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1.
Genome Res ; 32(6): 1112-1123, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35688483

RESUMO

The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.


Assuntos
Microbiota , Saliva , Humanos , Prevotella , RNA Ribossômico 16S , Saliva/microbiologia
2.
Nucleic Acids Res ; 51(13): 6593-6608, 2023 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-37326027

RESUMO

16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when interpreting their own findings in a broader context. To bridge this gap, we introduce dbBact - a novel pan-microbiome resource. dbBact combines manually curated information from studies across diverse habitats, creating a collaborative central repository of 16S rRNA amplicon sequence variants (ASVs), which are assigned multiple ontology-based terms. To date dbBact contains information from more than 1000 studies, which include 1500000 associations between 360000 ASVs and 6500 ontology terms. Importantly, dbBact offers a set of computational tools allowing users to easily query their own datasets against the database. To demonstrate how dbBact augments standard microbiome analysis we selected 16 published papers, and reanalyzed their data via dbBact. We uncovered novel inter-host similarities, potential intra-host sources of bacteria, commonalities across different diseases and lower host-specificity in disease-associated bacteria. We also demonstrate the ability to detect environmental sources, reagent-borne contaminants, and identify potential cross-sample contaminations. These analyses demonstrate how combining information across multiple studies and over diverse habitats leads to better understanding of underlying biological processes.


Assuntos
Bases de Conhecimento , Microbiota , Bactérias/genética , DNA Bacteriano/genética , Microbiota/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos
3.
Nature ; 551(7681): 457-463, 2017 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-29088705

RESUMO

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.


Assuntos
Biodiversidade , Planeta Terra , Microbiota/genética , Animais , Archaea/genética , Archaea/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , Ecologia/métodos , Dosagem de Genes , Mapeamento Geográfico , Humanos , Plantas/microbiologia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética
4.
BMC Biol ; 17(1): 47, 2019 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-31189482

RESUMO

BACKGROUND: Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks. RESULTS: Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5-1.9 weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics. CONCLUSIONS: These findings may lead to next-generation precision beauty products and therapies for skin disorders.


Assuntos
Cosméticos/efeitos adversos , Microbiota/efeitos dos fármacos , Higiene da Pele/efeitos adversos , Pele/efeitos dos fármacos , Adulto , Cosméticos/classificação , Feminino , Humanos , Masculino , Pele/química , Pele/microbiologia
5.
Proc Natl Acad Sci U S A ; 113(48): E7645-E7654, 2016 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-27849584

RESUMO

Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available. Here, we develop an approach to translate chemistries recovered from personal objects such as phones into a lifestyle sketch of the owner, using mass spectrometry and informatics approaches. Our results show that phones' chemistries reflect a personalized lifestyle profile. The collective repertoire of molecules found on these objects provides a sketch of the lifestyle of an individual by highlighting the type of hygiene/beauty products the person uses, diet, medical status, and even the location where this person may have been. These findings introduce an additional form of trace evidence from skin-associated lifestyle chemicals found on personal belongings. Such information could help a criminal investigator narrowing down the owner of an object found at a crime scene, such as a suspect or missing person.


Assuntos
Estilo de Vida , Espectrometria de Massas em Tandem/métodos , Adulto , Telefone Celular , Cromatografia Líquida de Alta Pressão , Feminino , Medicina Legal , Mãos , Humanos , Reprodutibilidade dos Testes , Pele/química
6.
Am J Epidemiol ; 185(2): 115-123, 2017 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-27986704

RESUMO

Prospective cohort studies are needed to assess the relationship between the fecal microbiome and human health and disease. To evaluate fecal collection methods, we determined technical reproducibility, stability at ambient temperature, and accuracy of 5 fecal collection methods (no additive, 95% ethanol, RNAlater Stabilization Solution, fecal occult blood test cards, and fecal immunochemical test tubes). Fifty-two healthy volunteers provided fecal samples at the Mayo Clinic in Rochester, Minnesota, in 2014. One set from each sample collection method was frozen immediately, and a second set was incubated at room temperature for 96 hours and then frozen. Intraclass correlation coefficients (ICCs) were calculated for the relative abundance of 3 phyla, 2 alpha diversity metrics, and 4 beta diversity metrics. Technical reproducibility was high, with ICCs for duplicate fecal samples between 0.64 and 1.00. Stability for most methods was generally high, although the ICCs were below 0.60 for 95% ethanol in metrics that were more sensitive to relative abundance. When compared with fecal samples that were frozen immediately, the ICCs were below 0.60 for the metrics that were sensitive to relative abundance; however, the remaining 2 alpha diversity and 3 beta diversity metrics were all relatively accurate, with ICCs above 0.60. In conclusion, all fecal sample collection methods appear relatively reproducible, stable, and accurate. Future studies could use these collection methods for microbiome analyses.


