155 research outputs found
Ξ¦CrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
peer-reviewedCrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (Ξ¦CrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102βkb in size, and has unusual structural traits. In addition, electron microscopy confirms that Ξ¦crAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, Ξ¦crAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks
RNA phage biology in a metagenomic era
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the βviral dark matterβ). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies
ΠΠ°ΠΊΡΠ΅ΡΠΈΠ°Π»ΡΠ½Π°Ρ ΡΡΠ°Π½ΡΠ»ΠΎΠΊΠ°ΡΠΈΡ ΠΈΠ· ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ°: ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅, ΠΈΠΌΠΌΡΠ½ΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅ ΠΈ ΠΏΠ°ΡΠΎΡΠΈΠ·ΠΈΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅ Π°ΡΠΏΠ΅ΠΊΡΡ
Bacterial translocation (BT) is both pathology and physiology phenomenon. In healthy newborns it accompanies the process of establishing the autochthonous intestinal microbiota and the host microbiome. In immunodeficiency it can be an aethio-pathogenetic link and a manifestation of infection or septic complications. The host colonization resistance to exogenous microbic colonizers is provided by gastrointestinal microbiota in concert with complex constitutional and adaptive defense mechanisms. BT may be result of barrier dysfunction and self-purification mechanisms involving the host myeloid cell phagocytic system and opsonins. Dynamic cell humoral response to microbial molecular patterns that occurs on the mucous membranes initiates receptor signaling pathways and cascade of reactions. Their vector and results are largely determined by cross-reactivity between microbiome and the host genome. Enterocyte barriers interacting with microbiota play leading role in providing adaptive, homeostatic and stress host reactivity. Microcirculatory ischemic tissue alterations and inflammatory reactions increase the intestinal barrier permeability and BT. These processes a well as mechanisms for apoptotic cells and bacteria clearance are justified to be of prospective research interest. The inflammatory and related diseases caused by alteration and dysfunction of the intestinal barrier are reasonably considered as diseases of single origin. Maternal microbiota affects the formation of the innate immune system and the microbiota of the newborn, including intestinal commensal translocation during lactation. Deeper understanding of intestinal barrier mechanisms needs complex microbiological, immunological, pathophysiological, etc. investigations using adequate biomodels, including gnotobiotic animals.ΠΠ°ΠΊΡΠ΅ΡΠΈΠ°Π»ΡΠ½Π°Ρ ΡΡΠ°Π½ΡΠ»ΠΎΠΊΠ°ΡΠΈΡ (ΠΠ’) ΠΈΠ· ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ° ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»ΡΠ΅Ρ ΠΏΠ°ΡΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΎΠ΅ ΠΈ ΡΠΈΠ·ΠΈΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΎΠ΅ ΡΠ²Π»Π΅Π½ΠΈΠ΅. ΠΠ’ Π½Π°Π±Π»ΡΠ΄Π°Π΅ΡΡΡ Π² ΠΏΡΠΎΡΠ΅ΡΡΠ΅ ΡΡΡΠ°Π½ΠΎΠ²Π»Π΅Π½ΠΈΡ Π°ΡΡΠΎΡ
