Culturable Bacteria Research Articles

Lactic Acid Bacteria-Derived Postbiotics as Adjunctive Agents in Breast Cancer Treatment to Boost the Antineoplastic Effect of a Conventional Therapeutic Comprising Tamoxifen and a New Drug Candidate: An Aziridine–Hydrazide Hydrazone Derivative

Breast cancer is associated with high mortality and morbidity rates. As about 20–30% of patients exhibiting ER-positive phenotype are resistant to hormonal treatment with the standard drug tamoxifen, finding new therapies is a necessity. Postbiotics, metabolites, and macromolecules isolated from probiotic bacteria cultures have been proven to have sufficient bioactivity to exert prohealth and anticancer effects, making them viable adjunctive agents for the treatment of various neoplasms, including breast cancer. In the current study, postbiotics derived from L. plantarum and L. rhamnosus cultures were assessed on an in vitro breast cancer model as potential adjunctive agents to therapy utilizing tamoxifen and a candidate aziridine–hydrazide hydrazone derivative drug. Cell viability and cell death processes, including apoptosis, were analyzed for neoplastic MCF-7 cells treated with postbiotics and synthetic compounds. Cell cycle progression and proliferation were analyzed by PI-based flow cytometry and Ki-67 immunostaining. Postbiotics decreased viability and triggered apoptosis in MCF-7, modestly affecting the cell cycle and showing a lack of negative impact on normal cell viability. Moreover, they enhanced the cytotoxic effect of tamoxifen and the new candidate drug toward MCF-7, accelerating apoptosis and the inhibition of proliferation. This illustrates postbiotics’ potential as natural adjunctive agents supporting anticancer therapy based on synthetic drugs.

Outcomes Following Different Management of Mycotic Infrarenal Abdominal Aortic Aneurysms.

The objective was to present our experience on managing mycotic infrarenal abdominal aortic aneurysm (MIAAA) through a retrospective cohort study. Data of patients with MIAAA managed in our center from July 2016 to October 2022 were retrospectively analyzed. The diagnosis of MIAAA was made based on: (1) preoperative clinical signs of infection; (2) elevated serologic infection parameters; (3) para-aneurysmal infection features on enhanced computed tomography; and (4) positive blood or tissue cultures. All the patients received standard antibiotic therapy. Surgical management including endovascular aneurysm repair (EVAR), initial EVAR followed by open re-operation, and initial open surgical repair (OSR) were conducted according to disease seriosity, physical condition, and patient's will. Infection index and clinical outcome were evaluated during the follow-up time. A total of 23 patients (21 men; averaged=66.3 years, range=49-79 years) were included, with a mean follow-up time of 19.9 months (range=1-75 months). Bacteria culture from blood or tissue specimen was positive in 15 patients (Salmonella, n=8; Escherichia coli, n=3; methicillin-sensitive Staphylococcus aureus [MSSA], n=1; Klebsiella pneumoniae, n=1; Staphylococcus epidermidis, n=1; Mycobacterium tuberculosis, n=1). Seven patients received OSR as the initial surgical intervention, whereas 14 patients chose EVAR instead. The 2 conservatively managed patients (refused surgery) died within 30 days. The 7 patients who received initial OSR survived till now. Among the 14 patients who underwent initial EVAR, infection deteriorated without exception (14/14, 100%). Three of these patients refused re-operation and died within 6 months. Eleven patients received secondary surgical intervention (10 cases of aneurysm and endograft resection, thorough debridement, subclavian to bi-femoral artery bypass, or in situ aorta reconstruction; 1 case of laparoscopic debridement) and 7 survived the follow-up time. The overall mortality rate was 39.1% (9/23). The mortality rates differed greatly following different intervention methods (merely antibiotic management, 100%; initial open operation, 0%; initial EVAR without secondary operation, 100%; initial EVAR plus secondary operation, 36.4%). Open surgical repair is still the first choice for hemodynamically stable and low-risk patients. Merely EVAR is related with disastrous results, which should be reserved as a temporary alternative for patients with ruptured aneurysms, hemodynamic instability or high surgical risk, and followed by timely secondary OSR. The management of mycotic or primary-infected aortic aneurysm is challenging; treatment remains controversial. Our center has reviewed our experience over the past 6 years and found that open surgical repair is still the first choice for hemodynamically stable and low-risk patients. Merely endovascular aneurysm repair (EVAR) is related with disastrous results, which should be reserved as a temporary alternative for patients with ruptured aneurysms, hemodynamic instability or high surgical risk, and followed by timely secondary open surgical repair.

