Subject: Life Sciences, Microbiology Keywords: compounds; microbiology; extract
Online: 22 April 2020 (06:09:21 CEST)
The current study aims to fermentation parameter for producing microbial products. Microwave parameters consist on 245 MHz, and 600-watt for 60 seconds. Ethyl acetate was the best solvent used for extraction purposes. Antioxidant properties were differentiated by blocking the oxidation of the linoleic acid with an inhibition rate of 73.13% at a concentration of 200 mg/mL, in addition to increasing its effectiveness for free radical extraction and reduction strength by increasing concentrations gradually. The bond ability to irons was lower compared to the EDTA-2Na, in addition to the obtained total content corresponding to phenolic compounds in the ethyl acetate extract of fermented rice (Koji) by A. flavus was 232.11 mg, on the basis of galic acid/mg. The stability of the antioxidant compounds of the ethyl acetate extract of fermented rice (Koji) by A. flavus was also studied; showing stability under neutral conditions, as well as at high temperatures (185 °C during two hours). However, no stability was obtained under acidic and alkaline conditions.
REVIEW | doi:10.20944/preprints202211.0259.v1
Subject: Life Sciences, Microbiology Keywords: Microbiology; fashion; design; education; biotechnology
Online: 14 November 2022 (11:24:04 CET)
Fashion industry is the second most polluting industry in the world representing a 2 trillion dollars and growing valuation (Pal, 2017). This dual context makes its challenges hard to address. From one side, fashion design education and practice systems have been perpetuating an industrial-focused approach which relies mostly in the economic improvement through fast cycles of product development (Pal, 2017). On the other side, fashion industry has also been closed to either multidisciplinary and transdisciplinary initiatives outside the scope of the artistic disciplines. Therefore, innovative approaches are needed to solve fashion industrial challenges. One of the most promising fields to tackle fashion current environment and technological problems is microbiology (Mazzoto et al., 2021). During the past 50 years, microbiology has played a vital role in solving human grand challenges in health, agriculture, food, and waste management sectors, and it also represents an opportunity for fashion industry as well. Microbiology biotechnological potential for the fashion industry relies mostly on the improvement of toxic waste bioremediation and the development of novel biomaterials and biomolecules. Moreover, the emergent field of synthetic biology is expanding the tools and approaches available, and they can already be seen in the development of engineered living materials that have functional properties (Mazzoto et al., 2021). Despite the urgent need for change, there is still a long way until a more sustainable fashion industry is achieved. Therefore, microbiological research and innovation need maturation to be able to scale-up and reach a global impact for tackling fashion industrial problems.
REVIEW | doi:10.20944/preprints201810.0328.v1
Subject: Life Sciences, Microbiology Keywords: Bifidobacterium breve; probiotics; pediatrics; therapeutic microbiology
Online: 15 October 2018 (17:03:26 CEST)
The human intestinal microbiota, establishing a symbiotic relationship with the host, plays a significant role for the human health. It is also well known that a disease status is frequently characterized by a dysbiotic condition of the gut. A probiotic treatment can represent an alternative therapy for enteric disorders and human pathologies not apparently linked to the gut environment. Among bifidobacteria, strains of the species Bifidobacterium breve are widely used in pediatrics. B. breve is the dominant species in the gut of breast-fed infants and it has also been isolated from human milk. It has antimicrobial activity against human pathogens, it does not possess transmissible antibiotic resistance traits, it is not cytotoxic and it has immuno-stimulating abilities. This review describes the applications of B. breve strains mainly for the prevention/treatment of pediatric pathologies. The target pathologies range from widespread gut diseases, including diarrhea and infant colics, to celiac disease, obesity, allergic and neurological disorders. Moreover, B. breve strains are used for the prevention of side infections in pre-term newborns and during antibiotic treatments or chemotherapy. With this documentation, we hope to increase knowledge on this species to boost the interest in the emerging discipline known as “therapeutic microbiology”.
ARTICLE | doi:10.20944/preprints202204.0114.v1
Subject: Life Sciences, Microbiology Keywords: Cystic Fibrosis; elexacaftor-tezacaftor-ivacaftor; microbiology; airway colonization
Online: 13 April 2022 (04:06:36 CEST)
The use of modulator drugs that target the cystic fibrosis transmembrane conductance regulator (CFTR) is the final frontier in the treatment of Cystic Fibrosis (CF), a genetic multiorgan disease. F508del is the most common mutation causing defective formation and function of CFTR. Elexacaftor-tezacaftor-ivacaftor is the first triple combination of CFTR modulators. Herein we report on a one-year case-control study that involved 26 patients with at least one F508del mutation. Patients were assigned to two similar groups, with patients with the worse clinical condition receiving treatment with the triple combination therapy. The study aims to define the clinical and especially microbiological implications of treatment administration. The treatment provided significant clinical benefits in terms of respiratory, pancreatic and sweat function. After one year of therapy, airway infection rates decreased and pulmonary exacerbations were dramatically reduced. Finally, treated patients reported a surprising improvement in their quality of life. The use of triple combination therapy has become essential in most CF people carrying the F508del mutation. While the clinical and instrumental benefits of treatment are thoroughly known, further investigations are needed to properly define its microbiological respiratory implications and establish the real advantage of life-long treatment with elexacaftor-tezacaftor-ivacaftor.
