Effects of glucose and lactate on <em>Streptococcus </em><em>mutans </em>abundance in a novel multispecies oral biofilm model

The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions. 38376204</strong

Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

The SynBioHub repository (synbiohub.org) is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g. the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation. SynBioHub also provides a central reference point for other resources to link to, delivering design information in a standardized format using the Synthetic Biology Open Language (SBOL). The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs

Assessing the potential application of bacteria-based self-healing cementitious materials for enhancing durability of wastewater treatment infrastructure

Wastewater treatment plants (WWTPs) around the world are mainly built using concrete. The continuous exposure to wastewater affects the durability of concrete structures and requires costly maintenance or replacement. Concrete production and repair represents ∼8% of the global anthropogenic CO2 emissions due to the use of cement, thus contributing to climate change. Developing a more sustainable cementitious material is therefore required for this vital health infrastructure. In this study, the feasibility of using bacteria-based self-healing (BBSH) cementitious materials for WWTPs is assessed by exposing BBSH mortar prisms to a continuous municipal wastewater flow and comparing their self-healing capacity to equivalent mortar prisms exposed to tap water. Microscopy imaging, water-flow tests and micro-CT analyses were performed to evaluate the self-healing efficiency of the mortar prisms, while SEM-EDX and Raman spectroscopy were used to characterise the healing products. Our work represents the first systematic study of the healing potential of BBSH in mortar exposed to wastewater. The results indicate that the purposely added bacteria are able to induce calcium carbonate precipitation when exposed to wastewater conditions. Moreover, if additional sources of calcium and carbon are embedded within the cement matrix, the rich bacterial community inherently present in the wastewater is capable of inducing calcium carbonate precipitation, even if no bacteria are purposely added to the mortar. The results of this study offer promising avenues for the construction of more sustainable wastewater infrastructure, with the potential of significantly reducing costs and simplifying the production process of BBSH concretes for this specific application

Lymphopenia: A predictive marker of disease severity in COVID-19 infection

Background. With the latest COVID-19 deaths reported to WHO now exceeding 3.3 million, COVID-19 has developed into a milestone of our medical generation, causing disruption in communities and hospital services. With complications raging from respiratory failure to inflammatory complication and even thrombotic events, we wanted to establish if lymphopenia is a predictive marker of disease severity in patients infected with SARS-CoV-2. Material and methods. 152 patients were included from 4 different departments of Colentina Clinical Hospital in this retrospective observational study beginning with July 2020 to March 2021. All of these patients were confirmed with COVID-19 by real-time reverse transcriptase polymerase chain reaction test for nasal and pharyngeal swab samples. As including criteria we have set the patients hospitalized confirmed with COVID-19, with at least 10 days of hospitalization. The data in demographic, basic clinical and laboratory characteristics and particular evolution was obtained from electronical medical records from each department involved in the study, by maintaining personal data confidentially. We set up criteria for lymphopenia as absolute lymphocyte count below 1.5 x 1000/µl, based on the laboratory reference values. The study group was divided into several groups: male and female, ICU (Intensive Care Unit) and non-ICU, deceased and released, lymphopenia at day 1 (day of admission to hospital) , lymphopenia at day 10 (10 days after hospital admission). Results. The age of the patients ranged from 17 to 92, with the median age of 57.62. Enrolled were 73 (47.4%) female patients and 79 (52.6%) male patients, with an ICU admission rate of 35.71% (55 patients), and a mortality rate of 21.43% (33 patients). Patients who have a severe form of COVID-19 and are admitted to the ICU for mechanical ventilation did not recover and died (p < 0.001). Male patients may have higher risk of requiring admission in ICU (p value = 0.357) and higher risk of death (p value = 0.241). Even in our small group of 152 patients, the elderly patients suffered a more severe form of the disease, which was reflected on the number of admission days (p = 0.07). In our specific population, based on the statistics, if we take the number of lymphocytes on the day of admission as the dependent factor, we can safely say that there is a statistically significant correlation between lymphopenia at day 1 and the ICU admission (p < 0.001) or death (p = 0.014). The number of lymphocytes following 10 days of admission is another prognostic marker as we can see from the results of statistic tests: there is a statistically significant correlation between lymphopenia at day 10 and the ICU admission (p < 0.001) or death (p < 0.001). Age is another predictive factor regarding the number of lymphocytes following 10 days of admission (r = -0.078 and p = 0.356). Conclusion. Lymphopenia is an easy-to-determine, efficient and reliable biomarker to establish the disease evolution in patients with COVID-19

Advancements in bacteria based self-healing concrete and the promise of modelling

In the last two decades self-healing of concrete through microbial based carbonate precipitation has emerged as a promising technology for making concrete structures more resilient and sustainable. Currently, progress in the field is achieved mainly through physical experiments, but their duration and cost are barriers to innovation and keep the number of large scale applications still very limited. Modelling and simulation of the phenomena underlying microbial based healing of concrete may provide a key to complement the experimental efforts, but their development is still in its infancy. In this review, we briefly present the field, introduce some key aspects emerged from the experiments, present the main ongoing developments in modelling and simulation of mineral and microbial systems, and discuss how their synergy may be accomplished to speed up progress in the near future

Spatial scaling of forest soil microbial communities across a temperature gradient.

Temperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa-area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental-scale description of temperature-dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama. Our results revealed that spatial scaling rates (z-values) of microbial communities varied with both taxonomic resolutions and phylogenetic groups. Additionally, microbial TAR z-values increased with temperature (r = 0.739, P &lt; 0.05), but were not correlated with other environmental variables tested (P &gt; 0.05), indicating that microbial spatial scaling rate is temperature-dependent. Understanding how temperature affects the spatial scaling of microbial biodiversity is of fundamental importance for preservation of soil biodiversity and management of ecosystems

In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in Spermine Synthase

Spermine synthase (SMS) is a key enzyme controlling the concentration of spermidine and spermine in the cell. The importance of SMS is manifested by the fact that single missense mutations were found to cause Snyder-Robinson Syndrome (SRS). At the same time, currently there are no non-synonymous single nucleoside polymorphisms, nsSNPs (harmless mutations), found in SMS, which may imply that the SMS does not tolerate amino acid substitutions, i.e. is not mutable.To investigate the mutability of the SMS, we carried out in silico analysis and in vitro experiments of the effects of amino acid substitutions at the missense mutation sites (G56, V132 and I150) that have been shown to cause SRS. Our investigation showed that the mutation sites have different degree of mutability depending on their structural micro-environment and involvement in the function and structural integrity of the SMS. It was found that the I150 site does not tolerate any mutation, while V132, despite its key position at the interface of SMS dimer, is quite mutable. The G56 site is in the middle of the spectra, but still quite sensitive to charge residue replacement.The performed analysis showed that mutability depends on the detail of the structural and functional factors and cannot be predicted based on conservation of wild type properties alone. Also, harmless nsSNPs can be expected to occur even at sites at which missense mutations were found to cause diseases

Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert

The Namib Dessert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East–West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East– West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68–97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert.Web of Scienc