Strategies to Enhance Cultivation of Anaerobic Bacteria from Gastrointestinal Tract of Chicken

Strategies to Enhance Cultivation of Anaerobic Bacteria from Gastrointestinal Tract of Chicken

Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle

IntroductionBovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples.MethodsThis pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing.ResultsNon-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads.DiscussionBy increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.

Development of a defined mixed starter culture for the improvement of Tej, Ethiopian honey wine.

Ethiopian honey wine, Tej, is the most popular traditionally fermented alcoholic beverage in Ethiopia. Owing to the spontaneous fermentation process, the final product is neither predictable nor consistent in quality. Attempts have not been made before to solve this problem. Thus, the aim of this study was to develop a potential mixed starter culture of yeast and lactic acid bacteria isolated from Tej samples for the production of Tej with consistent quality. One hundred seventy-seven lactic acid bacteria and 194 yeasts were isolated from 30 Tej samples collected from southwest Ethiopia. After sequentially testing the isolates towards physiological stress tolerance and desired metabolic products, 10 lactic acid bacteria and 10 yeast isolates were screened. Later, four lactic acid bacteria and four yeast isolates were found to be compatible in co-culture tests. Finally, the combination of lactic acid bacteria and yeast isolates was formulated using the design of expert version 7.0.0 software, and six formulates (F #1-6) were designed. Controlled Tej fermentation was performed under laboratory conditions using six lactic acid bacteria-yeast starter culture formulations. The sensory attributes, in terms of color, flavor, odor, turbidity, and overall acceptance analysis scored 4.8/5.0 (F #2) and 4.7/5.0 (F #6), with mean significant variations (p < 0.05) among the other formulates. These two formulates were considered the best-mixed starter cultures compared to the control and other formulates. Matrix-assisted laser desorption ionization-time of flight analysis revealed that the lactic acid bacteria starters (AAUL7 and AAUL10) belonged to Lactobacillus paracasei. While the yeast starters (AAUY2 and AAUY8) belonged to Saccharomyces cerevisiae. These mixed lactic acid bacteria-yeast starter cultures could be used as the best starter culture for the fermentation of Ethiopian honey wine, Tej, with consistent quality.

Deciphering the differentiated performance on electricity generation and COD degradation by Rhodopseudomonas-dominated bioanode in light or dark

Anoxygenic phototrophic bacteria is a promising catalyst for constructing bioanode, but the mixed culture with non-photosynthetic bacteria is inevitable in an open environment application. In this study, a Rhodopseudomonas-dominated mixed culture with other electrogenic bacteria was investigated for deciphering the differentiated performance on electricity generation in light or dark conditions. The kinetic study showed that reaction rate of OM degradation was 9 times higher than that under dark condition, demonstrating that OM degradation was enhanced by photosynthesis. However, CE under light condition was lower. It indicated that part of OM was used to provide hydrogen donors for the fixation of CO2 or hydrogen production in photosynthesis, decreasing the OM used for electron transfer. In addition, higher COD concentration was not conducive to electricity generation. EIS analysis demonstrated that higher OM concentration would increase Rct to hinder the transfer of electrons from bacteria to the electrode. Indirect and direct electron transfer were revealed by CV analysis for light and dark biofilm, respectively, and nanowires were also observed by SEM graphs, further revealing the differentiate performance. Microbial community analysis demonstrated Rhodopseudomonas was dominated in light and decreased in dark, but Geobacter increased apparently from light to dark, resulting in different power generation performance. The findings revealed the differentiated performance on electricity generation and pollutant removal by mixed culture of phototrophic bacteria in light or dark, which will improve the power generation from photo-microbial fuel cells.