ΡΠΎΠ½Π½ΠΎΠΉ ΠΊΠΈΡΠ΅ΡΠ½ΠΎΠΉ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΡ ΠΈ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΠΌΠ° Ρ
ΠΎΠ·ΡΠΈΠ½Π° ΠΏΡΠΈ Π²Π·Π°ΠΈΠΌΠΎΠ΄Π΅ΠΉΡΡΠ²ΠΈΠΈ Ρ ΠΊΠΎΠΌΠΌΠ΅Π½ΡΠ°Π»Π°ΠΌΠΈ, ΡΠΎΠΏΡΠΎΠ²ΠΎΠΆΠ΄Π°Ρ Π΅ΡΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΠΉ ΠΈΠΌΠΌΡΠ½ΠΎΠ³Π΅Π½Π΅Π·, ΠΈ ΠΏΡΠΈ ΠΏΠ°ΡΠΎΠ»ΠΎΠ³ΠΈΠΈ (Π½Π°ΠΏΡΠΈΠΌΠ΅Ρ, ΠΈΠΌΠΌΡΠ½ΠΎΠ΄Π΅ΡΠΈΡΠΈΡΠ°Ρ
), ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»ΡΡ ΡΡΠΈΠΎΠΏΠ°ΡΠΎΠ³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠ΅ Π·Π²Π΅Π½ΠΎ ΠΈΠ½ΡΠ΅ΠΊΡΠΈΠΎΠ½Π½ΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° ΠΈ ΡΠ΅ΠΏΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΎΡΠ»ΠΎΠΆΠ½Π΅Π½ΠΈΠΉ. ΠΠ²ΠΎΠ»ΡΡΠΈΠΎΠ½Π½ΠΎ Π²ΡΡΠ°Π±ΠΎΡΠ°Π½Π½ΡΠ΅ ΠΌΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌΡ Π²Π·Π°ΠΈΠΌΠΎΠ΄Π΅ΠΉΡΡΠ²ΠΈΡ Ρ
ΠΎΠ·ΡΠΈΠ½Π° ΠΈ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΡ, Π²Π·Π°ΠΈΠΌΠ½ΠΎ ΠΏΡΠΎΡΠΈΠ²ΠΎΠΏΠΎΠ»ΠΎΠΆΠ½ΠΎΠΉ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½Π½ΠΎΡΡΠΈ, ΠΎΠ±ΡΡΠ»ΠΎΠ²Π»Π΅Π½Ρ ΠΈΠ½Π²Π°Π·ΠΈΠΎΠ½Π½ΡΠΌΠΈ ΡΠ²ΠΎΠΉΡΡΠ²Π°ΠΌΠΈ ΠΌΠΈΠΊΡΠΎΠΎΡΠ³Π°Π½ΠΈΠ·ΠΌΠΎΠ² ΠΈ ΠΏΡΠΎΡΠΈΠ²ΠΎΡΡΠΎΡΡΠΈΠΌΠΈ ΠΈΠΌ Π·Π°ΡΠΈΡΠ½ΠΎ-Π±Π°ΡΡΠ΅ΡΠ½ΡΠΌΠΈ ΠΌΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌΠ°ΠΌΠΈ Ρ
ΠΎΠ·ΡΠΈΠ½Π°. ΠΠΎΠ»ΠΎΠ½ΠΈΠ·Π°ΡΠΈΠΎΠ½Π½Π°Ρ ΡΠ΅Π·ΠΈΡΡΠ΅Π½ΡΠ½ΠΎΡΡΡ Ρ
ΠΎΠ·ΡΠΈΠ½Π°, ΠΊΠΎΠ½ΡΠ°ΠΊΡΠΈΡΡΡΡΠ΅Π³ΠΎ Ρ ΡΠΊΠ·ΠΎΠ³Π΅Π½Π½ΠΎΠΉ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΠΎΠΉ, ΠΎΠ±Π΅ΡΠΏΠ΅ΡΠΈΠ²Π°Π΅ΡΡΡ ΠΊΠΎΠΌΠΏΠ»Π΅ΠΊΡΠΎΠΌ ΠΊΠΎΠ½ΡΡΠΈΡΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΡ
ΠΈ Π°Π΄Π°ΠΏΡΠΈΠ²Π½ΡΡ
ΠΌΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌΠΎΠ² Ρ Π²Π΅Π΄ΡΡΠΈΠΌ ΡΡΠ°ΡΡΠΈΠ΅ΠΌ ΠΊΠΎΠΌΠΌΠ΅Π½ΡΠ°Π»ΡΠ½ΠΎΠΉ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΡ. ΠT Π² ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠ΅ Π΄ΠΈΡΡΡΠ½ΡΠΈΠΈ Π±Π°ΡΡΠ΅ΡΠΎΠ² ΠΊΠΎΠ½ΡΡΠΎΠ»ΠΈΡΡΠ΅ΡΡΡ ΠΌΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌΠ°ΠΌΠΈ ΡΠ°ΠΌΠΎΠΎΡΠΈΡΠ΅Π½ΠΈΡ Ρ Π²ΠΎΠ²Π»Π΅ΡΠ΅Π½ΠΈΠ΅ΠΌ ΠΌΠΈΠ΅Π»ΠΎΠΈΠ΄Π½ΠΎΠΉ ΠΊΠ»Π΅ΡΠΎΡΠ½ΠΎΠΉ ΡΠ°Π³ΠΎΡΠΈΡΠ°ΡΠ½ΠΎΠΉ ΡΠΈΡΡΠ΅ΠΌΡ ΠΈ ΠΎΠΏΡΠΎΠ½ΠΈΠ½ΠΎΠ². ΠΠΎΠ·Π½ΠΈΠΊΠ°ΡΡΠ°Ρ Π½Π° ΡΠ»ΠΈΠ·ΠΈΡΡΡΡ
ΠΎΠ±ΠΎΠ»ΠΎΡΠΊΠ°Ρ
Π΄ΠΈΠ½Π°ΠΌΠΈΡΠ½ΠΎ ΡΠ°Π·Π²ΠΈΠ²Π°ΡΡΠ°ΡΡΡ ΠΊΠ»Π΅ΡΠΎΡΠ½ΠΎ-Π³ΡΠΌΠΎΡΠ°Π»ΡΠ½Π°Ρ ΡΠ΅Π°ΠΊΡΠΈΡ Π½Π° ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΡΠ΅ ΠΌΠΈΠΊΡΠΎΠ±Π½ΡΠ΅ ΠΏΠ°ΡΡΠ΅ΡΠ½Ρ ΠΈΠ½ΠΈΡΠΈΠΈΡΡΠ΅Ρ ΡΠ΅ΡΠ΅ΠΏΡΠΎΡΠ½ΠΎ-ΡΠΈΠ³Π½Π°Π»ΡΠ½ΡΠ΅ ΠΈ ΠΊΠ°ΡΠΊΠ°Π΄Π½ΡΠ΅ ΡΠ΅Π°ΠΊΡΠΈΠΈ, Π²Π΅ΠΊΡΠΎΡ ΠΈ ΡΠ΅Π·ΡΠ»ΡΡΠ°Ρ ΠΊΠΎΡΠΎΡΡΡ
ΠΎΠΏΡΠ΅Π΄Π΅Π»ΡΡΡΡΡ ΠΏΠ΅ΡΠ΅ΠΊΡΠ΅ΡΡΠ½ΡΠΌ Π²Π·Π°ΠΈΠΌΠΎΠ΄Π΅ΠΉΡΡΠ²ΠΈΠ΅ΠΌ Π³Π΅Π½ΠΎΠΌΠ° ΠΈ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΠΌΠ° Ρ
ΠΎΠ·ΡΠΈΠ½Π°. Π Π°ΡΡΠΌΠΎΡΡΠ΅Π½Π° ΡΠ»ΡΡΡΠ°ΡΡΡΡΠΊΡΡΡΠ° ΡΠ½ΡΠ΅ΡΠΎΡΠΈΡΠ°ΡΠ½ΡΡ
Π±Π°ΡΡΠ΅ΡΠΎΠ², Π²Π·Π°ΠΈΠΌΠΎΠ΄Π΅ΠΉΡΡΠ²ΡΡΡΠΈΡ
