Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes.

Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to "knock in" specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent.

Complex physiology and clinical implications of time-restricted eating.

Time-restricted eating (TRE) is a dietary intervention that limits food consumption to a specific time window each day. The effect of TRE on body weight and physiological functions has been extensively studied in rodent models, which have shown considerable therapeutic effects of TRE and important interactions among time of eating, circadian biology, and metabolic homeostasis. In contrast, it is difficult to make firm conclusions regarding the effect of TRE in people because of the heterogeneity in results, TRE regimens, and study populations. In this review, we 1) provide a background of the history of meal consumption in people and the normal physiology of eating and fasting; 2) discuss the interaction between circadian molecular metabolism and TRE; 3) integrate the results of preclinical and clinical studies that evaluated the effects of TRE on body weight and physiological functions; 4) summarize other time-related dietary interventions that have been studied in people; and 4) identify current gaps in knowledge and provide a framework for future research directions.

The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases.

The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.

Circadian Rhythms in the Pathogenesis and Treatment of Fatty Liver Disease.

Circadian clock proteins are endogenous timing mechanisms that control the transcription of hundreds of genes. Their integral role in coordinating metabolism has led to their scrutiny in a number of diseases, including nonalcoholic fatty liver disease (NAFLD). Discoordination between central and peripheral circadian rhythms is a core feature of nearly every genetic, dietary, or environmental model of metabolic syndrome and NAFLD. Restricting feeding to a defined daily interval (time-restricted feeding) can synchronize the central and peripheral circadian rhythms, which in turn can prevent or even treat the metabolic syndrome and hepatic steatosis. Importantly, a number of proteins currently under study as drug targets in NAFLD (sterol regulatory element-binding protein [SREBP], acetyl-CoA carboxylase [ACC], peroxisome proliferator-activator receptors [PPARs], and incretins) are modulated by circadian proteins. Thus, the clock can be used to maximize the benefits and minimize the adverse effects of pharmaceutical agents for NAFLD. The circadian clock itself has the potential for use as a target for the treatment of NAFLD.

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.

Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.

The effects of provider-prescribed obesogenic drugs on post-laparoscopic sleeve gastrectomy outcomes: a retrospective cohort study.

BACKGROUND: Laparoscopic sleeve gastrectomy (LSG) is one of the most commonly performed bariatric procedures and has proven effective in providing weight loss. However, considerable variance has been noted in the degree of weight loss. Physician prescription practices may be negatively affecting weight loss post-LSG and, thus, contributing to the broad range of weight loss outcomes. The aim of our study was to determine whether commonly prescribed obesogenic medications negatively affect weight loss outcomes post-LSG. SUBJECTS/METHODS: This single center retrospective cohort study performed at a University hospital included 323 patients (≥18 years) within the University California, San Diego Healthcare System who underwent LSG between 2007 and 2016. We identified a list of 32 commonly prescribed medications that have weight gain as a side effect. We compared the percent excess weight loss (%EWL) of patients divided into two groups based on post-LSG exposure to obesogenic medications. A linear regression model was used to analyze %EWL at 12 months post-LSG while controlling for age, initial body mass index (BMI), and use of leptogenic medications. RESULTS: A total of 150 patients (Meds group) were prescribed obesogenic medications within the one-year post-LSG follow up period, whereas 173 patients (Control group) were not prescribed obesogenic medications. The Meds group lost significantly less weight compared to the Control group (%EWL ± SEM at 12 months 53.8 ± 2.4 n = 78, 65.0 ± 2.6, n = 84 respectively, P = 0.002). This difference could not be attributed to differences in age, gender, initial BMI, co-morbidities, or prescription of leptogenic medications between the two groups. CONCLUSIONS: The use of provider-prescribed obesogenic medications was associated with worse weight loss outcomes post-LSG. Closer scrutiny of patient medications may be necessary to help improve outcomes of weight loss treatments.

Percutaneous Gastrostomy Device for the Treatment of Class II and Class III Obesity: Results of a Randomized Controlled Trial.