ARTICLE | doi:10.20944/preprints202104.0453.v1
Subject: Life Sciences, Biochemistry Keywords: high-pressure microbiology; deep biosphere; cultivation devices; decompression
Online: 17 April 2021 (08:46:55 CEST)
High temperatures (HT) and high hydrostatic pressures (HHP) are characteristic of deep-sea hydrothermal vents and other deep crustal settings. These environments host vast and diverse microbial populations, yet only a small fraction of those populations have been successfully cultured. This is due, in part, to the difficulty of sampling while maintaining these in situ conditions and also replicating those high-temperature and high-pressure conditions in the laboratory. In an effort to facilitate more HT-HHP cultivation, we present two HT-HHP batch culture incubation systems for cultivating deep-sea vent and subsurface (hyper)thermophilic microorganisms. One HT-HHP system can be used for batch cultivation up to 110 MPa and 121°C, and requires sample decompression during subsampling. The second HT-HHP system can be used to culture microorganisms up to 100 MPa and 160°C with variable-volume, pressure-retaining vessels that negate whole-sample decompression during subsampling. Here, we describe how to build cost effective heating systems for these two types of high-pressure vessels, as well as the protocols for HT-HHP microbial batch cultivation in both systems. Additionally, we demonstrate HHP transfer between the variable-volume vessels, which has utility in sampling and enrichment without decompression, laboratory isolation experiments, as well as HHP filtration.
ARTICLE | doi:10.20944/preprints202101.0051.v1
Subject: Keywords: water microbiology; ecotoxicology; Danube; wastewater; ichthyofauna; pollution indicators
Online: 4 January 2021 (15:00:04 CET)
Water and water habitats are essential to life and to the wellness of the communities that rely on them, as the Danube river is subject to human impact and vice versa, periodic surveys are required to determine the status of its pollution levels. In this work we used known microbiological indicators as well as physico-chemical ones to assess the ecotoxicological status of the Danube river from eleven locations partially forming the “Romanian–Bulgarian Danube Sector”. Most of the microbial communities found, and their densities, could be explained by point and diffuse sources scattered along the sector such as discharged household and farm wastewater, as well as nearby agricultural areas where fertilizers have been used and then leaked in the water stream during rainfalls. However, microbial data on non-point sources that lead to diffuse pollution of surface waters could be linked to such parameters and furthermore shown a slight correlation with the current status of fish communities.
ARTICLE | doi:10.20944/preprints201904.0161.v2
Subject: Life Sciences, Other Keywords: antimicrobial resistance; horizontal gene transfer; mathematical modelling; epidemiology; microbiology
Online: 6 May 2019 (10:59:05 CEST)
Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR, however its application to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies which focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria, and utilized our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture, and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap on the dynamics of transformation and transduction, and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.
REVIEW | doi:10.20944/preprints201810.0760.v1
Subject: Medicine & Pharmacology, Other Keywords: Multiplex serology, serosurveillance, vaccine monitoring, emerging diseases, clinical microbiology
Online: 1 November 2018 (18:02:59 CET)
High throughput multiplex serological systems enable the small developer to set up tests at small cost, for microbes for which there are no commercial tests, and for aspects which have not been addressed by them. An example is testing for Zika and Tick Borne Encephalitis virus antibodies, where antigenic cross-reactions make diagnosis problematic. Our technique variant, Suspension Multiplex Immunoassay (SMIA) allows many samples to be tested for antibodies to many antigens in a short time. Computational compensation for cross-reactions is possible if a SMIA panel contains most of the potentially cross-reacting antigens. Using antibody avidity and pattern of reactivity to whole virus and nonstructural protein, antibodies due to vaccination and infection, respectively, as well as probable degree of protection, can be determined with high throughput. These multiplex techniques hold great promise for future diagnostic development. Theoretically, even large scale serological monitoring, like blood donor pathogen testing, could be done inexpensively and rationally with multiplex serology developed in house. However, the quality control demands are steep and in most cases out of scope for a single laboratory. There remain however a number of clinical applications where in house multiplex serology can be performed with adequate quality control under high throughput conditions.
