Balances: a New Perspective for Microbiome Analysis

mSystems, Journal Year: 2018, Volume and Issue: 3(4)

Published: July 16, 2018

We propose a new algorithm for the identification of microbial signatures. These signatures can be used diagnosis, prognosis, or prediction therapeutic response based on an individual’s specific microbiota.

Language: Английский

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Human, animal and environmental contributors to antibiotic resistance in low-resource settings: integrating behavioural, epidemiological and One Health approaches

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2018, Volume and Issue: 285(1876), P. 20180332 - 20180332

Published: April 11, 2018

Antibiotic resistance (ABR) is recognized as a One Health challenge because of the rapid emergence and dissemination resistant bacteria genes among humans, animals environment on global scale. However, there paucity research assessing ABR contemporaneously in low-resource settings. This critical review seeks to identify extent low- middle-income countries (LMICs). Existing has highlighted hotspots for environmental contamination; food-animal production systems that are likely harbour reservoirs or promote transmission well high increasing human rates colonization with commensal such Escherichia coli . very few studies have integrated all three components spectrum understand dynamics prevalence community-acquired humans animals. Microbiological, epidemiological social science needed at community population levels across order fill large gaps knowledge

Language: Английский

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Epidemiology of the silent polio outbreak in Rahat, Israel, based on modeling of environmental surveillance data

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(45)

Published: Oct. 18, 2018

Israel experienced an outbreak of wild poliovirus type 1 (WPV1) in 2013-2014, detected through environmental surveillance the sewage system. No cases acute flaccid paralysis were reported, and epidemic subsided after a bivalent oral polio vaccination (bOPV) campaign. As we approach global eradication, will increasingly be only surveillance. We developed framework to convert quantitative polymerase chain reaction (qPCR) cycle threshold data into scaled WPV1 OPV1 concentrations for inference within deterministic, compartmental infectious disease transmission model. used this estimate curve dynamics, as well assess alternate scenarios. Our analysis estimates peaked late June, much earlier than previous derived from stool samples, although exact trajectory remains uncertain. basic reproduction number was 1.62 (95% CI 1.04-2.02). Model indicate that 59% 9-77%) susceptible individuals (primarily children under 10 years old) infected with over little more six months, mostly before campaign onset, averted 10% 1-24%) infections. monitoring qPCR can highly sensitive method enhance analytic brings public health relevance that, if systematically collected, guide eradication efforts.

Language: Английский

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Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet

Gut, Journal Year: 2021, Volume and Issue: 71(9), P. 1821 - 1830

Published: Nov. 22, 2021

Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response low FODMAP diet assess whether microbiota compositional functional shifts could provide insights into its mode of action.

Language: Английский

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Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila

mBio, Journal Year: 2021, Volume and Issue: 12(3)

Published: May 17, 2021

The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and only known species Verrucomicrobia phylum in mammalian gut. A high prevalence A. adult humans associated with leanness lower risk for development obesity diabetes. Four distinct phylogenetic groups have been described, but little about their relative abundance or how they impact human metabolic health. In this study, we isolated characterized 71 new strains from cohort children adolescents undergoing treatment obesity. Based on genomic phenotypic analysis these strains, found several phylogroup-specific phenotypes that may colonization GI tract modulate host functions, such as oxygen tolerance, adherence to epithelial cells, iron sulfur metabolism, bacterial aggregation. antibiotic-treated mice, phylogroups AmIV AmII outcompeted AmI strains. adolescents, were most prominent, observed variance single phylogroup dominance, switching occurring small subset patients. Overall, results highlight ecological principles determining which predominates are complex strain genetic diversity represent an important variable should be taken into account when making inferences microbe's its host's health.IMPORTANCE linked multiple positive health outcomes. There four phylogroups, yet vary ability influence largely unknown. performed identified traits adherence, acquisition likely differentially immunological humans, predominate at given time phylotype can switch individual. This collection provides foundation functional characterization effects multitude outcomes colonization, including protection obesity, diabetes, colitis, neurological diseases, well enhanced responses cancer immunotherapies.

Language: Английский

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Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

mSystems, Journal Year: 2018, Volume and Issue: 3(1)

Published: Jan. 8, 2018

The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes bacteria affect their ability flourish in gut under various conditions. Our analysis reveals that strain-level selection formula-fed infants drives enrichment beta-lactamase resistome. Using metagenomes, we built a machine learning model predict organisms community respond perturbation by antibiotics. This may eventually have clinical applications.

