Strain W3110 Research Articles

Evaluation of L-Asparaginase Purified from Pseudomonas Fluorescens as Inhibitor for Biofilm Producers in Dental Decays.

This study aimed to assess Pseudomonas fluorescens-purified L-Asparaginase's effectiveness as a broad-spectrum inhibitor of biofilm producers in dental decays. The 16S rRNA sequence was used to build a phylogenetic tree to calculate the evolutionary distance between the isolated bacterial strain SW3 and other species. The evolutionary history was inferred by using the neighbor-joining approach. The bacteria were identified from dental decays, including Staphylococcus aureus, Streptococcus mutans, Streptococcus oralis, and Streptococcus mitis. Each one of these isolates showed different degrees of biofilm development. Purified L-Asparaginase inhibited the most potent Gram-positive biofilm-forming bacteria (biofilm producers) with higher inhibition percentages against Streptococcus oralis and Streptococcus mitis, 65 - 73.8 % and 54.7 - 63%, respectively. The inhibition percentages increased with increasing concentration and reached up to 74 - 81% with Streptococcus oralis and 66 - 74% with Streptococcus mitis, while SW3 bacteria showed (100%). This strain was suggested SW3 (Pseudomonas spp.). Pseudomonas fluorescens bacterial strain isolated from rhizosphere soil produced extracellular L-Asparaginase when grown on as a substrate. L-Asparaginase was purified to homogeneity by using ammonium sulfate at 60% saturation, followed by gel filtration chromatography on a sephadex G-100 column, with a recovery yield of 49% and a purification fold of 2.22. L-Asparaginase had a promising use for removing and avoiding biofilm growth, implying that it might be used in the dental industry in the future.

Selecting Phosphorus-Solubilizing Strains of Purple Nonsulfur Bacteria Isolated From Pineapple Cultivated Acid Sulfate Soils

The presence of acid sulfate soils is such an obstacle for pineapple cultivation in Vietnam due to their low pH, high toxicity and poor nutrient availability, especially phosphorus (P), which is immobilized by cations in the soils. Therefore, the study occurred to select purple nonsulfur bacteria (PNSB) strains that can solubilize P under toxic and acidic conditions. There were 33 strains that can tolerate the acidic condition, and they were selected and tested for viability and P solubilization under conditions containing Al3+, Fe2+, and Mn2+ toxins. Four strains, including W15, W39, W42 and W48 suffered from growth inhibition by Al3+, Fe2+ and Mn2+ less than the other strains under both microaerobic light and aerobic dark conditions (ML and AD conditions). In addition, there were four strains (W15, W25, W42 and W48) solubilizing Al-P well (21.4-25.2 mg L-1), two strains (W23 and W42) solubilizing Fe-P well (15.9-17.3 mg L-1), and two strains (W17 and W42) solubilizing Ca-P well (23.0-36.4 mg L-1) under both ML and AD conditions. Ultimately, there were five strains selected (W17, W23, W25, W42 and W48) and identified as Rhodopseudomonas palustris strain W17 and W23, Cereibacter sphaeroides strain W23, W42 and W48 based on the 16S rRNA technique. The selected strains also produced ALA, EPS and siderophores at 1.31-2.19 mg L-1, 0.78-1.89 mg L-1, and 16.2-55.6%, respectively. Therefore, these strains were promising in providing nutrients for pineapples in the form of biofertilizer.

Drug efflux and lipid A modification by 4-L-aminoarabinose are key mechanisms of polymyxin B resistance in the sepsis pathogen Enterobacter bugandensis

A concern with the ESKAPE pathogen, Enterobacter bugandensis, and other species of the Enterobacter cloacae complex, is the frequent appearance of multidrug resistance against last-resort antibiotics, such as polymyxins. Here, we investigated the responses to polymyxin B (PMB) in two PMB-resistant E. bugandensis clinical isolates by global transcriptomics and deletion mutagenesis. In both isolates, the genes of the CrrAB-regulated operon, including crrC and kexD, displayed the highest levels of upregulation in response to PMB. ∆crrC and ∆kexD mutants became highly susceptible to PMB and lost the heteroresistant phenotype. Conversely, heterologous expression of CrrC and KexD proteins increased PMB resistance in a sensitive Enterobacter ludwigii clinical isolate and in the Escherichia coli K12 strain, W3110. The efflux pump, AcrABTolC, and the two component regulators, PhoPQ and CrrAB, also contributed to PMB resistance and heteroresistance. Additionally, the lipid A modification with 4-L-aminoarabinose (L-Ara4N), mediated by the arnBCADTEF operon, was critical to determine PMB resistance. Biochemical experiments, supported by mass spectrometry and structural modelling, indicated that CrrC is an inner membrane protein that interacts with the membrane domain of the KexD pump. Similar interactions were modeled for AcrB and AcrD efflux pumps. Our results support a model where drug efflux potentiated by CrrC interaction with membrane domains of major efflux pumps combined with resistance to PMB entry by the L-Ara4N lipid A modification, under the control of PhoPQ and CrrAB, confers the bacterium high-level resistance and heteroresistance to PMB.

