinct groups (I-V) and were isolated from the phytosphere of a number of plant species at a single geographical location. Of the collection pQBR103 (group I), which is known to confer a seasonal fitness benefit on a pseudomonad host, is the best studied. Determination and annotation of the pQBR103 sequence, in this thesis, has revealed it is large at 425 kb, and contains no 16S rRNA or other host "housekeeping" genes. It also revealed the likely mechanisms of plasmid replication and stability, but not of plasmid transfer. While traits of possible ecological function were identified, 80% of coding sequences could not be ascribed a function and 59% of the total coding capacity of pQBR103 constituted novel orphan genes. Therefore, the ecological function of this plasmid remains largely enigmatic. Having created an online database, of all publicly available complete plasmid genomes, the lack of functional assignment to pQBR103 may reflect the biases in plasmids previously chosen for sequencing. Building on the legacy of the plasmid sequence, genomic investigations were undertaken. In vitro, proteomic studies demonstrated pQBR103 is tightly regulated and affects host chromosomal responses to the environment. Diversity within the pQBR collection (groups I, III and IV) was assessed by PCR surveys and a custom pQBR103 microarray. Intergroup comparisons revealed no shared homology between group I and groups III or IV, other than common mer genes, suggesting independent evolutionary histories. Intragroup comparisons identified genetic instability and revealed a common genetic core, which contains the genes putatively responsible for stability and replication. These features are not clustered and there are relatively few repeat sequences, both of which contradict the modular paradigm described for other plasmids.

Published
2007

11. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Author

Karcher, Nicolai, Pasolli, Edoardo, Asnicar, Francesco, Huang, Kun D., Tett, Adrian, Manara, Serena, Armanini, Federica, Bain, Debbie, Duncan, Sylvia H., Louis, Petra, Zolfo, Moreno, Manghi, Paolo, Valles-Colomer, Mireia, Raffaetà, Roberta, Rota-Stabelli, Omar, Collado, Maria Carmen, Zeller, Georg, Falush, Daniel, Maixner, Frank, Walker, Alan W., Huttenhower, Curtis, and Segata, Nicola

Published
2020
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13. The person-to-person transmission landscape of the gut and oral microbiomes

Author

European Commission, National Cancer Institute (US), European Research Council, Simons Foundation, EMBO, 0000-0002-1988-6054, 0000-0001-7386-5572, 0000-0003-0846-6529, 0000-0003-3732-1468, 0000-0001-6371-528X, 0000-0002-4539-4811, 0000-0001-9450-9235, 0000-0001-6661-4046, 0000-0001-5212-1101, 0000-0002-8640-2662, 0000-0003-4144-2019, 0000-0002-5646-1004, 0000-0002-3872-347X, 0000-0002-7623-217X, 0000-0002-9128-9414, 0000-0001-8438-2322, 0000-0001-7831-8420, 0000-0002-7316-0772, 0000-0002-9795-0365, 0000-0001-7436-6919, 0000-0002-1583-5794, Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, María Carmen, Segata, Nicola, European Commission, National Cancer Institute (US), European Research Council, Simons Foundation, EMBO, 0000-0002-1988-6054, 0000-0001-7386-5572, 0000-0003-0846-6529, 0000-0003-3732-1468, 0000-0001-6371-528X, 0000-0002-4539-4811, 0000-0001-9450-9235, 0000-0001-6661-4046, 0000-0001-5212-1101, 0000-0002-8640-2662, 0000-0003-4144-2019, 0000-0002-5646-1004, 0000-0002-3872-347X, 0000-0002-7623-217X, 0000-0002-9128-9414, 0000-0001-8438-2322, 0000-0001-7831-8420, 0000-0002-7316-0772, 0000-0002-9795-0365, 0000-0001-7436-6919, 0000-0002-1583-5794, Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, María Carmen, and Segata, Nicola

Abstract

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Published
2023

15. Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Author

Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, and Segata, Nicola

Published
2019
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20. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