Ρ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΠΎΠΉ (ΡΠΈΠΌΠ±ΠΈΠΎΠ½ΡΡ ΠΈ ΠΏΠ°ΡΠΎΠ±ΠΈΠΎΠ½ΡΡ), Π² ΠΎΠ±Π΅ΡΠΏΠ΅ΡΠ΅Π½ΠΈΠΈ Π°Π΄Π°ΠΏΡΠ°ΡΠΈΠΎΠ½Π½ΠΎ-Π³ΠΎΠΌΠ΅ΠΎΡΡΠ°ΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΡΠ΅Π°ΠΊΡΠΈΠ²Π½ΠΎΡΡΠΈ Ρ
ΠΎΠ·ΡΠΈΠ½Π°. ΠΠ±ΠΎΡΠ½ΠΎΠ²Π°Π½Ρ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ ΠΌΠΈΠΊΡΠΎΡΠΈΡΠΊΡΠ»ΡΡΠΎΡΠ½ΠΎΠ³ΠΎ Π·Π²Π΅Π½Π° Π² ΠΏΠ°ΡΠΎΠ³Π΅Π½Π΅Π·Π΅ ΠΈΡΠ΅ΠΌΠΈΡΠ΅ΡΠΊΠΈΡ
ΡΠΊΠ°Π½Π΅Π²ΡΡ
ΠΏΠΎΠ²ΡΠ΅ΠΆΠ΄Π΅Π½ΠΈΠΉ ΠΈ Π²ΠΎΡΠΏΠ°Π»Π΅Π½ΠΈΡ, ΠΏΠΎΠ²ΡΡΠ°ΡΡΠΈΡ
ΠΏΡΠΎΠ½ΠΈΡΠ°Π΅ΠΌΠΎΡΡΡ ΠΊΠΈΡΠ΅ΡΠ½ΠΎΠ³ΠΎ Π±Π°ΡΡΠ΅ΡΠ° ΠΈ ΠΠ’, Π° ΡΠ°ΠΊΠΆΠ΅ ΠΌΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌΠΎΠ² ΠΎΡΠΈΡΠ΅Π½ΠΈΡ ΠΎΡ Π±Π°ΠΊΡΠ΅ΡΠΈΠΉ ΠΈ Π°ΠΏΠΎΠΏΡΠΎΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΊΠ»Π΅ΡΠΎΠΊ. ΠΠΎΡΠΏΠ°Π»ΠΈΡΠ΅Π»ΡΠ½ΡΠ΅ ΠΈ Π΄ΡΡΠ³ΠΈΠ΅ Π·Π°Π±ΠΎΠ»Π΅Π²Π°Π½ΠΈΡ, Π½Π°ΠΏΡΡΠΌΡΡ ΡΠ²ΡΠ·Π°Π½Π½ΡΠ΅ Ρ Π±Π°ΡΡΠ΅ΡΠ½ΡΠΌΠΈ Π½Π°ΡΡΡΠ΅Π½ΠΈΡΠΌΠΈ ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ°, ΠΎΠ±ΠΎΡΠ½ΠΎΠ²Π°Π½Π½ΠΎ ΡΡΠΈΡΠ°ΡΡΡΡ Π±ΠΎΠ»Π΅Π·Π½ΡΠΌΠΈ ΠΊΠΈΡΠ΅ΡΠ½ΠΎΠ³ΠΎ Π±Π°ΡΡΠ΅ΡΠ°. ΠΠ°ΡΠ΅ΡΠΈΠ½ΡΠΊΠ°Ρ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΠ° Π²Π»ΠΈΡΠ΅Ρ Π½Π° ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ Π²ΡΠΎΠΆΠ΄Π΅Π½Π½ΠΎΠ³ΠΎ ΠΈΠΌΠΌΡΠ½ΠΈΡΠ΅ΡΠ° ΠΈ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΡΡ Π½ΠΎΠ²ΠΎΡΠΎΠΆΠ΄Π΅Π½Π½ΠΎΠ³ΠΎ, Π² ΡΠΎΠΌ ΡΠΈΡΠ»Π΅ ΠΏΡΡΠ΅ΠΌ ΠΠ’ ΠΊΠΈΡΠ΅ΡΠ½ΡΡ
ΠΊΠΎΠΌΠΌΠ΅Π½ΡΠ°Π»ΠΎΠ² Ρ Π³ΡΡΠ΄Π½ΡΠΌ ΠΌΠΎΠ»ΠΎΠΊΠΎΠΌ. ΠΠ΅ΡΡΠΏΠ΅ΠΊΡΠΈΠ²Π½Ρ ΠΊΠΎΠΌΠΏΠ»Π΅ΠΊΡΠ½ΡΠ΅ ΠΌΠΈΠΊΡΠΎΠ±ΠΈΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅, ΠΈΠΌΠΌΡΠ½ΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅, ΠΏΠ°ΡΠΎΡΠΈΠ·ΠΈΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠ΅ ΠΈ Π΄ΡΡΠ³ΠΈΠ΅ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ Ρ ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΠ΅ΠΌ Π°Π΄Π΅ΠΊΠ²Π°ΡΠ½ΡΡ
Π±ΠΈΠΎΠΌΠΎΠ΄Π΅Π»Π΅ΠΉ, Π²ΠΊΠ»ΡΡΠ°Ρ Π³Π½ΠΎΡΠΎΠ±ΠΈΠΎΡΠΎΠ²
Abolishment of morphologyβbased taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy
of Viruses for the period of March 2021βMarch 2022. We provide an overview of the new taxa proposed in 2021, approved
by the Executive Committee, and ratifed by vote in 2022. Signifcant changes to the taxonomy of bacterial viruses were
introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22
families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved
Ruthenibacterium lactatiformans gen. nov., sp.nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces
Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18β:β1 Ο9, C18β:β1 Ο9 aldehyde, C16β:β0 and C16β:β1 Ο7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4β56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6β% similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2β% with Gemmiger formicilis ATCC 27749T and 88.9/88.8β% with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae , for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T)
Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa
peer-reviewedBackground
Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.