Whole genome analysis of Pseudomonas mandelii SW-3 and the insights into low-temperature adaptation.

Pseudomonas mandelii SW-3, isolated from the Napahai plateau wetland, can survive in cold environments. The mechanisms underlying the survival of bacteria in low temperatures and high altitudes are not yet fully understood. In this study, the whole genome of SW-3 was sequenced to identify the genomic features that may contribute to survival in cold environments. The results showed that the genome size of strain SW-3 was 6,538,059bp with a GC content of 59%. A total of 67 tRNAs, a 34,110bp prophage sequence, and a large number of metabolic genes were found. Based on 16S rRNA gene phylogeny and average nucleotide identity analysis among P. mandelii, SW-3 was identified as a strain belonging to P. mandelii. In addition, we clarified the mechanisms by which SW-3 survived in a cold environment, providing a basis for further investigation of host-phage interaction. P. mandelii SW-3 showed stress resistance mechanisms, including glycogen and trehalose metabolic pathways, and antisense transcriptional silencing. Furthermore, cold shock proteins and glucose 6-phosphate dehydrogenase may play pivotal roles in facilitating adaptation to cold environmental conditions. The genome-wide analysis provided us with a deeper understanding of the cold-adapted bacterium.

Antifungal Substances Produced by B. subtilis Strain W3.15 Inhibit the Fusarium oxysporum and Trigger Cellular Damage

Soybean Fusarium wilt and root rot disease caused by a necrotrophic ascomycete pathogen, F. oxysporum, triggered severe damage to the plant tissues and organs and impacted heavy losses. Biocontrol agents, Bacillus subtilis, were commonly used to produce a broad spectrum of antifungal substances and were gradually used in biocontrol studies for plant disease management. Investigation and determination of the inhibiting mechanism of antifungal substance produced by B. subtilis on F. oxysporum should be done to protect the soybean plant. This study revealed that basal nutrient broth (NB) gives the best antifungal activity. The stationary phase of the bacterial growth curve was obtained on two days of cultivation and showed the maximum antifungal activity against F. oxysporum. Ethyl acetate (EA) extraction of bacterial supernatant generated crude EA extract, which showed half inhibition (IC50) at 306.42 µg/ml obtained from the dose-response regression curve. Post-treatment mycelia of F. oxysporum with bacterial extract were demonstrated as hyphal deformation followed by malondialdehyde (MDA) accumulation. Furthermore, cellular leakage on fungal cells that may be triggered by antifungal compounds from strain W3.15 occurred. Last, the related antifungal compounds were predicted to be epicatechin and benzophenone from the LC-MS/MS analysis of crude EA extract. Accordingly, the biocontrol agent B. subtilis strain W3.15 promises a strong potency for biofungicide development.

Yields and product comparison between Escherichia coli BL21 and W3110 in industrially relevant conditions: anti-c-Met scFv as a case study

