NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.

Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variants, thereby achieving a good balance between sensitivity and precision. A comparative evaluation of NanoMGT, using a simulated multi-strain sample of seven bacterial species, demonstrated superior performance relative to existing tools and the advantages of using a threshold-based filtering approach to calling minority variants in ONT's sequencing data. NanoMGT's potential as a post-binning tool in metagenomic pipelines is particularly notable, enabling researchers to more accurately determine specific alleles and understand strain diversity in microbial communities. Our findings have significant implications for clinical diagnostics, environmental microbiology, and the broader field of genomics. The findings offer a reliable and efficient approach to marker gene typing in complex metagenomic samples.

Dominant strain shift in the invasive fall armyworm (Lepidoptera: Noctuidae) populations in Thailand as inferred from mitochondrial COI and nuclear Tpi genes.

The fall armyworm, Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera: Noctuidae), is a significant global pest, that exhibits 2 discernible strains, corn strain (CS) and rice strain (RS). After initial detection in the eastern hemisphere in 2016, the dominant strain was identified as RS based only on cytochrome C oxidase subunit I (COI) mitochondrial gene from limited samples from various countries, including Thailand. This study aimed to assess strain and haplotype variation in the S. frugiperda populations in Thailand using both mitochondrial COI and nuclear triosephosphate isomerase (Tpi) genes. Analyses of COI sequences (n = 105) revealed 2 predominant haplotypes, COICSh4 (82.86%) and COIRSh1 (17.14%), and the analyses of Tpi sequences (n = 99) revealed 6 haplotypes, with TpiCa1a (53.53%) being the most prevalent. Of the 98 caterpillar samples, the majority exhibited true CS (83.67%) for both genes. Meanwhile, interstrain hybrids, indicated by gene discordance, accounted for the minority (16.33%). Interestingly, despite the initial dominance of RS during the 2018 outbreak, the current study identified CS as the prevalent strain across all localities in Thailand. These findings suggested a shift in S. frugiperda dynamics in Thailand that was possibly influenced by factors, such as competitive exclusion principle, pesticide usage in rice cultivation, and preferences for corn over rice. Our study suggests a need to reexamine the previous reports of rice-strain dominance in various countries in the eastern hemisphere after the initial invasion.

Screening of a Saccharomyces cerevisiae Strain with High 3-Methylthio-1-Propanol Yield and Optimization of Its Fermentation Conditions.

3-Methylthio-1-propanol (3-Met) is an important flavor compound in various alcoholic beverages such as Baijiu and Huangjiu. To maintain the content of 3-Met in these alcoholic beverages, it is necessary to screen a micro-organism with high yield of 3-Met from the brewing environment. In this study, the ability of yeast strains from the Baijiu brewing to produce 3-Met was analyzed, aiming to obtain yeast with high-yield 3-Met, and its fermentation conditions were optimized. Firstly, 39 yeast strains were screened using 3-Met conversion medium. The results showed that the majority of the strains from Baijiu brewing sources could produce 3-Met, and nearly half of the strains produced more than 0.5 g/L of 3-Met. Among these, yeast F10404, Y03401, and Y8#01, produced more than 1.0 g/L of 3-Met, with yeast Y03401 producing the highest amount at 1.30 g/L. Through morphological observation, physiological and biochemical analysis, and molecular biological identification, it was confirmed that yeast Y03401 was a Saccharomyces cerevisiae. Subsequently, the optimal fermentation conditions for 3-Met production by this yeast were obtained through single-factor designs, Plackett-Burman test, steepest ascent path design and response surface methodology. When the glucose concentration was 60 g/L, yeast extract concentration was 0.8 g/L, L-methionine concentration was 3.8 g/L, initial pH was 4, incubation time was 63 h, inoculum size was 1.6%, shaking speed was 150 rpm, loading volume was 50 mL/250 mL, and temperature was 26 °C, the content of 3-Met produced by S. cerevisiae Y03401 reached a high level of 3.66 g/L. It was also noteworthy that, in contrast to other study findings, this yeast was able to create substantial amounts of 3-Met even in the absence of L-methionine precursor. Based on the clear genome of S. cerevisiae and its characteristics in 3-Met production, S. cerevisiae Y03401 had broad prospects for application in alcoholic beverages such as Baijiu.

Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data.

Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors' (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions.

Laboratory tests and analysis of drug resistance in non-tuberculous mycobacteria.

Background: This study analyzed the laboratory diagnosis results and drug resistance of patients infected with non-tuberculous mycobacterium (NTM). Methods: We collected information on patients with positive indicators of NTM infection at the Henan Provincial Chest Hospital from 2020 to 2022. Acid-fast smear, mycobacterium culture, QB-SPOT assay, GeneXpert MTB/RIF assay, immunoglobulin E test, tuberculosis antibody test, and microplate method for drug sensitivity test were analyzed using strain identification as the gold standard. Results: The 242 cases of NTM infection were predominantly detected with slow-growing mycobacteria (a detection rate of 87.19%), among which Mycobacterium intracellulare (66.53%), Mycobacterium avium (15.70%), and Mycobacterium chelonei/abscessus complex (11.16%) ranked the top three in terms of the isolation rate. Males patients accounted for a higher proportion (58.26%) than females (41.74%), and the majority of them were over 60 years (50.83%). Among laboratory tests for patients with NTM infection, mycobacterium culture showed a highest detected rate (87.20%) among laboratory tests. The results of the drug sensitivity test demonstrated that the resistance rate of NTM was generally high. Moreover, the Mycobacterium avium complex with the highest isolation rate showed 100% resistant to doxycycline and minocycline, but exhibited relatively high sensitivity to moxifloxacin (a resistance rate of 7.89%) and rifabutin (a resistance rate of 13.16%). The Mycobacterium chelonei/abscessus complex was 100% resistant to doxycycline and relatively sensitive to cefoxitin (29.17%) and clarithromycin (37.50%). Conclusion: The NTM species isolated by the Henan Provincial Chest Hospital is dominated by Mycobacterium intracellulare and the highest positive rate is detected by mycobacterium culture among laboratory tests. NTM infection generally exhibits a high rate of drug resistance. Accordingly, the accurate diagnosis of NTM diseases requires enhanced drug sensitivity testing to provide patients with targeted combination drug treatment.

Evidence of the Ability of Microsatellite Method to Distinguish Cannabis Strains with High Cannabinoid Content.

Introduction: Cannabis is a plant with high potential for use in several sectors of the industry; however, it is also a controversial crop due to its tetrahydrocannabinol (THC) content. Moreover, the plant has a rather unclarified classification. Traditionally, two types of Cannabis have been distinguished, hemp as a source of fiber and low THC content, and marijuana with high THC levels, which is used as a drug. With the increasing use of CBD strains and wide range of commercially used THC strains, it is becoming paramount to be able to develop an easy and reliable method for Cannabis strain differentiation. The use of simple sequence repeat markers, or microsatellites, seems to be an applicable choice. Materials and Methods: In this study, 52 strains of Cannabis with variable cannabinoid content were collected from growers from different geographical regions and analyzed using 17 different microsatellite markers. For more precise differentiation, five strains were selected and a higher number of individuals of each were analyzed. Results: Fragment analysis and cluster analysis showed that when one to three individual plants per strain were analyzed, the method was able to classify these samples into distinguishable groups with similar gene structure. They also revealed that when a larger sample set was used (10 individual plants per strain), highly specific strain clusters could be fully discriminated. Conclusion: Our study involved the highest number of cannabinoid-rich strains up to now and showed that the microsatellite method can be used to reliably differentiate Cannabis strains and show their relationships.

Pollution status and distribution characteristics of indoor air bacteria in subway stations and compartments in a city of Central South China / 环境与职业医学

