Gut microbiome, big data and machine learning to promote precision medicine for cancer

G Cammarota, G Ianiro, A Ahern, C Carbone… - Nature reviews …, 2020 - nature.com
The gut microbiome has been implicated in cancer in several ways, as specific microbial
signatures are known to promote cancer development and influence safety, tolerability and …

RESCRIPt: Reproducible sequence taxonomy reference database management

MS Robeson, DR O'Rourke, BD Kaehler… - PLoS computational …, 2021 - journals.plos.org
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

A Regueira‐Iglesias, C Balsa‐Castro… - Molecular Oral …, 2023 - Wiley Online Library
The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from
different works has gained particular relevance in the literature in recent years. The large …

[PDF][PDF] QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet… - 2018 - peerj.com
We present QIIME 2, an opensource microbiome data science platform accessible to users
spanning the microbiome research ecosystem, from scientists and engineers to clinicians …

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

E Bolyen, JR Rideout, MR Dillon, NA Bokulich… - Nature …, 2019 - nature.com
To the Editor—Rapid advances in DNA-sequencing and bioinformatics technologies in the
past two decades have substantially improved understanding of the microbial world. This …

A catalogue of 1,167 genomes from the human gut archaeome

CM Chibani, A Mahnert, G Borrel, A Almeida… - Nature …, 2022 - nature.com
The human gut microbiome plays an important role in health, but its archaeal diversity
remains largely unexplored. In the present study, we report the analysis of 1,167 …

QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data

M Estaki, L Jiang, NA Bokulich… - Current protocols in …, 2020 - Wiley Online Library
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the
popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully …

q2-longitudinal: longitudinal and paired-sample analyses of microbiome data

NA Bokulich, MR Dillon, Y Zhang, JR Rideout… - …, 2018 - Am Soc Microbiol
Studies of host-associated and environmental microbiomes often incorporate longitudinal
sampling or paired samples in their experimental design. Longitudinal sampling provides …

Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota

S Kawamoto, K Uemura, N Hori, L Takayasu… - Nature Cell …, 2023 - nature.com
The elucidation of the mechanisms of ageing and the identification of methods to control it
have long been anticipated. Recently, two factors associated with ageing—the accumulation …

Man-made microbial resistances in built environments

A Mahnert, C Moissl-Eichinger, M Zojer… - Nature …, 2019 - nature.com
Antimicrobial resistance is a serious threat to global public health, but little is known about
the effects of microbial control on the microbiota and its associated resistome. Here we …