Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes.

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.

Photo-Mediated RAFT Step-Growth Polymerization With Diacrylate Monomers: Investigating Versatility and Oxygen Tolerance.

Photomediated reversible addition fragmentation chain transfer (RAFT) step-growth polymerization is performed using a trithiocarbonate-based chain transfer agent (CTA) and acrylate-based monomers both with and without a photocatalyst. The versatility of photo-mediated RAFT step-growth is demonstrated by one-pot synthesis of a graft copolymer via sequential monomer addition. Furthermore, oxygen-tolerant photo-mediated RAFT step-growth is demonstrated, facilitated by the appropriate selection of photocatalyst and solvent pair (zinc tetraphenyl porphyrin [ZnTPP] and dimethyl sulfoxide [DMSO]), enabling ultralow volume polymerization under open-air conditions.

A Minimalist Method for Fully Oxygen-Tolerant RAFT Polymerization through Sulfur-Centered Trithiocarbonate Radical Initiation.

In recent years, the fully oxygen-tolerant reversible deactivation radical polymerization (RDRP) has become a highly researched area. In this contribution, a new and minimalist method is successfully employed to accomplish fully oxygen-tolerant reversible addition-fragmentation chain transfer (RAFT) polymerization using bis(trithiocarbonate) disulfides (BisTTC) as an iniferter agent, where the released sulfur-centered trithiocarbonate (TTC) radical can initiate monomer. Furthermore, polymerization kinetics revealed the typical "living" features of this polymerization system. More importantly, by high-throughput screening, it is found that dodecyl-substituted TTC is responsible for the fully oxygen-tolerant RAFT polymerization though trithiocarbonate radical initiation and R radical deoxygenation. It is believed that trithiocarbonate radical initiation strategy provides a powerful and minimalist tool for fully oxygen-tolerant RDRPs.

Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance.

In [NiFe]-hydrogenases, the active-site Ni is coordinated by four cysteine-S ligands (Cys; C), two of which are bridging to the Fe(CO)(CN)2 fragment. Substitution of a single Cys residue by selenocysteine (Sec; U) occurs occasionally in nature. Using a recent method for site-specific Sec incorporation into proteins, each of the four Ni-coordinating cysteine residues in the oxygen-tolerant Escherichia coli [NiFe]-hydrogenase-1 (Hyd-1) has been replaced by U to identify its importance for enzyme function. Steady-state solution activity of each Sec-substituted enzyme (on a per-milligram basis) is lowered, although this may reflect the unquantified presence of recalcitrant inactive/immature/misfolded forms. Protein film electrochemistry, however, reveals detailed kinetic data that are independent of absolute activities. Like native Hyd-1, the variants have low apparent KMH2 values, do not produce H2 at pH 6, and display the same onset overpotential for H2 oxidation. Mechanistically important differences were identified for the C576U variant bearing the equivalent replacement found in native [NiFeSe]-hydrogenases, its extreme O2 tolerance (apparent KMH2 and Vmax [solution] values relative to native Hyd-1 of 0.13 and 0.04, respectively) implying the importance of a selenium atom in the position cis to the site where exogenous ligands (H-, H2, O2) bind. Observation of the same unusual electrocatalytic signature seen earlier for the proton transfer-defective E28Q variant highlights the direct role of the chalcogen atom (S/Se) at position 576 close to E28, with the caveat that Se is less effective than S in facilitating proton transfer away from the Ni during H2 oxidation by this enzyme.

Oxygen tolerance in anaerobes as a virulence factor and a health-beneficial property.

