Improved mouse models of the small intestine microbiota using region-specific sampling from humans

Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.

Stretchable and Self-Adhesive Humidity-Sensing Patch for Multiplexed Non-Contact Sensing

The slippage of moisture-sensitive materials from substrates during bending or stretching is a common issue that causes baseline drift and even failure of the flexible humidity sensors, which are essential components of wearable electronic devices. In this study, we report a stretchable, self-adhesive, and transparent humidity-sensing electronic patch comprising liquid metal particle electrodes with a stretchable serpentine structure and a humidity-sensing layer made of Ti3C2Tx MXene/carboxymethyl cellulose. This patch is constructed on a soft-hard integrated heterostructure substrate and demonstrates stable humidity-sensitive response performance at 100% tensile strain, along with autonomous adhesion to human skin. Additionally, it exhibits maximum response (1145.4%) at 90% relative humidity (RH), fast response and recovery time (1.4/5.9 s), elevated sensitivity (64.63%/% RH), and preserved humidity sensing under deformation, as well as easy scalability for multiplexed detection. We further illustrate the patch's potential applications in healthcare and environmental monitoring through a non-contact security door control system and wind monitor system. Our proposed strain-isolation strategy can be extended to other rigid conductive materials and stretchable substrates, providing a feasible mechanism for producing stretchable electronic skin patches.

Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle

Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.

Cellulolytic bacteria in the large intestine of mammals

The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of interest since the nineteenth century. Cellulolytic bacteria are key participants in this breakdown process of cellulose, which is otherwise indigestible by the host. They critically contribute to host nutrition and health through the production of short-chain fatty acids, in addition to maintaining the balance of intestinal microbiota. Despite this key role, cellulolytic bacteria have not been well studied. In this review, we first retrace the history of the discovery of cellulolytic bacteria in the large intestine. We then focus on the current knowledge of cellulolytic bacteria isolated from the large intestine of various animal species and humans and discuss the methods used for isolating these bacteria. Moreover, we summarize the enzymes and the mechanisms involved in cellulose degradation. Finally, we present the contribution of these bacteria to the host.

Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities

Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.

Soft Elastomers with Programmable Stiffness as Strain-Isolating Substrates for Stretchable Electronics

Stretchable electronics are of rapidly increasing interest due to their unique ability to function under complex deformations. Strain isolation of stiff functional components from the substrate represents a key challenge in the development of stretchable electronics since their mechanical mismatch may yield undesirable strains to degrade the device performance. The results presented here report an approach to develop a soft strain-isolating polymer substrate with programmable stiffness by spatioselective ultraviolet exposure for stretchable electronics. The approach being compatible with the well-established lithographic process reduces the fabrication complexity significantly and offers a simple yet robust strain-isolation mechanism to ensure the system stretchability of more than 100%. Combined experimental and numerical studies reveal the fundamental aspects of the design, fabrication, and operation of the strain-isolating substrate. Demonstration of this concept in a stretchable inorganic metal-based resistive temperature sensor and a stretchable organic photodiode array with unusually high performance shows the simplicity of the approach and the robustness in strain isolation in both component and device levels. This type of strain-isolation design not only creates promising routes for potential scalable manufacturing of stretchable electronics but also engineering opportunities for stretchable electronics involving the integration of various functional components, which require the quantitative control of the strain levels to achieve optimal performance.

Gene-Centric Metagenome Analysis Reveals Gene Clusters for Carbon Monoxide Conversion and Validates Isolation of a Clostridial Acetogen for C2 Chemical Production

Syngas fermentation is largely dependent on acetogens that occur in various anaerobic environmental samples including soil, sediment, and feces. Here the authors report the metagenomic isolation of acetogens for C2 chemical production from syngas. Screening acetogens for C2 chemical production typically involves detecting the presence of the Wood-Ljungdahl Pathway for carbon monoxide conversion. The authors collect samples from river-bed sediments potentially having conditions suitable for carbon monoxide-converting anaerobes, and enrich the samples under carbon monoxide selection pressure. Changes in the microbial community during the experimental procedure are investigated using both amplicon and shotgun metagenome sequencing. Combined next-generation sequencing techniques enabl in situ tracking of the major acetogenic bacterial group and lead to the discovery of a 16 kb of gene cluster for WLP. The authors isolat an acetogenic clostridial strain from the enrichment culture (strain H21-9). The functional activity of H21-9 is confirmed by its high level of production of C2 chemicals from carbon monoxide (77.4 mM acetate and 2.5 mM of ethanol). This approach of incorporating experimental enrichment with metagenomic analysis can facilitate the discovery of novel strains from environmental habitats by tracking target strains during the screening process, combined with validation of their functional activity.

Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide

Supercritical carbon dioxide (scCO2) is an attractive substitute for conventional organic solvents due to its unique transport and thermodynamic properties, its renewability and labile nature, and its high solubility for compounds such as alcohols, ketones, and aldehydes. However, biological systems that use scCO2 are mainly limited to in vitro processes due to its strong inhibition of cell viability and growth. To solve this problem, we used a bioprospecting approach to isolate a microbial strain with the natural ability to grow while exposed to scCO2. Enrichment culture and serial passaging of deep subsurface fluids from the McElmo Dome scCO2 reservoir in aqueous media under scCO2 headspace enabled the isolation of spore-forming strain Bacillus megaterium SR7. Sequencing and analysis of the complete 5.51 Mbp genome and physiological characterization revealed the capacity for facultative anaerobic metabolism, including fermentative growth on a diverse range of organic substrates. Supplementation of growth medium with L-alanine for chemical induction of spore germination significantly improved growth frequencies and biomass accumulation under scCO2 headspace. Detection of endogenous fermentative compounds in cultures grown under scCO2 represents the first observation of bioproduct generation and accumulation under this condition. Culturing development and metabolic characterization of B. megaterium SR7 represent initial advancements in the effort toward enabling exploitation of scCO2 as a sustainable solvent for in vivo bioprocessing.

A Novel Cellulase Produced by a Newly Isolated Trichoderma virens

Screening and obtaining a novel high activity cellulase and its producing microbe strain is the most important and essential way to improve the utilization of crop straw. In this paper, we devoted our efforts to isolating a novel microbe strain which could produce high activity cellulase. A novel strain Trichoderma virens ZY-01 was isolated from a cropland where straw is rich and decomposed, by using the soil dilution plate method with cellulose and Congo red. The strain has been licensed with a patent numbered ZL 201210295819.6. The cellulase activity in the cultivation broth could reach up to 7.4 IU/mL at a non-optimized fermentation condition with the newly isolated T. virens ZY-01. The cellulase was separated and purified from the T. virens culture broth through (NH₄)₂SO₄ fractional precipitation, anion-exchange chromatography and gel filtration chromatography. With the separation process, the CMC specific activity increased from 0.88 IU/mg to 31.5 IU/mg with 35.8 purification fold and 47.04% yield. Furthermore, the enzymatic properties of the cellulase were investigated. The optimum temperature and pH is 50 °C and pH 5.0 and it has good thermal stability. Zn²⁺, Ca²⁺ and Mn²⁺ could remarkably promote the enzyme activity. Conversely, Cu²⁺ and Co²⁺ could inhibit the enzymatic activity. This work provides a new highly efficient T. virens strain for cellulase production and shows good prospects in practical application.