The Gut Microbiome: Reaching the Promise Through Discovery— Advancing Knowledge and Discovery of the Gut Microbiome in the Age of Precision Medicine

2020 ◽  
Author(s):  
Beth A. McCormick ◽  
Eugene B. Chang
Keyword(s):  
Precision Medicine ◽  
Gut Microbiome

BIOBOARD

2018 ◽  
Vol 22 (11) ◽  
pp. 61-64
Keyword(s):  
Neuropathic Pain ◽  
Side Effects ◽  
Precision Medicine ◽  
Nobel Prize ◽  
Gut Microbiome ◽  
Asia Pacific ◽  
Chemotherapy Side Effects ◽  
The World

ASIA-PACIFIC – Precision medicine for diagnosing and treating neuropathic pain. ASIA-PACIFIC – Antibiotics overuse causes imbalanced gut microbiome. ASIA-PACIFIC – Bright lights, big CITI. REST OF THE WORLD – 2018 Nobel Prize in Physiology or Medicine winners. REST OF THE WORLD – Women more prone to selected chemotherapy side-effects.

AI-aided Data Mining in Gut Microbiome: The Road to Precision Medicine

2021 ◽  
Author(s):  
Xiaoqing Jiang ◽  
Congmin Xu ◽  
Qian Guo ◽  
Huaiqiu Zhu
Keyword(s):  
Data Mining ◽  
Precision Medicine ◽  
Gut Microbiome ◽  
The Road

scholarly journals Plasma metabolomic profiles enhance precision medicine for volunteers of normal health

2015 ◽  
Vol 112 (35) ◽  
pp. E4901-E4910 ◽  
Author(s):  
Lining Guo ◽  
Michael V. Milburn ◽  
John A. Ryals ◽  
Shaun C. Lonergan ◽  
Matthew W. Mitchell ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Gut Microbiome ◽  
Disease Risk ◽  
Disease Diagnosis ◽  
Carnitine Deficiency ◽  
Great Promise ◽  
Therapeutic Effects ◽  
Metabolic Abnormalities ◽  
Next Generation Sequencing Ngs ◽  
Normal Health

Precision medicine, taking account of human individuality in genes, environment, and lifestyle for early disease diagnosis and individualized therapy, has shown great promise to transform medical care. Nontargeted metabolomics, with the ability to detect broad classes of biochemicals, can provide a comprehensive functional phenotype integrating clinical phenotypes with genetic and nongenetic factors. To test the application of metabolomics in individual diagnosis, we conducted a metabolomics analysis on plasma samples collected from 80 volunteers of normal health with complete medical records and three-generation pedigrees. Using a broad-spectrum metabolomics platform consisting of liquid chromatography and GC coupled with MS, we profiled nearly 600 metabolites covering 72 biochemical pathways in all major branches of biosynthesis, catabolism, gut microbiome activities, and xenobiotics. Statistical analysis revealed a considerable range of variation and potential metabolic abnormalities across the individuals in this cohort. Examination of the convergence of metabolomics profiles with whole-exon sequences (WESs) provided an effective approach to assess and interpret clinical significance of genetic mutations, as shown in a number of cases, including fructose intolerance, xanthinuria, and carnitine deficiency. Metabolic abnormalities consistent with early indications of diabetes, liver dysfunction, and disruption of gut microbiome homeostasis were identified in several volunteers. Additionally, diverse metabolic responses to medications among the volunteers may assist to identify therapeutic effects and sensitivity to toxicity. The results of this study demonstrate that metabolomics could be an effective approach to complement next generation sequencing (NGS) for disease risk analysis, disease monitoring, and drug management in our goal toward precision care.

Host microbiomes in tumor precision medicine: how far are we?