Results
In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I)Β and amino acids, as well as defense mechanisms.
Conclusions
Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2β165Tβ=βDSM 17677Tβ=βJCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768Tβ=βNCIMB 13872T).This research was conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273, a Science Foundation Irelandβs Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number SFI/14/SP APC/B3032, and a research grant from Janssen Biotech, Inc
Π ΠΠΠ ΠΠΠΠ’ΠΠ ΠΠΠΠΠΠΠ‘Π’ΠΠ§ΠΠ‘ΠΠΠ Π’ΠΠ‘Π’-Π‘ΠΠ‘Π’ΠΠΠ« ΠΠΠ― Π ΠΠΠΠΠ ΠΠΠΠΠΠΠΠΠΠΠΠ ΠΠΠΠΠΠΠ‘Π’ΠΠΠ Π ΠΠΠ ΠΠ ΠΠ‘Π’ΠΠ’Π«, ΠΠ‘ΠΠΠΠΠΠΠΠ ΠΠ ΠΠΠΠΠ§ΠΠ‘Π’ΠΠΠΠΠΠ ΠΠΠ’ΠΠΠ¦ΠΠ ΠΠ ΠΠ ΠΠΠΠ PCA3 Π ΠΠ‘ΠΠΠΠ ΠΠΠ§Π ΠΠΠ’ΠΠΠΠ ΠΠ’-ΠΠ¦Π Π Π ΠΠΠΠΠ Π ΠΠΠΠ¬ΠΠΠΠ ΠΠ ΠΠΠΠΠ
The wide introduction of prostatic specific antigen (PSA) determination into clinical practice has resulted in a larger number of prostate biopsies, while the lower age threshold for PSA has led to a larger number of unnecessary prostate biopsies. Hence, there is a need for new biomarkers that can detect prostate cancer. Π CΠ3 is a noncoding messenger ribonucleic acid (mRNA) that is expressed exclusively in prostate cells.Β The aim of the study Β has been to develop a diagnostic test system for early non-invasive detection of prostateΒ cancer based on PCA3 mRNA levels in urine sediment using quantitative reverse transcription polymerase chain reaction (qRT-PCR). As part of the study, a laboratory diagnostic test system prototype has been designed, an application methodology has been developed and specificity and sensitivity data of the method has been assessed. The diagnostic system has demonstrated its ability to detect significantly elevated levels of PCAΒ 3/Β KLKΒ 3 in samples from prostate cancer (PCa) patients compared with those from healthy men. The findings have shown relatively high diagnostic sensitivity, specificity and negative-predictive values for an early non-invasive screening of prostate cancerΠ¨ΠΈΡΠΎΠΊΠΎΠ΅ Π²Π½Π΅Π΄ΡΠ΅Π½ΠΈΠ΅ Π² ΠΊΠ»ΠΈΠ½ΠΈΡΠ΅ΡΠΊΡΡ ΠΏΡΠ°ΠΊΡΠΈΠΊΡ ΠΎΠΏΡΠ΅Π΄Π΅Π»Π΅Π½ΠΈΡ ΡΠΎΠ΄Π΅ΡΠΆΠ°Π½ΠΈΡ ΠΏΡΠΎΡΡΠ°ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΡΠΏΠ΅ΡΠΈΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ Π°Π½ΡΠΈΠ³Π΅Π½Π° (ΠΠ‘Π) ΠΏΡΠΈΠ²Π΅Π»ΠΎ ΠΊ ΡΠ²Π΅Π»ΠΈΡΠ΅Π½ΠΈΡ ΡΠΈΡΠ»Π° Π²ΡΠΏΠΎΠ»Π½ΡΠ΅ΠΌΡΡ