Background Bacteria are the most diverse and widely sourced microorganisms in the indoor air of subway stations, where pathogenic bacteria can spread through the air, leading to increased health risks. Objective To understand the status and distribution characteristics of indoor air bacterial pollution in subway stations and compartments in a city of Central South China, and to provide a scientific basis for formulating intervention measures to address indoor air bacteria pollution in subways. Methods Three subway stations and the compartments of trains parking there in a city in Central South China were selected according to passenger flow for synchronous air sampling and monitoring. Temperature, humidity, wind speed, carbon dioxide (CO2), fine particulate matter (PM2.5), and inhalable particulate matter (PM10) were measured by direct reading method. In accordance with the requirements of Examination methods for public places-Part 3: Airborne microorganisms (GB/T 18204.3-2013), air samples were collected at a flow rate of 28.3 L·min−1, and total bacterial count was estimated. Bacterial microbial species were identified with a mass spectrometer and pathogenic bacteria were distinguished from non-pathogenic bacteria according to the Catalogue of pathogenic microorganisms transmitted to human beings issued by National Health Commission. Kruskal-Wallis H test was used to compare the subway hygiene indicators in different regions and time periods, and Bonferroni test was used for pairwise comparison. Spearman correlation test was used to evaluate the correlation between CO2 concentration and total bacterial count. Results The pass rates were 100.0% for airborne total bacteria count, PM2.5, and PM10 in the subway stations and train compartments, 94.4% for temperature and wind speed, 98.6% for CO2, but 0% for humidity. The overall median (P25, P75) total bacteria count was 177 (138,262) CFU·m−3. Specifically, the total bacteria count was higher in station halls than in platforms, and higher during morning peak hours than during evening peak hours (P<0.05). A total of 874 strains and 82 species were identified by automatic microbial mass spectrometry. The results of identification were all over 9 points, and the predominant bacteria in the air were Micrococcus luteus (52.2%) and Staphylococcus hominis (9.8%). Three pathogens, Acinetobacter baumannii (0.3%), Corynebacterium striatum (0.1%), and Staphylococcus epidermidis bacilli (2.2%) were detected in 23 samples (2.6%), and the associated locations were mainly distributed in train compartments during evening rush hours. Conclusion The total bacteria count in indoor air varies by monitoring sites of subway stations and time periods, and there is a risk of opportunistic bacterial infection. Attention should be paid to cleaning and disinfection during peak passenger flow hours in all areas.

Growth Kinetics of Prodigiosin (Food Color) Produced by Novel Serratia marcescens bhu prodig Under Submerged Fermentation (SMF).

Prodigiosin is a promising food color due to its antibacterial, antimalarial, antimycotic characteristics, immunomodulating, and antitumor activities. Novel prodigiosin producing strain isolated from sugarcane field soil of Banaras Hindu University, India, characterized as Serratia marcescens bhu prodig by 16 sRNA. The effect of carbon, nitrogen source, and physical parameters (pH and temperature) on pigment yield was studied. The highest amount of pigment produced, which was 800.95 ± 0.05 mg/L, was detected when sorbitol and peptone were used as nitrogen and carbon source with pH 7 at 30 °C. The optimized condition scale-up in a bioreactor with a working capacity of 3.0 L, gave maximum pigment yield of 825 ± 0.05 mg/L with µ (Maximum specific growth rate), Yp/x, which represents the product yield coefficient, and Yp/s, which signifies the specific product yield coefficient and productivity of 0.3/h, 0.62, 0.80, and 0.02 g/L/h, respectively, after 72 h of cultivation in submerged fermentation (SMF). The isolated pigment was characterized as prodigiosin by the analysis of spectral data and GC-MS. The mass spectrophotometry investigation characterized pigment as 4-methoxy-5(5 methyl-4-pentyl-2H-pyrrol-2-ylidene)- 2,2-bipyrrole ring structure. The GC-MS chromatogram showed m/z of 323, representing prodigiosin. The prodigiosin yield and productivity obtained in the current finding were higher than in previous reports.

cgMSI: pathogen detection within species from nanopore metagenomic sequencing data.

BACKGROUND: Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential tool for rapid pathogen detection due to its fast turnaround time. However, identifying pathogen within species is nontrivial for nanopore sequencing data due to the high sequencing error rate. RESULTS: We developed the core gene alleles metagenome strain identification (cgMSI) tool, which uses a two-stage maximum a posteriori probability estimation method to detect pathogens at strain level from nanopore metagenomic sequencing data at low computational cost. The cgMSI tool can accurately identify strains and estimate relative abundance at 1× coverage. CONCLUSIONS: We developed cgMSI for nanopore metagenomic pathogen detection within species. cgMSI is available at https://github.com/ZHU-XU-xmu/cgMSI .

Strain Identification and Drug Resistance Analysis of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in Nontuberculous Mycobacterial Lung Disease.

