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1.
J Nutr ; 151(2): 423-433, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33021315

RESUMO

BACKGROUND: Diet affects the human gastrointestinal microbiota. Blood and urine samples have been used to determine nutritional biomarkers. However, there is a dearth of knowledge on the utility of fecal biomarkers, including microbes, as biomarkers of food intake. OBJECTIVES: This study aimed to identify a compact set of fecal microbial biomarkers of food intake with high predictive accuracy. METHODS: Data were aggregated from 5 controlled feeding studies in metabolically healthy adults (n = 285; 21-75 y; BMI 19-59 kg/m2; 340 data observations) that studied the impact of specific foods (almonds, avocados, broccoli, walnuts, and whole-grain barley and whole-grain oats) on the human gastrointestinal microbiota. Fecal DNA was sequenced using 16S ribosomal RNA gene sequencing. Marginal screening was performed on all species-level taxa to examine the differences between the 6 foods and their respective controls. The top 20 species were selected and pooled together to predict study food consumption using a random forest model and out-of-bag estimation. The number of taxa was further decreased based on variable importance scores to determine the most compact, yet accurate feature set. RESULTS: Using the change in relative abundance of the 22 taxa remaining after feature selection, the overall model classification accuracy of all 6 foods was 70%. Collapsing barley and oats into 1 grains category increased the model accuracy to 77% with 23 unique taxa. Overall model accuracy was 85% using 15 unique taxa when classifying almonds (76% accurate), avocados (88% accurate), walnuts (72% accurate), and whole grains (96% accurate). Additional statistical validation was conducted to confirm that the model was predictive of specific food intake and not the studies themselves. CONCLUSIONS: Food consumption by healthy adults can be predicted using fecal bacteria as biomarkers. The fecal microbiota may provide useful fidelity measures to ascertain nutrition study compliance.


Assuntos
Dieta , Ingestão de Alimentos , Fezes/microbiologia , Adulto , Idoso , Biomarcadores , Microbioma Gastrointestinal , Humanos , Pessoa de Meia-Idade , Adulto Jovem
2.
Genes (Basel) ; 11(2)2020 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-32033187

RESUMO

The hippocampus is involved in learning and memory and undergoes significant growth and maturation during the neonatal period. Environmental insults during this developmental timeframe can have lasting effects on brain structure and function. This study assessed hippocampal DNA methylation and gene transcription from two independent studies reporting reduced cognitive development stemming from early life environmental insults (iron deficiency and porcine reproductive and respiratory syndrome virus (PRRSv) infection) using porcine biomedical models. In total, 420 differentially expressed genes (DEGs) were identified between the reduced cognition and control groups, including genes involved in neurodevelopment and function. Gene ontology (GO) terms enriched for DEGs were associated with immune responses, angiogenesis, and cellular development. In addition, 116 differentially methylated regions (DMRs) were identified, which overlapped 125 genes. While no GO terms were enriched for genes overlapping DMRs, many of these genes are known to be involved in neurodevelopment and function, angiogenesis, and immunity. The observed altered methylation and expression of genes involved in neurological function suggest reduced cognition in response to early life environmental insults is due to altered cholinergic signaling and calcium regulation. Finally, two DMRs overlapped with two DEGs, VWF and LRRC32, which are associated with blood brain barrier permeability and regulatory T-cell activation, respectively. These results support the role of altered hippocampal DNA methylation and gene expression in early life environmentally-induced reductions in cognitive development across independent studies.


Assuntos
Biomarcadores/análise , Transtornos Cognitivos/etiologia , Metilação de DNA , Exposição Ambiental/efeitos adversos , Epigênese Genética , Hipocampo/patologia , Animais , Animais Recém-Nascidos , Diferenciação Celular , Transtornos Cognitivos/metabolismo , Transtornos Cognitivos/patologia , Ilhas de CpG , Feminino , Hipocampo/metabolismo , Suínos
3.
Sci Rep ; 6: 26083, 2016 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-27188581

RESUMO

Interstitial cystitis/bladder pain syndrome (IC) is associated with significant morbidity, yet underlying mechanisms and diagnostic biomarkers remain unknown. Pelvic organs exhibit neural crosstalk by convergence of visceral sensory pathways, and rodent studies demonstrate distinct bacterial pain phenotypes, suggesting that the microbiome modulates pelvic pain in IC. Stool samples were obtained from female IC patients and healthy controls, and symptom severity was determined by questionnaire. Operational taxonomic units (OTUs) were identified by16S rDNA sequence analysis. Machine learning by Extended Random Forest (ERF) identified OTUs associated with symptom scores. Quantitative PCR of stool DNA with species-specific primer pairs demonstrated significantly reduced levels of E. sinensis, C. aerofaciens, F. prausnitzii, O. splanchnicus, and L. longoviformis in microbiota of IC patients. These species, deficient in IC pelvic pain (DIPP), were further evaluated by Receiver-operator characteristic (ROC) analyses, and DIPP species emerged as potential IC biomarkers. Stool metabolomic studies identified glyceraldehyde as significantly elevated in IC. Metabolomic pathway analysis identified lipid pathways, consistent with predicted metagenome functionality. Together, these findings suggest that DIPP species and metabolites may serve as candidates for novel IC biomarkers in stool. Functional changes in the IC microbiome may also serve as therapeutic targets for treating chronic pelvic pain.


Assuntos
Bactérias/classificação , Biomarcadores/análise , Cistite Intersticial/patologia , Fezes/química , Fezes/microbiologia , Metaboloma , Bexiga Urinária/patologia , Adulto , Bactérias/genética , Análise por Conglomerados , DNA Ribossômico/química , DNA Ribossômico/genética , Feminino , Humanos , Metagenômica , Pessoa de Meia-Idade , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Inquéritos e Questionários , Adulto Jovem
4.
J Proteome Res ; 3(6): 1289-91, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15595740

RESUMO

Recent progress in genomics, proteomics, and bioinformatics enables unprecedented opportunities to examine the evolutionary history of molecular, cellular, and developmental pathways through phylogenomics. Accordingly, we have developed a motif analysis tool for phylogenomics (Phylomat, http://alg.ncsa.uiuc.edu/pmat) that scans predicted proteome sets for proteins containing highly conserved amino acid motifs or domains for in silico analysis of the evolutionary history of these motifs/domains. Phylomat enables the user to download results as full protein or extracted motif/domain sequences from each protein. Tables containing the percent distribution of a motif/domain in organisms normalized to proteome size are displayed. Phylomat can also align the set of full protein or extracted motif/domain sequences and predict a neighbor-joining tree from relative sequence similarity. Together, Phylomat serves as a user-friendly data-mining tool for the phylogenomic analysis of conserved sequence motifs/domains in annotated proteomes from the three domains of life.


Assuntos
Evolução Molecular , Filogenia , Proteínas/química , Proteômica/métodos , Algoritmos , Motivos de Aminoácidos , Biologia Computacional , Bases de Dados de Proteínas , Humanos , Internet , Fragmentos de Peptídeos , Estrutura Terciária de Proteína , Alinhamento de Sequência
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