OBJECTIVES: The AspireAssist System (AspireAssist) is an endoscopic weight loss device that is comprised of an endoscopically placed percutaneous gastrostomy tube and an external device to facilitate drainage of about 30% of the calories consumed in a meal, in conjunction with lifestyle (diet and exercise) counseling. METHODS: In this 52-week clinical trial, 207 participants with a body-mass index (BMI) of 35.0-55.0 kg/m2 were randomly assigned in a 2:1 ratio to treatment with AspireAssist plus Lifestyle Counseling (n=137; mean BMI was 42.2±5.1 kg/m2) or Lifestyle Counseling alone (n=70; mean BMI was 40.9±3.9 kg/m2). The co-primary end points were mean percent excess weight loss and the proportion of participants who achieved at least a 25% excess weight loss. RESULTS: At 52 weeks, participants in the AspireAssist group, on a modified intent-to-treat basis, had lost a mean (±s.d.) of 31.5±26.7% of their excess body weight (12.1±9.6% total body weight), whereas those in the Lifestyle Counseling group had lost a mean of 9.8±15.5% of their excess body weight (3.5±6.0% total body weight) (P<0.001). A total of 58.6% of participants in the AspireAssist group and 15.3% of participants in the Lifestyle Counseling group lost at least 25% of their excess body weight (P<0.001). The most frequently reported adverse events were abdominal pain and discomfort in the perioperative period and peristomal granulation tissue and peristomal irritation in the postoperative period. Serious adverse events were reported in 3.6% of participants in the AspireAssist group. CONCLUSIONS: The AspireAssist System was associated with greater weight loss than Lifestyle Counseling alone.

Functional Local Input to Layer 5 Pyramidal Neurons in the Rat Visual Cortex.

Pyramidal neurons in layer 5 of the neocortex can be differentiated into 3 cell subtypes: 1) short regular spiking (SH), 2) tall regular spiking (TR), and 3) tall burst spiking (TB), based on their morphological and electrophysiological properties. We characterized the functional excitatory local input to these 3 cell subtypes in rat primary visual cortex using laser-scanning photostimulation. Although all cell types received significant input from all cortical layers, SH neurons received stronger input from layer 4 and weaker input from layer 5 than did tall pyramidal cells. However, the laminar input to the 2 populations of tall pyramidal cells was indistinguishable. Simultaneous paired recording were then used to calculate a correlation probability (CP) to infer the proportion of shared input based on the occurrence of simultaneous synaptic potentials. Tall pairs of matched type had significantly higher CPs compared with unmatched pairs, suggesting that subpopulations of layer 4, 5, and 6 neurons preferentially connect to each tall cell type. Hence, this study shows that unconnected but matching pairs of tall pyramidal neurons, but not short pyramidal neurons, receive functional input from different interconnected networks within layers 4, 5, and 6.

Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study.

OBJECTIVE: In the setting where two individuals are genetically similar, epigenetic mechanisms could account for discordance in the presence or absence of non-alcoholic fatty liver disease (NAFLD). This study investigated if serum microRNAs (miRs) could explain discordance in NAFLD. DESIGN: This is a cross-sectional analysis of a prospective cohort study of 40 (n=80) twin-pairs residing in Southern California. All participants underwent a standardised research visit, liver MRI using proton-density fat fraction to quantify fat content and miR profiling of their serum. RESULTS: Among the 40 twin-pairs, there were 6 concordant for NAFLD, 28 were concordant for non-NAFLD and 6 were discordant for NAFLD. The prevalence of NAFLD was 22.5% (18/80). Within the six discordant twins, a panel of 10 miRs differentiated the twin with NAFLD from the one without. Two of these miRs, miR-331-3p and miR-30c, were also among the 21 miRs that were different between NAFLD and non-NAFLD groups (for miR-331-3p: 7.644±0.091 vs 8.057±0.071, respectively, p=0.004; for miR-30c: 10.013±0.126 vs 10.418±0.086, respectively, p=0.008). Both miRs were highly heritable (35.9% and 10.7%, respectively) and highly correlated with each other (R=0.90, p=2.2×10(-16)) suggesting involvement in a common mechanistic pathway. An interactome analysis of these two miRs showed seven common target genes. CONCLUSIONS: Using a novel human twin-study design, we demonstrate that discordancy in liver fat content between the twins can be explained by miRs, and that they are heritable.

Targeting Dysbiosis for the Treatment of Liver Disease.

The gut microbiome is composed of a vast number of microbes in the gastrointestinal tract, which benefit host metabolism, aid in digestion, and contribute to normal immune function. Alterations in microbial composition can result in intestinal dysbiosis, which has been implicated in several diseases including obesity, inflammatory bowel disease, and liver diseases. Over the past several years, significant interactions between the intestinal microbiota and liver have been discovered, with possible mechanisms for the development as well as progression of liver disease and promising therapeutic targets to either prevent or halt the progression of liver disease. In this review the authors examine mechanisms of dysbiosis-induced liver disease; highlight current knowledge regarding the role of dysbiosis in nonalcoholic liver disease, alcoholic liver disease, and cirrhosis; and discuss potential therapeutic targets.

Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation.

The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders.

Differences in Weight Loss Between Persons on Standard Balanced vs Nutrigenetic Diets in a Randomized Controlled Trial.

BACKGROUND & AIMS: Many companies provide genetic tests for obesity-related polymorphisms (nutrigenetics) and make dietary recommendations for weight loss that are based on the results. We performed a randomized controlled trial to determine whether more participants who followed a nutrigenetic-guided diet lost ≥5% of their body weight than participants on a standard balanced diet for 8 and 24 weeks. METHODS: We performed a prospective study of 51 obese or overweight U.S. veterans on an established weight management program at the Veterans Administration San Diego Healthcare System (the MOVE! program). Participants were randomly assigned to groups placed on a nutrigenetic-guided diet (balanced, low-carbohydrate, low-fat, or Mediterranean; n = 30) or a standard balanced diet (n = 21). Nutrigenetic diets were selected on the basis of results from the Pathway FIT test. RESULTS: There was no significant difference in the percentage of participants on the balanced diet vs the nutrigenetic-guided diet who lost 5% of their body weight at 8 weeks (35.0% ± 20.9% vs 26.9% ± 17.1%, respectively; P = .28) or at 24 weeks. Both groups had difficulty adhering to the diets. However, adherence to the nutrigenetic-guided diet correlated with weight loss (r = 0.74; P = 4.0 × 10(-5)), but not adherence to standard therapy (r = 0.34; P = .23). Participants who had low-risk polymorphisms for obesity lost more weight than all other participants at 8 weeks (5.0% vs 2.9%, respectively; P = .02) and had significantly greater reductions in body mass index (6.4% vs 3.6%, respectively; P = .03) and waist circumference (6.5% vs 2.6%, respectively; P = .02) at 24 weeks. CONCLUSIONS: In a prospective study, a nutrigenetic-based diet did not increase weight loss compared with a standard balanced diet. However, genetic features can identify individuals most likely to benefit from a balanced diet weight loss strategy; these findings require further investigation. ClinicalTrials.gov number: NCT01859403.

Control of Eating Attributes and Weight Loss Outcomes over One Year After Sleeve Gastrectomy.

PURPOSE: Sleeve gastrectomy (SG) is a commonly performed metabolic-bariatric surgery, but its effectiveness is variable and difficult to predict. Our study aimed to compare control of eating (CoE) attributes pre- and post-SG depending on the achievement of optimal weight loss target at 1 year post-SG. MATERIALS AND METHODS: A prospective longitudinal cohort study using the CoE Questionnaire, pre-SG, and postoperatively at 3, 6, and 12 months was conducted. Total weight loss (TWL) ≥ 25% at 12 months post-SG was set as an optimal weight loss target. RESULTS: Forty-one patients (80.5% females, mean age 41.7 ± 10.6) were included. Sex, age, baseline weight, BMI, and smoking status were all comparable. At 3 months post-SG, "difficulty to control eating" score became significantly different between ≥ 25%TWL and < 25%TWL groups (7 [0-50] vs. 17 [5-63], p = 0.042). At 6 months, it was followed by "feeling of fullness," "frequency of food cravings," and "difficulty to resist cravings" demonstrating significant differences between ≥ 25%TWL and < 25%TWL groups. At 12 months, significant differences between groups were observed in "feeling hungry," "difficulty to resist cravings," "eating in response to cravings," and difficulty to control eating scores. CONCLUSION: Individuals with obesity who achieved a target of ≥ 25%TWL at 1 year post-SG have an early improvement in overall eating control at 3 months that steadily persists at 6 and 12 months. Improvements in other aspects tend to follow later, at 6 and 12 months. These findings may assist in identifying individuals with inadequate response to help attain optimal weight loss targets and developing a prognostic model to identify predictors of successful weight loss.

Stronger control of eating 3 months after sleeve gastrectomy predicts successful weight loss outcomes at one year.