2022 ◽  
Vol 29 ◽  
Author(s):  
Federica D'Amico ◽  
Monica Barone ◽  
Teresa Tavella ◽  
Simone Rampelli ◽  
Patrizia Brigidi ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Gut Microbiome ◽  
Fecal Microbiota Transplantation ◽  
Current Knowledge ◽  
Safety Information ◽  
Fecal Microbiota ◽  
Response To Therapy ◽  
Bioinformatic Tools ◽  
Therapeutic Outcomes

Abstract: The human gut microbiome has received a crescendo of attention in recent years, due to the countless influences on human pathophysiology, including cancer. Research on cancer and anticancer therapy is constantly looking for new hints to improve the response to therapy while reducing the risk of relapse. In this scenario, the gut microbiome and the plethora of microbial-derived metabolites are considered a new opening in the development of innovative anticancer treatments for a better prognosis. This narrative review summarizes the current knowledge on the role of the gut microbiome in the onset and progression of cancer, as well as in response to chemo-immunotherapy. Recent findings regarding the tumor microbiome and its implications for clinical practice are also commented on. Current microbiome-based intervention strategies (i.e., prebiotics, probiotics, live biotherapeutics and fecal microbiota transplantation) are then discussed, along with key shortcomings, including a lack of long-term safety information in patients who are already severely compromised by standard treatments. The implementation of bioinformatic tools applied to microbiomics and other omics data, such as machine learning, has an enormous potential to push research in the field, enabling the prediction of health risk and therapeutic outcomes, for a truly personalized precision medicine.

scholarly journals Pharmacomicrobiology of Methotrexate in Rheumatoid Arthritis: Gut Microbiome as Predictor of Therapeutic Response

2021 ◽  
Vol 12 ◽  
Author(s):  
Huanhuan Yan ◽  
Ru Sui ◽  
Hongwei Xue ◽  
Chong Gao ◽  
Xiaofeng Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Precision Medicine ◽  
Gut Microbiome ◽  
Clinical Status ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Bacterial Strains ◽  
Joint Deformity ◽  
Subsequent Response ◽  
Anti Inflammatory

Rheumatoid arthritis (RA) is a disabling autoimmune disease with invasive arthritis as the main manifestation and synovitis as the basic pathological change, which can cause progressive destruction of articular cartilage and bone, ultimately leading to joint deformity and loss of function. Since its introduction in the 1980s and its widespread use in the treatment of RA, low-dose methotrexate (MTX) therapy has dramatically changed the course and outcome of RA treatment. The clinical use of this drug will be more rational with a better understanding of the pharmacology, anti-inflammatory mechanisms of action and adverse reaction about it. At present, the current clinical status of newly diagnosed RA is that MTX is initiated first regardless of the patients’ suitability. But up to 50% of patients could not reach adequate clinical efficacy or have severe adverse events. Prior to drug initiation, a prognostic tool for treatment response is lacking, which is thought to be the most important cause of the situation. A growing body of studies have shown that differences in microbial metagenomes (including bacterial strains, genes, enzymes, proteins and/or metabolites) in the gastrointestinal tract of RA patients may at least partially determine their bioavailability and/or subsequent response to MTX. Based on this, some researchers established a random forest model to predict whether different RA patients (with different gut microbiome) would respond to MTX. Of course, MTX, in turn, alters the gut microbiome in a dose-dependent manner. The interaction between drugs and microorganisms is called pharmacomicrobiology. Then, the concept of precision medicine has been raised. In this view, we summarize the characteristics and anti-inflammatory mechanisms of MTX and highlight the interaction between gut microbiome and MTX aiming to find the optimal treatment for patients according to individual differences and discuss the application and prospect of precision medicine.

Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine

2018 ◽  
Vol 24 (10) ◽  
pp. 2142-2154 ◽  
Author(s):  
Francesca De Filippis ◽  
Paola Vitaglione ◽  
Rosario Cuomo ◽  
Roberto Berni Canani ◽  
Danilo Ercolini
Keyword(s):  
Precision Medicine ◽  
Gut Microbiome ◽  
Dietary Interventions

Gut microbiome, big data and machine learning to promote precision medicine for cancer

2020 ◽  
Vol 17 (10) ◽  
pp. 635-648 ◽  
Author(s):  
Giovanni Cammarota ◽  
Gianluca Ianiro ◽  
Anna Ahern ◽  
Carmine Carbone ◽  
Andriy Temko ◽  
...  
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Precision Medicine ◽  
Gut Microbiome

scholarly journals Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes

2021 ◽  
Author(s):  
Shaqed Carasso ◽  
Bettina Fishman ◽  
Liel Stelmach Lask ◽  
Tamar Shochat ◽  
Naama Geva-Zatorsky ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Precision Medicine ◽  
Mood Disorders ◽  
Chronic Diseases ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Metagenomic Analysis ◽  
Metagenomic Sequencing ◽  
Diurnal Activity ◽  
Microbiome Composition

Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of extreme chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, the factors that shape chronotypes remain poorly understood. Here, we assessed whether chronotypes are associated with different gut microbiome composition. Using metagenomic sequencing, we established a distinct signature associated with chronotype that involves two bacterial genera Alistipes (elevated in "larks") and Lachnospira (elevated in "owls). We have identified four metabolic pathways (e.g. gluconegonesis) that were associated with early chronotype.

Folate and vitamin B-12 deficiencies additively impaired memory function and disturbed the gut microbiota in amyloid-β infused rats

2019 ◽  
pp. 1-13 ◽  
Author(s):  
Sunmin Park ◽  
Sunna Kang ◽  
Da Sol Kim
Keyword(s):  
Insulin Resistance ◽  
Gut Microbiota ◽  
Insulin Signaling ◽  
Gut Microbiome ◽  
Metabolic Diseases ◽  
Memory Function ◽  
Amyloid Β ◽  
Impaired Memory ◽  
Ca1 Region ◽  
Folate And Vitamin B12

Abstract. Folate and vitamin B12(V-B12) deficiencies are associated with metabolic diseases that may impair memory function. We hypothesized that folate and V-B12 may differently alter mild cognitive impairment, glucose metabolism, and inflammation by modulating the gut microbiome in rats with Alzheimer’s disease (AD)-like dementia. The hypothesis was examined in hippocampal amyloid-β infused rats, and its mechanism was explored. Rats that received an amyloid-β(25–35) infusion into the CA1 region of the hippocampus were fed either control(2.5 mg folate plus 25 μg V-B12/kg diet; AD-CON, n = 10), no folate(0 folate plus 25 μg V-B12/kg diet; AD-FA, n = 10), no V-B12(2.5 mg folate plus 0 μg V-B12/kg diet; AD-V-B12, n = 10), or no folate plus no V-B12(0 mg folate plus 0 μg V-B12/kg diet; AD-FAB12, n = 10) in high-fat diets for 8 weeks. AD-FA and AD-VB12 exacerbated bone mineral loss in the lumbar spine and femur whereas AD-FA lowered lean body mass in the hip compared to AD-CON(P < 0.05). Only AD-FAB12 exacerbated memory impairment by 1.3 and 1.4 folds, respectively, as measured by passive avoidance and water maze tests, compared to AD-CON(P < 0.01). Hippocampal insulin signaling and neuroinflammation were attenuated in AD-CON compared to Non-AD-CON. AD-FAB12 impaired the signaling (pAkt→pGSK-3β) and serum TNF-α and IL-1β levels the most among all groups. AD-CON decreased glucose tolerance by increasing insulin resistance compared to Non-AD-CON. AD-VB12 and AD-FAB12 increased insulin resistance by 1.2 and 1.3 folds, respectively, compared to the AD-CON. AD-CON and Non-AD-CON had a separate communities of gut microbiota. The relative counts of Bacteroidia were lower and those of Clostridia were higher in AD-CON than Non-AD-CON. AD-FA, but not V-B12, separated the gut microbiome community compared to AD-CON and AD-VB12(P = 0.009). In conclusion, folate and B-12 deficiencies impaired memory function by impairing hippocampal insulin signaling and gut microbiota in AD rats.

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