Effects of exogenous autoinducer-2 precursor on the ability of Lactiplantibacillus plantarum SH7 to degrade biogenic amines: In vitro and in a dry-sausage model

The effects of the exogenous autoinducer-2 (AI-2) precursor, 4,5-dihydroxy-2,3-pentanedione (DPD; 0, 300, 600, and 900 nmol/L), on the degradation capacity of Lactiplantibacillus plantarum SH7 toward biogenic amines (BA) were investigated both in vitro and in a dry-sausage model. L. plantarum SH7 exhibited a significant increase in BA-degradation capacity (putrescine, cadaverine, and histamine) under DPD treatments compared to the absence of DPD treatment in vitro. Additionally, a significant increase in the production of AI-2 signal molecule and diamine oxidase in L. plantarum SH7 was observed with the addition of exogenous DPD (p < 0.05). In the dry-sausage model, the contents of BAs (tryptamine, 2-phenethylamine, putrescine, cadaverine, and histamine) significantly decreased with the addition of DPD (p < 0.05). Meanwhile, the sausage with 600-nM DPD exhibited the lowest cadaverine content (11.13 mg/kg), while the sausage with 900-nM DPD exhibited the lowest tryptamine, putrescine, and histamine contents (12.44, 11.15, and 13.21 mg/kg, respectively). Results suggest that an optimal concentration of exogenous DPD can enhance the capacity of L. plantarum SH7 to degrade BAs and that the degradation of BAs by L. plantarum SH7 may be dependent on the LuxS/AI-2 quorum sensing (QS) system. This study provides the theoretical basis for the development of functional starter cultures of lactic acid bacteria with BA-degradation ability based on targeted LuxS/AI-2 QS system regulation and reducing the accumulation of BAs in fermented meat products.

Bacterial Micro-Aggregates as Inoculum in Animal Models of Implant-Associated Infections

Is it time to rethink the inoculum of animal models of implant-associated infections (IAI)? Traditionally, animal models of IAI are based on inoculation with metabolically active overnight cultures of planktonic bacteria or pre-grown surface-attached biofilms. However, such inoculums do not mimic the clinical initiation of IAI. Therefore, the present study aimed to develop a clinically relevant inoculum of low metabolic micro-aggregated bacteria. The porcine Staphylococcus aureus strain S54F9 was cultured in Tryptone Soya Broth (TSB) for seven days to facilitate the formation of low metabolic micro-aggregates. Subsequently, the aggregated culture underwent filtration using cell strainers of different pore sizes to separate micro-aggregates. Light microscopy was used to evaluate the aggregate formation and size in the different fractions, while isothermal microcalorimetry was used to disclose a low metabolic activity. The micro-aggregate fraction obtained with filter size 5-15 μm (actual measured mean size 32 μm) was used as inoculum in a porcine implant-associated osteomyelitis (IAO) model and compared to a standard overnight planktonic inoculum and a sham inoculum of 0.9% saline. The micro-aggregate and planktonic inoculums caused IAO with the re-isolation of S. aureus from soft tissues, bones, and implants. However, compared to their planktonic counterpart, neither of the micro-aggregate inoculated animals showed signs of osteomyelitis, i.e., sequester, osteolysis, and pus at gross inspection. Furthermore, inoculation with low metabolic micro-aggregates resulted in a strong healing response with pronounced osteoid formation, comparable to sham animals. In conclusion, the formation and separation of low metabolic bacterial micro-aggregates into various size fractions is possible, however, planktonic bacteria were still seen in all size fractions. Inoculation with micro-aggregates caused a less-aggressive osteomyelitis i.e. combination of infected tissue and strong healing response. Therefore, the use of low metabolic micro-aggregates could be a relevant inoculum for animal models of less-aggressive and thereby slower developing IAI and add in to our understanding of the host-implant-bacteria interactions in slow-onset low-grade infections.