Author

Maixner, Frank, primary, Sarhan, Mohamed S., additional, Huang, Kun D., additional, Tett, Adrian, additional, Schoenafinger, Alexander, additional, Zingale, Stefania, additional, Blanco-Míguez, Aitor, additional, Manghi, Paolo, additional, Cemper-Kiesslich, Jan, additional, Rosendahl, Wilfried, additional, Kusebauch, Ulrike, additional, Morrone, Seamus R., additional, Hoopmann, Michael R., additional, Rota-Stabelli, Omar, additional, Rattei, Thomas, additional, Moritz, Robert L., additional, Oeggl, Klaus, additional, Segata, Nicola, additional, Zink, Albert, additional, Reschreiter, Hans, additional, and Kowarik, Kerstin, additional

Published
2021
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22. Additional file 1 of Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Author

Karcher, Nicolai, Pasolli, Edoardo, Asnicar, Francesco, Huang, Kun D., Tett, Adrian, Manara, Serena, Armanini, Federica, Bain, Debbie, Duncan, Sylvia H., Louis, Petra, Zolfo, Moreno, Manghi, Paolo, Valles-Colomer, Mireia, Raffaetà, Roberta, Rota-Stabelli, Omar, Collado, Maria Carmen, Zeller, Georg, Falush, Daniel, Maixner, Frank, Walker, Alan W., Huttenhower, Curtis, and Segata, Nicola

Abstract

Additional file 1. Supplementary Figures.

Published
2020
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23. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

Author

Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric Steven, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J., Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric Steven, Huttenhower, Curtis, Knip, Mikael, and Xavier, Ramnik J.

Abstract

Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child's life. We identified mother-to-child bacterial transmission events and describe the incidence of family-specific antibiotic resistance genes. We observed two inheritance patterns across multiple species, where often the mother's dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant gut. In families where the secondary strain of B. uniformis was inherited, a starch utilization gene cluster that was absent in the mother's dominant strain was identified in the child, suggesting the selective advantage of a mother's secondary strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high resolution and give insights into early colonization of the infant gut. Using longitudinal metagenomic sequencing from 44 mother/child pairs, Yassour et al. characterized mother-to-child strain transmission patterns. While mothers' dominant strains were often inherited, nondominant secondary strain transmissions were also observed. Microbial functional analysis reveals that inherited maternal secondary strains may have a selective advantage to colonize infant guts., National Institutes of Health (Grant 1DP3DK094338–01)

Published
2020

25. Additional file 8: of Genomic and metagenomic insights into the microbial community of a thermal spring

Author

Pedron, Renato, Esposito, Alfonso, Bianconi, Irene, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Cristofolini, Mario, Segata, Nicola, and Jousson, Olivier

Abstract

Figure S3. Presence (blue)/absence (yellow) heatmap displaying only the gene families found to be significantly over- (or under-)represented in genomes deriving from one of the four sampling sites. (PPTX 1073Â kb)

Published
2019
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26. Additional file 9: of Genomic and metagenomic insights into the microbial community of a thermal spring

Author

Pedron, Renato, Esposito, Alfonso, Bianconi, Irene, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Cristofolini, Mario, Segata, Nicola, and Jousson, Olivier

Abstract

Figure S4. Anviâ O plots displaying the clustering patterns of assembled contigs along with their coverage by each metagenome. Leftmost graph shows the contigs clustered only by sequence composition (i.e., tetrameric signature); rightmost graph clusters the contigs only by their differential coverage; middle graph, combination of differential coverage and tetrameric composition. (PPTX 829Â kb)

Published
2019
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27. Additional file 3: of Genomic and metagenomic insights into the microbial community of a thermal spring

Author

Pedron, Renato, Esposito, Alfonso, Bianconi, Irene, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Cristofolini, Mario, Segata, Nicola, and Jousson, Olivier

Abstract

Figure S1a. Rank abundance plots of the families detected using MetaPhlAn2 in the four metagenomes. y-axis, abundances (expressed as percentage of the reads mapping on taxonomically informative marker genes); x-axis, families detected. (PPTX 471Â kb)

Published
2019
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28. Additional file 6: of Genomic and metagenomic insights into the microbial community of a thermal spring