Assuntos
Fezes/microbiologia , Microbiota , Manejo de Espécimes/métodos , Adulto , Feminino , Voluntários Saudáveis , Humanos , Masculino , Temperatura
7.
Appl Environ Microbiol ; 83(10)2017 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-28258145

RESUMO

To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at -80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the "gold standard" method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.IMPORTANCE The collection of fecal samples in prospective cohort studies is essential to provide the opportunity to study the effect of the human microbiota on numerous health conditions. However, these collection methods have not been adequately tested in low- and middle-income countries. We present estimates of technical reproducibility, stability at ambient temperature for 4 days, and accuracy comparing a "gold standard" for fecal samples in no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test cards, and fecal immunochemical test tubes in a study conducted in Bangladesh. Fecal occult blood test cards and fecal samples stored in 95% ethanol or RNAlater adequately preserve fecal samples in this setting. Therefore, new studies in low- and middle-income countries should include collection of fecal samples using fecal occult blood test cards, 95% ethanol, or RNAlater for prospective cohort studies.


Assuntos
Bactérias/isolamento & purificação , Fezes/microbiologia , Microbiota , Manejo de Espécimes/métodos , Adulto , Bactérias/classificação , Bactérias/genética , Bangladesh , Fezes/química , Feminino , Congelamento , Humanos , Masculino , Pessoa de Meia-Idade , Manejo de Espécimes/instrumentação
8.
Nucleic Acids Res ; 41(22): e205, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24214960

RESUMO

The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.


Assuntos
Bactérias/classificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos , Acetobacter/genética , Acetobacter/isolamento & purificação , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Drosophila melanogaster/microbiologia , Humanos , Modelos Estatísticos , Saliva/microbiologia , Wolbachia/genética , Wolbachia/isolamento & purificação
9.
Cell Rep Med ; 5(7): 101651, 2024 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-39019007

RESUMO

Gut microbial imbalance is noted in Crohn's disease (CD), but the specific bacteria associated with CD vary between studies. Chen et al.1 pair CD patients with their healthy first-degree relatives to mitigate some of the environmental and genetic effects.


Assuntos
Doença de Crohn , Microbioma Gastrointestinal , Doença de Crohn/microbiologia , Doença de Crohn/genética , Humanos , Microbioma Gastrointestinal/genética , Família
10.
Mol Metab ; : 101985, 2024 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-38977130

RESUMO

OBJECTIVE: Excessive consumption of added sugars has been linked to the rise in obesity and associated metabolic abnormalities. Non-nutritive sweeteners (NNSs) offer a potential solution to reduce sugar intake, yet their metabolic safety remains debated. This study aimed to systematically assess the long-term metabolic effects of commonly used NNSs under both normal and obesogenic conditions. METHODS: To ensure consistent sweetness level and controlling for the acceptable daily intake (ADI), eight weeks old C57BL/6 male mice were administered with acesulfame K (ace K, 535.25 mg/L), aspartame (411.75 mg/L), sucralose (179.5 mg/L), saccharin (80 mg/L), or steviol glycoside (Reb M, 536.25 mg/L) in the drinking water, on the background of either regular or high-fat diets (in high fat diet 60% of calories from fat). Water or fructose-sweetened water (82.3.gr/L), were used as controls. Anthropometric and metabolic parameters, as well as microbiome composition, were analyzed following 20-weeks of exposure. RESULTS: Under a regular chow diet, chronic NNS consumption did not significantly affect body weight, fat mass, or glucose metabolism as compared to water consumption, with aspartame demonstrating decreased glucose tolerance. In diet-induced obesity, NNS exposure did not increase body weight or alter food intake. Exposure to sucralose and Reb M led to improved insulin sensitivity and decreased weight gain. Reb M specifically was associated with increased prevalence of colonic Lachnospiracea bacteria. CONCLUSIONS: Long-term consumption of commonly used NNSs does not induce adverse metabolic effects, with Reb M demonstrating a mild improvement in metabolic abnormalities. These findings provide valuable insights into the metabolic impact of different NNSs, aiding in the development of strategies to combat obesity and related metabolic disorders.