Heterotrophic bacteria isolated from a chloraminated system accelerate chloramine decay

This work comprehensively demonstrates the ability of heterotrophic bacteria, isolated from a chloraminated system, to decay chloramine. This study non-selectively isolated 62 cultures of heterotrophic bacteria from a water sample (0.002 mg-N/L nitrite and 1.42 mg/L total chlorine) collected from a laboratory-scale reactor system; most of the isolates (93.3%) were Mycobacterium sp. Three species of Mycobacterium and one species of Micrococcus were inoculated to a basal inorganic medium with initial concentrations of acetate (from 0 to 24 mg-C/L) and 1.5 mg/L chloramine. Bacterial growth coincided with declines in the concentrations of chloramine, acetate, and ammonium. Detailed experiments with one of the Mycobacterium sp. isolates suggest that the common mechanism of chloramine loss is auto-decomposition likely mediated by chloramine-decaying proteins. The ability of the isolates to grow and decay chloramine underscores the important role of heterotrophic bacteria in the stability of chloramine in water-distribution systems. Existing strategies based on controlling nitrification should be augmented to include minimising heterotrophic bacteria.

Diversity of Culturable Gut Bacteria in Natural Aphid Populations and Their Contribution to Insecticide Degradation

Microorganisms in insects play pivotal roles in various aspects, including nutrition, development, protection, physiology, and behavior. Aphids, a distinct group of insects that feed on plant sap, have been the focus of research exploring the intricate relationships between microbes and insects. While extensive investigations have delved into the obligate endosymbionts in aphids, there remains a gap in understanding the diversity of gut microbes and other associated microorganisms. This study employed culture-dependent methods to isolate microorganisms from diverse aphid species (Aphis gossypii, A. nerii, A. craccivora, Hysteroneura setariae, and Myzus persicae). The results identified three bacterial phyla (Firmicutes, Proteobacteria, Actinobacteria), belonging to families such as Bacillaceae, Corynebacteriaceae, Micrococcaceae, Morganellaceae, Staphylococcaceae, and Xanthomonadaceae. Bacillus emerged as the predominant taxon, with Aphis craccivora exhibiting both high abundance and an even distribution of bacteria. Both A. craccivora and A. gossypii displayed a diverse array of bacterial species, with A. gossypii exhibiting the highest dominance index. Hysteroneura setariae showcased a diverse dominance of bacteria among aphids. Notably, the microorganisms Exiguobacterium indicum MPB-2 and Pseudomonas hibiscicola CCF 2-2 demonstrated the ability to degrade imidacloprid at a rate of 18-22%. This finding emphasizes their capacity to utilize insecticides as sole sources of carbon and nitrogen, ultimately benefiting the fitness of the insects. This study contributes to our understanding of the microorganisms presented in aphids. Highlighting the efficacy of culture-dependent methods in unveiling the diversity of these microscopic organisms.

3D printed kombucha biomaterial as a tissue scaffold and L929 cell cytotoxicity assay

AbstractTissue engineering includes the construction of tissue‐organ scaffold. The advantage of three‐dimensional scaffolds over two‐dimensional scaffolds is that they provide homeostasis for a longer time. The microbial community in Symbiotic culture of bacteria and yeast (SCOBY) can be a source for kombucha (kombu tea) production. In this study, it was aimed to investigate the usage of SCOBY, which produces bacterial cellulose, as a biomaterial and 3D scaffold material. 3D printable biomaterial was obtained by partial hydrolysis of oolong tea and black tea kombucha biofilms. In order to investigate the usage of 3D kombucha biomaterial as a tissue scaffold, “L929 cell line 3D cell culture” was created and cell viability was tested in the biomaterial. At the end of the 21st day, black tea showed 51% and oolong tea 73% viability. The cytotoxicity of the materials prepared by lyophilizing oolong and black tea kombucha beverages in fibroblast cell culture was determined. Black tea IC50 value: 7.53 mg, oolong tea IC50 value is found as 6.05 mg. Fibroblast viability in 3D biomaterial + lyophilized oolong and black tea kombucha beverages, which were created using the amounts determined to these values, were investigated by cell culture Fibroblasts in lyophilized and 3D biomaterial showed viability of 58% in black tea and 78% in oolong tea at the end of the 7th day. In SEM analysis, it was concluded that fibroblast cells created adhesion to the biomaterial. 3D biomaterial from kombucha mushroom culture can be used as tissue scaffold and biomaterial.