Oxygen tolerance of anaerobes is a virulence factor, but can also be a beneficial property. Many species have evolved to tolerate or take advantage of the presence of low, especially nanaerobic (≤0.14 %) oxygen concentrations. Oxygen tolerance is genus-, species- and strain-dependent according to their protective mechanisms. It was better expressed in some pathogenic species such as Bacteroides fragilis, Clostridioides difficile, and Clostridium perfringens, as well as in Akkermansia muciniphila than in other potential probiotics such as Alistipes, Blautia and Roseburia spp. Different degrees of oxygen sensitivity were found between the strains of Anaerostipes, Faecalibacterium, and Bifidobacterium spp. Importantly, clostridial spores and anaerobes in biofilms are protected from oxidation. Rubrerythrins and flavodiiron proteins and two regulators (sigma factor B and PerR) contribute to C. difficile protection from reactive oxygen species (ROS). The frequent pathogen, B. fragilis, has numerous protective factors such as enzymes (catalase, superoxide dismutase, alkyl hydroperoxidase, thioredoxin peroxidase, and aerobic-type NrdAB ribonucleotide reductase), and nanaerobic respiration. Seven proteins confer strain-specific oxygen adaptation of Faecalibacterium prausnitzii. Oxygen tolerance protects anaerobes from ROS, shields their DNA and modulates gene expression. Furthermore, oxygen can induce mutations leading to antibiotic resistance as shown in Prevotella melaninogenica. Some Faecalibacterium, Anaerostipes, Bifidobacterium, and Akkermansia strains from the intestinal microbiota exhibiting oxygen tolerance may become next-generation probiotic candidates. Further studies are needed to reveal oxygen effects on more anaerobic species and strains, and the influence of oxygen on antibiotic resistance. More studies on oxygen-tolerant probiotic strains can be useful to optimize biotechnological methods.

Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus.

BACKGROUND: The promising yet barely investigated anaerobic species Phocaeicola vulgatus (formerly Bacteroides vulgatus) plays a vital role for human gut health and effectively produces organic acids. Among them is succinate, a building block for high-value-added chemicals. Cultivating anaerobic bacteria is challenging, and a detailed understanding of P. vulgatus growth and metabolism is required to improve succinate production. One significant aspect is the influence of different gas concentrations. CO2 is required for the growth of P. vulgatus. However, it is a greenhouse gas that should not be wasted. Another highly interesting aspect is the sensitivity of P. vulgatus towards O2. In this work, the effects of varying concentrations of both gases were studied in the in-house developed Respiratory Activity MOnitoring System (RAMOS), which provides online monitoring of CO2, O2, and pressure under gassed conditions. The RAMOS was combined with a gas mixing system to test CO2 and O2 concentrations in a range of 0.25-15.0 vol% and 0.0-2.5 vol%, respectively. RESULTS: Changing the CO2 concentration in the gas supply revealed a CO2 optimum of 3.0 vol% for total organic acid production and 15.0 vol% for succinate production. It was demonstrated that the organic acid composition changed depending on the CO2 concentration. Furthermore, unrestricted growth of P. vulgatus up to an O2 concentration of 0.7 vol% in the gas supply was proven. The viability decreased rapidly at concentrations larger than or equal to 1.3 vol% O2. CONCLUSIONS: The study showed that P. vulgatus requires little CO2, has a distinct O2 tolerance and is therefore well suited for industrial applications.

Progress in the study of functional genes related to direct seeding of rice.

Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.

Visible Light-ATRP Driven by Tris(2-Pyridylmethyl)Amine (TPMA) Impurities in the Open Air.

Atom transfer radical polymerization (ATRP) of oligo(ethylene oxide) monomethyl ether methacrylate (OEOMA500 ) in water is enabled using CuBr2 with tris(2-pyridylmethyl)amine (TPMA) as a ligand under blue or green-light irradiation without requiring any additional reagent, such as a photo-reductant, or the need for prior deoxygenation. Polymers with low dispersity (D = 1.18-1.25) are synthesized at high conversion (>95%) using TPMA from three different suppliers, while no polymerization occurred with TPMA is synthesized and purified in the laboratory. Based on spectroscopic studies, it is proposed that TPMA impurities (i.e., imine and nitrone dipyridine), which absorb blue and green light, can act as photosensitive co-catalyst(s) in a light region where neither pure TPMA nor [(TPMA)CuBr]+ absorbs light.

Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp.

OBJECTIVES: Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp. METHODS: Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests. RESULTS: Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp. CONCLUSIONS: The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.

Augmenting the Performance of Hydrogenase for Aerobic Photocatalytic Hydrogen Evolution via Solvent Tuning.