11.
Gut Microbes ; 16(1): 2309682, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38324278

RESUMO

Spinal cord injury (SCI) is a devastating event that significantly changes daily function and quality of life and is linked to bowel and bladder dysfunction and frequent antibiotic treatment. We aimed to study the composition of the gut microbiome in individuals with SCI during the initial sub-acute rehabilitation process and during the chronic phase of the injury. This study included 100 fecal samples from 63 participants (Median age 40 years, 94% males): 13 cases with SCI in the sub-acute phase with 50 longitudinal samples, 18 cases with chronic SCI, and 32 age and gender-matched controls. We show, using complementary methods, that the time from the injury was a dominant factor linked with gut microbiome composition. Surprisingly, we demonstrated a lack of gut microbial recovery during rehabilitation during the sub-acute phase, with further deviation from the non-SCI control group in the chronic ambulatory SCI group. To generalize the results, we were able to show significant similarity of the signal when comparing to a previous cohort with SCI, to subjects from the American Gut Project who reported low physical activity, and to subjects from another population-based cohort who reported less normal stool consistency. Restoration of the microbiome composition may be another desirable measure for SCI recovery in the future, but further research is needed to test whether such restoration is associated with improved neurological outcomes and quality of life.


Assuntos
Microbioma Gastrointestinal , Microbiota , Traumatismos da Medula Espinal , Masculino , Humanos , Adulto , Feminino , Qualidade de Vida , Exercício Físico
12.
Nat Commun ; 15(1): 3764, 2024 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-38704361

RESUMO

Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.


Assuntos
Doença de Crohn , Dieta , Microbioma Gastrointestinal , População Rural , População Urbana , Doença de Crohn/microbiologia , Doença de Crohn/genética , Humanos , Masculino , Feminino , China/epidemiologia , Adulto , Israel/epidemiologia , Metabolômica , Estudos de Coortes , Pessoa de Meia-Idade , Fezes/microbiologia , Íleo/microbiologia , Íleo/metabolismo , Transcriptoma , Adulto Jovem
13.
Br J Haematol ; 160(4): 477-86, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23252482

RESUMO

The ability to sequence nucleic acids at an unprecedented pace and decreased costs using massive parallel sequencing (MPS) strongly affects biomedical research. Here we applied MPS for the detection of rare, clinically relevant mutations in a chronic myeloid leukaemia (CML) patient. Tyrosine kinase inhibitors revolutionized CML therapy but in some patients the disease progresses due to resistance-conferring mutations. MPS was applied herein to monitor such mutations in BCR-ABL1 transcripts at different time points. The large volume of sequencing data increases sensitivity compared to direct sequencing and allows detection of marginally represented and previously uncharacterized mutations. We detected changes in the frequency of mutated clones including the emergence and disappearance of the resistance-associated ABL1 T315I mutation. We also observed correlation in appearance of adjacent mutations, and exploited this observation to demonstrate the existence of mutated clones at the time of diagnosis. A tool is provided for detection of low frequency single nucleotide variants/mutations from deep coverage MPS data, applicable to clinical translation of advanced sequencing technologies.


Assuntos
Proteínas de Fusão bcr-abl/genética , Leucemia Mieloide de Fase Crônica/genética , Mutação/genética , Adulto , Análise Mutacional de DNA/métodos , Resistencia a Medicamentos Antineoplásicos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Polimorfismo de Nucleotídeo Único/genética
14.
Sci Rep ; 13(1): 2007, 2023 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-36737654

RESUMO

We aimed to determine microbial signature linked with lung cancer (LC) diagnosis and to define taxa linked with durable clinical benefit (DCB) of advanced LC patients. Stool samples for microbial 16S amplicon sequencing and clinical data were collected from 75 LC patients (50 of which were treated with checkpoint inhibitors) and 31 matched healthy volunteers. We compared LC to healthy controls and patients with DCB to those without. LC patients had lower α-diversity and higher between-subject diversity. Random Forests model to differentiate LC cases from controls ROC-AUC was 0.74. Clostridiales, Lachnospiraceae, and Faecalibacterium prausnitzii taxa abundance was decreased in LC compared to controls. High Akkermansia muciniphila correlated with DCB (HR 4.26, 95% CI 1.98-9.16), not only for the immunotherapy-treated patients. In addition, high Alistipes onderdonkii (HR 3.08, 95% CI 1.34-7.06) and high Ruminococcus (HR 7.76, 95% CI 3.23-18.65) correlated with DCB.Our results support the importance of gut microbiome in LC. We have validated the apparent predictive value of Akkermansia muciniphila, and highlighted Alistipes onderdonkii and Ruminococcus taxa correlation with DCB. Upon additional validations those can be used as biomarkers or as targets for future therapeutic interventions.