The abundance and pathogenicity of microbes in automobile air conditioning filters across the typical cities of China and Europe

Bioaerosols are widely distributed in urban air and can be transmitted across the atmosphere, biosphere, and anthroposphere, resulting in infectious diseases. Automobile air conditioning (AAC) filters can trap airborne microbes. In this study, AAC filters were used to investigate the abundance and pathogenicity of airborne microorganisms in typical Chinese and European cities. Culturable bacteria and fungi concentrations were determined using microbial culturing. High-throughput sequencing was employed to analyze microbial community structures. The levels of culturable bioaerosols in Chinese and European cities exhibited disparities (Analysis of Variance, P < 0.01). The most dominant pathogenic bacteria and fungi were similar in Chinese (Mycobacterium: 18.2–18.9 %; Cladosporium: 23.0–30.2 %) and European cities (Mycobacterium: 15.4–37.7 %; Cladosporium: 18.1–29.3 %). Bartonella, Bordetella, Alternaria, and Aspergillus were also widely identified. BugBase analysis showed that microbiomes in China exhibited higher abundances of mobile genetic elements (MGEs) and biofilm formation capacity than those in Europe, indicating higher health risks. Through co-occurrence network analysis, heavy metals such as zinc were found to correlate with microorganism abundance; most bacteria were inversely associated, while fungi exhibited greater tolerance, indicating that heavy metals affect the growth and reproduction of bioaerosol microorganisms. This study elucidates the influence of social and environmental factors on shaping microbial community structures, offering practical insights for preventing and controlling regional bioaerosol pollution.

Degradation of pretilachlor and fenclorim and effects of these compounds on bacterial communities under anaerobic condition.

Pretilachlor and safener fenclorim are the main components of herbicides widely applied to control weeds. Although some pure cultures of bacteria and fungi which degraded these compounds under aerobic conditions were isolated, no isolated pretilachlor- and fenclorim-degrading bacterial strains under anaerobic condition had been available. In this study, the degradation of these compounds and the effects of them on bacterial community structures were investigated under anaerobic conditions. The dissipation rates of pretilachlor and fenclorim in slurries were in the order: soil from paddy field ≈ sediment from river > sediment from mangrove. Moreover, three pretilachlor-degrading bacterial strains (Pseudomonas sp. Pr1, Proteiniclasticum sp. Pr2 and Paracoccus denitrificans Pr3) and two fenclorim-degrading strains (Dechloromonas sp. Fe1 and Ralstonia pickettii Fe2) isolated from a slurry of paddy soil utilized the substrates as sole carbon and energy sources under anaerobic conditions. The degradation of pure pretilachlor and fenclorim at various concentrations by corresponding mixed pure cultures followed the Michaelis-Menten model, with the maximum degradation was 3.10 ± 0.31µM/day for pretilachlor, and 2.08 ± 0.18µM/day for fenclorim. During the degradation, 2-chloro-N-(2,6-diethylphenyl) acetamide and 2,6-dimethylaniline were produced in pretilachlor degradation, and benzene was a product of fenclorim degradation. The synergistic degradation of both substrates by all isolated bacteria reduced the metabolites concentrations accumulated in media. This study provides valuable information on effects of pretilachlor and fenclorim on bacterial communities in soil and sediments, and degradation of these substrates by isolated bacteria under anaerobic condition.

Bacterial extracellular vesicles: biotechnological perspective for enhanced productivity.

