Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

BACKGROUND: The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset. RESULTS: We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10 % increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92 % for TFF and PEG, 82.4 % for LIT). Our methods obtained lower relative abundance of the Myoviridae family (<16 %) as compared to the reference protocol (22 %). This decline, however, was not considered a true loss of Myoviridae phages but rather a greater level of extraction of Siphoviridae phages (TFF and PEG >32.5 %, LIT 22.6 %), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy. CONCLUSIONS: Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior to HTS in phage-metavirome studies. Our methods can be easily modified, being thus applicable and adjustable for in principle any solid environmental material in dissolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0131-4) contains supplementary material, which is available to authorized users

Industrial, Collaborative and Mobile Robotics in Latin America: Review of Mechatronic Technologies for Advanced Automation

Mechatronics and Robotics (MaR) have recently gained importance in product development and manufacturing settings and applications. Therefore, the Center for Space Emerging Technologies (C-SET) has managed an international multi-disciplinary study to present, historically, the first Latin American general review of industrial, collaborative, and mobile robotics, with the support of North American and European researchers and institutions. The methodology is developed by considering literature extracted from Scopus, Web of Science, and Aerospace Research Central and adding reports written by companies and government organizations. This describes the state-of-the-art of MaR until the year 2023 in the 3 Sub-Regions: North America, Central America, and South America, having achieved important results related to the academy, industry, government, and entrepreneurship; thus, the statistics shown in this manuscript are unique. Also, this article explores the potential for further work and advantages described by robotic companies such as ABB, KUKA, and Mecademic and the use of the Robot Operating System (ROS) in order to promote research, development, and innovation. In addition, the integration with industry 4.0 and digital manufacturing, architecture and construction, aerospace, smart agriculture, artificial intelligence, and computational social science (human-robot interaction) is analyzed to show the promising features of these growing tech areas, considering the improvements to increase production, manufacturing, and education in the Region. Finally, regarding the information presented, Latin America is considered an important location for investments to increase production and product development, taking into account the further proposal for the creation of the LATAM Consortium for Advanced Robotics and Mechatronics, which could support and work on roboethics and education/R+D+I law and regulations in the Region. Doi: 10.28991/ESJ-2023-07-04-025 Full Text: PD

Methylmercury exposure in a subsistence fishing community in Lake Chapala, Mexico: an ecological approach

<p>Abstract</p> <p>Background</p> <p>Elevated concentrations of mercury have been documented in fish in Lake Chapala in central Mexico, an area that is home to a large subsistence fishing community. However, neither the extent of human mercury exposure nor its sources and routes have been elucidated.</p> <p>Methods</p> <p>Total mercury concentrations were measured in samples of fish from Lake Chapala; in sections of sediment cores from the delta of Rio Lerma, the major tributary to the lake; and in a series of suspended-particle samples collected at sites from the mouth of the Lerma to mid-Lake. A cross-sectional survey of 92 women ranging in age from 18-45 years was conducted in three communities along the Lake to investigate the relationship between fish consumption and hair mercury concentrations among women of child-bearing age.</p> <p>Results</p> <p>Highest concentrations of mercury in fish samples were found in carp (mean 0.87 ppm). Sediment data suggest a pattern of moderate ongoing contamination. Analyses of particles filtered from the water column showed highest concentrations of mercury near the mouth of the Lerma. In the human study, 27.2% of women had >1 ppm hair mercury. On multivariable analysis, carp consumption and consumption of fish purchased or captured from Lake Chapala were both associated with significantly higher mean hair mercury concentrations.</p> <p>Conclusions</p> <p>Our preliminary data indicate that, despite a moderate level of contamination in recent sediments and suspended particulate matter, carp in Lake Chapala contain mercury concentrations of concern for local fish consumers. Consumption of carp appears to contribute significantly to body burden in this population. Further studies of the consequences of prenatal exposure for child neurodevelopment are being initiated.</p

Association between solar insolation and a history of suicide attempts in bipolar I disorder