Objective: To evaluate the clinical value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in detecting Nontuberculous mycobacteria (NTM). Methods: The clinical data of 172 patients with suspected NTM lung disease were collected from our hospital from January 1, 2018, to December 30, 2021. The results were compared with those of BACTEC MGIT 960 in liquid culture and gene chip. This study also utilised MALDI-TOF MS to detect macrolide (MA) and amikacin (Am) mutations. Results: One hundred thirty-seven cases of NTM pulmonary disease were confirmed by identifying the NTM gene chip in bronchoalveolar lavage fluid and/or MALDI-TOF MS detection. The positive predictive value and negative predictive value were 100% (131/131) and 85.37% (35/41), respectively, and the consistency of the two methods was high (kappa=0.899). For the drug resistance detection of MAs, the consistency rate between MALDI-TOF MS detection and drug sensitivity detection was 97.71% (128/131), the sensitivity was 81.25% (13/16) and the specificity was 100% (115/115). The positive and negative predictive values were 100% (13/13) and 93.75% (115/118), respectively. There was no coincidental consistency between the two methods, and the consistency was high (P<0.001, kappa=0.884). For the drug resistance test of Am, the consistency rate between the MALDI-TOF MS test and the drug sensitivity test was 93.13% (122/131), the sensitivity was 93.52% (101/108), the specificity was 90.91% (21/23) and the positive predictive value and negative predictive value were 98.06% (101/103) and 75.00% (21/28), respectively. The two methods had high consistency, and the consistency was not coincidental (P<0.001, kappa=0.781). Conclusion: Utilising MALDI-TOF MS has a good consistency with the drug resistance gene chip method and can be a rapid and effective method to identify strains and drug resistance of NTM. Therefore, it has certain clinical application value in patients with suspected NTM lung disease.

Efficient short time pretreatment on lignocellulosic waste using an isolated fungus Trametes sp. W-4 for the enhancement of biogas production.

Biological pretreatment to the lignocellulosic waste prior to anaerobic digestion is a popular method to increase biogas production. However, the long time needed for the pretreatment is not suitable to the practical application. A fungus strain, which could produce many kinds of lignocellulosic enzymes including CMCase, FPase, xylanase and laccase, was isolated from the soil of Tibet in this study. The fungus was identified as Trametes sp. W-4 by morphological and molecular characterization. The optimum culture temperature was 30 °C and the optimum nitrogen source was peptone. Under the optimum fermentation condition, the activity of CMCase, FPase, xylanase and laccase could reach 2.73 U/mL, 0.41 U/mL, 0.29 U/mL, and 1.11 U/mL, respectively. The results of pretreatment of Trametes sp. W-4 on the mixtures of high land barley straw, cow manure and pig manure for enhancement of biogas production showed that a very short time pretreatment of 3 days could obtain the highest cumulative methane production of 111.51 mL/g-VS, which was 63.81% higher than that of the control group of 68.07 mL/g-VS. The finding indicated that Trametes sp. W-4 pretreatment could be a candidate for the improving of biogas production from lignocellulosic waste.

Strategies for the Identification and Assessment of Bacterial Strains with Specific Probiotic Traits.

Early in the 1900s, it was proposed that health could be improved and senility delayed by manipulating gut microbiota with the host-friendly bacteria found in yogurt. Later, in 1990, the medical community reconsidered this idea and today probiotics represent a developed area of research with a billion-dollar global industry. As a result, in recent decades, increased attention has been paid to the isolation and characterization of novel probiotic bacteria from fermented foods and dairy products. Most of the identified probiotic strains belong to the lactic acid bacteria group and the genus Bifidobacterium. However, current molecular-based knowledge has allowed the identification and culture of obligatory anaerobic commensal bacteria from the human gut, such as Akkermansia spp. and Faecalibacterium spp., among other human symbionts. We are aware that the identification of new strains of these species does not guarantee their probiotic effects and that each effect must be proved through in vitro and in vivo preclinical studies before clinical trials (before even considering it as a probiotic strain). In most cases, the identification and characterization of new probiotic strain candidates may lack the appropriate set of in vitro experiments allowing the next assessment steps. Here, we address some innovative strategies reported in the literature as alternatives to classical characterization: (i) identification of alternatives using whole-metagenome shotgun sequencing, metabolomics, and multi-omics analysis; and (ii) probiotic characterization based on molecular effectors and/or traits to target specific diseases (i.e., inflammatory bowel diseases, colorectal cancer, allergies, among others).