This work showcases the performance of [NiFeSe] hydrogenase from Desulfomicrobium baculatum for solar-driven hydrogen generation in a variety of organic-based deep eutectic solvents. Despite its well-known sensitivity towards air and organic solvents, the hydrogenase shows remarkable performance under an aerobic atmosphere in these solvents when paired with a TiO2 photocatalyst. Tuning the water content further increases hydrogen evolution activity to a TOF of 60±3 s-1 and quantum yield to 2.3±0.4 % under aerobic conditions, compared to a TOF of 4 s-1 in a purely aqueous solvent. Contrary to common belief, this work therefore demonstrates that placing natural hydrogenases into non-natural environments can enhance their intrinsic activity beyond their natural performance, paving the way for full water splitting using hydrogenases.

Overcoming the Oxygen Dilemma in Photoredox Catalysis: Near-Infrared (NIR) Light-Triggered Peroxynitrite Generation for Antibacterial Applications.

The peroxynitrite anion (ONOO- ) is closely associated with many diseases and the creation of ONOO- donors is an essential means of understanding its pathophysiological functions. However, it is challenging to develop ONOO- donors due to the difficulties in simultaneously producing highly reactive and short-lived nitric oxide (NO) and superoxide anion (O2 ⋅- ). Here, we report a novel strategy for constructing ONOO- donors by combining near-infrared (NIR)-mediated type I photosensitization and photoredox catalysis. The key design using a Nile blue analogue that can serve as both a type I photosensitizer and a metal-free photocatalyst. Intriguingly, the formation of O2 ⋅- via type I photosensitization avoids oxygen interference and instead activates nitrobenzofurazan-based NO donors via oxygen-tolerant NIR photoredox catalysis. The simultaneous release of O2 ⋅- and NO leads to ONOO- release, showing both antibacterial and antibiofilm activities.

Design of an Oxygen-Tolerant Photo-RAFT System for Protein-Polymer Conjugation Achieving High Bioactivity.

Protein-polymer conjugates have significant potential in pharmaceutical and biomedical applications. To enable their widespread use, robust conjugation techniques are crucial. This study introduces a photo-initiated reversible addition-fragmentation chain-transfer (Photo-RAFT) polymerization system that exhibits excellent oxygen tolerance. This system allows for the synthesis of protein-polymer conjugates with high bioactivity under mild and aerobic conditions. Three photocatalytic systems utilizing Eosin Y (EY) as the photocatalyst with two different cocatalysts (ascorbic acid and triethanolamine) were investigated, each generating distinct reactive oxygen species (ROS) such as singlet oxygen, superoxide, hydrogen peroxide, and hydroxyl radicals. The impact of these ROS on three model proteins (lysozyme, albumin, and myoglobin) was evaluated, demonstrating varying bioactivities based on the ROS produced. The EY/TEOA system was identified as the optimal photo-RAFT initiating system, enabling the preparation of protein-polymer conjugates under aerobic conditions while maintaining high protein enzymatic activity. To showcase the potential of this approach, lysozyme-poly(dimethylaminoethyl acrylate) conjugates were successfully prepared and exhibited enhanced antimicrobial property against Gram-positive and Gram-negative bacteria.

Oxygen-Tolerant RAFT Polymerization Catalyzed by a Recyclable Biomimetic Mineralization Enhanced Biological Cascade System.

An enzyme cascade system including glucose oxidase (GOx) and iron porphyrin (DhHP-6) is encapsulated in a metal-organic framework called zeolitic imidazolate framework-8 (ZIF-8) through one-step facile synthesis. The composite (GOx&DhHP-6@ZIF-8) is then used to initiate oxygen-tolerant reversible addition-fragmentation chain-transfer polymerization for different methacrylate monomers, such as 2-diethylaminoethyl methacrylate, 2-hydroxyethyl methacrylate, and poly(ethylene glycol) methyl ether methacrylate (Mn = 500 g mol-1 ). The composite shows the robustness toward solvent and temperatures, all polymerizations using above monomers and catalyzing by GOx&DhHP-6@ZIF-8 exhibits high monomer conversion (>85%) and narrow molar mass dispersity (<1.3). Besides, acrylic and acrylamide monomers such as 2-hydroxyethyl acrylate and N,N-dimethylacrylamide are also carried to demonstrate the broad applicability. Proton nuclear magnetic resonance characterization and chain extension experiments confirm the retaining end groups of the resultant polymers, which is a significant feature of living polymerization. More importantly, the process of recycling the composite through a centrifuge is simplistic, and the composite still maintains similar activity compared to the original composites after five times. This low-cost and easily separated composite catalyst represents a versatile strategy to synthesize well-defined functional polymers suitable for industrial-scale production.