IntroductionIn the biopharmaceutical industry, Escherichia coli is one of the preferred expression hosts for large-scale production of therapeutic proteins. Although increasing the product yield is important, product quality is a major factor in this industry because greatest productivity does not always correspond with the highest quality of the produced protein. While some post-translational modifications, such as disulphide bonds, are required to achieve the biologically active conformation, others may have a negative impact on the product’s activity, effectiveness, and/or safety. Therefore, they are classified as product associated impurities, and they represent a crucial quality parameter for regulatory authorities.ResultsIn this study, fermentation conditions of two widely employed industrial E. coli strains, BL21 and W3110 are compared for recombinant protein production of a single-chain variable fragment (scFv) in an industrial setting. We found that the BL21 strain produces more soluble scFv than the W3110 strain, even though W3110 produces more recombinant protein in total. A quality assessment on the scFv recovered from the supernatant was then performed. Unexpectedly, even when our scFv is correctly disulphide bonded and cleaved from its signal peptide in both strains, the protein shows charge heterogeneity with up to seven distinguishable variants on cation exchange chromatography. Biophysical characterization confirmed the presence of altered conformations of the two main charged variants.ConclusionsThe findings indicated that BL21 is more productive for this specific scFv than W3110. When assessing product quality, a distinctive profile of the protein was found which was independent of the E. coli strain. This suggests that alterations are present in the recovered product although the exact nature of them could not be determined. This similarity between the two strains’ generated products also serves as a sign of their interchangeability. This study encourages the development of innovative, fast, and inexpensive techniques for the detection of heterogeneity while also provoking a debate about whether intact mass spectrometry-based analysis of the protein of interest is sufficient to detect heterogeneity in a product.

Effect of chromosomal integration on catalytic performance of a multi-component P450 system in Escherichia coli.

Cytochromes P450 are useful biocatalysts in synthetic chemistry and important bio-bricks in synthetic biology. Almost all bacterial P450s require separate redox partners for their activity, which are often expressed in recombinant Escherichia coli using multiple plasmids. However, the application of CRISPR/Cas recombineering facilitated chromosomal integration of heterologous genes which enables more stable and tunable expression of multi-component P450 systems for whole-cell biotransformations. Herein, we compared three E. coli strains W3110, JM109, and BL21(DE3) harboring three heterologous genes encoding a P450 and two redox partners either on plasmids or after chromosomal integration in two genomic loci. Both loci proved to be reliable and comparable for the model regio- and stereoselective two-step oxidation of (S)-ketamine. Furthermore, the CRISPR/Cas-assisted integration of the T7 RNA polymerase gene enabled an easy extension of T7 expression strains. Higher titers of soluble active P450 were achieved in E. coli harboring a single chromosomal copy of the P450 gene compared to E. coli carrying a medium copy pET plasmid. In addition, improved expression of both redox partners after chromosomal integration resulted in up to 80% higher (S)-ketamine conversion and more than fourfold increase in total turnover numbers.

Metabolic stress constrains microbial L-cysteine production in Escherichia coli by accelerating transposition through mobile genetic elements

BackgroundL-cysteine is an essential chemical building block in the pharmaceutical-, cosmetic-, food and agricultural sector. Conventionally, L-cysteine production relies on the conversion of keratinous biomass mediated by hydrochloric acid. Today, fermentative production based on recombinant E. coli, where L-cysteine production is streamlined and facilitated by synthetic plasmid constructs, is an alternative process at industrial scale. However, metabolic stress and the resulting production escape mechanisms in evolving populations are severely limiting factors during industrial biomanufacturing. We emulate high generation numbers typically reached in industrial fermentation processes with Escherichia coli harbouring L-cysteine production plasmid constructs. So far no genotypic and phenotypic alterations in early and late L-cysteine producing E. coli populations have been studied.ResultsIn a comparative experimental design, the E. coli K12 production strain W3110 and the reduced genome strain MDS42, almost free of insertion sequences, were used as hosts. Data indicates that W3110 populations acquire growth fitness at the expense of L-cysteine productivity within 60 generations, while production in MDS42 populations remains stable. For the first time, the negative impact of predominantly insertion sequence family 3 and 5 transposases on L-cysteine production is reported, by combining differential transcriptome analysis with NGS based deep plasmid sequencing. Furthermore, metabolic clustering of differentially expressed genes supports the hypothesis, that metabolic stress induces rapid propagation of plasmid rearrangements, leading to reduced L-cysteine yields in evolving populations over industrial fermentation time scales.ConclusionThe results of this study implicate how selective deletion of insertion sequence families could be a new route for improving industrial L-cysteine or even general amino acid production using recombinant E. coli hosts. Instead of using minimal genome strains, a selective deletion of certain IS families could offer the benefits of adaptive laboratory evolution (ALE) while maintaining enhanced L-cysteine production stability.

Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium.

Keratin-rich wastes, mainly in the form of feathers, are recalcitrant residues generated in high amounts as by-products in chicken farms and food industry. Polylactic acid (PLA) is the second most common biodegradable polymer found in commercial plastics, which is not easily degraded by microbial activity. This work reports the 3.8-Mb genome of Bacillus altitudinis B12, a highly efficient PLA- and keratin-degrading bacterium, with potential for environmental friendly biotechnological applications in the feed, fertilizer, detergent, leather, and pharmaceutical industries. The whole genome sequence of B. altitudinis B12 revealed that this strain (which had been previously misclassified as Bacillus pumilus B12) is closely related to the B. altitudinis strains ER5, W3, and GR-8. A total of 4056 coding sequences were annotated using the RAST server, of which 2484 are core genes of the pan genome of B. altitudinis and 171 are unique to this strain. According to the sequence analysis, B. pumilus B12 has a predicted secretome of 353 proteins, among which a keratinase and a PLA depolymerase were identified by sequence analysis. The presence of these two enzymes could explain the characterized PLA and keratin biodegradation capability of the strain.

CycA-Dependent Glycine Assimilation Is Connected to Novobiocin Susceptibility in Escherichia coli.

Escherichia coli serine hydroxymethyltransferase (GlyA) converts serine to glycine, and glyA mutants are auxotrophic for glycine. CycA is a transporter that mediates glycine uptake. Deleting glyA in E. coli strain W3110 led to activation of CysB, which was related to novobiocin (NOV) susceptibility. Moreover, deleting glyA resulted in increased sensitivity to NOV, and this could be reversed by high concentrations of glycine. Reverse mutants of ΔglyA were selected and one of them had a mutation in yrdC, the gene encoding threonylcarbamoyl-AMP synthase. Subsequent proteome analysis showed that deleting glyA led to increased expression of TcyP and TdcB, making this bacterium dependent on CycA for glycine assimilation. Furthermore, deleting cycA in a ΔglyA background caused a severe growth defect on Luria-Bertani medium, which could be complemented by high concentrations of exogenous glycine. Mutation of yrdC led to decreased expression of TdcB but increased expression of ThrA/B/C and LtaE, which favored the conversion of threonine to glycine and thus avoided the dependence on CycA. Correspondingly, deleting of tcyP, tdcB, or gshA could reverse the NOV-sensitive phenotype of ΔglyA mutants. Overexpression of cycA resulted in increased sensitivity to NOV, whereas deleting this gene caused NOV resistance. Moreover, overexpression of cycA led to increased accumulation of NOV upon drug treatment. Therefore, inactivation of glyA in E. coli led to CycA-dependent glycine assimilation, which enhanced the accumulation of NOV and then made the bacterium more sensitive to this drug. These findings broaden our understanding of glycine metabolism and mechanisms of NOV susceptibility. IMPORTANCE Novobiocin (NOV) has been used in clinical practice as an ATPase inhibitor for decades. However, because it has been withdrawn from the market, pharmaceutical companies are searching for other ATPase inhibitors. Thus, probing the mechanisms of susceptibility to NOV will be beneficial to those efforts. In this study, we showed that inactivation of glyA in E. coli led to CycA-dependent glycine assimilation, which accompanied the accumulation of NOV and thereby increased the sensitivity to this drug. To date, this is the first report demonstrating the linkage between glycine assimilation and NOV susceptibility, and it is also the first report showing that YrdC is able to modulate the metabolic flux of threonine.

Effective 5-aminolevulinic acid production via T7 RNA polymerase and RuBisCO equipped Escherichia coli W3110.

Chromosome-based engineering is a superior approach for gene integration generating a stable and robust chassis. Therefore, an effective amplifier, T7 RNA polymerase (T7RNAP) from bacteriophage, has been incorporated into Escherichia coli W3110 by site-specific integration. Herein, we performed the 5-aminolevulinic acid (5-ALA) production in four T7RNAP-equipped W3110 strains using recombinant 5-aminolevulinic synthase and further explored the metabolic difference in best strain. The fastest glucose consumption resulted in the highest biomass and the 5-ALA production reached to 5.5 g/L; thus, the least by-product of acetate was shown in RH strain in which T7RNAP was inserted at HK022 phage attack site. Overexpression of phosphoenolpyruvate (PEP) carboxylase would pull PEP to oxaloacetic acid in tricarboxylic acid cycle, leading to energy conservation and even no acetate production, thus, 6.53 g/L of 5-ALA was achieved. Amino acid utilization in RH deciphered the major metabolic flux in α-ketoglutaric acid dominating 5-ALA production. Finally, the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulokinase were expressed for carbon dioxide recycling; a robust and efficient chassis toward low-carbon assimilation and high-level of 5-ALA production up to 11.2 g/L in fed-batch fermentation was established.

Enhanced recombinant carbonic anhydrase in T7RNAP-equipped Escherichia coli W3110 for carbon capture storage and utilization (CCSU)

Sulfurihydrogenibium yellowstonense carbonic anhydrase (SyCA) is a well-known thermophilic CA for carbon mineralization. To broaden the applications of SyCA, the activity of SyCA was improved through stepwise engineering and in different cultural conditions, as well as extended to co-expression with other enzymes. The engineered W3110 strains with 4 different T7 RNA polymerase levels were employed for SyCA production. As a result, the best strain WT7L cultured in modified M9 medium with temperature shifted from 37 to 30 °C after induction increased SyCA activity to 9122 U/mL. The SyCA whole-cell biocatalyst was successfully applied for carbon capture and storage (CCS) of CaCO3. Furthermore, SyCA was applied for low-carbon footprint synthesis of 5-aminolevulinic acid (5-ALA) and cadaverine (DAP) by coupling with ALA synthetase (ALAS) and lysine decarboxylase (CadA), suppressing CO2 release to −6.1 g-CO2/g-ALA and −2.53 g-CO2/g-DAP, respectively. Harnessing a highly active SyCA offers a complete strategy for CCSU in a green process.

Ammonium Sensitivity of Biological Nitrogen Fixation by Anaerobic Diazotrophs in Cultures and Benthic Marine Sediments

AbstractNew bioavailable nitrogen (N) from biological nitrogen fixation (BNF) is critical for the N budget and productivity of marine ecosystems. Nitrogen‐fixing organisms typically inactivate BNF when less metabolically costly N sources, like ammonium (NH4+), are available. Yet, several studies have observed BNF in benthic marine sediments linked to anaerobic sulfate‐reducing bacteria and fermenting firmicutes despite high porewater NH4+ concentrations (10–1,500 μM). To better understand the regulating controls and importance of benthic marine BNF, we evaluate BNF sensitivity to NH4+ in benthic diazotrophs using incubations of increasing biogeochemical complexity. BNF by cultures of model anaerobic diazotrophs (sulfate‐reducer Desulfovibrio vulgaris var. Hildenborough, fermenter Clostridium pasteurianum strain W5), sulfate‐reducing sediment enrichment cultures, and sediments from three Northeastern salt marshes (USA) is highly sensitive to external NH4+. BNF is inhibited by NH4+ beyond an apparent threshold [NH4+] of 2 μM in liquid cultures, most closely reflecting the true cellular sensitivity of BNF to NH4+. Sediment slurries exhibited an apparent threshold [NH4+] of 9 μM. Consistent with other studies, we find SRB‐like nitrogenase (nifH) gene and transcripts are prevalent in sediments. Our survey of porewater NH4+ data from diverse sediments suggests the broad applicability of inhibition thresholds measured here and confinement of benthic BNF to surficial sediments. Variations in BNF inhibition timing, NH4+ uptake rate, sediment composition, and biophysics could affect measurements of the apparent sensitivity of benthic BNF to NH4+. We propose NH4+ transporter affinity as a fundamental mechanistic constraint on NH4+ control of cellular BNF to improve biogeochemical models of N cycling.

Crude oil hydrocarbon degradation efficiency of indigenous bacterial strains isolated from contaminated sites in Nigeria

The crude oil degradation potential of bacterial isolates from three contaminated sites in Nigeria were investigated. Seven bacterial isolates namely Pseudomonas aeruginosa strain W15, Pseudomonas aeruginosa strain N3R, Serratia marcescens strain N4, Providencia vermicola strain W8, Serratia marcescens strain W13, Pseudomonas aeruginosa strain W11 and Pseudomonas protegens strain P7 were isolated and identified using molecular methods. Isolates N4, N3 and W13 showed higher % total petroleum hydrocarbon (TPH) degradation of 79.26%, 78.96% and 78.69% respectively than W15, P7, W8 and W11 with % TPH degradation of 68.96%, 62.14%, 59.75% and 59.00% respectively. W13 showed the fastest degradation rate with 78.72% within the first 14 days of incubation; however, after the 14th day, there was no progressive change in % TPH. W11 showed degradation of wider range of hydrocarbon components originally in the crude oil as well as the complete degradation of most intermediates formed. The isolates showed good degradation potentials for bioremediation applications.

