The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained ...popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
•Factors driving the timing and government closure and containment responses to COVID-19 for 150 countries are examined.•Authoritarian regimes tended have weaker policy responses initially but pursed ...more aggressive policies later on.•Unitary regimes tended to have stronger policy measures early on relative to federalist states but relaxed them soonerUnitary regimes tended to have stronger policy measures early on after the pandemic hit relative to federalist states but relaxed them sooner.•Responses of countries with greater freedom and those spending less on public health started slow but caught up later.The policy response of countries with greater freedom and those spending less on public health started slow but caught up in around three months.•Policy implications are discussed as the how nations should prepare for future pandemics.
Factors that drove the early timing and strictness of government responses to COVID-19 for over 150 countries are examined using the daily Coronavirus Government Response Tracker data provided by the University of Oxford. Results show that authoritarian regimes tended to have an initial policy response somewhat weaker relative to democratic regimes at the early stages of the pandemic but pursed more aggressive containment policies over the latter part of the six-month period analyzed. Unitary regimes tended to have stronger policy measures in place early on relative to federalist states but relaxed these restrictions sooner. Countries with greater freedom (political rights and civil liberties) and those that spend less on public health also exhibited slower early policy responses, but caught up within three to four months after the pandemic reached their country. There is no evidence that women leaders, viewed as a whole, put in place more aggressive polices to combat the virus relative to their male counterparts. Nor is there any evidence that either island nations or countries that experienced the start of the pandemic later in the global wave pursued different policies that other nations. Policy implications are discussed as the how nations should prepare for future pandemics.
The microbiota of the mammalian gastrointestinal (GI) tract consists of diverse populations of commensal bacteria that interact with host physiological function. Dysregulating these populations, ...through exogenous means such as antibiotics or dietary changes, can have adverse consequences on the health of the host. Studies from laboratories such as ours have demonstrated that exposure to psychological stressors disrupts the population profile of intestinal microbiota. To date, such studies have primarily focused on prolonged stressors (repeated across several days) and have assessed fecal bacterial populations. It is not known whether shorter stressors can also impact the microbiota, and whether colonic mucosa-associated populations can also be affected. The mucosa-associated microbiota exist in close proximity to elements of the host immune system and the two are tightly interrelated. Therefore, alterations in these populations should be emphasized. Additionally, stressors can induce differential responses in anxiety-like behavior and corticosterone outputs in variant strains of mice. Thus, whether stressor exposure can have contrasting effects on the colonic microbiota in inbred C57BL/6 mice and outbred CD-1 mice was also examined.
In the present study, we used high throughput pyrosequencing to assess the effects of a single 2-hour exposure to a social stressor, called social disruption (SDR), on colonic mucosa-associated microbial profiles of C57BL/6 mice. The data indicate that exposure to the stressor significantly changed the community profile and significantly reduced the relative proportions of two genera and one family of highly abundant intestinal bacteria, including the genus Lactobacillus. This finding was confirmed using a quantitative real-time polymerase chain reaction (qPCR) technique. The use of qPCR also identified mouse strain-specific differences in bacterial abundances. L. reuteri, an immunomodulatory species, was decreased in stressor-exposed CD-1 mice, but not C57BL/6 mice.
These data illustrate that stressor exposure can affect microbial populations, including the lactobacilli, that are closely associated with the colonic mucosa. Because the lactobacilli can have beneficial effects on human health, stressor-induced reductions of their population could have important health implications.
In this study, the collective microbial diversity in anaerobic digesters was examined using a meta-analysis approach. All 16S rRNA gene sequences recovered from anaerobic digesters available in ...public databases were retrieved and subjected to phylogenetic and statistical analyses. As of May 2010, 16,519 bacterial and 2869 archaeal sequences were found in GenBank. The bacterial sequences were assigned to 5926 operational taxonomic units (OTUs, based on ⩾97% sequence identity) representing 28 known bacterial phyla, with Proteobacteria (1590 OTUs), Firmicutes (1352 OTUs), Bacteroidetes (705 OTUs), and Chloroflexi (693 OTUs) being predominant. Archaeal sequences were assigned to 296 OTUs, primarily Methanosaeta and the uncharacterized WSA2 group. Nearly 60% of all sequences could not be classified to any established genus. Rarefaction analysis indicates that approximately 60% of bacterial and 90% of archaeal diversity in anaerobic digesters has been sampled. This analysis of the global bacterial and archaeal diversity in AD systems can guide future studies to further examine the microbial diversity involved in AD and development of comprehensive analytical tools.
The study of the church is a prominent issue among New Testament writers. Though the church has progressed and may look different in the twenty-first century than it did in the first century, its ...purpose and function described in the New Testament ought to remain the same. One such progression that many modern churches have promoted is the use of multiple locations. The multi-campus phenomenon of the church is a recent development in the history of Christianity. Even more popular and perhaps even more acceptable is the multiple gatherings of the church that occur in one place but at different times. In many ways, the multi-site and multiple-service church are an application of the hierarchical structure of the church which developed in the third century. Such practices compromise the principle of congregationalism, foundational to Baptist churches, for the benefit of pragmatic purposes. Therefore, this article will argue a necessary connection between congregationalism and the assembly to show that the local church is to be a physical and singular gathering of covenanted believers at one time and in one location.
Nelson argues that the current intertwined environmental crises--not just climate change, but also zoonotic disease pandemics, pollution, food insecurity, and biodiversity loss--are scientific ...problems; they are also economic and technological problems. But most notably, they are ethical problems that demand an ethical response. These environmental crises have grown out of ethical assumptions that Western nations have made over centuries about our proper role in the natural world. Recognizing and challenging these assumptions could transform our relationship with the Earth and shift public attitudes, allowing new approaches to policy decisions and motivating scientists to incorporate ethics into how they think about, talk about, and conduct their research. Continuing to separate ethics from science, on the other hand, will likely result in more incomplete, and ultimately ineffective, responses to each crisis.
Studies have demonstrated cross-reactivity of anti-dengue virus (DENV) antibodies in human sera against Zika virus (ZIKV), promoting increased ZIKV infection in vitro. However, the correlation ...between in vitro and in vivo findings is not well characterized. Thus, we evaluated the impact of heterotypic flavivirus immunity on ZIKV titers in biofluids of rhesus macaques. Animals previously infected (≥420 days) with DENV2, DENV4, or yellow fever virus were compared to flavivirus-naïve animals following infection with a Brazilian ZIKV strain. Sera from DENV-immune macaques demonstrated cross-reactivity with ZIKV by antibody-binding and neutralization assays prior to ZIKV infection, and promoted increased ZIKV infection in cell culture assays. Despite these findings, no significant differences between flavivirus-naïve and immune animals were observed in viral titers, neutralizing antibody levels, or immune cell kinetics following ZIKV infection. These results indicate that prior infection with heterologous flaviviruses neither conferred protection nor increased observed ZIKV titers in this non-human primate ZIKV infection model.
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