Π±ΠΈΠΎΠΏΡΠΈΠΉ ΠΏΡΠΎΡΡΠ°ΡΡ, Π° ΡΠ½ΠΈΠΆΠ΅Π½ΠΈΠ΅ ΠΏΠΎΡΠΎΠ³Π° Π²ΠΎΠ·ΡΠ°ΡΡΠ½ΡΡ
Π½ΠΎΡΠΌ ΠΠ‘Π β ΠΊ ΡΠ²Π΅Π»ΠΈΡΠ΅Π½ΠΈΡ ΡΠΈΡΠ»Π° Π½Π΅ΠΎΠΏΡΠ°Π²Π΄Π°Π½Π½ΡΡ
Π±ΠΈΠΎΠΏΡΠΈΠΉ. Π ΡΠ²ΡΠ·ΠΈ Ρ ΡΡΠΈΠΌ Π²ΠΎΠ·Π½ΠΈΠΊΠ»Π° Π½Π΅ΠΎΠ±Ρ
ΠΎΠ΄ΠΈΠΌΠΎΡΡΡ Π² Π½ΠΎΠ²ΡΡ
Π±ΠΈΠΎΠΌΠ°ΡΠΊΠ΅ΡΠ°Ρ
ΡΠ°ΠΊΠ° ΠΏΡΠ΅Π΄ΡΡΠ°ΡΠ΅Π»ΡΠ½ΠΎΠΉ ΠΆΠ΅Π»Π΅Π·Ρ. Π Π‘Π3 β Π½Π΅ΠΊΠΎΠ΄ΠΈΡΡΡΡΠ°Ρ ΠΌΠ ΠΠ, ΠΊΠΎΡΠΎΡΠ°Ρ ΡΠΊΡΠΏΡΠ΅ΡΡΠΈΡΡΠ΅ΡΡΡ ΠΈΡΠΊΠ»ΡΡΠΈΡΠ΅Π»ΡΠ½ΠΎ ΠΊΠ»Π΅ΡΠΊΠ°ΠΌΠΈ ΠΏΡΠ΅Π΄ΡΡΠ°ΡΠ΅Π»ΡΠ½ΠΎΠΉ ΠΆΠ΅Π»Π΅Π·Ρ. Π¦Π΅Π»ΡΡ Π΄Π°Π½Π½ΠΎΠΉ ΡΠ°Π±ΠΎΡΡ Π±ΡΠ»ΠΎ ΡΠ°Π·ΡΠ°Π±ΠΎΡΠ°ΡΡ Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΡΡ ΡΠ΅ΡΡ-ΡΠΈΡΡΠ΅ΠΌΡ Π΄Π»Ρ ΡΠ°Π½Π½Π΅ΠΉ Π½Π΅ΠΈΠ½Π²Π°Π·ΠΈΠ²Π½ΠΎΠΉ Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΠΊΠΈ ΡΠ°ΠΊΠ° ΠΏΡΠΎΡΡΠ°ΡΡ, ΠΎΡΠ½ΠΎΠ²Π°Π½Π½ΠΎΠΉ Π½Π° ΠΊΠΎΠ»ΠΈΡΠ΅ΡΡΠ²Π΅Π½Π½ΠΎΠΉ Π΄Π΅ΡΠ΅ΠΊΡΠΈΠΈ ΠΌΠ ΠΠ Π³Π΅Π½Π° Π Π‘Π3 Π² ΠΎΡΠ°Π΄ΠΊΠ΅ ΠΌΠΎΡΠΈ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠΌ ΠΏΠΎΠ»ΠΈΠΌΠ΅ΡΠ°Π·Π½ΠΎΠΉ ΡΠ΅ΠΏΠ½ΠΎΠΉ ΡΠ΅Π°ΠΊΡΠΈΠΈ (ΠΠ¦Π ) Π² ΡΠ΅ΠΆΠΈΠΌΠ΅ ΡΠ΅Π°Π»ΡΠ½ΠΎΠ³ΠΎ Π²ΡΠ΅ΠΌΠ΅Π½ΠΈ ΡΠΎΠΏΡΡΠΆΠ΅Π½Π½ΠΎΠΉ Ρ ΠΎΠ±ΡΠ°ΡΠ½ΠΎΠΉ ΡΡΠ°Π½ΡΠΊΡΠΈΠΏΡΠΈΠ΅ΠΉ (ΠΠ’). Π ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠ΅ Π±ΡΠ» ΡΠΎΠ·Π΄Π°Π½ Π»Π°Π±ΠΎΡΠ°ΡΠΎΡΠ½ΡΠΉ ΠΎΠ±ΡΠ°Π·Π΅Ρ Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΠΠ¦Π -ΡΠ΅ΡΡ-ΡΠΈΡΡΠ΅ΠΌΡ ΠΈ ΠΎΡΡΠ°Π±ΠΎΡΠ°Π½Π° ΠΌΠ΅ΡΠΎΠ΄ΠΈΠΊΠ° Π΅Π³ΠΎ ΠΏΡΠΈΠΌΠ΅Π½Π΅Π½ΠΈΡ. ΠΠΎΠ»ΡΡΠ΅Π½Ρ Π΄Π°Π½Π½ΡΠ΅ ΠΎ ΡΠΏΠ΅ΡΠΈΡΠΈΡΠ½ΠΎΡΡΠΈ ΠΈ ΡΡΠ²ΡΡΠ²ΠΈΡΠ΅Π»ΡΠ½ΠΎΡΡΠΈ ΡΠ°Π·ΡΠ°Π±ΠΎΡΠ°Π½Π½ΠΎΠ³ΠΎ ΠΌΠ΅ΡΠΎΠ΄Π°. ΠΠΎΠΊΠ°Π·Π°Π½Π° ΡΠΏΠΎΡΠΎΠ±Π½ΠΎΡΡΡ Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΡΠΈΡΡΠ΅ΠΌΡ Π²ΡΡΠ²Π»ΡΡΡ Π·Π½Π°ΡΠΈΡΠ΅Π»ΡΠ½ΠΎΠ΅ ΠΏΡΠ΅Π²ΡΡΠ΅Π½ΠΈΠ΅ ΠΏΠ°ΡΠ°ΠΌΠ΅ΡΡΠ° PCA3/KLK3 Π² ΠΎΠ±ΡΠ°Π·ΡΠ°Ρ
Π±ΠΈΠΎΠΌΠ°ΡΠ΅ΡΠΈΠ°Π»Π°, ΠΏΠΎΠ»ΡΡΠ΅Π½Π½ΠΎΠ³ΠΎ ΠΎΡ Π±ΠΎΠ»ΡΠ½ΡΡ
ΡΠ°ΠΊΠΎΠΌ ΠΏΡΠΎΡΡΠ°ΡΡ, ΠΏΠΎ ΡΡΠ°Π²Π½Π΅Π½ΠΈΡ Ρ ΠΎΠ±ΡΠ°Π·ΡΠ°ΠΌΠΈ ΠΎΡ Π·Π΄ΠΎΡΠΎΠ²ΡΡ
ΠΈΠ½Π΄ΠΈΠ²ΠΈΠ΄ΡΡΠΌΠΎΠ². Π Ρ
ΠΎΠ΄Π΅ ΠΏΡΠΎΠ²Π΅Π΄Π΅Π½Π½ΡΡ
ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠΉ ΡΡΡΠ°Π½ΠΎΠ²Π»Π΅Π½Ρ Π΄ΠΎΡΡΠ°ΡΠΎΡΠ½ΠΎ Π²ΡΡΠΎΠΊΠΈΠ΅ ΠΏΠΎΠΊΠ°Π·Π°ΡΠ΅Π»ΠΈ Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΡΡΠ²ΡΡΠ²ΠΈΡΠ΅Π»ΡΠ½ΠΎΡΡΠΈ, ΡΠΏΠ΅ΡΠΈΡΠΈΡΠ½ΠΎΡΡΠΈ ΠΈ Π½Π΅Π³Π°ΡΠΈΠ²Π½ΠΎΠΉ ΠΏΡΠ΅Π΄ΡΠΊΠ°Π·Π°ΡΠ΅Π»ΡΠ½ΠΎΠΉ ΡΠ΅Π½Π½ΠΎΡΡΠΈ Π΄Π»Ρ ΡΠ°Π½Π½Π΅Π³ΠΎ Π½Π΅ΠΈΠ½Π²Π°Π·ΠΈΠ²Π½ΠΎΠ³ΠΎ ΡΠΊΡΠΈΠ½ΠΈΠ½Π³ΠΎΠ²ΠΎ ΠΎΠ±Π½Π°ΡΡΠΆΠ΅Π½ΠΈΡ ΡΠ°ΠΊΠ° ΠΏΡΠ΅Π΄ΡΡΠ°ΡΠ΅Π»ΡΠ½ΠΎΠΉ ΠΆΠ΅Π»Π΅Π·Ρ.Β
