Water is a preservative of microbes

Quantifying fecal and plasma short-chain fatty acids in healthy Thai individuals

Short-chain fatty acids (SCFAs) are involved in important physiological processes such as gut health and immune response, and changes in SCFA levels can be indicative of disease. Despite the importance of SCFAs in human health and disease, reference values for fecal and plasma SCFA concentrations in healthy individuals are scarce. To address this gap in current knowledge, we developed a simple and reliable derivatization-free GC-TOFMS method for quantifying fecal and plasma SCFAs in healthy individuals. We targeted six linear- and seven branched-SCFAs, obtaining method recoveries of 73-88% and 83-134% in fecal and plasma matrices, respectively. The developed methods are simpler, faster, and more sensitive than previously published methods and are well suited for large-scale studies. Analysis of samples from 157 medically confirmed healthy individuals showed that the total SCFAs in the feces and plasma were 34.1 ± 15.3 µmol/g and 60.0 ± 45.9 µM, respectively. In fecal samples, acetic acid (Ace), propionic acid (Pro), and butanoic acid (But) were all significant, collectively accounting for 89% of the total SCFAs, whereas the only major SCFA in plasma samples was Ace, constituting of 93% of the total plasma SCFAs. There were no statistically significant differences in the total fecal and plasma SCFA concentrations between sexes or among age groups. The data revealed, however, a positive correlation for several nutrients, such as carbohydrate, fat, iron from vegetables, and water, to most of the targeted SCFAs. This is the first large-scale study to report SCFA reference intervals in the plasma and feces of healthy individuals, and thereby delivers valuable data for microbiome, metabolomics, and biomarker research.

The Biologically Active Biopolymer Silk: The Antibacterial Effects of Solubilized Bombyx mori Silk Fibroin with Common Wound Pathogens

Antibacterial properties are desirable in wound dressings. Silks, among many material formats, have been investigated for use in wound care. However, the antibacterial properties of liquid silk are poorly understood. The aim of this study is to investigate the inherent antibacterial properties of a Bombyx mori silk fibroin solution. Silk fibroin solutions containing ≥ 4% w/v silk fibroin do not support the growth of two common wound pathogens, Staphylococcus aureus and Pseudomonas aeruginosa. When liquid silk is added to a wound pad and placed on inoculated culture plates mimicking wound fluid, silk is bacteriostatic. Viability tests of the bacterial cells in the presence of liquid silk show that cells remain intact within the silk but could not be cultured. Liquid silk appears to provide a hostile environment for S. aureus and P. aeruginosa and inhibits growth without disrupting the cell membrane. This effect can be beneficial for wound healing and supports future healthcare applications for silk. This observation also indicates that liquid silk stored prior to processing is unlikely to experience microbial spoilage.

A Novel Comprehensive Therapeutic Approach to the Challenges of Chronic Wounds: A Brief Review and Clinical Experience Report

Following the clinical perspective and concept that a healthy body will not develop chronic wounds, the central approach for the treatment described here is based on an understanding of how the body transforms the wound microenvironment from a non-healing to a healing state. As part of a comprehensive treatment regimen that includes OCM™ (complete matrix), wound preparation, and skin protectant formulations, the OCM contains components for complete wound healing by attending to the individual needs required to promote the closure of each unique chronic wound. During application of the comprehensive treatment regimen in independent investigator-led trials, the total wound percentage average reduction over the first 4 weeks of treatment was 60% across multiple wound types; median time to total wound closure was 6.9 weeks. Safety testing of the OCM formulation shows no potential allergenicity, no potential sensitization, and no known product-related adverse events. Clinical trials evaluating the OCM formulation as part of the comprehensive treatment regimen of multiple wound types are underway. Results of clinical trials and real-world experiences will expand current knowledge of the wound-healing potential of this novel product.

Ecology theory disentangles microbial dichotomies

Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.

Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars

Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.

Extremely chaotolerant and kosmotolerant Aspergillus atacamensis - a metabolically versatile fungus suitable for recalcitrant biosolid treatment

