Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut DOI Creative Commons
Teagan L. Brown, Oliver J. Charity, Evelien M. Adriaenssens

et al.

Current Opinion in Microbiology, Journal Year: 2022, Volume and Issue: 70, P. 102229 - 102229

Published: Nov. 5, 2022

While they are the most abundant biological entities on planet, role of bacteriophages (phages) in microbiome remains enigmatic and understudied. With a rise number metagenomics studies publication highly efficient phage mining programmes, we now have extensive data genomic taxonomic diversity (mainly) DNA wide range environments. In addition, higher throughput quality sequencing is allowing for strain-level reconstructions genomes from metagenomes. These factors will ultimately help us to understand these phages play as part specific microbial communities, enabling tracking individual virus through space time. Using lessons learned latest metagenomic studies, focus two explicit aspects within microbiome, their ecological structuring bacterial populations, contribution functioning by encoding auxiliary metabolism genes.

Language: Английский

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut DOI Creative Commons
Ann Gregory, Olivier Zablocki, Ahmed A. Zayed

et al.

Cell Host & Microbe, Journal Year: 2020, Volume and Issue: 28(5), P. 724 - 740.e8

Published: Aug. 24, 2020

Language: Английский

Citations

523
The human virome: assembly, composition and host interactions DOI Open Access
Guanxiang Liang, Frederic D. Bushman

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(8), P. 514 - 527

Published: March 30, 2021

Language: Английский

Citations

429
Microbiome and cancer DOI Creative Commons
Nyssa Cullin, Camila Azevedo Antunes, Ravid Straussman

et al.

Cancer Cell, Journal Year: 2021, Volume and Issue: 39(10), P. 1317 - 1341

Published: Sept. 9, 2021

Language: Английский

Citations

362
Microbiota succession throughout life from the cradle to the grave DOI
Cameron Martino, Amanda Hazel Dilmore, Zachary M. Burcham

et al.

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(12), P. 707 - 720

Published: July 29, 2022

Language: Английский

Citations

154
Fecal filtrate transplantation protects against necrotizing enterocolitis DOI Creative Commons
Anders Brunse, Ling Deng, Xiaoyu Pan

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(3), P. 686 - 694

Published: Sept. 22, 2021

Abstract Necrotizing enterocolitis (NEC) is a life-threatening gastrointestinal disorder afflicting preterm infants, which currently unpreventable. Fecal microbiota transplantation (FMT) promising preventive therapy, but the transfer of pathogenic microbes or toxic compounds raise concern. Removal bacteria from donor feces by micropore filtering may reduce this risk bacterial infection, while residual bacteriophages could maintain NEC-preventive effects. We aimed to assess preclinical efficacy and safety fecal filtrate (FFT). Using material healthy suckling piglets, we compared rectal FMT administration (FMT, n = 16) with cognate FFT either (FFTr, 14) oro-gastric (FFTo, 13) saline (CON, in preterm, cesarean-delivered piglets as models for infants. assessed gut pathology analyzed mucosal luminal viral composition using 16S rRNA gene amplicon meta-virome sequencing. Finally, used isolated ileal mucosa, coupled RNA-Seq, gauge host response different treatments. Oro-gastric completely prevented NEC, was confirmed microscopy, whereas did not perform better than control. increased diversity reduced Proteobacteria relative abundance mucosa An induction immunity observed FFT. As infants are extremely vulnerable infections, rational strategies need incontestable profiles. show clinically relevant animal model that FFT, opposed FMT, efficiently prevents NEC without any recognizable side

Language: Английский

Citations

107
Mutualistic interplay between bacteriophages and bacteria in the human gut DOI
Andrey N. Shkoporov, Christopher Turkington, Colin Hill

et al.

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(12), P. 737 - 749

Published: June 30, 2022

Language: Английский

Citations

105
Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome DOI Creative Commons
Carter Merenstein, Guanxiang Liang, Samantha A. Whiteside

et al.

mBio, Journal Year: 2021, Volume and Issue: 12(4)

Published: Aug. 17, 2021

Viral infection of the respiratory tract can be associated with propagating effects on airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated in coronavirus disease 2019 (COVID-19) its relationship to severity, systemic immunologic features, outcomes. We examined 507 oropharyngeal, nasopharyngeal, endotracheal samples from 83 hospitalized COVID-19 patients as well non-COVID healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae Redondoviridae quantified by qPCR. found that had upper greater change over time than critically ill without COVID-19. Oropharyngeal diversity at first point correlated inversely severity during hospitalization. Microbiome composition was also immune parameters blood, measured lymphocyte/neutrophil ratios profiling peripheral blood mononuclear cells. Intubated showed patient-specific lung frequently highly dynamic, prominence Staphylococcus. more frequent colonization higher titers severe Machine learning analysis demonstrated integrated features early sampling points high power discriminate ultimate level severity. Thus, are disturbed correlate parameters, Future studies should address clinical consequences COVID-19, possible use biomarkers, role bacterial taxa identified here pathogenesis. IMPORTANCE caused acute syndrome 2 (SARS-CoV-2) tract, results variable outcomes ranging minimal illness death, but reasons for this not understood. small each markedly abnormal compared people differed Early tracked reached hospitalization, blood. These findings raise questions about mechanisms linking SARS-CoV-2 other microbial inhabitants airway, including whether might regulate and/or serve biomarkers

Language: Английский

Citations

104
PhaTYP: predicting the lifestyle for bacteriophages using BERT DOI Creative Commons
Jiayu Shang, Xubo Tang, Yanni Sun

et al.

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Oct. 17, 2022

Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating cannot keep pace fast accumulation sequenced phages, computational method predicting lifestyles has become an attractive alternative. Despite some promising results, prediction remains difficult because limited known annotations sheer amount contigs assembled from metagenomic data. In particular, most existing tools precisely predict short contigs. this work, we develop PhaTYP (Phage TYPe tool) to improve accuracy on We design different training tasks, self-supervised fine-tuning overcome difficulties. rigorously tested compared four state-of-the-art methods: DeePhage, PHACTS, PhagePred BACPHLIP. The results show that outperforms all these achieves more stable performance addition, demonstrated utility analyzing human neonates' gut This application shows is a useful means studying data extend our understanding microbial communities.

Language: Английский

Citations

104
Expanding known viral diversity in the healthy infant gut DOI Creative Commons
Shiraz A. Shah, Ling Deng, Jonathan Thorsen

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(5), P. 986 - 998

Published: April 10, 2023

Abstract The gut microbiome is shaped through infancy and impacts the maturation of immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis lysogeny, with latter being especially prominent infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes standardized detection methods. Here we systematically resolved diversity faecal viromes from 647 1-year-olds belonging Copenhagen Prospective Studies on Asthma Childhood 2010, an unselected Danish cohort healthy mother–child pairs. By assembly curation uncovered 10,000 species 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, Caudoviricetes class. Hosts determined for 79% phage using clustered regularly interspaced short palindromic repeat spacers within same children. Typical Bacteroides -infecting crAssphages outnumbered undescribed families infecting Clostridiales Bifidobacterium . Phage lifestyles conserved at family level, 33 virulent 118 temperate families. Virulent phages more abundant, while ones prevalent diverse. Together, found this study expand existing taxonomy provide a resource aiding future virome research.

Language: Английский

Citations

93
Gut microbiome and breast-feeding: Implications for early immune development DOI Creative Commons
Erin C. Davis,

Vanessa P Castagna,

David A. Sela

et al.

Journal of Allergy and Clinical Immunology, Journal Year: 2022, Volume and Issue: 150(3), P. 523 - 534

Published: Sept. 1, 2022

Language: Английский

Citations

73