Assuntos
Microbioma Gastrointestinal , Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/diagnóstico , Bacteroidetes , Verrucomicrobia , Clostridiales
15.
Sci Rep ; 13(1): 20513, 2023 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-37993670

RESUMO

Disruption of intestinal epithelial functions is linked to Crohn disease (CD) pathogenesis. We identified a widespread reduction in the expression of long non-coding RNAs (lncRNAs) including LHFPL3-AS2 in the treatment-naïve CD ileum of the RISK pediatric cohort. We validated the reduction of LHFPL3-AS2 in adult CD and noted a further reduction in patients with more severe CD from the RISK cohort. LHFPL3-AS2 knockdown in Caco-2 cells robustly affected epithelial monolayer morphogenesis with markedly reduced confluency and spreading, showing atypical rounding, and clumping. mRNA-seq analysis of LHFPL3-AS2 knockdown cells highlighted the reduction of genes and pathways linked with apical polarity, actin bundles, morphogenesis, and the b-catenin-TCF4 complex. LHFPL3-AS2 knockdown significantly reduced the ability of cells to form an internal lumen within the 3-dimensional (3D) cyst model, with mislocalization of actin and adherent and tight junction proteins, affecting epithelial polarity. LHFPL3-AS2 knockdown also resulted in defective mitotic spindle formation and consequent reduction in epithelial proliferation. Altogether, we show that LHFPL3-AS2 reduction affects epithelial morphogenesis, polarity, mitotic spindle formation, and proliferation, which are key processes in maintaining epithelial homeostasis in CD. Reduced expression of LHFPL3-AS2 in CD patients and its further reduction with ileal ulceration outcome, emphasizes its significance in this context.


Assuntos
Doença de Crohn , RNA Longo não Codificante , Adulto , Humanos , Criança , Células CACO-2 , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Doença de Crohn/genética , Actinas/genética , Proliferação de Células/genética , Íleo/metabolismo , Linhagem Celular Tumoral
16.
J Crohns Colitis ; 17(6): 960-971, 2023 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-36655602

RESUMO

BACKGROUND AND AIMS: Widespread dysregulation of long non-coding RNAs [lncRNAs] including a reduction in GATA6-AS1 was noted in inflammatory bowel disease [IBD]. We previously reported a prominent inhibition of epithelial mitochondrial functions in ulcerative colitis [UC]. However, the connection between reduction of GATA6-AS1 expression and attenuated epithelial mitochondrial functions was not defined. METHODS: Mucosal transcriptomics was used to conform GATA6-AS1 reduction in several treatment-naïve independent human cohorts [n=673]. RNA pull-down followed by mass spectrometry was used to determine the GATA6-AS1 interactome. Metabolomics and mitochondrial respiration following GATA6-AS1 silencing in Caco-2 cells were used to elaborate on GATA6-AS1 functions. RESULTS: GATA6-AS1 showed predominant expression in gut epithelia using single cell datasets. GATA6-AS1 levels were reduced in Crohn's disease [CD] ileum and UC rectum in independent cohorts. Reduced GATA6-AS1 lncRNA was further linked to a more severe UC form, and to a less favourable UC course. The GATA6-AS1 interactome showed robust enrichment for mitochondrial proteins, and included TGM2, an autoantigen in coeliac disease that is induced in UC, CD and coeliac disease, in contrast to GATA6-AS1 reduction in these cohorts. GATA6-AS1 silencing resulted in induction of TGM2, and this was coupled with a reduction in mitochondrial membrane potential and mitochondrial respiration, as well as in a reduction of metabolites linked to aerobic respiration relevant to mucosal inflammation. TGM2 knockdown in GATA6-AS1-deficient cells rescued mitochondrial respiration. CONCLUSIONS: GATA6-AS1 levels are reduced in UC, CD and coeliac disease, and in more severe UC forms. We highlight GATA6-AS1 as a target regulating epithelial mitochondrial functions, potentially through controlling TGM2 levels.


Assuntos
Doença Celíaca , Colite Ulcerativa , Doença de Crohn , Humanos , Colite Ulcerativa/genética , Colite Ulcerativa/metabolismo , Células CACO-2 , Mucosa Intestinal/metabolismo , Doença de Crohn/metabolismo , Reto , Inflamação/metabolismo , Mitocôndrias/metabolismo , Fator de Transcrição GATA6/metabolismo
17.
JCI Insight ; 8(14)2023 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-37261910