Using unique ORFan genes as strain-specific identifiers for Escherichia coli.

BACKGROUND: Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers. RESULTS: Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible. CONCLUSIONS: The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.

Enhanced production of cordycepic acid from Cordyceps cicadae isolated from a wild environment.

Cordyceps acid is an active component of Cordyceps cicadae and has a variety of medicinal uses, including anti-tumor effects, the prevention of cerebral hemorrhaging and myocardial infarction, and the inhibition of a wide range of bacteria. The objectives of this study were to identify C. cicadae fungi and optimize the culture conditions to obtain a high yield of cordycepic acid. First, a wild C. cicadae was identified by morphological observation and rDNA sequence analysis. Secondly, the optimal fermentation conditions were determined using a single-factor method, a Plackett-Burman design, and a Box-Behnken response surface. Finally, using the yield of fruit bodies and the content of cordyceps acid as indices, combined with a single-factor experiment and a response surface design, the best combination of conditions for cultivation was determined. The results showed that the best combination was as follows: sucrose 2%, tryptone 2%, KH2PO4 0.4%, MgSO4·7H2O 0.4%, an initial pH of the fermentation liquid of 7.0, 5% inoculum, fermentation for 4.5 d, a ratio of medium to liquid of 1:1.7, illumination intensity 150 Lux, illumination time 15 h per day, and 70% humidity. The content of cordycepic acid in the fruiting bodies developed in cultivation was 2.07-fold higher than that in the wild C. cicadae. This study provides a theoretical basis for the large-scale cultivation of C. cicadae with a high concentration of cordycepic acid.

Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.

The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.

Isolation and Identification of Arisaema Cum Bile Fermentation Strain and Preliminary Investigation on Its Compound Strain Fermentation / 中国实验方剂学杂志

ObjectiveIn order to solve the problem that the quality and stability of Arisaema Cum Bile in the fermentation process with hybrid bacteria were not easy to control， the microorganism in the fermentation process of Arisaema Cum Bile was isolated and identified， the dominant strains were screened and the fermentation process of Arisaema Cum Bile with compound bacteria was investigated. MethodThe submerged culture during the fermentation process of Arisaema Cum Bile was taken out for strain separation and purification. Bacteria and fungi multiphase identification and detection methods and automatic microbial analysis system were used to analyze and compare DNA sequences and identify microorganisms. The isolated and identified strains were respectively inoculated and fermented. After screening the dominant strains， a preliminary exploration of compound strain fermentation were carried out. The contents of index components in Arisaema Cum Bile fermented by compound strain and traditional Arisaema Cum Bile were compared by ultra-performance liquid chromatography-triple quadrupole tandem mass spectrometry （UPLC-QqQ-MS/MS）. Mmobile phase was 0.1% formic acid acetonitrile solution （A）-0.1% formic acid aqueous solution （B） for gradient elution （0-2 min， 35%-45%A； 2-10 min， 45%-48%A； 10-12 min， 48%-100%A； 12-12.01 min， 100%-35%A； 12.01-15 min， 35%-65%A）， the flow rate was set at 0.35 mL·min-1. The mass spectrographic analysis employed electrospray ionization （ESI）， negative ion acquisition mode and multiple reaction monitoring （MRM） scanning mode were adopted to collect information， the collection range was m/z 50-1 000. ResultEight microorganisms were isolated and identified from the submerged culture of Arisaema Cum Bile. Among them， Enterococcus sp. （anaerobic） and E. casseliflavus were selected as the dominant strains in the fermentation process. Compared with the traditional fermentation method， the contents of chenodeoxycholic acid， hyodeoxycholic acid and hyocholic acid in free cholic acid increased by 1.76， 0.06， 0.19 mg·g-1， respectively. In bound cholic acid， glycochenodeoxycholic acid， taurochenodeoxycholic acid， glycohyodeoxycholic acid， taurohyodeoxycholic acid， glycohyocholic acid， taurine porcine cholic acid decreased by 0.63， 0.23， 0.26， 0.16， 0.03， 0.04 mg·g-1， respectively. ConclusionArisaema Cum Bile with compound strain fermentation （Enterococcus sp. and E. casseliflavus） can be fermented more completely， the fermentation cycle can be shortened， and the quality and stability of products can be improved.