Reproducible protocols for metagenomic analysis of human faecal phageomes
peer-reviewedAll sequence data used in the analyses were deposited in the Sequence read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA407341. Sample IDs, meta data and corresponding accession numbers are summarised in Additional file 2: Table S2. All raw count tables, 16S taxonomic assignments, BLAST top hits for viral contigs and R code used for the analysis are available at (https://figshare.com/s/71163558b4f78e3e7ed6).Background
Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing.
The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.
Results
Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at +β4Β Β°C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.
Conclusions
The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results
ΠΠ·ΡΡΠ΅Π½ΠΈΠ΅ Π²ΠΈΠ΄ΠΎΠ²ΠΎΠ³ΠΎ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΡ Π±Π°ΠΊΡΠ΅ΡΠΈΠΉ ΡΠΎΠ΄Π° Bifidobacterium ΠΊΠΈΡΠ΅ΡΠ½ΠΎΠΉ ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΡ Ρ ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΠ΅ΠΌ ΠΌΠ΅ΡΠΎΠ΄Π° MALDI-TOF ΠΌΠ°ΡΡ-ΡΠΏΠ΅ΠΊΡΡΠΎΠΌΠ΅ΡΡΠΈΠΈ
Background: The members of genus Bifidobacterium represent a significant part of intestinal microbiota in adults and predominate in infants. Species repertoire of the intestinal bifidobacteria is known to be subjected to major changes with age; however, many details of this process are still to be elucidated.Objective: Our aim was to study the diversity of intestinal bifidobacteria and changes of their qualitative and quantitative composition characteristics during the process of growing up using MALDI-TOF mass-spectrometric analysis of pure bacterial cultures.Methods: A cross-sectional study of bifidobacteria in the intestinal microbiota was performed in 93 healthy people of the ages from 1 month to 57 years. Strains were identified using Microflex LT MALDI-TOF MS, the confirmation was performed by 16S rRNA gene fragment sequencing.Results: 93% of isolated bifidobacterial strains were successfully identified using MALDI-TOF mass-spectrometry. At least two of the strains from each species were additionally identified by 16S rRNA gene fragment sequencing, in all of the cases the results were the same. It was shown that the total concentration of bifidobacteria decreases with age (p 0.001) as well as the frequency of isolation of Bifidobacterium bifidum (p =0.020) and Bifidobacterium breve (p 0.001), and the frequency of isolation of Bifidobacterium adolescentis, increases (p 0.001), representing the continuous process of transformation of microbiota.Conclusion: The method of MALDI-TOF mass spectrometry demonstrated the ability to perform rapid and reliable identification of bifidobacteria that allowed the study of changes in the quantitative and qualitative characteristics of human microbiota in the process of growing up.ΠΡΠ΅Π΄ΡΡΠ°Π²ΠΈΡΠ΅Π»ΠΈ ΡΠΎΠ΄Π° Bifidobacterium ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»ΡΡΡ Π·Π½Π°ΡΠΈΡΠ΅Π»ΡΠ½ΡΡ ΡΠ°ΡΡΡ ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΡ ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ° Π²Π·ΡΠΎΡΠ»ΡΡ
Π»ΡΠ΄Π΅ΠΉ ΠΈ ΡΠΈΡΠ»Π΅Π½Π½ΠΎ Π΄ΠΎΠΌΠΈΠ½ΠΈΡΡΡΡ Π² ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΠ΅ ΠΌΠ»Π°Π΄Π΅Π½ΡΠ΅Π². ΠΠ·Π²Π΅ΡΡΠ½ΠΎ, ΡΡΠΎ Π²ΠΈΠ΄ΠΎΠ²ΠΎΠΉ ΡΠΎΡΡΠ°Π² ΠΊΠΈΡΠ΅ΡΠ½ΡΡ
Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ ΠΏΠΎΠ΄Π²Π΅ΡΠ³Π°Π΅ΡΡΡ ΡΠΈΠ»ΡΠ½ΡΠΌ ΠΈΠ·ΠΌΠ΅Π½Π΅Π½ΠΈΡΠΌ Ρ Π²ΠΎΠ·ΡΠ°ΡΡΠΎΠΌ, ΠΎΠ΄Π½Π°ΠΊΠΎ ΠΌΠ½ΠΎΠ³ΠΈΠ΅ Π΄Π΅ΡΠ°Π»ΠΈ ΡΡΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° ΠΎΡΡΠ°ΡΡΡΡ Π½Π΅ΡΡΠ½ΡΠΌΠΈ.Π¦Π΅Π»Ρ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ: ΠΈΠ·ΡΡΠΈΡΡ Π²ΠΈΠ΄ΠΎΠ²ΠΎΠ΅ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΠ΅ Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ° ΠΈ ΠΈΠ·ΠΌΠ΅Π½Π΅Π½ΠΈΡ ΠΈΡ
ΠΊΠ°ΡΠ΅ΡΡΠ²Π΅Π½Π½ΠΎΠ³ΠΎ ΠΈ ΠΊΠΎΠ»ΠΈΡΠ΅ΡΡΠ²Π΅Π½Π½ΠΎΠ³ΠΎ ΡΠΎΡΡΠ°Π²Π° Π² ΠΏΡΠΎΡΠ΅ΡΡΠ΅ Π²Π·ΡΠΎΡΠ»Π΅Π½ΠΈΡ ΡΠ΅Π»ΠΎΠ²Π΅ΠΊΠ° ΠΏΡΠΈ ΠΏΠΎΠΌΠΎΡΠΈ ΡΠ΅Ρ
Π½ΠΎΠ»ΠΎΠ³ΠΈΠΈ MALDI-TOF ΠΌΠ°ΡΡ-ΡΠΏΠ΅ΠΊΡΡΠΎΠΌΠ΅ΡΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ Π°Π½Π°Π»ΠΈΠ·Π° Π±Π΅Π»ΠΊΠΎΠ²ΡΡ
ΠΏΡΠΎΡΠΈΠ»Π΅ΠΉ ΡΠΈΡΡΡΡ
ΠΊΡΠ»ΡΡΡΡ.ΠΠ΅ΡΠΎΠ΄Ρ: ΠΊΡΠΎΡΡ-ΡΠ΅ΠΊΡΠΈΠΎΠ½Π½ΠΎΠ΅ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠ΅ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΡ Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ Π² ΡΠΎΡΡΠ°Π²Π΅ Π½ΠΎΡΠΌΠ°Π»ΡΠ½ΠΎΠΉ ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΡ ΠΊΠΈΡΠ΅ΡΠ½ΠΈΠΊΠ° ΠΏΡΠΎΠ²Π΅Π΄Π΅Π½ΠΎ Ρ 93 ΡΠ΅Π»ΠΎΠ²Π΅ΠΊ Π² Π²ΠΎΠ·ΡΠ°ΡΡΠ΅ ΠΎΡ 1 ΠΌΠ΅Ρ Π΄ΠΎ 57 Π»Π΅Ρ. ΠΡΡΡΠ΅ΡΡΠ²Π»ΡΠ»ΠΈ Π²ΡΠ΄Π΅Π»Π΅- Π½ΠΈΠ΅ ΡΠΈΡΡΡΡ