Obligate halophily is extremely rare in fungi. Nevertheless, Aspergillus atacamensis (strain EXF-6660), isolated from a salt water-exposed cave in the Coastal Range hills of the hyperarid Atacama Desert in Chile, is an obligate halophile, with a broad optimum range from 1.5 to 3.4 M of NaCl. When we tested its ability to grow at varied concentrations of both kosmotropic (NaCl, KCl, and sorbitol) and chaotropic (MgCl2, LiCl, CaCl2, and glycerol) solutes, stereoscopy and laser scanning microscopy revealed the formation of phialides and conidia. A. atacamensis EXF-6660 grew up to saturating levels of NaCl and at 2.0 M concentration of the chaotropic salt MgCl2. Our findings confirmed that A. atacamensis is an obligate halophile that can grow at substantially higher MgCl2 concentrations than 1.26 M, previously considered as the maximum limit supporting prokaryotic life. To assess the fungus' metabolic versatility, we used the phenotype microarray technology Biolog FF MicroPlates. In the presence of 2.0 M NaCl concentration, strain EXF-6660 metabolism was highly versatile. A vast repertoire of organic molecules (~95% of the substrates present in Biolog FF MicroPlates) was metabolized when supplied as sole carbon sources, including numerous polycyclic aromatic hydrocarbons, benzene derivatives, dyes, and several carbohydrates. Finally, the biotechnological potential of A. atacamensis for xenobiotic degradation and biosolid treatment was investigated. Interestingly, it could remove biphenyls, diphenyl ethers, different pharmaceuticals, phenols, and polyaromatic hydrocarbons. Our combined findings show that A. atacamensis EXF-6660 is a highly chaotolerant, kosmotolerant, and xerotolerant fungus, potentially useful for xenobiotic and biosolid treatments.

The Pareto principle: To what extent does it apply to resource acquisition in stable microbial communities and thereby steer their geno-/ecotype compositions and interactions between their members?

The Pareto principle, or 20:80 rule, describes resource distribution in stable communities whereby 20% of community members acquire 80% of a key resource. In this Burning Question, we ask to what extent the Pareto principle applies to the acquisition of limiting resources in stable microbial communities; how it may contribute to our understanding of microbial interactions, microbial community exploration of evolutionary space, and microbial community dysbiosis; and whether it can serve as a benchmark of microbial community stability and functional optimality?

Scientific novelty beyond the experiment

Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

Preparation and Application of Directed Vat Set Indigenous Freeze-Drying Lentilactobacillus hilgardii Q19 Starter in Winemaking

In order to prepare a better direct vat set for malolactic fermentation (MLF) in high ethanol and low pH wines, the high-ethanol- and low-temperature-tolerant strain Lentilactobacillus hilgardii Q19, which was isolated from the eastern foothill of the Helan Mountain wine region in China, was used to prepare a direct vat set by vacuum freeze-drying. A superior freeze-dried lyoprotectant was obtained to create the starting culture by selecting, combining, and optimizing numerous lyoprotectants with higher protection for Q19 by using a single-factor experiment and response surface approach. Finally, the Lentilactobacillus hilgardii Q19 direct vat set was inoculated in Cabernet Sauvignon wine to carry out MLF on a pilot scale, with commercial starter culture Oeno1 as control. The volatile compounds, biogenic amines, and ethyl carbamate content were analyzed. The results showed that a combination of 8.5 g/100 mL skimmed milk powder, 14.5 g/100 mL yeast extract powder, and 6.0 g/100 mL sodium hydrogen glutamate offered better protection; with this lyoprotectant, there were (4.36 ± 0.34) × 10¹¹ CFU/g cells after freeze-drying, and it showed an excellent ability to degrade L-malic acid and could successfully finish MLF. In addition, in terms of aroma and wine safety, compared with Oeno1, the quantity and complexity of volatile compounds were increased after MLF, and biogenic amines and ethyl carbamate were produced less during MLF. We conclude that the Lentilactobacillus hilgardii Q19 direct vat set could be applied as a new MLF starter culture in high-ethanol wines.

Silicon nanoparticles: A promising approach for control of Pseudomonas aeruginosa biofilms

Objectives

The current study aimed to investigate the control and treatment of biofilm-producing isolates of Pseudomonas aeruginosa using silicon nanoparticles (SiNPs).

Materials and Methods

Biofilm-producing isolates of P. aeruginosa were recovered from various food samples and identified through fluorescent green colony formation on selective and differential media, as well as the amplification of oprI and oprL genes. Tube methods, Congo-red agar method, and scanning electron microscopy (SEM) were used to study biofilm phenotypes. The effect of SiNPs was evaluated by broth dilution assay.