Author

Pedron, Renato, Esposito, Alfonso, Bianconi, Irene, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Cristofolini, Mario, Segata, Nicola, and Jousson, Olivier

Abstract

Figure S2. Venn diagram showing the distribution of functions in the four metagenomes. Each ellipse corresponds to the metagenome of a site; the overlapping areas represents the functions that are either shared among- or unique to- each site. Unique functions are explicitly annotated. (PPTX 988Â kb)

Published
2019
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29. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Author

European Research Council, Tett, Adrian, Huang, Kun D., Asnicar, Francesco, Fehlner-Peach, Hannah, Pasolli, Edoardo, Karcher, Nicolai, Armanini, Federica, Manghi, Paolo, Bonham, Kevin, Zolfo, Moreno, De Filippis, Francesca, Magnabosco, Cara, Bonneau, Richard, Lusingu, John, Amuasi, John, Reinhard, Karl, Rattei, Thomas, Boulund, Fredrik, Engstrand, Lars, Zink, Albert, Collado, María Carmen, Littman, Dan R., Eibach, Daniel, Ercolini, Danilo, Rota-Stabelli, Omar, Huttenhower, Curtis, Maixner, Frank, Segata, Nicola, European Research Council, Tett, Adrian, Huang, Kun D., Asnicar, Francesco, Fehlner-Peach, Hannah, Pasolli, Edoardo, Karcher, Nicolai, Armanini, Federica, Manghi, Paolo, Bonham, Kevin, Zolfo, Moreno, De Filippis, Francesca, Magnabosco, Cara, Bonneau, Richard, Lusingu, John, Amuasi, John, Reinhard, Karl, Rattei, Thomas, Boulund, Fredrik, Engstrand, Lars, Zink, Albert, Collado, María Carmen, Littman, Dan R., Eibach, Daniel, Ercolini, Danilo, Rota-Stabelli, Omar, Huttenhower, Curtis, Maixner, Frank, and Segata, Nicola

Abstract

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

Published
2019

30. Author Correction:Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (Nature Medicine, (2019), 25, 4, (667-678), 10.1038/s41591-019-0405-7)

Author

Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, Segata, Nicola, Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, and Segata, Nicola

Abstract

In the version of this article initially published, the affiliation for Chiara Pozzi, Sara Gandini and Davide Serrano was given as the European Institute of Oncology. The correct affiliation is IEO, European Institute of Oncology IRCCS. In addition, the data for age, BMI and sex were missing from Table 1 for the HanniganGD_2018 dataset, and consequently for the totals of all datasets. These data are given in Table 1 here. The errors have been corrected in the HTML and PDF versions of the article.(table Presented).

Published
2019

31. Additional file 1: of Profiling microbial strains in urban environments using metagenomic sequencing data

Author

Zolfo, Moreno, Asnicar, Francesco, Manghi, Paolo, Pasolli, Edoardo, Tett, Adrian, and Segata, Nicola

Abstract

Figure S1. Scatterplot contrasting for each sample the number of successfully profiled species against the metagenome size (in million reads). Each dot corresponds to a sample in the MetaSUB dataset. The number of detected species was calculated with MetaPhlAn2 by requiring a species to have a relative abundance higher than 0.5% within the sample. (PDF 113Â kb)

Published
2018
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32. Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

Author

Fehlner-Peach, Hannah, primary, Magnabosco, Cara, additional, Raghavan, Varsha, additional, Scher, Jose U., additional, Tett, Adrian, additional, Cox, Laura M., additional, Gottsegen, Claire, additional, Watters, Aaron, additional, Wiltshire-Gordon, John D., additional, Segata, Nicola, additional, Bonneau, Richard, additional, and Littman, Dan R., additional

Published
2019
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33. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Author

