Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study.

Oral microbiome dysbiosis has been associated with various local and systemic human diseases such as dental caries, periodontal disease, obesity, and cardiovascular disease. Bacterial composition may be affected by age, oral health, diet, and geography, although information about the natural variation found in the general public is still lacking. In this study, citizen-scientists used a crowdsourcing model to obtain oral bacterial composition data from guests at the Denver Museum of Nature & Science to determine if previously suspected oral microbiome associations with an individual's demographics, lifestyle, and/or genetics are robust and generalizable enough to be detected within a general population. Consistent with past research, we found bacterial composition to be more diverse in youth microbiomes when compared to adults. Adult oral microbiomes were predominantly impacted by oral health habits, while youth microbiomes were impacted by biological sex and weight status. The oral pathogen Treponema was detected more commonly in adults without recent dentist visits and in obese youth. Additionally, oral microbiomes from participants of the same family were more similar to each other than to oral microbiomes from non-related individuals. These results suggest that previously reported oral microbiome associations are observable in a human population containing the natural variation commonly found in the general public. Furthermore, these results support the use of crowdsourced data as a valid methodology to obtain community-based microbiome data

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.

Immediate freezing at -20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods-95% ethanol, FTA cards, and the OMNIgene Gut kit-can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive

Dramatic Plays as a Tool to Educate Young African-American Females about HIV/AIDS

Rates of HIV/AIDS transmission have increased substantially, particularly among young African American women. According to the Centers for Disease Control and Prevention (CDC), HIV/AIDS is the number one killer for African American women aged 25 to 34. Given that many of these young women are contracting the disease in their late teens and early twenties, there is a need to develop interventions that directly address the needs of this group. The current study sought to assess the effectiveness of theater in increasing knowledge of HIV/AIDS and the likelihood of healthier sexual behavior and choices among 219 young African American women 18 to 39 years of age. Paired sample t-tests revealed that there were significant mean differences in knowledge and intended safe sex behavior after viewing the play. Young women who viewed the play reported increased knowledge of HIV and reported a higher likelihood of engaging in safer sex. Given the high rates of HIV/AIDS among young African American women, more innovative educational and prevention techniques are needed

Toward a predictive understanding of Earth’s microbiomes to address 21st century challenges

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e00714-16, doi:10.1128/mBio.00714-16.Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.E.L.B. is supported by the Genomes-to-Watersheds Subsurface Biogeochemical Research Scientific Focus Area, and T.R.N. is supported by ENIGMA-Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov) Scientific Focus Area, funded by the U.S. Department of Energy (US DOE), Office of Science, Office of Biological and Environmental Research under contract no. DE-AC02- 05CH11231 to Lawrence Berkeley National Laboratory (LBNL). M.E.M. is also supported by the US DOE, Office of Science, Office of Biological and Environmental Research under contract no. DE-AC02-05CH11231. Z.G.C. is supported by National Science Foundation Integrative Organismal Systems grant #1355085, and by US DOE, Office of Biological and Environmental Research grant # DE-SC0008182 ER65389 from the Terrestrial Ecosystem Science Program. M.J.B. is supported by R01 DK 090989 from the NIH. T.J.D. is supported by the US DOE Office of Science’s Great Lakes Bioenergy Research Center, grant DE-FC02- 07ER64494. J.L.G. is supported by Alfred P. Sloan Foundation G 2-15-14023. R.K. is supported by grants from the NSF (DBI-1565057) and NIH (U01AI24316, U19AI113048, P01DK078669, 1U54DE023789, U01HG006537). K.S.P. is supported by grants from the NSF DMS- 1069303 and the Gordon & Betty Moore Foundation (#3300)

The Juvenile Justice Behavioral Health Services Cascade: A New Framework for Measuring Unmet Substance Use Treatment Services Needs Among Adolescent Offenders

