In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls DOI Open Access

Julia Isenring,

Lea Bircher, Annelies Geirnaert

et al.

Microbiome Research Reports, Journal Year: 2023, Volume and Issue: 2(1), P. 2 - 2

Published: Jan. 1, 2023

The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional medical research focusing on HGM modulation strategies as means of improving host is steadily increasing. In vitro fermentation models offer valid complement to animal studies when it comes the mechanistic exploration novel approaches their direct effects composition activity, while excluding interfering effects. However, cultivation can be challenging due its high oxygen sensitivity difficulties accurately modeling physio-chemical complexity environment. Despite increased use models, there no consensus about appropriate model selection operation, sometimes leading major deficiencies study design result interpretation. this review paper, we aim analyze crucial aspects application, setup data validation interpretation models. When carefully designed implemented, powerful strategy for isolating investigating biotic abiotic factors HGM, well evaluating controlled environment akin gut. Furthermore, complementary combining different vivo strengthen studies.

Language: Английский

CheckV assesses the quality and completeness of metagenome-assembled viral genomes DOI Creative Commons
Stephen Nayfach, Antônio Pedro Camargo, Frederik Schulz

et al.

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(5), P. 578 - 585

Published: Dec. 21, 2020

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness these vary considerably. Here we present CheckV, an automated pipeline for identifying closed genomes, estimating genome fragments removing flanking host regions integrated proviruses. CheckV estimates by comparing with a large database complete including 76,262 systematic search publicly available metatranscriptomes metaviromes. After validation on mock datasets comparison to existing methods, applied diverse collections metagenome-assembled sequences, IMG/VR Global Ocean Virome. This revealed 44,652 high-quality genomes (that is, >90% complete), although vast majority were small fragments, which highlights challenge assembling short-read metagenomes. Additionally, found that removal contamination substantially improved accurate identification auxiliary metabolic genes interpretation viral-encoded functions.

Language: Английский

Citations

1044
Massive expansion of human gut bacteriophage diversity DOI Creative Commons

Luis F. Camarillo-Guerrero,

Alexandre Almeida, Guillermo Rangel-Piñeros

et al.

Cell, Journal Year: 2021, Volume and Issue: 184(4), P. 1098 - 1109.e9

Published: Feb. 1, 2021

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not restricted to single species, across phylogenetically distinct species. Epidemiological analysis uncovered 280 VCs found at least 5 continents highly prevalent phage clade with features reminiscent p-crAssphage. This high-quality, large-scale catalog will improve future virome studies enable bacteriophages.

Language: Английский

Citations

471
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
A Roadmap for Genome-Based Phage Taxonomy DOI Creative Commons
Dann Turner, Andrew M. Kropinski, Evelien M. Adriaenssens

et al.

Viruses, Journal Year: 2021, Volume and Issue: 13(3), P. 506 - 506

Published: March 18, 2021

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect state of provide a roadmap for future, including abolition order Caudovirales families Myoviridae, Podoviridae, Siphoviridae. Furthermore, specify guidelines demarcation species, genus, subfamily family-level ranks tailed

Language: Английский

Citations

418
Interactions between bacterial and phage communities in natural environments DOI
Anne Chevallereau, Benoît J. Pons, Stineke van Houte

et al.

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(1), P. 49 - 62

Published: Aug. 9, 2021

Language: Английский

Citations

412
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome DOI Creative Commons
Stephen Nayfach, David Páez-Espino, Lee Call

et al.

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(7), P. 960 - 970

Published: June 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.

Language: Английский

Citations

408
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
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses DOI Creative Commons
Simon Roux, David Páez-Espino, I-Min A. Chen

et al.

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D764 - D775

Published: Oct. 9, 2020

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections their cellular hosts, viruses can reshape microbial community structure drive global nutrient cycling. Over the past decade, viral sequences identified from genomes metagenomes have provided an unprecedented view genome diversity in nature. Since 2016, IMG/VR database has access to largest collection obtained (meta)genomes. Here, we present third version IMG/VR, composed 18 373 cultivated 2 314 329 uncultivated (UViGs), nearly tripling total number compared previous version. These clustered into 935 362 Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs now reported as single contigs, integrated proviruses bins, annotated a new standardized pipeline quality estimation using CheckV, taxonomic classification reflecting latest ICTV update, expanded host taxonomy prediction. The interface enables users efficiently browse, search, select based features and/or sequence similarity. v3 is available at https://img.jgi.doe.gov/vr, underlying data download https://genome.jgi.doe.gov/portal/IMG_VR.

Language: Английский

Citations

315
Network analysis methods for studying microbial communities: A mini review DOI Creative Commons
Monica Steffi Matchado, Michael Lauber, Sandra Reitmeier

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 2687 - 2698

Published: Jan. 1, 2021

Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex contiguous environments. They engage numerous inter- intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful deciphering microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom ranging simple correlation- conditional dependence-based methods. We highlight common biases encountered profiles discuss mitigation strategies employed by different tools their trade-off with increased computational complexity. Finally, current limitations that motivate further method development inter-kingdom robustly comprehensively characterize environments the future.

Language: Английский

Citations

219
Gut Microbiota Interact With the Brain Through Systemic Chronic Inflammation: Implications on Neuroinflammation, Neurodegeneration, and Aging DOI Creative Commons

Yi Mou,

Yu Du, Lixing Zhou

et al.

Frontiers in Immunology, Journal Year: 2022, Volume and Issue: 13

Published: April 7, 2022

It has been noticed in recent years that the unfavorable effects of gut microbiota could exhaust host vigor and life, yet knowledge theory are just beginning to be established. Increasing documentation suggests microbiota–gut–brain axis not only impacts brain cognition psychiatric symptoms but also precipitates neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s (PD), multiple sclerosis (MS). How blood–brain barrier (BBB), a machinery protecting central nervous system (CNS) from systemic circulation, allows risky factors derived translocated into seems paradoxical. For unique anatomical, histological, immunological properties underpinning its permeable dynamics, BBB regarded biomarker associated with neural pathogenesis. The permeability mice rats caused by GM dysbiosis raises question how metabolites change causes pathophysiology neuroinflammation neurodegeneration (NF&ND) aging, pivotal multidisciplinary field tightly immune chronic inflammation. If all, microbiota-induced inflammation (GM-SCI) mainly refers excessive mucosal immunity dysregulation, which is often influenced dietary components age, produced at interface intestinal (IB) or exacerbated after IB disruption, initiates various common diseases along dispersal routes, eventually impairs integrity cause NF&ND aging. To illustrate roles affected inflammatory “leaky” resulting their metabolites, we reviewed selected publications, including role barrier, influences on permeability, NF&ND, add depth bridging inflammation, plausible mechanism indispensable for corruption was highlighted; namely, maintenance cues cytokines, may help understand play major

Language: Английский

Citations

209