Drivers and determinants of strain dynamics following fecal microbiota transplantation DOI Creative Commons
Thomas Schmidt, Simone S. Li, Oleksandr M Maistrenko

и другие.

Nature Medicine, Год журнала: 2022, Номер 28(9), С. 1902 - 1912

Опубликована: Сен. 1, 2022

Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre post intervention, treatment ten different disease indications. We quantified strain-level 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization recipient resilience were mostly independent outcomes, accurately predictable using LASSO-regularized regression models that accounted host, procedural variables. Recipient factors donor-recipient complementarity, encompassing entire communities to individual strains, main determinants population dynamics, providing insights into underlying processes shape post-FMT gut microbiome. Applying an ecology-based framework our findings indicated parameters may inform development more effective, targeted therapies in future, suggested how patient stratification can be used enhance donor or displacement microbes practice.

Язык: Английский

Antibiotic resistance in the environment DOI Open Access
D. G. Joakim Larsson, Carl‐Fredrik Flach

Nature Reviews Microbiology, Год журнала: 2021, Номер 20(5), С. 257 - 269

Опубликована: Ноя. 4, 2021

Язык: Английский

Процитировано

1779
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database DOI Creative Commons
Brian Alcock,

William Huynh,

Romeo Chalil

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D690 - D699

Опубликована: Окт. 20, 2022

Abstract The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation interpretation of resistomes. As version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, 5057 detection models that can be used by accompanying Gene Identifier (RGI) software annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation likelihood-based Mycobacterium tuberculosis, addition disinfectants antiseptics plus their associated ARGs, systematic resistance-modifying agents. This includes 180 new families, 15 drug classes, 1 resistance mechanism, two ontological relationships: evolutionary_variant_of is_small_molecule_inhibitor. In silico prediction resistomes prevalence statistics ARGs has been 377 pathogens, 21,079 chromosomes, 2,662 islands, 41,828 plasmids 155,606 whole-genome shotgun assemblies, resulting in collation 322,710 unique ARG allele New features CARD:Live collection community submitted isolate resistome data introduction standardized character Short Names support machine learning efforts.

Язык: Английский

Процитировано

891
Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects DOI Creative Commons
Tanvir Mahtab Uddin, Arka Chakraborty, Ameer Khusro

и другие.

Journal of Infection and Public Health, Год журнала: 2021, Номер 14(12), С. 1750 - 1766

Опубликована: Окт. 25, 2021

Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents also a variety of other medicinal applications. In the battle against microbes, antibiotics certainly blessing human civilization by saving millions lives. Globally, caused multidrug-resistant (MDR) bacteria are on rise. being combat diversified infections. Synthetic biology techniques, in combination with molecular, functional genomic, metagenomic studies bacteria, plants, even marine invertebrates aimed at unlocking world's natural products faster previous methods antibiotic discovery. There currently only few viable remedies, potential preventive limited number antibiotics, thereby necessitating discovery innovative approaches antimicrobial therapies. MDR is facilitated biofilms, which makes infection control complex. this review, we spotlighted comprehensively various aspects viz. overview era, mode actions development mechanisms resistance future strategies fight emerging resistant threat.

Язык: Английский

Процитировано

810
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR DOI Creative Commons
Robert Olson,

Rida Assaf,

Thomas Brettin

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D678 - D689

Опубликована: Ноя. 9, 2022

Abstract The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing growing body genome sequence other omics-related data. In this report, we describe merger PAThosystems Integration (PATRIC), Influenza Research Database (IRD) Virus Pathogen Analysis (ViPR) BRCs form Bacterial Viral (BV-BRC) https://www.bv-brc.org/. combined BV-BRC leverages functionality bacterial viral resources provide a unified data model, enhanced web-based visualization analysis tools, bioinformatics services, powerful suite command line tools that benefit research communities.