Piriformospora indica and Azotobacter chroococcum Consortium Facilitates Higher Acquisition of N, P with Improved Carbon Allocation and Enhanced Plant Growth in Oryza sativa.

The soil microbiome contributes to nutrient acquisition and plant adaptation to numerous biotic and abiotic stresses. Numerous studies have been conducted over the past decade showing that plants take up nutrients better when associated with fungi and additional beneficial bacteria that promote plant growth, but the mechanisms by which the plant host benefits from this tripartite association are not yet fully understood. In this article, we report on a synergistic interaction between rice (Oryza sativa), Piriformospora indica (an endophytic fungus colonizing the rice roots), and Azotobacter chroococcum strain W5, a free-living nitrogen-fixing bacterium. On the basis of mRNA expression analysis and enzymatic activity, we found that co-inoculation of plant roots with the fungus and the rhizobacterium leads to enhanced plant growth and improved nutrient uptake compared to inoculation with either of the two microbes individually. Proteome analysis of O. sativa further revealed that proteins involved in nitrogen and phosphorus metabolism are upregulated and improve nitrogen and phosphate uptake. Our results also show that A. chroococcum supports colonization of rice roots by P. indica, and consequentially, the plants are more resistant to biotic stress upon co-colonization. Our research provides detailed insights into the mechanisms by which microbial partners synergistically promote each other in the interaction while being associated with the host plant.

A common SSD1 truncation is toxic to cells entering quiescence and promotes sporulation.

Ssd1p is an RNA binding protein in Saccharomyces cerevisiae that plays an important role in cell division, cell fate decisions, stress response and virulence. Lab strain W303 encodes the terminal truncation ssd1-2, which is typically interpreted to be a loss of function allele. We have shown that ssd1-2 is toxic to mpt5-Δ mutants and to diploids entering stationary phase and quiescence. The ssd1-Δ null shows no toxicity, indicating that ssd1-2 is disrupting an essential function that does not solely require Ssd1p. ssd1-2 cells are also more sensitive to stress than ssd1-Δ . These phenotypes are recessive to SSD1-1 . In contrast, ssd1-2 plays a dominant role in promoting sporulation.

Population dynamics and crude oil degrading ability of bacterial consortia of isolates from oil-contaminated sites in Nigeria.

Application of bacterial consortium of hydrocarbon degraders to crude oil-contaminated site can enhance bioremediation. This study evaluated the population dynamics and crude oil degradation abilities of various consortia developed from bacterial strains isolated from crude oil-contaminated sites using crude oil-supplemented Bushnell Haas media. Each consortium consisted of three bacterial strains and was designated as Consortium A (Serratia marcescens strain N4, Pseudomonas aeruginosa strain N3R, Pseudomonas aeruginosa strain W11), B (Pseudomonas aeruginosa strain N3R, Pseudomonas aeruginosa strain W11, Pseudomonas protegens strain P7), C (Serratia marcescens strain N4, Pseudomonas aeruginosa strain W11, Pseudomonas protegens strain P7), and D (Pseudomonas aeruginosa strain W15, Providencia vermicola strain W8, Serratia marcescens strain W13). There was progressive decline in the populations of Serratia marcescens strains in the consortia as the incubation period progressed. This may have led to reduction in their synergistic contribution and, subsequently, total degradation ability of crude oil by the consortia. The gravimetric analyses showed that Consortium D produced the highest % crude oil degradation of 29.66% compared to Consortia A, B, and C with 23.73%, 11.86%, and 19.49% respectively. Based on gas chromatography-mass spectrometry analyses, Consortium D produced the highest percentage total petroleum hydrocarbon degradation of 73.65% compared to 68.24%, 68.94%, and 69.19% produced by Consortia A, B, and C respectively. The biodegradation potential of Consortium D also demonstrates the significance of using isolates from the same isolation site in development of consortium for bioremediation.