ARTICLE | doi:10.20944/preprints201802.0090.v1
Subject: Life Sciences, Microbiology Keywords: antibiotics; geomicrobiology; Illumina sequencing; microbiome diversity; Streptomyces; Cave microbiology
Online: 12 February 2018 (16:30:42 CET)
Moonmilk are cave carbonate deposits that host a rich microbiome including antibiotic-producing Actinobacteria making these speleothems appealing for bioprospecting. Here we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave “Grotte des Collemboles” via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9 to 23% of the total bacterial population. Next to actinobacterial OTUs attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of OTUs unlinked to the culturable Streptomyces strains previously isolated from the same deposits. 43% of OTUs were shared between the three studied collection points while 34% were exclusive to one deposit indicating that distinct speleothems host their own population despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.
ARTICLE | doi:10.20944/preprints202106.0052.v1
Subject: Life Sciences, Biochemistry Keywords: antibiotics; conventional; microbiology; microfluidics; microscopy; mycobacterium smegmatis; population; single cell
Online: 2 June 2021 (08:32:03 CEST)
To reveal rare phenotypes in bacterial populations conventional microbiology tools should be advanced to generate rapid, quantitative, accurate and high-throughput data. The main drawbacks of widely used traditional methods for antibiotic studies include low sampling rate and averaging data for population measurements. To overcome these limitations microfluidic-microscopy systems have great promise to produce quantitative single-cell data with high sampling rates. Using Mycobacterium smegmatis cells we applied both conventional assays and a microfluidic-microscopy method to reveal antibiotic-tolerance mechanisms of wild type and the msm2570::Tnmutant cells. Our results revealed that the enhanced antibiotic tolerance mechanism of the msm2570::Tn mutant was due to the low number of lysed cells during the antibiotic exposure compared with wild-type cells. This is the first study that characterized the antibiotic-tolerance phenotype of the msm2570::Tn mutant that has a transposon insertion in the msm2570 gene encoding a putative xanthine/uracil permease, which enrolls in uptake of nitrogen compound during nitrogen limitation. The experimental results indicate that the msm2570::Tn mutant can be further interrogated to reveal antibiotic killing mechanisms, in particularly, antibiotics those targets cell wall integrity.
ARTICLE | doi:10.20944/preprints202104.0299.v1
Subject: Life Sciences, Biochemistry Keywords: ddPCR, droplet digital PCR, environmental samples, environmental DNA, soil microbiology
Online: 12 April 2021 (12:48:11 CEST)
Droplet digital polymerase chain reaction (ddPCR) is a method used to detect and quantify nu-cleic acids even when present in exceptionally low numbers. While it has proven to be valuable for clinical studies, it has failed to be widely adopted for environmental and applied studies. Due to the complexity of the chemical and biological composition of environmental samples, protocols tailored to clinical studies are not appropriate, and results are difficult to interpret. We used en-vironmental DNA samples originating from field studies to determine a protocol for environ-mental samples. Samples included field soils which had been inoculated with the soil fungus Rhizophagus irregularis (environmental positive control), field soils that had not been inoculat-ed and the targeted fungus was not naturally present (environmental negative control), and root samples from both field categories. To control for the effect of soil inhibitors, we also in-cluded DNA samples of an organismal control extracted from pure fungal spores (organismal positive control). Finally, we included a no-template control consisting only of the PCR reaction reagents and nuclease free water instead of template DNA. Using original data, we examined which factors contribute to poor resolution in root and soil samples and propose best practises to ensure accuracy and repeatability. Furthermore, we evaluated manual and automatic threshold determination methods and we propose a novel protocol based on multiple controls that is more appropriate for environmental samples.
ARTICLE | doi:10.20944/preprints202205.0070.v1
Subject: Life Sciences, Microbiology Keywords: phototrophic bacteria; phototrophic extracellular electron uptake; comparative genomics; transcriptomics; environmental microbiology
Online: 6 May 2022 (09:35:45 CEST)
Rhodovulum spp. are anoxygenic photosynthetic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). Recently, our group isolated 15 strains of R. sulfidophilum to observe this metabolism in marine phototrophs. Our group previously observed carbon dioxide fixation coupled to phototrophic iron oxidation (photoferrotrophy) and pEEU in AB26 and identified a novel di-heme c¬-type cytochrome EeuP important for pEEU but not photoferrotrophy. Taxonomic re-evaluation based on 16S and pufM phylogenetic analyses led us to re-classify two isolates, AB26 and AB19, as Rhodovulum visakhapatnamense. The AB26 genome consists of 4,380,746 base-pairs, including two plasmids, and encodes 4,296 predicted protein-coding genes. AB26 contains 22 histidine kinases, 20 response regulators, and dedicates ~16% of its genome to transport. Transcriptomic data under aerobic, photoheterotrophy, photoautotrophy, and pEEU reveals how gene expression varies between metabolisms. Lastly, we use transcriptomic data for a comparative genomic analysis of potential pEEU-relevant genes between all 15 isolates. With these data we identify potential pEEU capable phototrophs within these isolates, and likely molecular mechanisms of pEEU.