Language: Английский

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A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

mSystems, Journal Year: 2017, Volume and Issue: 2(6)

Published: Nov. 15, 2017

Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion range of research to investigate how the diversity microbiome among its members impact function, where function be measured as exometabolites. allows for exometabolite profiling coupled with genome mining, transcript analysis, measurements member productivity population size. It also facilitate discovery natural products that are only produced within consortia. Thus, this has utility address questions about possible occur both engineered ecosystems.

Language: Английский

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Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

mSystems, Journal Year: 2019, Volume and Issue: 4(4)

Published: Aug. 12, 2019

Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, metagenome-assembled genomes (MAGs) were reconstructed metagenomic data sets derived Hexadella detritifera, cf. and Stylissa flabelliformis Phylogenetic taxonomic analyses revealed three MAGs represent two new species within genus Nitrosopumilus one novel genus, for which we propose names "CandidatusUNitrosopumilus hexadellus," detritiferus," "CandidatusUCenporiarchaeum stylissum" (the U superscript indicates taxon uncultured). Comparison of these Sponge Earth Microbiome Project "CaUCenporiarchaeum has been exclusively detected in can hence be classified as a specialist, while "CaUNitrosopumilus detritiferus" hexadellus" also outside sponge holobiont likely lead generalist lifestyle. sponge-associated signatures indicate functional lifestyle, related nutrient transport metabolism, restriction-modification, defense mechanisms, host interactions. Each exhibited distinct traits, suggesting they have reached different stages evolutionary adaptation and/or occupy ecological niches hosts. Our study therefore offers insights into symbiosis between symbionts.IMPORTANCE Sponges ecologically important models understand evolution symbiotic interactions metazoans microbial symbionts. commonly found sponges, but potential adaptations host-associated lifestyle largely unknown. Here, present compare genomic predicted those closely We degrees specialization environment reflected distribution molecular metabolic properties. results may sponges.

Language: Английский

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Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

mBio, Journal Year: 2020, Volume and Issue: 11(2)

Published: Feb. 29, 2020

Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental microbe-microbe interactions act simultaneously on community structure, making microbiome dynamics challenging predict. The coral is essential health of reefs sensitive environmental changes. Here, we develop a dynamic model determine structure associated with surface mucus layer (SML) corals using temperature as an factor network factor. was validated comparing predicted relative abundances taxa from sample data. SML Pseudodiploria strigosa collected across reef zones in Bermuda, where inner outer exposed distinct thermal profiles. A shotgun metagenomics approach used describe taxonomic composition microbiome. By simulating annual fluctuations at each zone, output statistically identical observed further applied six scenarios that combined different profiles investigate influence these two accuracy. best profile closest local environment, regardless profile. Our shows P. Bermuda primarily structured seasonal scale, while secondary driver.IMPORTANCE Coral dysbiosis (i.e., shifts or complete loss symbionts) caused changes key player decline worldwide. Multiple water column surrounding biological However, including only external factor, our proved be successful describing developed this study potential tool predict under conditions.

Language: Английский

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The human archaeome: methodological pitfalls and knowledge gaps

Emerging Topics in Life Sciences, Journal Year: 2018, Volume and Issue: 2(4), P. 469 - 482

Published: Dec. 14, 2018

Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite long time that methanogenic are substantial components the human gastrointestinal tract (GIT) oral cavity, knowledge on archaeome very limited. Various methodological problems contribute to invisibility archaeome, resulting in severe gaps contradictory information. Similar bacteriome, archaeal biogeography was found be site-specific, forming (i) thaumarchaeal skin landscape, (ii) (methano)euryarchaeal GIT (iii) mixed skin/GIT landscape nose, (iv) woesearchaeal lung including numerous unknown clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal wide diversity high quantity signatures various tissues, up 1 : ratios appendix nose samples. The interacts closely bacteriome body cells, whereas roles human-associated respect health only sparsely described. Methanogenic methane production correlated many issues, constipation, periodontitis multiple sclerosis. However, one most burning questions — do pathogens exist? still remains obscure date.

Language: Английский

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