RESUMO

Ulcerative colitis (UC), Crohn's disease (CD), and celiac disease are prevalent intestinal inflammatory disorders with nonsatisfactory therapeutic interventions. Analyzing patient data-driven cohorts can highlight disease pathways and new targets for interventions. Long noncoding RNAs (lncRNAs) are attractive candidates, since they are readily targetable by RNA therapeutics, show relative cell-specific expression, and play key cellular functions. Uniformly analyzing gut mucosal transcriptomics from 696 subjects, we have highlighted lncRNA expression along the gastrointestinal (GI) tract, demonstrating that, in control samples, lncRNAs have a more location-specific expression in comparison with protein-coding genes. We defined dysregulation of lncRNAs in treatment-naive UC, CD, and celiac diseases using independent test and validation cohorts. Using the Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) inception UC cohort, we defined and prioritized lncRNA linked with UC severity and prospective outcomes, and we highlighted lncRNAs linked with gut microbes previously implicated in mucosal homeostasis. HNF1A-AS1 lncRNA was reduced in all 3 conditions and was further reduced in more severe UC form. Similarly, the reduction of HNF1A-AS1 ortholog in mice gut epithelia showed higher sensitivity to dextran sodium sulfate-induced colitis, which was coupled with alteration in the gut microbial community. These analyses highlight prioritized dysregulated lncRNAs that can guide future preclinical studies for testing them as potential targets.


Assuntos
Doença Celíaca , Colite Ulcerativa , Doença de Crohn , RNA Longo não Codificante , Animais , Camundongos , Colite Ulcerativa/genética , Doença de Crohn/genética , RNA Longo não Codificante/genética , Doença Celíaca/genética , Transcriptoma , Estudos Prospectivos
18.
Nucleic Acids Res ; 38(19): e179, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-20699269

RESUMO

Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets.


Assuntos
Alelos , Triagem de Portadores Genéticos/métodos , Análise de Sequência de DNA/métodos , Algoritmos , Simulação por Computador , Humanos
19.
Genome Biol ; 23(1): 61, 2022 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-35197084

RESUMO

BACKGROUND: Gut microbial alteration is implicated in inflammatory bowel disease but is noted in other diseases. Systematic comparison to define similarities and specificities is hampered since most studies focus on a single disease. RESULTS: We develop a pipeline to compare between disease cohorts starting from the raw V4 16S amplicon sequence variants. Including 12,838 subjects, from 59 disease cohorts, we demonstrate a predominant shared signature across diseases, indicating a common bacterial response to different diseases. We show that classifiers trained on one disease cohort predict relatively well other diseases due to this shared signal, and hence, caution should be taken when using such classifiers in real-world scenarios, where diseases are intermixed. Based on this common signature across a large array of diseases, we develop a universal dysbiosis index that successfully differentiates between cases and controls across various diseases and can be used for prioritizing fecal donors and samples with lower disease probability. Finally, we identify a set of IBD-specific bacteria, which can direct mechanistic studies and design of IBD-specific microbial interventions. CONCLUSIONS: A robust non-specific general response of the gut microbiome is detected in a large array of diseases. Disease classifiers may confuse between different diseases due to this shared microbial response. Our universal dysbiosis index can be used as a tool to prioritize fecal samples and donors. Finally, the IBD-specific taxa may indicate a more direct association to gut inflammation and disease pathogenesis, and those can be further used as biomarkers and as future targets for interventions.


Assuntos
Colite Ulcerativa , Doença de Crohn , Microbioma Gastrointestinal , Doenças Inflamatórias Intestinais , Bactérias/genética , Colite Ulcerativa/microbiologia , Doença de Crohn/microbiologia , Disbiose/microbiologia , Fezes/microbiologia , Humanos , Doenças Inflamatórias Intestinais/microbiologia
20.
Cureus ; 14(2): e22487, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35371778

RESUMO

Background Nosocomial infections are a significant health concern. Following surgery, infections are most commonly associated with the surgical site, yet there are other potential sources for infections after surgical interventions. Identification of the source of infections can be very challenging. Methodology An outbreak of postoperative infections following surgery led to intensive care unit (ICU) admission of patients immediately after the surgical procedure. The blood cultures of two patients were positive for Citrobacter freundii. The only connection between all cases was the anesthesiologist. An epidemiological inquiry could not definitively identify the source of the outbreak. Therefore, we utilized an RNA sequencing technique to evaluate the microbiome of the anesthesiologist and compared the results to bacteria cultured from the bloodstream of the two patients. Results The anesthesiologist's microbiome contained amplicons that were identical to those of the bacteria in the patient's bloodstream. Because Citrobacter freundii is an uncommon source of bloodstream infections, and in the normal human microbiome, the results establish the source of a cluster of infections to the anesthesiologist. Conclusions In cases of nosocomial infections, when conventional microbiological techniques do not clearly establish the source of the infection, using 16S RNA sequencing should be considered.

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