REVIEW | doi:10.20944/preprints202004.0172.v2
Subject: Life Sciences, Cell & Developmental Biology Keywords: Wolbachia; Drosophila; Symbiosis; Cellular microbiology; Cellular differentiation; Epigenetics; Transcription; Translation; Proteolysis
Online: 28 April 2020 (09:18:03 CEST)
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signalling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia’s diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
COMMUNICATION | doi:10.20944/preprints202007.0012.v1
Subject: Keywords: COVID-19; football; soccer; microbiology; microdroplets; saliva; SARS-CoV-2, sport; soccer; surfaces; transmission; viruses
Online: 3 July 2020 (05:13:30 CEST)
Safely resuming sporting events while the coronavirus is spreading is challenging – yet possible – if the science is taken into account. Two main ways the coronavirus can spread among football players is through air-suspended microdroplets (and possibly aerosols), and via contact with contaminated surfaces. Here we estimated virus survival in dried saliva droplets on a football pitch (i.e., on the grass) and on the ball itself, and compared these measures between mid-day and nighttime matches. We find, based on experiments with the enveloped phage Phi6 – a surrogate for SARS-Cov-2 – that while the virus survives reasonably well on both pitch and ball during a nighttime match (~10% survival), virtually no viruses survived the 90-minute duration of a mid-day match on a hot, sunny day. These results, taken together with studies reporting rapid deactivation of coronavirus in aerosols by sunlight, suggest that playing football in mid-day reduces the likelihood of transmission between players, and thus increases players’ safety.
ARTICLE | doi:10.20944/preprints202208.0026.v1
Subject: Biology, Plant Sciences Keywords: rhizosphere; phyllosphere; endophyte; plant microbiome; plant mycobiome; rare microbiome; fungi; bacteria; microbes; soil microbiology; inoculum; microbial ecology
Online: 1 August 2022 (15:22:30 CEST)
A plant’s health and productivity is influenced by its associated microbes. Although the common microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (eg. specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum, and pea. Plants were grown inside sealed jars on sterile sand or field soil. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon, however judging by read abundance, up to half of the mycobiome consists of uncommon fungal cells, while less than 11% of bacterial endophytes are rare. Uncommon seed transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes that most heavily colonized shoots, to a lesser extent roots and least of all rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon seed transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
ARTICLE | doi:10.20944/preprints202105.0042.v1
Subject: Life Sciences, Biophysics Keywords: viral particles; radiobiology; RNA detection; microbiology; matter identification; particle physics; physical modelling; particle accelerators in environmental studies
Online: 10 May 2021 (15:35:15 CEST)
This study presents a methodology to reveal traces of viral particles, as aerosol with known chemical and molecular structure, in a sample by means of photon and electron interactions. The method is based on Monte Carlo simulations and on the analysis of photon-electron fluxes-spectra through energy channels counts as a function of different aerosol viral concentrations in the air sample and looking at the peculiar photon/electron interactions with the potential abnormal atomic hydrogen (H), oxygen (O), carbon (C), and phosphorus (P) compositions present in the air sample as a function of living and nonliving matter with PO4 group RNA/DNA strands in a cluster configuration.
Subject: Life Sciences, Virology Keywords: anti-viral; COVID-19; SARS-CoV-2; autophagy; chloroquine; hydroxychloroquine; immunology; infection; inflammation; lysophagy; microbiology; Plaquenil; SARS; virophagy
Online: 23 May 2020 (10:45:40 CEST)
At a time when the world faces an emotional breakdown, crushing our dreams if not taking our lives, we realize that together we must fight the war against the COVID-19 outbreak even if almost the majority of the scientific community finds itself confined to home. Every day, like everyone else, we, scientists, listen to the latest news with its promises and announcements. Across the world, a surge of clinical trials trying to cure or slow down the coronavirus pandemic has been launched to bring hope instead of fear and despair. One first proposed clinical trial has drawn worldwide hype to the benefit of chloroquine (CQ), a well-known and broadly used anti-malarial drug, in the treatment of patients infected by the recently emerged deadly coronavirus (SARS-CoV-2). We should consider this information in the light of the long-standing anti-inflammatory and anti-viral properties of CQ-related drugs. Yet, none of the articles promoting the use of CQ in the current pandemic evoked a possible molecular or cellular mechanism of action that could account for any efficacy. Here, given the interaction of viruses with macroautophagy (hereafter referred to as autophagy), a CQ-sensitive anti-viral safeguard pathway, we would like to discuss the pros, but also the cons concerning the current therapeutic options targeting this process.