Uncovering Akkermansia muciniphila resilience or susceptibility to different temperatures, atmospheres and gastrointestinal conditions.

Data regarding Akkermansia muciniphila viability under stress remains scarce despite its beneficial potential. Therefore, the main goal was to assess A. muciniphila culturability when exposed to different temperatures, atmospheres and gastrointestinal simulated conditions. Cultivable cell numbers A. muciniphila remain high after refrigerated and room temperatures oxygen exposure, and gastrointestinal passage.

Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview.

Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.

Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins.

Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.

An Oxygen Paradox: Catalytic Use of Oxygen in Radical Photopolymerization.

A peculiar radical polymerization reaction is presented in which oxygen serves as a cocatalyst, alongside triethylamine, to provide activation with light in the far-red (690 nm, 3 mW cm-2 ) of the PET-RAFT process in the presence of zinc(II) (2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetraphenylporphyrin) as photocatalyst. Apart from the ability to exert temporal control by switching the light on or off, this system possesses the exciting capability of inducing temporal control by removal or reintroduction of oxygen. Furthermore, this multicomponent catalytic system was typified by controlled polymerizations of various acrylate and acrylamide monomers, which all resulted in well-defined polymers with low dispersity (<1.2). The process displayed excellent living characteristics that were demonstrated through chain extensions and a range of degrees of polymerization (200-1600).

The Difference Se Makes: A Bio-Inspired Dppf-Supported Nickel Selenolate Complex Boosts Dihydrogen Evolution with High Oxygen Tolerance.

Inspired by the metal active sites of [NiFeSe]-hydrogenases, a dppf-supported nickel(II) selenolate complex (dppf=1,1'-bis(diphenylphosphino)ferrocene) shows high catalytic activity for electrochemical proton reduction with a remarkable enzyme-like H2 evolution turnover frequency (TOF) of 7838 s-1 under an Ar atmosphere, which markedly surpasses the activity of a dppf-supported nickel(II) thiolate analogue with a low TOF of 600 s-1 . A combined study of electrochemical experiments and DFT calculations shed light on the catalytic process, suggesting that selenium atom as a bio-inspired proton relay plays a key role in proton exchange and enhancing catalytic activity of H2 production. For the first time, this type of Ni selenolate-containing electrocatalyst displays a high degree of O2 and H2 tolerance. Our results should encourage the development of the design of highly efficient oxygen-tolerant Ni selenolate molecular catalysts.

Aerobic Conditions Enhance the Photocatalytic Stability of CdS/CdOx Quantum Dots.

Photocatalytic H2 production through water splitting represents an attractive route to generate a renewable fuel. These systems are typically limited to anaerobic conditions due to the inhibiting effects of O2 . Here, we report that sacrificial H2 evolution with CdS quantum dots does not necessarily suffer from O2 inhibition and can even be stabilised under aerobic conditions. The introduction of O2 prevents a key inactivation pathway of CdS (over-accumulation of metallic Cd and particle agglomeration) and thereby affords particles with higher stability. These findings represent a possibility to exploit the O2 reduction reaction to inhibit deactivation, rather than catalysis, offering a strategy to stabilise photocatalysts that suffer from similar degradation reactions.

An Oxygen-Tolerant PET-RAFT Polymerization for Screening Structure-Activity Relationships.

The complexity of polymer-protein interactions makes rational design of the best polymer architecture for any given biointerface extremely challenging, and the high throughput synthesis and screening of polymers has emerged as an attractive alternative. A porphyrin-catalysed photoinduced electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) polymerisation was adapted to enable high throughput synthesis of complex polymer architectures in dimethyl sulfoxide (DMSO) on low-volume well plates in the presence of air. The polymerisation system shows remarkable oxygen tolerance, and excellent control of functional 3- and 4-arm star polymers. We then apply this method to investigate the effect of polymer structure on protein binding, in this case to the lectin concanavalin A (ConA). Such an approach could be applied to screen the structure-activity relationships for any number of polymer-protein interactions.