The dynamics of a family’s gut microbiota reveal variations on a theme

Abstract Background It is clear that the structure and function of the human microbiota has significant impact on maintenance of health and yet the factors that give rise to an adult microbiota are poorly understood. A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome. Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old. Results Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member. Interestingly, there was a significant core membership to the family members’ microbiota where the abundance of this core accounted for the differences between individuals. It was clear that the introduction of solids represents a significant transition in the development of a mature microbiota. This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales. Although the children and mother shared essentially the identical diet and environment, the children’s microbiotas were not significantly more similar to their mother than they were to their father. Conclusions This analysis underscores the complex interactions that give rise to a personalized microbiota and suggests the value of studying families as a surrogate for longitudinal studies.http://deepblue.lib.umich.edu/bitstream/2027.42/109502/1/40168_2014_Article_54.pd

Pilot Testing of Peak Alpha Frequency Stability During Repetitive Transcranial Magnetic Stimulation

Over half of those diagnosed with post-traumatic stress disorder (PTSD) have comorbid major depressive disorder (MDD), and rates are even higher among military veterans. Transcranial magnetic stimulation (TMS) may be a safe and efficacious treatment for PTSD, both with and without comorbid MDD. Still, the mechanism of action of TMS is not fully understood, and it remains unclear which stimulation techniques (e.g., target regions, pulse strength/frequency, waveform) optimize treatment for these patients. Recent research indicated that a patient's unique individualized alpha frequency (IAF) may be used to guide brain stimulation treatment, and emerging data suggests that stimulation synchronized to the IAF may be efficacious for MDD. However, to our knowledge there are no studies to date that evaluate the stability of IAF over time in patients with comorbid PTSD and MDD. To this end, we used an eight-lead electroencephalography (EEG) system to record IAF before and after a course of TMS. Stimulation parameters were informed by prior studies of TMS for comorbid PTSD and MDD and included 5 Hz TMS to the left dorsolateral prefrontal cortex, at 120% of motor threshold, 3,000–4,000 pulses per session for up to 40 sessions. We tested whether IAF was changed with a course of TMS therapy and evaluated whether IAF predicted clinical outcomes. We observed no significant changes in IAF from baseline to post-treatment, and there was no relationship between IAF and clinical symptom change. These data demonstrate the stability of IAF with TMS and indicate its utility as a trait marker for future brain stimulation studies. This work does not support the use of IAF as predictor of clinical response to TMS as administered

Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

Background: The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking are associated with differences in the oral and gut microbiota, in comparison to non-smoking controls. Methods: We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Results: Tobacco smokers had significantly different bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with a higher relative abundance of Prevotella (P = 0.006) and lowered Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. Discussion: The current pilot data demonstrate that tobacco smoking is associated with signicant differences in the oral and gut microbiome in humans. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted

Beyond Blackboards: Engaging Underserved Middle School Students in Engineering

Beyond Blackboards is an inquiry-centered, after-school program designed to enhance middle school students’ engagement with engineering through design-based experiences focused on the 21st Century Engineering Challenges. Set within a predominantly lowincome, majority-minority community, our study aims to investigate the impact of Beyond Blackboards on students’ interest in and understanding of engineering, as well as their ability to align their educational and career plans. We compare participants’ and nonparticipants’ questionnaire responses before the implementation and at the end of the program’s first academic year. Statistically significant findings indicate a school-wide increase in students’ interest in engineering careers, supporting a shift in school culture. However, only program participants showed increased enjoyment of design-based strategies, understanding of what engineers do, and awareness of the steps for preparing for an engineering career. These quantitative findings are supported by qualitative evidence from participant focus groups highlighting the importance of mentors in shaping students’ awareness of opportunities within engineering

Meeting the ISTE Challenge in the Field: An Overview of the First Six Distinguished Achievement Award Winning Programs

The 2002 National Educational Technology Standards (NETS) Distinguished Achievement Awards, sponsored by the International Society for Technology in Education (ISTE), were awarded to six teacher education programs across the United States. The awards recognize institutions that exemplify successful integration of the National Educational Technology Standards for Teachers (NETS[solid dot]T) into teacher education programs. Institutions across the country completed an extensive application process to be selected one of the first six recipients of the ISTE Distinguished Achievement award. This process included online documentation that demonstrated the program\u27s implementation of the NETS[solid dot]T models and practices. This article provides a means of uniting various programs and program developers (teacher educators and instructional technologists) by looking at the most common obstacles they face in the pursuit of appropriate infusion of technology into teacher education programs and workable solutions for overcoming those obstacles

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi

A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon’s second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults

Examining the neural mechanisms of rTMS: a naturalistic pilot study of acute and serial effects in pharmacoresistant depression

IntroductionPrevious studies have demonstrated the effectiveness of therapeutic repetitive transcranial magnetic stimulation (rTMS) to treat pharmacoresistant depression. Nevertheless, these trials have primarily focused on the therapeutic and neurophysiological effects of rTMS following a long-term treatment course. Identifying brain-based biomarkers of early rTMS therapeutic response remains an important unanswered question. In this pilot study, we examined the effects of rTMS on individuals with pharmacoresistant depression using a graph-based method, called Functional Cortical Networks (FCN), and serial electroencephalography (EEG). We hypothesized that changes in brain activity would occur early in treatment course.MethodsA total of 15 patients with pharmacoresistant depression underwent five rTMS sessions (5Hz over the left dorsolateral prefrontal cortex, 120%MT, up to 4,000 pulses/session). Five participants received additional rTMS treatment, up to 40 sessions. Resting EEG activity was measured at baseline and following every five sessions, using 64-channel EEG, for 10 minutes with eyes closed. An FCN model was constructed using time-varying graphs and motif synchronization. The primary outcome was acute changes in weighted-node degree. Secondary outcomes included serial FFT-based power spectral analysis and changes in depressive symptoms measured by the 9-Item Patient Health Questionnaire (PHQ-9) and the 30-item Inventory of Depressive Symptoms-Self Report (IDS-SR).ResultsWe found a significant acute effect over the left posterior area after five sessions, as evidenced by an increase in weighted-node degree of 37,824.59 (95% CI, 468.20 to 75,180.98) and a marginal enhancement in the left frontal region (t (14) = 2.0820, p = 0.056). One-way repeated measures ANOVA indicated a significant decrease in absolute beta power over the left prefrontal cortex (F (7, 28) = 2.37, p = 0.048) following ten rTMS sessions. Furthermore, a significant clinical improvement was observed following five rTMS sessions on both PHQ-9 (t (14) = 2.7093, p = 0.017) and IDS-SR (t (14) = 2.5278, p = 0.024) and progressed along the treatment course.DiscussionOur findings suggest that FCN models and serial EEG may contribute to a deeper understanding of mechanisms underlying rTMS treatment. Additional research is required to investigate the acute and serial effects of rTMS in pharmacoresistant depression and assess whether early EEG changes could serve as predictors of therapeutic rTMS response

Deltaic and Coastal Sediments as Recorders of Mediterranean Regional Climate and Human Impact Over the Past Three Millennia

This work was financially supported by the MISTRALS/PaleoMex program and by the Project of Strategic Interest NextData PNR 2011–2013 (www. nextdataproject.it). Lionel Savignan is thanked for his participation in the biomarker analysis. Radiocarbon datings for core KESC9-14 have been funded by Institut Carnot Ifremer-EDROME (grant A0811101). We also thank the Holocene North-Atlantic Gyres and Mediterranean Overturning dynamic through Climate Changes (HAMOC) project for financial support. The biomarker data presented here are available in the supporting information.Peer reviewedPublisher PD

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases