The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

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

doi:10.1016/j.chom.2019.08.018

Cited by 347 publications

(461 citation statements)

References 147 publications

(240 reference statements)

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“…The gut microbiome is influenced by several factors including diet [2], physical activity [3], use of antibiotics [4], and other lifestyle-related conditions. Studies comparing the microbiome of rural and industrialized communities have also shown that dietary and lifestyle changes linked to Westernization have played a pivotal role in the loss of many microbial taxa and in the rise of others [5][6][7][8][9][10][11][12][13][14]. Although it is difficult to establish causality and mechanisms for these links [15,16], recent studies have extended the identifiable members of the human microbiome to now cover > 90% of its overall diversity [11], which is a prerequisite for advancing the understanding of the role of microbes in human physiology and metabolism.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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BackgroundHumans 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.ResultsWe 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.ConclusionsThe 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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…indicating high genomic diversity of the different species 140 as well as a high differentiation among 513 strains of the same species, as for instance P. copri 141 . It is well documented that bacteria can 514 modulate the lymphocyte differentiation by the SCFAs (as previously 142 ), whose composition can 515 vary (qualitatively and quantitatively) based on the inflammatory status, as we have recently shown 516 for different intestinal gastrointestinal pathologies, such as celiac disease, adenomatous polyposis and 517 CRC 143 .…”

Section: Statistical Analysis Of the Association Between Tissue Micromentioning

confidence: 99%

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Niccolai

Russo

Baldi

et al. 2020

Preprint

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20Background: Colorectal cancer (CRC) is a widespread disease that represents an example of chronic 21 inflammation-associated tumor. In fact, the immune system, besides protecting the host from 22Aim: The cellular and molecular characterization of the immune response and the evaluation of GM 33 composition in healthy and tumor mucosa, focusing on the correlation between cytokines' profile and 34 GM signature. 35 36 Methods: We collected tumoral (CRC) and healthy (CRC-S) mucosa samples of 45 CRC patients. 37 For each sample, we characterized the Tissue Infiltrating Lymphocytes (TIL)'s subset profile and the 38 GM composition. In addition, in 14 CRC patients, we evaluated the CRC and CRC-S molecular 39 inflammatory response (26 cytokines/chemokines) and we correlated this profile with GM 40 composition using the Dirichlet Multinomial Regression. 41 42Results: The analysis of T cells subsets distribution showed that CRC samples displayed higher 43 percentages of Th17, Th2, Tregs, Tc17, Tc1/Tc17, and Tcreg, compared to CRC-S. Notably, also the 44 number of Th9 was higher, even if not significantly, in CRC tissue compared to healthy one. In 45 addition, we found that MIP-1α, IL-1β, IL-2, IP-10, IL-6, IL-8, IL-17A, IFN-γ, TNF-α, MCP-1, IL-46 1α, P-selectin and IL-9 were significantly increased in CRC compared to CRC-S. Moreover, the GM 47 analysis revealed that CRC samples had significantly higher levels of Fusobacteria, Proteobacteria, 48Fusobacterium, Ruminococcus2 (Lachnospiraceae family) and Ruminococcus (Ruminococcaceae 49 family) than CRC-S. Finally, we found that the abundance of Prevotella spp in CRC samples was 50 negatively correlated with IL-17A and positively with IL-9. In addition, the abundance of Bacteroides 51and Escherichia/Shigella species in CRC samples showed a negative association with IL-9 and IP-10 52 respectively. 53 54 Conclusions: Our data show a clear dissimilarity of inflammatory profile and GM composition 55 between the tumor and the adjacent healthy tissue, displaying the generation of a peculiar CRC 56 microenvironment. Interestingly, relating the tissue cytokine profile with the GM composition, we 57 confirmed the presence of a bidirectional crosstalk between the immune response and the host's 58 commensal microorganisms; in detail, we documented for the first time that Prevotella spp. and 59 Bacteroides spp. are correlated (positively and negatively, respectively) with the IL-9, whose role in 60 CRC development is still debated. 61 62 63

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“…Then, to determine whether the paleofeces DNA exhibits appropriate molecular behavior for aDNA, such as DNA damage, the merged reads from each sample were mapped to the genome of Prevotella copri (DSM 18205), and mapDamage 2.0 (Jonsson, Ginolhac, Schubert, Johnson, & Orlando, 2013) was used to measure the frequency of nucleotide deaminations that are characteristic of aDNA. P. copri was selected because it has been reported in both human and dog gut microbiota (Li et al, 2017;Tett et al, 2019).…”

Section: Assessment Of Paleofeces Microbial Preservationmentioning

confidence: 99%

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

Hagan

Hofman

Hübner

et al. 2019

American J Phys Anthropol

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Objectives: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. Methods:In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP). Results:Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.Conclusions: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies. K E Y W O R D S

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The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Cited by 347 publications

References 147 publications

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

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

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

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