Язык: Английский

Процитировано

640
Majorbio Cloud: A one‐stop, comprehensive bioinformatic platform for multiomics analyses DOI Creative Commons
Yi Ren, Yu Guo,

Caiping Shi

и другие.

iMeta, Год журнала: 2022, Номер 1(2)

Опубликована: Март 16, 2022

The platform consists of three modules, which are pre-configured bioinformatic pipelines, cloud toolsets, and online omics' courses. pipelines not only combine analytic tools for metagenomics, genomes, transcriptome, proteomics metabolomics, but also provide users with powerful convenient interactive analysis reports, allow them to analyze mine data independently. As a useful supplement the bioinformatics wide range toolsets can further meet needs daily biological processing, statistics, visualization. rich courses multi-omics state-of-art researchers in communication knowledge sharing.

Язык: Английский

Процитировано

533
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome DOI Creative Commons
Stephen Nayfach, David Páez-Espino, Lee Call

и другие.

Nature Microbiology, Год журнала: 2021, Номер 6(7), С. 960 - 970

Опубликована: Июнь 24, 2021

Bacteriophages have important roles in the ecology of human gut microbiome but are under-represented reference databases. To address this problem, we assembled Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available stool metagenomes. Over 75% represent double-stranded DNA phages infect members Bacteroidia and Clostridia classes. Based on sequence clustering identified 54,118 candidate species, 92% which were not found existing The improves detection viruses metagenomes accounts for nearly 40% CRISPR spacers Bacteria Archaea. We also produced a 459,375 protein clusters to explore functional potential virome. This revealed tens thousands diversity-generating retroelements, use error-prone reverse transcription mutate target genes may be involved molecular arms race between their bacterial hosts.

Язык: Английский

Процитировано

419
Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation DOI Creative Commons
Sara Federici,

Sharon Kredo‐Russo,

Rafael Valdés‐Mas

и другие.

Cell, Год журнала: 2022, Номер 185(16), С. 2879 - 2898.e24

Опубликована: Авг. 1, 2022

Язык: Английский

Процитировано

328
Profiling the human intestinal environment under physiological conditions DOI Creative Commons
Dari Shalon, Rebecca N. Culver, Jessica A. Grembi

и другие.

Nature, Год журнала: 2023, Номер 617(7961), С. 581 - 591

Опубликована: Май 10, 2023

The spatiotemporal structure of the human microbiome

Язык: Английский

Процитировано

275
Distribution of antibiotic resistance genes in the environment DOI Creative Commons
Mei Zhuang, Yigal Achmon, Yuping Cao

и другие.

Environmental Pollution, Год журнала: 2021, Номер 285, С. 117402 - 117402

Опубликована: Май 19, 2021

The prevalence of antibiotic resistant bacteria (ARB) and resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats environment are under threat due to excessive use antibiotics evolutionary changes occurring resistome. ARB ARGs from farms, cities hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate water, soil, air. We present global picture resistome by examining ARG-related papers retrieved PubMed published last 30 years (1990-2020). Natural Language Processing (NLP) was used retrieve 496,640 papers, out which 9374 passed filtering test were further analyzed determine distribution diversity ARG subtypes. revealed seven families together with their respective subtypes different on six continents. Asia, especially China, had highest number related compared other countries/regions/continents. belonging multidrug, glycopeptide, β-lactam most common reports hospitals sulfonamide tetracycline WWTPs, soil. also highlight 'omics' tools research, describe some factors that shape development resistome, suggest future work needed better understand goal show nature order encourage collaborate research efforts aimed at reducing negative impacts One Health concept.

Язык: Английский

Процитировано

245
Pharokka: a fast scalable bacteriophage annotation tool DOI Creative Commons
George Bouras, Roshan Nepal, Ghais Houtak

и другие.

Bioinformatics, Год журнала: 2022, Номер 39(1)

Опубликована: Дек. 1, 2022

Abstract Summary In recent years, there has been an increasing interest in bacteriophages, which led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, is a need for rapid and consistent annotation tool dedicated bacteriophages. Existing tools either are not designed specifically bacteriophages or web- email-based require significant manual curation, makes their integration into bioinformatic pipelines challenging. Pharokka was created provide that annotates genomes easily, rapidly consistently with standards compliant outputs. Moreover, requires only two lines code install use takes under 5 min run average 50-kb genome. Availability implementation implemented Python available as bioconda package using ‘conda -c pharokka’. The source on GitHub (https://github.com/gbouras13/pharokka). tested Linux-64 MacOSX machines Windows Linux Virtual Machine.

Язык: Английский

Процитировано

230