Background: Weight loss response to sleeve gastrectomy (SG) is variable and predicting the effectiveness of surgery is challenging and elusive. The aim of our study was to assess and quantify the association between eating control and weight loss outcomes and identify the control of eating (CoE) attributes during the early postoperative period that might predict good vs. poor response to SG at one year. Methods: A prospective longitudinal cohort study using the Control of Eating Questionnaire (CoEQ) was designed as a series before and at 3-, 6-, and 12-months post-SG. Primary outcomes were changes in CoE attributes and percent of total weight loss (%TWL) 12-months post-surgery. Subjects were categorized based on %TWL as good (GR, ≥25 %) or poor responders (PR, <25 %). A receiver operating characteristic and logistic regression analyses were performed. Results: We included 41 participants (80.5% females, 51.2% Hispanic, mean age 41.7±10.6, median baseline body mass index (BMI) 43.6 kg/m2 [range 35.2-66.3]) who completed the CoEQ at all four timepoints. The "Difficulty to control eating" score at 3 months revealed the highest area under the curve (AUC) (AUC 0.711; 95%CI 0.524-0.898; p=0.032). In a trade-off between a high Youden index and high sensitivity, the "Difficulty to control eating" score of 7 at 3 months was identified as the optimal cut-off for distinguishing between GRs and PRs. Score ≤7 at 3 months was strongly independently associated with a successful weight loss target of 25%TWL at one-year post-SG (Relative Risk 4.43; 95%CI 1.06-18.54; p=0.042). Conclusion: "Difficulty to control eating" score at 3 months post-SG is an independent early predictor of optimal response (achieving a successful TWL target of ≥25 % at one-year post-SG). Our results support the utility of this easy-to-administer validated tool for predicting the effectiveness of SG and may assist in identifying individuals with suboptimal response early and helping them with interventions to attain optimal weight loss targets.

Engineered bacterial therapeutics for detecting and treating CRC.

Despite an overall decrease in occurrence, colorectal cancer (CRC) remains the third most common cause of cancer deaths in the USA. Detection of CRC is difficult in high-risk groups, including those with genetic predispositions, with disease traits, or from certain demographics. There is emerging interest in using engineered bacteria to identify early CRC development, monitor changes in the adenoma and CRC microenvironment, and prevent cancer progression. Novel genetic circuits for cancer therapeutics or functions to enhance existing treatment modalities have been tested and verified in vitro and in vivo. Inclusion of biocontainment measures would prepare strains to meet therapeutic standards. Thus, engineered bacteria present an opportunity for detection and treatment of CRC lesions in a highly sensitive and specific manner.

Time of sample collection is critical for the replicability of microbiome analyses.

As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur. One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5-7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.

Harnessing the power within: engineering the microbiome for enhanced gynecologic health.

Abstract: Although numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions. Lay summary: Manipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.

Live Biotherapeutic Products as Cancer Treatments.

Almost every aspect of cancer can be influenced by microbiota including tumor onset, progression, and response to therapy. The increasing evidence of the role of microbiota in human health and disease has reinvigorated the interest in designing microbial products that can affect cancer outcomes. Researchers have made numerous attempts to develop safe, engineered biotherapeutic products for cancer treatment using synthetic biology tools. Despite the progress, only Bacillus Calmette-Guérin is approved for human use. Here, we highlight the recent advances and current challenges in using live bacteria as cancer therapeutics.

Complete Genome Sequence of an Escherichia coli Strain Isolated from Laboratory Mouse Stool for Use as a Chassis for Transgene Delivery to the Murine Microbiome.

Tools to explore functional changes in the microbiome are limited. Here, we report the complete genome sequence of a strain of Escherichia coli that was isolated from murine stool. This sequence will provide essential information to further develop this tool, and similar tools, to explore the complex murine microbiome.

Obesity, Chronic Stress, and Stress Reduction.

The obesity epidemic is caused by the misalignment between human biology and the modern food environment, which has led to unhealthy eating patterns and behaviors and an increase in metabolic diseases. This has been caused by the shift from a "leptogenic" to an "obesogenic" food environment, characterized by the availability of unhealthy food and the ability to eat at any time of day due to advances in technology. Binge Eating Disorder (BED) is the most commonly diagnosed eating disorder, characterized by recurrent episodes of binge eating and a sense of loss of control over eating, and is treated with cognitive-behavioral therapy-enhanced (CBT-E). Shift work, especially night shift work, can disrupt the body's natural circadian rhythms and increase the risk of obesity and other negative health consequences, such as cardiovascular disease and metabolic syndrome. One dietary approach to address circadian dysregulation is time-restricted eating (TRE), which involves restricting food intake to specific periods of the day to synchronize the body's internal clock with the external environment. TRE has been found to cause modest weight loss and improve metabolic outcomes such as insulin sensitivity and blood pressure, but the extent to which it is beneficial may depend on adherence and other factors such as caloric restriction.