The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

Cell Host & Microbe, Год журнала: 2020, Номер 28(5), С. 724 - 740.e8

Опубликована: Авг. 24, 2020

Язык: Английский

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The human virome: assembly, composition and host interactions

Nature Reviews Microbiology, Год журнала: 2021, Номер 19(8), С. 514 - 527

Опубликована: Март 30, 2021

Язык: Английский

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The oral microbiome: Role of key organisms and complex networks in oral health and disease

Periodontology 2000, Год журнала: 2021, Номер 87(1), С. 107 - 131

Опубликована: Авг. 31, 2021

Abstract States of oral health and disease reflect the compositional functional capacities of, as well interspecies interactions within, microbiota. The cavity exists a highly dynamic microbial environment that harbors many distinct substrata microenvironments house diverse communities. Specific to cavity, nonshedding dental surfaces facilitate development complex polymicrobial biofilm communities, characterized not only by microbes comprising them, but cumulatively their activities. Adding this complexity, faces near‐constant environmental challenges, including those from host diet, salivary flow, masticatory forces, introduction exogenous microbes. composition microbiome is shaped throughout life factors genetics, maternal transmission, factors, such dietary habits, hygiene practice, medications, systemic factors. This ecosystem presents opportunities for dysbiosis periodontal diseases. application both in vitro culture‐independent approaches has broadened mechanistic understandings communities within environmental, local, underpinnings influence dynamics microbiome. Here, we review present knowledge current understanding influences challenges upon system encourage homeostasis or provoke perturbation, thus contribute states disease.

Язык: Английский

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Interactions between bacterial and phage communities in natural environments

Nature Reviews Microbiology, Год журнала: 2021, Номер 20(1), С. 49 - 62

Опубликована: Авг. 9, 2021

Язык: Английский

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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

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

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Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

Cell Host & Microbe, Год журнала: 2019, Номер 26(6), С. 764 - 778.e5

Опубликована: Ноя. 19, 2019

Язык: Английский

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Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota–Immune System Interplay. Implications for Health and Disease

Nutrients, Год журнала: 2021, Номер 13(2), С. 699 - 699

Опубликована: Фев. 22, 2021

The most prevalent diseases of our time, non-communicable (NCDs) (including obesity, type 2 diabetes, cardiovascular and some types cancer) are rising worldwide. All them share the condition an “inflammatory disorder”, with impaired immune functions frequently caused or accompanied by alterations in gut microbiota. These multifactorial maladies also have common malnutrition related to physiopathology. In this context, diet is greatest modulator system–microbiota crosstalk, much interest, new challenges, arising area precision nutrition as a way towards treatment prevention. It fact that westernized (WD) partly responsible for increased prevalence NCDs, negatively affecting both microbiota system. Conversely, other nutritional approaches, such Mediterranean (MD), positively influence system microbiota, proposed not only potential tool clinical management different disease conditions, but prevention health promotion globally. Thus, purpose review determine regulatory role components WD MD interplay, order understand, create awareness of, over key components.

Язык: Английский

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Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Март 20, 2021

Abstract Background Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information viral community within agricultural waste. There currently ~ 2.7 million dairy cattle in UK producing 7–8% their own bodyweight manure daily, and 28 tonnes annually. To avoid pollution freshwaters, must stored spread accordance with guidelines set by DEFRA. Manures used as fertiliser, widely over crop fields, yet about composition. We analysed virome slurry a 5-month period using short long-read sequencing. Results Hybrid sequencing uncovered more high-quality genomes than long or short-reads alone; yielding 7682 vOTUs, 174 which were complete genomes. The was highly diverse dominated lytic bacteriophage, majority represent novel genera (~ 98%). Despite constant influx efflux slurry, composition diversity extremely stable time, 55% vOTUs detected all samples period. Functional annotation revealed range auxiliary metabolic genes features present community, including agriculturally relevant virulence factor VapE, distributed across different phage that predicted infect several hosts. Furthermore, we identified an abundance phage-encoded diversity-generating retroelements, previously thought rare Additionally, group crAssphages, lineages only found human gut. Conclusions complex, genera, many not recovered alone. Phages encode wide AMGs constrained particular groups hosts, determinants putative ARGs. application land may therefore driver bacterial antimicrobial resistance environment.

Язык: Английский

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Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

International Journal of Molecular Sciences, Год журнала: 2020, Номер 21(8), С. 2668 - 2668

Опубликована: Апрель 11, 2020

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well numerous disease etiologies. Dominated by bacteria, the also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in past two decades, these non-bacterial microorganisms, their functional roles, interaction one another or host immune system have not been widely explored. This review covers recent findings on communities gastrointestinal involvement health disease, particular focus pathophysiology inflammatory bowel disease.

Язык: Английский

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

Frontiers in Immunology, Год журнала: 2022, Номер 13

Опубликована: Апрель 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

Язык: Английский

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