In many international studies, rates of completed suicide and suicide attempts have a seasonal pattern that peaks in spring or summer. This exploratory study investigated the association between solar insolation and a history of suicide attempt in patients with bipolar I disorder. Solar insolation is the amount of electromagnetic energy from the Sun striking a surface area on Earth. Data were collected previously from 5536 patients with bipolar I disorder at 50 collection sites in 32 countries at a wide range of latitudes in both hemispheres. Suicide related data were available for 3365 patients from 310 onset locations in 51 countries. 1047 (31.1%) had a history of suicide attempt. There was a significant inverse association between a history of suicide attempt and the ratio of mean winter solar insolation/mean summer solar insolation. This ratio is smallest near the poles where the winter insolation is very small compared to the summer insolation. This ratio is largest near the equator where there is relatively little variation in the insolation over the year. Other variables in the model that were positively associated with suicide attempt were being female, a history of alcohol or substance abuse, and being in a younger birth cohort. Living in a country with a state-sponsored religion decreased the association. (All estimated coefficients p <0.01). In summary, living in locations with large changes in solar insolation between winter and summer may be associated with increased suicide attempts in patients with bipolar disorder. Further investigation of the impacts of solar insolation on the course of bipolar disorder is needed.Peer reviewe

Variations in seasonal solar insolation are associated with a history of suicide attempts in bipolar I disorder

Background: Bipolar disorder is associated with circadian disruption and a high risk of suicidal behavior. In a previous exploratory study of patients with bipolar I disorder, we found that a history of suicide attempts was associated with differences between winter and summer levels of solar insolation. The purpose of this study was to confirm this finding using international data from 42% more collection sites and 25% more countries. Methods: Data analyzed were from 71 prior and new collection sites in 40 countries at a wide range of latitudes. The analysis included 4876 patients with bipolar I disorder, 45% more data than previously analyzed. Of the patients, 1496 (30.7%) had a history of suicide attempt. Solar insolation data, the amount of the sun’s electromagnetic energy striking the surface of the earth, was obtained for each onset location (479 locations in 64 countries). Results: This analysis confirmed the results of the exploratory study with the same best model and slightly better statistical significance. There was a significant inverse association between a history of suicide attempts and the ratio of mean winter insolation to mean summer insolation (mean winter insolation/mean summer insolation). This ratio is largest near the equator which has little change in solar insolation over the year, and smallest near the poles where the winter insolation is very small compared to the summer insolation. Other variables in the model associated with an increased risk of suicide attempts were a history of alcohol or substance abuse, female gender, and younger birth cohort. The winter/summer insolation ratio was also replaced with the ratio of minimum mean monthly insolation to the maximum mean monthly insolation to accommodate insolation patterns in the tropics, and nearly identical results were found. All estimated coefficients were significant at p &lt; 0.01. Conclusion: A large change in solar insolation, both between winter and summer and between the minimum and maximum monthly values, may increase the risk of suicide attempts in bipolar I disorder. With frequent circadian rhythm dysfunction and suicidal behavior in bipolar disorder, greater understanding of the optimal roles of daylight and electric lighting in circadian entrainment is needed

Deciphering the association networks of mycobiome communities among the elderly Danes

Changes of microbial communities have been linked to frailty in elderly, yet the presence of fungal communities and their associations are little understood. This study attemps to identify biologically meaningful gut microbial fungal associations during aging. Faecal samples of 100 Danes of 65 years or older were collected, and sequenced by high-throughput tag-encoded sequencing of ITS2 gene fragments. The sequences were analysed using QIIME and CoNet to characterise fungal communities, and generate association networks, respectively. HbA1c, identified as the principal node, was grouped into 3 clusters based on glycated glucose levels. The clusters correspond to the phyla Ascomycota, Basidiomycota and Zygomycota, with the genera Penicillium, Candida, and Aspergillus being particularly abundant within each cluster. Interestingly, Bray-Curtis dissimilarity matrices showed significant (P<0.05) variation between clusters. These findings suggest that the presences of specific gut mycobiome members are associated with glycemic behaviours among the healthy individuals of the elderly Danish population

Deciphering the association networks of mycobiome communities among the elderly Danes

Changes of microbial communities have been linked to frailty in elderly, yet the presence of fungal communities and their associations are little understood. This study attemps to identify biologically meaningful gut microbial fungal associations during aging. Faecal samples of 100 Danes of 65 years or older were collected, and sequenced by high-throughput tag-encoded sequencing of ITS2 gene fragments. The sequences were analysed using QIIME and CoNet to characterise fungal communities, and generate association networks, respectively. HbA1c, identified as the principal node, was grouped into 3 clusters based on glycated glucose levels. The clusters correspond to the phyla Ascomycota, Basidiomycota and Zygomycota, with the genera Penicillium, Candida, and Aspergillus being particularly abundant within each cluster. Interestingly, Bray-Curtis dissimilarity matrices showed significant (P<0.05) variation between clusters. These findings suggest that the presences of specific gut mycobiome members are associated with glycemic behaviours among the healthy individuals of the elderly Danish population