ΠΊΡΠ»ΡΡΡΡ ΠΈ ΠΈΡ
ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΠΊΠ°ΡΠΈΡ Π½Π° ΠΏΡΠΈΠ±ΠΎΡΠ΅ Microflex LT MALDI-TOF MS (Bruker Daltonics, ΠΠ΅ΡΠΌΠ°Π½ΠΈΡ), ΠΏΠΎΠ΄ΡΠ²Π΅ΡΠΆΠ΄Π΅Π½ΠΈΠ΅ ΡΠ΅Π°Π»ΠΈΠ·ΠΎΠ²ΡΠ²Π°Π»ΠΈ Ρ ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΠ΅ΠΌ ΡΠ΅ΠΊΠ²Π΅Π½ΠΈΡΠΎΠ²Π°Π½ΠΈΡ ΡΡΠ°Π³ΠΌΠ΅Π½ΡΠ° Π³Π΅Π½Π° 16S ΡΠ ΠΠ.Π Π΅Π·ΡΠ»ΡΡΠ°ΡΡ: Ρ ΠΏΡΠΈΠΌΠ΅Π½Π΅Π½ΠΈΠ΅ΠΌ MALDI-TOF ΠΌΠ°ΡΡ-ΡΠΏΠ΅ΠΊΡΡΠΎΠΌΠ΅ΡΡΠΈΠΈ Π±ΡΠ»ΠΎ ΡΡΠΏΠ΅ΡΠ½ΠΎ ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΡΠΈΡΠΎΠ²Π°Π½ΠΎ 93% Π²ΡΠ΄Π΅Π»Π΅Π½Π½ΡΡ
ΡΡΠ°ΠΌΠΌΠΎΠ² Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ. ΠΠΈΠ½ΠΈΠΌΡΠΌ ΠΏΠΎ 2 ΠΏΡΠ΅Π΄ΡΡΠ°Π²ΠΈΡΠ΅Π»Ρ ΠΎΡ ΠΊΠ°ΠΆΠ΄ΠΎΠ³ΠΎ ΠΈΠ· Π²ΠΈΠ΄ΠΎΠ² Π±ΡΠ»ΠΈ Π΄ΠΎΠΏΠΎΠ»Π½ΠΈΡΠ΅Π»ΡΠ½ΠΎ ΠΎΠΏΡΠ΅Π΄Π΅Π»Π΅Π½Ρ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠΌ ΡΠ΅ΠΊΠ²Π΅Π½ΠΈΡΠΎΠ²Π°Π½ΠΈΡ ΡΡΠ°Π³ΠΌΠ΅Π½ΡΠ° Π³Π΅Π½Π° 16SΡΠ ΠΠ; Π²ΠΎ Π²ΡΠ΅Ρ
ΡΠ»ΡΡΠ°ΡΡ
ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΡ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ² ΡΠΎΠ²ΠΏΠ°Π»ΠΈ. ΠΠΎΠΊΠ°Π·Π°Π½ΠΎ, ΡΡΠΎ Ρ Π²ΠΎΠ·ΡΠ°ΡΡΠΎΠΌ ΠΏΡΠΎΠΈΡΡ
ΠΎΠ΄ΠΈΡ ΡΠ½ΠΈΠΆΠ΅Π½ΠΈΠ΅ ΠΎΠ±ΡΠ΅ΠΉ ΠΊΠΎΠ½ΡΠ΅Π½ΡΡΠ°ΡΠΈΠΈ Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ (p 0,001), ΡΠΌΠ΅Π½ΡΡΠ°Π΅ΡΡΡ Π²ΡΡΡΠ΅ΡΠ°Π΅ΠΌΠΎΡΡΡ Π²ΠΈΠ΄ΠΎΠ² Bifidobacterium bifidum (p =0,020) ΠΈ Bifidobacterium breve (p 0,001), Π° Π²ΡΡΡΠ΅ΡΠ°Π΅ΠΌΠΎΡΡΡ Π²ΠΈΠ΄Π° Bifidobacterium adolescentis ΡΠ²Π΅Π»ΠΈΡΠΈΠ²Π°Π΅ΡΡΡ (p 0,001), ΠΎΡΡΠ°ΠΆΠ°Ρ ΠΏΠΎΡΡΠ΅ΠΏΠ΅Π½Π½ΡΠ΅ ΠΏΡΠΎΡΠ΅ΡΡΡ ΠΏΠ΅ΡΠ΅ΡΡΡΠΎΠΉΠΊΠΈ ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΡ.ΠΠ°ΠΊΠ»ΡΡΠ΅Π½ΠΈΠ΅: ΠΌΠ΅ΡΠΎΠ΄ MALDI-TOF ΠΌΠ°ΡΡ-ΡΠΏΠ΅ΠΊΡΡΠΎΠΌΠ΅ΡΡΠΈΠΈ ΠΏΠΎΠΊΠ°Π·Π°Π» Π²ΠΎΠ·ΠΌΠΎΠΆΠ½ΠΎΡΡΡ Π±ΡΡΡΡΠΎΠΉ ΠΈ Π½Π°Π΄Π΅ΠΆΠ½ΠΎΠΉ ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΠΊΠ°ΡΠΈΠΈ Π±ΠΈΡΠΈΠ΄ΠΎΠ±Π°ΠΊΡΠ΅ΡΠΈΠΉ, ΠΏΠΎΠ·Π²ΠΎΠ»ΠΈΠ²ΡΠ΅ΠΉ ΠΏΡΠΎΠ²Π΅ΡΡΠΈ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠ΅ ΠΈΠ·ΠΌΠ΅Π½Π΅Π½ΠΈΠΉ ΠΊΠΎΠ»ΠΈΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΡ
ΠΈ ΠΊΠ°ΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΡ
ΠΏΠΎΠΊΠ°Π·Π°ΡΠ΅Π»Π΅ΠΉ ΠΌΠΈΠΊΡΠΎΡΠ»ΠΎΡΡ ΡΠ΅Π»ΠΎΠ²Π΅ΠΊΠ° Π² ΠΏΡΠΎΡΠ΅ΡΡΠ΅ Π²Π·ΡΠΎΡΠ»Π΅Π½ΠΈ
Stability of the human gut virome and effect of gluten-free diet
The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition
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