Tett, Adrian, primary, Huang, Kun D., additional, Asnicar, Francesco, additional, Fehlner-Peach, Hannah, additional, Pasolli, Edoardo, additional, Karcher, Nicolai, additional, Armanini, Federica, additional, Manghi, Paolo, additional, Bonham, Kevin, additional, Zolfo, Moreno, additional, De Filippis, Francesca, additional, Magnabosco, Cara, additional, Bonneau, Richard, additional, Lusingu, John, additional, Amuasi, John, additional, Reinhard, Karl, additional, Rattei, Thomas, additional, Boulund, Fredrik, additional, Engstrand, Lars, additional, Zink, Albert, additional, Collado, Maria Carmen, additional, Littman, Dan R., additional, Eibach, Daniel, additional, Ercolini, Danilo, additional, Rota-Stabelli, Omar, additional, Huttenhower, Curtis, additional, Maixner, Frank, additional, and Segata, Nicola, additional

Published
2019
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34. Consumer Safety Considerations of Skin and Oral Microbiome Perturbation

Author

McBain, Andrew J., primary, O’Neill, Catherine A., additional, Amezquita, Alejandro, additional, Price, Laura J., additional, Faust, Karoline, additional, Tett, Adrian, additional, Segata, Nicola, additional, Swann, Jonathan R., additional, Smith, Adrian M., additional, Murphy, Barry, additional, Hoptroff, Michael, additional, James, Gordon, additional, Reddy, Yugandhar, additional, Dasgupta, Anindya, additional, Ross, Tom, additional, Chapple, Iain L., additional, Wade, William G., additional, and Fernandez-Piquer, Judith, additional

Published
2019
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35. Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

Author

De Filippis, Francesca, primary, Pasolli, Edoardo, additional, Tett, Adrian, additional, Tarallo, Sonia, additional, Naccarati, Alessio, additional, De Angelis, Maria, additional, Neviani, Erasmo, additional, Cocolin, Luca, additional, Gobbetti, Marco, additional, Segata, Nicola, additional, and Ercolini, Danilo, additional

Published
2019
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37. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Author

Pasolli, Edoardo, primary, Asnicar, Francesco, additional, Manara, Serena, additional, Zolfo, Moreno, additional, Karcher, Nicolai, additional, Armanini, Federica, additional, Beghini, Francesco, additional, Manghi, Paolo, additional, Tett, Adrian, additional, Ghensi, Paolo, additional, Collado, Maria Carmen, additional, Rice, Benjamin L., additional, DuLong, Casey, additional, Morgan, Xochitl C., additional, Golden, Christopher D., additional, Quince, Christopher, additional, Huttenhower, Curtis, additional, and Segata, Nicola, additional

Published
2019
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38. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Author

European Commission, LEO Pharma Foundation, Fondazione Caritro, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Gorfer, Valentina, Fedi, Sabina, Armanini, Federica, Truong, Duy Tin, Manara, Serena, Zolfo, Moreno, Beghini, Francesco, Bertorelli, Roberto, de Sanctis, Veronica, Bariletti, Ilaria, Canto, Rosarita, Clementi,Rosanna, Cologna,Marina, Crifò, Tiziana, Cusumano, Giuseppina, Gottardi, Stefania, Innamorati, Claudia, Masè,Caterina, Postai,Daniela, Savoi, Daniela, Duranti, Sabrina, Lugli, Gabriele Andrea, Mancabelli, Leonardo, Turroni, Francesca, Ferrario, Chiara, Milani, Christian, Mangifesta, Marta, Anzalone, Rosaria, Viappiani, Alice, Yassour, Moran, Vlamakis, Hera, Xavier, Ramnik, Collado, María Carmen, Koren,Omry, Tateo, Saverio, Soffiati,Massimo, Pedrotti, Anna, Ventura, Marco, Huttenhower, Curtis, Bork, Peer, Segata, Nicola, European Commission, LEO Pharma Foundation, Fondazione Caritro, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Gorfer, Valentina, Fedi, Sabina, Armanini, Federica, Truong, Duy Tin, Manara, Serena, Zolfo, Moreno, Beghini, Francesco, Bertorelli, Roberto, de Sanctis, Veronica, Bariletti, Ilaria, Canto, Rosarita, Clementi,Rosanna, Cologna,Marina, Crifò, Tiziana, Cusumano, Giuseppina, Gottardi, Stefania, Innamorati, Claudia, Masè,Caterina, Postai,Daniela, Savoi, Daniela, Duranti, Sabrina, Lugli, Gabriele Andrea, Mancabelli, Leonardo, Turroni, Francesca, Ferrario, Chiara, Milani, Christian, Mangifesta, Marta, Anzalone, Rosaria, Viappiani, Alice, Yassour, Moran, Vlamakis, Hera, Xavier, Ramnik, Collado, María Carmen, Koren,Omry, Tateo, Saverio, Soffiati,Massimo, Pedrotti, Anna, Ventura, Marco, Huttenhower, Curtis, Bork, Peer, and Segata, Nicola

Abstract

The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.

Published
2018

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

Author

Yassour, Moran, primary, Jason, Eeva, additional, Hogstrom, Larson J., additional, Arthur, Timothy D., additional, Tripathi, Surya, additional, Siljander, Heli, additional, Selvenius, Jenni, additional, Oikarinen, Sami, additional, Hyöty, Heikki, additional, Virtanen, Suvi M., additional, Ilonen, Jorma, additional, Ferretti, Pamela, additional, Pasolli, Edoardo, additional, Tett, Adrian, additional, Asnicar, Francesco, additional, Segata, Nicola, additional, Vlamakis, Hera, additional, Lander, Eric S., additional, Huttenhower, Curtis, additional, Knip, Mikael, additional, and Xavier, Ramnik J., additional

Published
2018
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41. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Author

Ferretti, Pamela, primary, Pasolli, Edoardo, additional, Tett, Adrian, additional, Asnicar, Francesco, additional, Gorfer, Valentina, additional, Fedi, Sabina, additional, Armanini, Federica, additional, Truong, Duy Tin, additional, Manara, Serena, additional, Zolfo, Moreno, additional, Beghini, Francesco, additional, Bertorelli, Roberto, additional, De Sanctis, Veronica, additional, Bariletti, Ilaria, additional, Canto, Rosarita, additional, Clementi, Rosanna, additional, Cologna, Marina, additional, Crifò, Tiziana, additional, Cusumano, Giuseppina, additional, Gottardi, Stefania, additional, Innamorati, Claudia, additional, Masè, Caterina, additional, Postai, Daniela, additional, Savoi, Daniela, additional, Duranti, Sabrina, additional, Lugli, Gabriele Andrea, additional, Mancabelli, Leonardo, additional, Turroni, Francesca, additional, Ferrario, Chiara, additional, Milani, Christian, additional, Mangifesta, Marta, additional, Anzalone, Rosaria, additional, Viappiani, Alice, additional, Yassour, Moran, additional, Vlamakis, Hera, additional, Xavier, Ramnik, additional, Collado, Carmen Maria, additional, Koren, Omry, additional, Tateo, Saverio, additional, Soffiati, Massimo, additional, Pedrotti, Anna, additional, Ventura, Marco, additional, Huttenhower, Curtis, additional, Bork, Peer, additional, and Segata, Nicola, additional

Published
2018
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48. Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism

Author

Korecka, Agata, primary, Dona, Anthony, additional, Lahiri, Shawon, additional, Tett, Adrian James, additional, Al-Asmakh, Maha, additional, Braniste, Viorica, additional, D’Arienzo, Rossana, additional, Abbaspour, Afrouz, additional, Reichardt, Nicole, additional, Fujii-Kuriyama, Yoshiaki, additional, Rafter, Joseph, additional, Narbad, Arjan, additional, Holmes, Elaine, additional, Nicholson, Jeremy, additional, Arulampalam, Velmurugesan, additional, and Pettersson, Sven, additional

Published
2016
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49. Exploring Vertical Transmission of Bifidobacteria from Mother to Child

Author

Milani, Christian, primary, Mancabelli, Leonardo, additional, Lugli, Gabriele Andrea, additional, Duranti, Sabrina, additional, Turroni, Francesca, additional, Ferrario, Chiara, additional, Mangifesta, Marta, additional, Viappiani, Alice, additional, Ferretti, Pamela, additional, Gorfer, Valentina, additional, Tett, Adrian, additional, Segata, Nicola, additional, van Sinderen, Douwe, additional, and Ventura, Marco, additional

Published
2015
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