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

Blanco-Míguez, Aitor; Beghini, Francesco; Cumbo, Fabio; McIver, Lauren J.; Thompson, Kelsey N.; Zolfo, Moreno; Manghi, Paolo; Dubois, Léonard; Huang, Kun; 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; Spector, Tim D.; Franzosa, Eric A.; Pasolli, Edoardo; Asnicar, Francesco; Huttenhower, Curtis; Segata, Nicola

doi:10.1038/s41587-023-01688-w

Cited by 400 publications

(281 citation statements)

References 111 publications

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“…Raw reads were quality checked and adapter-trimmed using Trimgalore (Supplementary Table S1) (43). Metaphlan was used to identify relative species abundance of sequence reads (44). Sequences were aligned using RSEM (45) to the C. difficile strain 630 reference GCA_000009205.2 under the accession number AM180355 (PRJNA78) (46,47).…”

Section: Methodsmentioning

confidence: 99%

Butyrate enhances Clostridioides difficile sporulationin vitro

Baldassare

Bhattacharjee

Coles

et al. 2023

Preprint

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Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile. Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with alternative metabolic and related C. difficile regulatory pathways, such as the carbon catabolite repressor, CcpA. Collectively, these data suggest that butyrate may signal alternative C. difficile metabolic pathways, thus modifying its growth and virulence to persist in the gut environment.

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Section: Methodsmentioning

confidence: 99%

Butyrate enhances Clostridioides difficile sporulationin vitro

Baldassare

Bhattacharjee

Coles

et al. 2023

Preprint

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“…(v.0.36) to acquire clean data for subsequent analysis. Species‐level profiling of fecal microbiome was performed via MetaPhlAn4 9 . with default parameters and marker gene database (mpa vJan21 CHOCOPhlAnSGB 202103).…”

Section: Methodsmentioning

confidence: 99%

Baseline gut microbiome features prior to SARS‐CoV‐2 infection are associated with host symptoms in and post COVID‐19

Zuo,

Liang,

Huang

et al. 2023

Journal of Medical Virology

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The human gut microbiome varies substantially across individuals and populations and differentially tames our immunity at steady‐state. Hence, we hypothesize that the large heterogeneity of gut microbiomes at steady‐state may shape our baseline immunity differentially, and then mediate discrepant immune responses and symptoms when one encounters a viral infection, such as SARS‐CoV‐2 infection. To validate this hypothesis, we conducted an exploratory, longitudinal microbiome‐COVID‐19 study involving homogenous young participants from two geographically different regions in China. Subjects were recruited and sampled of fecal specimens before the 3‐week surge window of COVID‐19 (between December 11 and December 31, 2022) in China, and then were followed up for assessment of COVID‐19 and post‐COVID‐19 manifestations. Our data showed that the baseline gut microbiome composition was intricately associated with different COVID‐19 manifestations, particularly gastrointestinal involvement and post‐COVID‐19 lingering symptoms, in both an individual‐ and population‐dependent manner. Our study intriguingly for the first time highlight that the gut microbiome at steady‐state may prepare us differentially for weathering a respiratory viral infection.

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“…Species-level microbial taxonomic analysis and their relative abundances were performed by MetaPhlAn (v 4.0.2). 27 Default parameters were used, which used unique clade-specific marker genes identified from ∼154 700 reference genomes to unequivocally detect the taxonomic clades present in a microbiome sample (species level), including eukaryotic microbes, bacteria, archaea, and viruses.…”

Section: Methodsmentioning

confidence: 99%