Bacterial extracellular vesicles (BEVs) are non-replicative nanostructures released by Gram-negative and Gram-positive bacteria as a survival mechanism and inter- and intraspecific communication mechanism. Due to BEVs physical, biochemical, and biofunctional characteristics, there is interest in producing and using them in developing new therapeutics, vaccines, or delivery systems. However, BEV release is typically low, limiting their application. Here, we provide a biotechnological perspective to enhance BEV production, highlighting current strategies. The strategies include the production of hypervesiculating strains through gene modification, bacteria culture under stress conditions, and artificial vesicles production. We discussed the effect of these production strategies on BEVs types, morphology, composition, and activity. Furthermore, we summarized general aspects of BEV biogenesis, functional capabilities, and applications, framing their current importance and the need to produce them in abundance. This review will expand the knowledge about the range of strategies associated with BEV bioprocesses to increase their productivity and extend their application possibilities.

Characterization of bacterial cellulose produced by the KomEt strain isolated from a kombucha SCOBY

Bacterial cellulose (BC) is gaining interest, due to its actual and potential applications in the biomedical, cosmetics and textile industries. In this study, mechanical, thermal, and chemical properties of BC produced from a novel strain, isolated from a kombucha symbiotic culture of bacteria and yeast (SCOBY), were evaluated. The highest obtained yields with this strain, after a 10-day fermentation, were 496 ± 14 g/L (native hydrated) and 19 ± 1 g/L (dry). Compression, including relaxation, and traction tests were performed on BC membranes in a hydrated state. The tested material revealed a 3-phase compression behaviour with a compression modulus of 235 ± 50 Pa. In terms of relaxation in water, BC membranes showed plastic deformation past 50 % compression. Regarding BC membrane under traction, analysis showed a 1090 ± 410 kPa Young Modulus, a 50 ± 10 % Elongation at Break and a 270 ± 80 kPa Ultimate Tensile Strength (UTS). Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) indicated that BC begins its degradation around 290 °C. Fourier-Transform Infrared spectroscopy (FTIR) of freeze-dried BC membranes confirmed the obtained biofilm to be BC. The results of this study provide valuable information on the potential applications of BC membranes in different industries including textile, biomedical and as a low-cost alternative to some synthetic polymers.

Evaluation of pathogen spread risk from excavated landfill

Landfill is a huge pathogen reservoir and needs special attention. Herein, the distribution and spread risk of pathogen were assessed in excavated landfill scenario. The results show that landfill excavation will greatly increase the risk of environmental microbial contamination. The highest total concentration of culturable bacteria among landfill refuse, topsoil and plant leaves was found to be as high as 1010 CFU g−1. Total coliforms, Hemolytic bacteria, Staphylococcus aureus, Salmonella, Enterococci, and Fecal coliforms were detected in the landfill surrounding environment. Notably, pathogens were more likely to adhere to plant leaves, making it an important source of secondary pathogens. The culturable bacteria concentration in the air samples differed with the landfill zone with different operation status, and the highest culturable bacteria concentration was found in the excavated area of the landfill (3.3 × 104 CFU m−3), which was the main source of bioaerosol release. The distribution of bioaerosols in the downwind outside of the landfill showed a tendency of increasing and then decreasing, and the highest concentration of bioaerosols outside of the landfill (6.56 × 104 CFU m−3) was significantly higher than that in the excavated area of the landfill. The risk of respiratory inhalation was the main pathway leading to infection, whereas the HQin (population inhalation hazardous quotient) at 500 m downwind the excavation landfill was still higher than 1, indicating that the neighboring residents were exposed to airborne microbial pollutants. The results of the study provide evidence for bioaerosols control protective measures taken to reduce health risk from the excavated landfill.

Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium.

The bacterial species 'Candidatus Alkanivorans nitratireducens' was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies1,2, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation. The regulation of this switch or the nature of potential syntrophic partnerships with other microorganisms remains unclear. Here, we describe anaerobic multispecies cultures of bacteria which couple the oxidation of propane and butane to nitrate reduction and the oxidation of ammonium (anammox). Batch tests with 15N-isotope labelling and multi-omic analyses collectively supported a syntrophic partnership between 'Ca. A. nitratireducens' and anammox bacteria, with the former species mediating nitrate-driven oxidation of SCGAs, supplying the latter with nitrite for the oxidation of ammonium. The elimination of nitrite accumulation by the anammox substantially increased SCGA and nitrate consumption rates, whereas suppressing DNRA. Removing ammonium supply led to its eventual production, the accumulation of nitrite, and the upregulation of DNRA gene expression for the abundant 'Ca. A. nitratireducens'. Increasing the supply of SCGA had a similar effect in promoting DNRA. Our results suggest that 'Ca. A. nitratireducens' switches to DNRA to alleviate oxidative stress caused by nitrite accumulation, giving further insight into adaptability and ecology of this microorganism. Our findings also have important implications for the understanding of the fate of nitrogen and SCGAs in anaerobic environments.

Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State.

Growing evidence points to the presence of differentially culturable tubercle bacteria (DCTB) in clinical specimens from individuals with active tuberculosis (TB) disease. These bacteria are unable to grow on solid media but can resuscitate in liquid media. Given the epidemiological success of certain clinical genotype families of Mycobacterium tuberculosis, we hypothesize that different strains may have distinct mechanisms of adaptation and tolerance. We used an in vitro carbon starvation model to determine the propensity of strains from lineages 2 and 4 that included the Beijing and LAM families respectively, to generate DCTB. Beijing strains were associated with a greater propensity to produce DCTB compared to LAM strains. Furthermore, LAM strains required culture filtrate (CF) for resuscitation whilst starved Beijing strains were not dependent on CF. Moreover, Beijing strains showed improved resuscitation with cognate CF, suggesting the presence of unique growth stimulatory molecules in this family. Analysis of starved Beijing and LAM strains showed longer cells, which with resuscitation were restored to a shorter length. Cell wall staining with fluorescent D-amino acids identified strain-specific incorporation patterns, indicating that cell surface remodeling during resuscitation was distinct between clinical strains. Collectively, our data demonstrate that M. tuberculosis clinical strains from different genotype lineages have differential propensities to generate DCTB, which may have implications for TB treatment success.

Nucleic Acid Plate Culture: Label-Free and Naked-Eye-Based Digital Loop-Mediated Isothermal Amplification in Hydrogel with Machine Learning.

Digital nucleic acid amplification enables the absolute quantification of single molecules. However, due to the ultrasmall reaction volume in the digital system (i.e., short light path), most digital systems are limited to fluorescence signals, while label-free and naked-eye readout remain challenging. In this work, we report a digital nucleic acid plate culture method for label-free, ultrasimple, and naked-eye nucleic acid analysis. As simple as the bacteria culture, the nanoconfined digital loop-mediated isothermal amplification was performed by using polyacrylamide (PAM) hydrogel as the amplification matrix. The nanoconfinement of PAM hydrogel with an ionic polymer chain can remarkably accelerate the amplification of target nucleic acids and the growth of inorganic byproducts, namely, magnesium pyrophosphate particles (MPPs). Compared to that in aqueous solutions, MPPs trapped in the hydrogel with enhanced light scattering characteristics are clearly visible to the naked eye, forming white "colony" spots that can be simply counted in a label-free and instrument-free manner. The MPPs can also be photographed by a smartphone and automatically counted by a machine-learning algorithm to realize the absolute quantification of antibiotic-resistant pathogens in diverse real samples.

Kombucha as a Health-Beneficial Drink for Human Health.

Kombucha is a unique fermented beverage made from a symbiotic culture of yeast and bacteria. Kombucha is normally based on black tea added to water, then sugar is added as a substrate for fermentation in this beverage. This unique beverage is composed of amino acids, flavonoids, vitamins, and some active enzymes. Several beneficial health effects such as antioxidant, antimicrobial effects have been reported as a result of probiotics and prebiotics presence. These health effects of kombucha are attributed to its bioactive chemical and biological agents of probiotics bacteria e.g., Gluconobacter, Acetobacter and yeasts like Saccharomyces sps., along with glucuronic acid as the main sources of the health protection. This review focuses on the beneficial effects of Kombucha including antimicrobial, antioxidant, anti-cancer antidiabetic properties, as well as liver protection, treat of gastrointestinal problems, AIDS, gastric ulcers, obesity (and energy production), detoxification, and skin health.