[Screening of plant growth-promoting rhizobacteria and its effect on seed germination of Polygonum multiflorum].

In this study, the rhizobacteria and actinomycetes of Polygonum multiflorum were screened for the strains with indole acetic acid(IAA)-producing capacity by Salkowski method, the siderophore-producing strains by Chrome Azurol S(CAS) assay, and the strains with inorganic phosphorus-solubilizing capacity by PKO inorganic phosphorus medium. The strains were identified by morphological identification, physiological and biochemical characteristics, and 16 S rDNA sequences. Furthermore, the effect of growth-promoting strains on the seed germination and development of P. multiflorum was tested. The results showed that among 196 strains, two strains F17 and F42 were found to be capable of producing IAA and siderophore and solubilizing inorganic phosphorus simulta-neously. For F17 and F42, the results are listed below: 38.65 and 33.64 mg·L~(-1) for IAA production, 0.85 and 0.49 for siderophore-producing capacities(A_s/A_r), and 1.35 and 1.70 for inorganic phosphorus-solubilizing capacities(D/d), respectively. Comprehensive analysis revealed that strains F17 and F42 were identified as Pseudochrobactrum asacharolyticum and Bacillus aryabhattai, respectively, and both could significantly promote the seed germination of P. multiflorum.

Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer.

This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus. We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed 'sibling' strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

Antimicrobial Activity and Identification of the Biosynthetic Gene Cluster of X-14952B From Streptomyces sp. 135.

The bacterial genus Streptomyces is an important source of antibiotics, and genome mining is a valuable tool to explore the potential of microbial biosynthesis in members of this genus. This study reports an actinomycete strain 135, which was isolated from Qinghai-Tibet Plateau in China and displayed broad antimicrobial activity. The fermentation broth of strain 135 displayed strong antifungal activity (>70%) against Sclerotinia sclerotiorum, Botrytis cinerea, Valsa mali, Phytophthora capsici, Glomerella cingulata, Magnaporthe grisea, Bipolaris maydis, Exserohilum turcicum in vitro, meanwhile possessed significant preventive and curative efficacy against S. sclerotiorum, Gaeumannomyces graminis, and P. capsici on rape leaves (54.04 and 74.18%), wheat (90.66 and 67.99%), and pepper plants (79.33 and 66.67%). X-14952B showed the greatest antifungal activity against S. sclerotiorum and Fusarium graminearum which the 50% inhibition concentration (EC50) were up to 0.049 and 0.04 µg/mL, respectively. Characterization of strain 135 using a polyphasic approach revealed that the strain displayed typical features of the genus Streptomyces. 16S rRNA gene sequencing and phylogenetic analysis demonstrated that the isolate was most closely related to and formed a clade with Streptomyces huasconensis HST28T (98.96% 16S rRNA gene sequence similarity). Average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values in strain 135 and related type strains were both below the threshold of species determination (91.39 and 56.5%, respectively). OrthoANI values between strain 135 and related type strains are under the cutoff of determining species (<95%). The biosynthetic gene cluster (BGC) designated to X-14952B biosynthesis was identified through genome mining and the possible biosynthesis process was deduced.

Bacterial Sub-Species Typing Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: What Is Promising?

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial to also be able to use the technology as a fast way to detect clinically relevant clones of bacterial species. However, studies to this aim have often had limited success. The methods used for data acquisition, processing and data interpretation are highly diverse amongst studies on MALDI-TOF MS sub-species typing. In addition to this, feasibility may depend on the bacterial species and strains investigated, making it difficult to determine what methods may or may not work. In our paper, we have reviewed recent research on MALDI-TOF MS typing of bacterial strains. Although we found a lot of variation amongst the methods used, there were approaches shared by multiple research groups. Multiple spectra of the same isolate were often combined before further analysis for strain distinction. Many groups used a protein extraction step to increase resolution in their MALDI-TOF MS results. Peaks at a high mass range were often excluded for data interpretation. Three groups have found ways to determine feasibility of MALDI-TOF MS typing for their set of strains at an early stage of their project.