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Article
Open AccessGenomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles
The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries t...
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Chapter
CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea
The CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/ CRISPR-Associated Genes) and CRISPR/Cmr systems (Cmr: Cas module-RAMP (Repeat-Associated Mysterious Proteins)) provide the basis for a...
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Chapter
Archaeal Type II Toxin-Antitoxins
A few of the bacterial type II TA systems, primarily those involved in translational inhibition, occur widely throughout the archaeal domain. Using a bioinformatic approach, the frequency and distribution of t...
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Article
A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species
A newly isolated single-tailed fusiform virus, Sulfolobus tengchongensis spindle-shaped virus STSV2, from Hamazui, China, is characterised. It contains a double-stranded modified DNA genome of 76,107 bp and is en...
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Article
An updated evolutionary classification of CRISPR–Cas systems
CRISPR–Cas systems provide archaea and bacteria with adaptive immunity against viruses and plasmids.
CRISPR...
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Chapter
Archaeal Viruses and Their Interactions with CRISPR-Cas Systems
Our knowledge of archaeal viruses has increased rapidly over the past four decades since the discovery of the archaeal domain. Most surprising has been the morphological diversity of crenarchaeal viruses that ...
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Article
Open AccessVirulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 64...
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Article
Open AccessPrenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial
Maternal dietary interventions during pregnancy with fish oil and high dose vitamin D have been shown to reduce the incidence of asthma and wheeze in offspring, potentially through microbial effects in pregnan...
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Article
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on ...
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Article
Large-scale association analyses identify host factors influencing human gut microbiome composition
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microb...
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Article
Open AccessGenome binning of viral entities from bulk metagenomics data
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the g...
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Article
Open AccessExpanding known viral diversity in the healthy infant gut
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial ...
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Article
Open AccessThe airway microbiota of neonates colonized with asthma-associated pathogenic bacteria
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown t...
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Article
The infant gut virome is associated with preschool asthma risk independently of bacteria
Bacteriophage (also known as phage) communities that inhabit the gut have a major effect on the structure and functioning of bacterial populations, but their roles and association with health and disease in ea...
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Article
Open AccessCo-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition
In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes...
