Salivary Transcriptome and Mitochondrial Analysis of Autism Spectrum Disorder Children Compared to Healthy Controls.

Autism rates have been reported to be increasing rapidly in industrialized societies. The pathology most often combines neurological symptoms associated with language and social impairments with gastrointestinal symptoms. This study aimed to measure differences in oral metatranscriptome and mitochondrial health between ASD children and neurotypical USA and Colombia ("Blue Zone") children.

Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness.

It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129).

A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study.

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples.

An accurate aging clock developed from large-scale gut microbiome and human gene expression data.

Accurate measurement of the biological markers of the aging process could provide an "aging clock" measuring predicted longevity and enable the quantification of the effects of specific lifestyle choices on healthy aging. Using machine learning techniques, we demonstrate that chronological age can be predicted accurately from (1) the expression level of human genes in capillary blood and (2) the expression level of microbial genes in stool samples. The latter uses a very large metatranscriptomic dataset, stool samples from 90,303 individuals, which arguably results in a higher quality microbiome-aging model than prior work.

Detecting salivary host and microbiome RNA signature for aiding diagnosis of oral and throat cancer.

Objective: Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) can go undetected resulting in late detection and poor outcomes. We describe the development and validation of CancerDetect for Oral & Throat cancer™ (CDOT), to detect markers of OSCC and/or OPSCC within a high-risk population.

Material And Methods: We collected saliva samples from 1,175 individuals who were 50 years or older, or adults with a tobacco use history.

Comparison of the gut microbiome composition between men with erectile dysfunction and a matched cohort: a pilot study.

Background: To-date there have been minimal studies to investigate an association between the gut microbiome and erectile dysfunction. There have been many inflammatory diseases linked to gut microbiome dysbiosis; such as cardiovascular disease and metabolic syndrome. These same inflammatory diseases have been heavily linked to erectile dysfunction.

Investigating the association between the symptoms of women with Fibromyalgia, Digestive function, and markers of the microbiota of the Gastrointestinal Tract (The FIDGIT Study): study protocol.

Background: Fibromyalgia a common idiopathic condition affecting around 1.4% of adults globally. Its signature symptom is chronic widespread pain, with a constellation of somatic and psychological symptoms.

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes.

Background: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes.

Methods: Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368).

A clinically validated human saliva metatranscriptomic test for global systems biology studies.

The authors report here the development of a high-throughput, automated, inexpensive and clinically validated saliva metatranscriptome test that requires less than 100 μl of saliva. RNA is preserved at the time of sample collection, allowing for ambient-temperature transportation and storage for up to 28 days. Critically, the RNA preservative is also able to inactivate pathogenic microorganisms, rendering the samples noninfectious and allowing for safe and easy shipping.

Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses.

Objectives: Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated by the constant presence of mutated, emerging, and novel pathogens. One of the most common sites of infection by many pathogens is the human throat.

The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer.

Despite advances in cancer treatment, the 5-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluated machine-learning (ML) classifiers using metatranscriptomic data from saliva samples (n = 433) collected from oral premalignant disorders (OPMD), OC patients (n = 71) and normal controls (n = 171). Our diagnostic classifiers yielded a receiver operating characteristics (ROC) area under the curve (AUC) up to 0.

Gut Microbiome Activity Contributes to Prediction of Individual Variation in Glycemic Response in Adults.

Limiting postprandial glycemic response (PPGR) is an important intervention in reducing the risk of chronic metabolic diseases and has been shown to impart significant health benefits in people with elevated levels of blood sugar. In this study, we collected gut microbiome activity data by assessing the metatranscriptome, and we measured the glycemic responses of 550 adults who consumed more than 30,000 meals, collectively, from omnivore or vegetarian/gluten-free diets. We demonstrate that gut microbiome activity, anthropometric factors, and food macronutrients modulate individual variation in glycemic response.

A clinically validated human capillary blood transcriptome test for global systems biology studies.

To prevent and treat chronic diseases, including cancer, a global application of systems biology is needed. We report here a whole blood transcriptome test that needs only 50 μl of capillary (fingerprick) blood. This test is suitable for global applications because the samples are preserved at ambient temperature for up to 4 weeks and the RNA preservative inactivates all pathogens, enabling safe transportation.

Correction: California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals.

[This corrects the article DOI: 10.1371/journal.pone.

California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals.

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions.

A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health.

A functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome's functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intrasample variability, rapid changes, and RNA degradation.

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal.

Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development.

Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients.

Background: Acute Coronary Syndrome (ACS) is a leading cause of morbidity and mortality. Perturbed gut- microbiota (dysbiosis) and increased intestinal permeability (leaky-gut) with translocation of bacterial antigens, play critical role in obesity and metabolic syndrome, which are also major ACS risk factors. Additionally, Trimethylamine-N-Oxide (TMAO), a metabolite produced by phylum Proteobacteria in gut is implicated in developing ACS.

High-throughput phenotyping of cell-to-cell interactions in gel microdroplet pico-cultures.

Microbiomes exert significant influence on our planet's ecology. Elucidating the identities of individual microbes within these communities and how they interact is a vital research imperative. Using traditional plating and culturing methods, it is impractical to assess even a small fraction of the interactions that exist within microbial communities.

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages.

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y.

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater.

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive released to the environment as a result of weapons manufacturing and testing worldwide. At Los Alamos National Laboratory, the Technical Area (TA) 16 260 Outfall discharged high-explosives-bearing water from a high-explosives-machining facility to Cañon de Valle during 1951 through 1996. These discharges served as a primary source of high-explosives and inorganic-element contamination in the area.

Molecular Dissection of Induced Platinum Resistance through Functional and Gene Expression Analysis in a Cell Culture Model of Bladder Cancer.

We report herein the development, functional and molecular characterization of an isogenic, paired bladder cancer cell culture model system for studying platinum drug resistance. The 5637 human bladder cancer cell line was cultured over ten months with stepwise increases in oxaliplatin concentration to generate a drug resistant 5637R sub cell line. The MTT assay was used to measure the cytotoxicity of several bladder cancer drugs.

Building International Genomics Collaboration for Global Health Security.

Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications.

First Complete Genome Sequence of Felis catus Gammaherpesvirus 1.

We sequenced the complete genome of Felis catus gammaherpesvirus 1 (FcaGHV1) from lymph node DNA of an infected cat. The genome includes a 121,556-nucleotide unique region with 87 predicted open reading frames (61 gammaherpesvirus conserved and 26 unique) flanked by multiple copies of a 966-nucleotide terminal repeat.