Mechanistic study of antimonate reduction by Escherichia coli W3110

Microbial-assisted antimonate [Sb(V)] reduction immobilizes this redox-sensitive metalloid in the subsurface. Most indigenous aerobes in antimony (Sb)-contaminated areas do not contain Sb(V)-reducing genes but can resist high levels of Sb(V) threat. Herein, to unravel the mechanisms of Sb(V) resistance by aerobes, we used Escherichia coli W3110 as a model aerobe and incubated it with 10 μM Sb(V). We found that strain W3110, without known Sb(V)-reducing genes, was able to reduce Sb(V) to Sb(III). Our transcriptome analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) results show that the Sb(V) threat at the 10 μM level had a negligible effect on the gene expression of strain W3110. In vitro incubation experiments further indicate that Sb(V) reduction was attributable to extracellular polymeric substances (EPS). Moreover, the three-dimensional excitation-emission matrix fluorescence spectroscopy reveals that the tryptophan-like components in EPS were involved in Sb(V) binding as evidenced by its weakened fluorescence intensity upon Sb(V) addition. The FTIR and XPS analyses indicate that hemiacetal and amide groups in EPS contributed to the reduction of Sb(V). Preculture with 10 μM Sb(V) did not exhibit a significant difference in Sb(V)-reducing capacity, suggesting that Sb(V) stress probably did not stimulate EPS secretion of W3110. Our results highlight the importance of EPS as the first line of defense against toxins, especially for those bacteria without such functional genes.

Stenotrophomonas nematodicola sp. nov., isolated from Caenorhabditis elegans.

A Gram stain-negative, coccoid rod-shaped, motile by gliding, facultatively aerobic bacterium, designated W5, was isolated from Caenorhabditis elegans samples in BaotianmanNatural Reserve (33° 27' 47'' N; 111° 48' 32'' E), Nanyang, China. The isolate was characterized taxonomically using a polyphasic approach. The 16S rRNA gene of strain W5 exhibited 98.1-99.7% similarity to the 16S rRNA genes of members of the genus Stenotrophomonas, and < 98.0% similarities to those of other bacterial species in the family Lysobacteraceae. The most closely related strains were Stenotrophomonas rhizophila JCM 13333T (99.7%) and Stenotrophomonasbentonitica DSM 103927T (99.2%). The predominant respiratory quinone of the isolate is Q-8. The major fatty acids are iso-C15:0 (38.2%) and antesio-C15:0 (16.6%). The draft genome of strain W5 had a length of 4,402,751bp and a DNA G + C content of 67.3mol%. The ANI values between the draft genomes of strain W5 and its closest phylogenetic neighbors S. rhizophila JCM 1333T and S. bentonitica DSM 103927T were 84.7% and 85.0%, respectively. The DDH value between W5 and S. rhizophila JCM 13333T was 30.8%, which was the highest DDH level. We propose that strain W5 represents a novel bacterial species with the name Stenotrophomonas nematodicola sp. nov. and W5 as the type strain. The type strain is W5 (= CPCC 101271T = CGMCC 19401T = KCTC XXXT).

Bifidobacterium longum W11: Uniqueness and individual or combined clinical use in association with rifaximin.

Strains belonging to bifidobacteria have been documented as being helpful in adults with intestinal dysbiosis conditions, like those related to irritable bowel syndrome (IBS). This review aims to present the most relevant evidence regarding the efficacy of Bifidobacterium longum W11, a Bifidobacterium used in clinical settings for conditions such as IBS and inflammatory bowel disease. The following electronic databases were systematically searched up to August 2020: MEDLINE (via PubMed), EMBASE, Cochrane Central Database of Controlled Trials (via CENTRAL), Google Scholar, and Clinicaltrials.gov. Data arising from pooled analysis, 7 invitro/pharmacological studies, 7 clinical trials including 1 randomized, double-blind and placebo-controlled, showed that the probiotic strain B.longum W11 has been extensively studied for its efficacy in subjects with IBS with constipation, leading to a significant reduction in symptoms. In particular, its role in alleviating constipation was also confirmed in subjects for whom a low-calorie weight-loss diet led to the slowing down of gut motility. The probiotic characteristics of B. longum W11 were further demonstrated in the treatment of minimal hepatic encephalopathy and hepatic disease. The most remarkable trait of B. longum W11 is its non-transmissible antibiotic resistance, due to a nucleotide polymorphism mutation in the rpoB gene, making it resistant to antibiotics of the rifampicin group, including rifaximin. The co-administration of B. longum W11 and rifaximin in patients with symptomatic uncomplicated diverticular disease brought about a further significant improvement in the clinical condition compared to patients treated with rifaximin alone. B. longum W11 is a probiotic which could synergize with rifaximin as an adjuvant to antibiotic treatment. Taken altogether these findings demonstrate the clinical role of the strain W11 both in some functional and in some inflammatory bowel diseases.