Results

The biofilm assay revealed that these isolates formed biofilms on glass surfaces within 72 hr of incubation. Scanning electron micrographs showed that the biofilm communities were composed of multicellular clusters of P. aeruginosa encased in matrix material. However, these isolates were unable to form biofilms on SiNPs-coated surfaces. The results showed that the planktonic isolates of P. aeruginosa were comparatively sensitive to the antibacterial properties of SiNPs, with minimum inhibitory concentration (MIC) ranging from 100 to 200 µg/ml. Contrarily, the biofilms were found to be 500 times more tolerant to the highest concentration of SiNPs (MIC of 500 µg/ml) and were more resistant. Under static conditions, the sedimentation of SiNPs resulted in their ineffectiveness. However, under shaking conditions, the biofilms were effectively dispersed and the cells were lysed. The results showed that SiNPs were effective against both the planktonic and the metabolically inactive forms of P. aeruginosa.

Conclusion

This study suggests that SiNPs could be a useful tool for preventing the formation of biofilms and removing pre-existing biofilms.

Biophysical Manipulation of the Extracellular Environment by Eurotium halophilicum

Eurotium halophilicum is psychrotolerant, halophilic, and one of the most-extreme xerophiles in Earth's biosphere. We already know that this ascomycete grows close to 0 °C, at high NaCl, and-under some conditions-down to 0.651 water-activity. However, there is a paucity of information about how it achieves this extreme stress tolerance given the dynamic water regimes of the surface habitats on which it commonly occurs. Here, against the backdrop of global climate change, we investigated the biophysical interactions of E. halophilicum with its extracellular environment using samples taken from the surfaces of library books. The specific aims were to examine its morphology and extracellular environment (using scanning electron microscopy for visualisation and energy-dispersive X-ray spectrometry to identify chemical elements) and investigate interactions with water, ions, and minerals (including analyses of temperature and relative humidity conditions and determinations of salt deliquescence and water activity of extracellular brine). We observed crystals identified as eugsterite (Na₄Ca(SO₄)₃·2H₂O) and mirabilite (Na₂SO₄·10H₂O) embedded within extracellular polymeric substances and provide evidence that E. halophilicum uses salt deliquescence to maintain conditions consistent with its water-activity window for growth. In addition, it utilizes a covering of hair-like microfilaments that likely absorb water and maintain a layer of humid air adjacent to the hyphae. We believe that, along with compatible solutes used for osmotic adjustment, these adaptations allow the fungus to maintain hydration in both space and time. We discuss these findings in relation to the conservation of books and other artifacts within the built environment, spoilage of foods and feeds, the ecology of E. halophilicum in natural habitats, and the current episode of climate change.

The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network

Most microbes reside in oligotrophic environments for extended periods of time, requiring survival strategies that maintain proliferative capacity. We demonstrate that the non-spore-forming Lactococcus lactis KF147 progressively activates the expression of stress-associated functions in response to the declining growth rate elicited by prolonged retentostat cultivation, which coincides with up to 10⁴ -fold increased stress tolerance. Our findings provide a quantified view of the transcription and stress-tolerance adaptations underlying the growth-survival trade-off in L. lactis, and exemplify the hard-wiring of this trade-off in the lactococcal gene regulation network.

The darkest microbiome-a post-human biosphere

Microbial technology is exceptional among human activities and endeavours in its range of applications that benefit humanity, even exceeding those of chemistry. What is more, microbial technologists are among the most creative scientists, and the scope of the field continuously expands as new ideas and applications emerge. Notwithstanding this diversity of applications, given the dire predictions for the fate of the surface biosphere as a result of current trajectories of global warming, the future of microbial biotechnology research must have a single purpose, namely to help secure the future of life on Earth. Everything else will, by comparison, be irrelevant. Crucially, microbes themselves play pivotal roles in climate (Cavicchioli et al., Nature Revs Microbiol 17: 569-586, 2019). To enable realization of their full potential in humanity's effort to survive, development of new and transformative global warming-relevant technologies must become the lynchpin of microbial biotechnology research and development. As a consequence, microbial biotechnologists must consider constraining their usual degree of freedom, and re-orienting their focus towards planetary-biosphere exigences. And they must actively seek alliances and synergies with others to get the job done as fast as humanly possible; they need to enthusiastically embrace and join the global effort, subordinating where necessary individual aspirations to the common good (the amazing speed with which new COVID-19 diagnostics and vaccines were developed and implemented demonstrates what is possible given creativity, singleness of purpose and funding). In terms of priorities, some will be obvious, others less so, with some only becoming revealed after dedicated effort yields new insights/opens new vistas. We therefore refrain from developing a priority list here. Rather, we consider what is likely to happen to the Earth's biosphere if we (and the rest of humanity) fail to rescue it. We do so with the aim of galvanizing the formulation and implementation of strategic and financial science policy decisions that will maximally stimulate the development of relevant new microbial technologies, and maximally exploit available technologies, to repair existing environmental damage and mitigate against future deterioration.