Overview—Substance use and substance use disorders are highly prevalent among youth under juvenile justice (JJ) supervision, and related to delinquency, psychopathology, social problems, risky sex and sexually transmitted infections, and health problems. However, numerous gaps exist in the identification of behavioral health (BH) problems and in the subsequent referral, initiation and retention in treatment for youth in community justice settings. This reflects both organizational and systems factors, including coordination between justice and BH agencies. Methods and Results—This paper presents a new framework, the Juvenile Justice Behavioral Health Services Cascade (“Cascade”), for measuring unmet substance use treatment needs to illustrate how the cascade approach can be useful in understanding service delivery issues and identifying strategies to improve treatment engagement and outcomes for youth under community JJ supervision. We discuss the organizational and systems barriers for linking delinquent youth to BH services, and explain how the Cascade can help understand and address these barriers. We provide a detailed description of the sequential steps and measures of the Cascade, and then offer an example of its application from the Juvenile Justice – Translational Research on Interventions for Adolescents in the Legal System project (JJ-TRIALS), a multi-site research cooperative funded by the National Institute on Drug Abuse. Conclusion—As illustrated with substance abuse treatment, the Cascade has potential for informing and guiding efforts to improve behavioral health service linkages for adolescent offenders, developing and testing interventions and policies to improve interagency and cross-systems coordination, and informing the development of measures and interventions for improving the implementation of treatment in complex multisystem service settings

Antiretroviral Adherence Following Prison Release in a Randomized Trial of the imPACT Intervention to Maintain Suppression of HIV Viremia

Many people living with HIV (PLWH) pass through correctional facilities each year, a large proportion of whom do not maintain viral suppression following release. We examined the effects of imPACT, an intervention designed to promote post-release viral suppression, on antiretroviral therapy (ART) adherence. PLWH awaiting release from prisons in two southern states were randomized to imPACT (consisting of motivational interviewing, care linkage coordination, and text message medication reminders) versus standard care (SC). ART adherence, measured by unannounced monthly telephone pill counts, was compared between study arms over 6 months post-release. Of 381 participants eligible for post-release follow-up, 302 (79%) completed ≥ 1 of 6 possible pill counts (median: 4; IQR 1–6). Average adherence over follow-up was 80.3% (95% CI 77.5, 83.1) and 81.0% (78.3, 83.6) of expected doses taken in the imPACT and SC arms, respectively. There was no difference between arms when accounting for missing data using multiple imputation (mean difference = − 0.2 percentage points [− 3.7, 3.3]), controlling for study site and week of follow-up. Of the 936 (40.9%) pill counts that were missed, 212 (22.7%) were due to re-incarceration. Those who missed pill counts for any reason were more likely to be unsuppressed, suggesting that they had lower adherence. However, missingness was balanced between arms. Among PLWH released from prison, ART adherence averaged > 80% in both study arms over 6 months—a level higher than seen with most other chronic diseases. However, missing data may have led to an overestimate of adherence. Factors independent of the intervention influence ART adherence in this population and should be identified to inform future targeted interventions

Using the gut microbiota as a novel tool for examining colobine primate GI health

Primates of the Colobinae subfamily are highly folivorous. They possess a sacculated foregut and are believed to rely on a specialized gut microbiota to extract sufficient energy from their hard-to-digest diet. Although many colobines are endangered and would benefit from captive breeding programs, maintaining healthy captive populations of colobines can be difficult since they commonly suffer from morbidity and mortality due to gastrointestinal (GI) distress of unknown cause. While there is speculation that this GI distress may be associated with a dysbiosis of the gut microbiota, no study has directly examined the role of the gut microbiota in colobine GI health. In this study, we used high-throughput sequencing to examine the gut microbiota of three genera of colobines housed at the San Diego Zoo: doucs (Pygathrix) (N=7), colobus monkeys (Colobus) (N=4), and langurs (Trachypithecus) (N=5). Our data indicated that GI-healthy doucs, langurs, and colobus monkeys possess a distinct gut microbiota. In addition, GI-unhealthy doucs exhibited a different gut microbiota compared to GI-healthy individuals, including reduced relative abundances of anti-inflammatory Akkermansia. Finally, by comparing samples from wild and captive Asian colobines, we found that captive colobines generally exhibited higher relative abundances of potential pathogens such as Desulfovibrio and Methanobrevibacter compared to wild colobines, implying an increased risk of gut microbial dysbiosis. Together, these results suggest an association between the gut microbiota and GI illness of unknown cause in doucs. Further studies are necessary to corroborate these findings and determine cause-and-effect relationships. Additionally, we found minimal variation in the diversity and composition of the gut microbiota along the colobine GI tract, suggesting that fecal samples may be sufficient for describing the colobine gut microbiota. If these findings can be validated in wild individuals, it will facilitate the rapid expansion of colobine gut microbiome research

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.

Background: Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment.Results: Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA.Conclusions: Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA