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Lee Sua,Cho Min,Sadowsky Michael J.,Jang Jeonghwan 한국미생물학회 2023 The journal of microbiology Vol.61 No.9
Nitrate ( NO3 −) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3 − have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas ( N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3 −-removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3 − in several field studies. NO3 − removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3 − to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3 − pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3 − from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3 − in WBR, and perspectives to enhance WBR performance in the future.
Microbial source tracking using metagenomics and other new technologies
Raza Shahbaz,Kim Jungman,Sadowsky Michael J.,Unno Tatsuya 한국미생물학회 2021 The journal of microbiology Vol.59 No.3
The environment is under siege from a variety of pollution sources. Fecal pollution is especially harmful as it disperses pathogenic bacteria into waterways. Unraveling origins of mixed sources of fecal bacteria is difficult and microbial source tracking (MST) in complex environments is still a daunting task. Despite the challenges, the need for answers far outweighs the difficulties experienced. Advancements in qPCR and next generation sequencing (NGS) technologies have shifted the traditional culture-based MST approaches towards culture independent technologies, where communitybased MST is becoming a method of choice. Metagenomic tools may be useful to overcome some of the limitations of community-based MST methods as they can give deep insight into identifying host specific fecal markers and their association with different environments. Adoption of machine learning (ML) algorithms, along with the metagenomic based MST approaches, will also provide a statistically robust and automated platform. To compliment that, ML-based approaches provide accurate optimization of resources. With the successful application of ML based models in disease prediction, outbreak investigation and medicine prescription, it would be possible that these methods would serve as a better surrogate of traditional MST approaches in future.
Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease
엄태길,김용성,최창환,Michael J. Sadowsky,Tatsuya Unno 한국미생물학회 2018 The journal of microbiology Vol.56 No.3
Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified > 200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci resulting in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti- TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.
Shamseldin, A.,El-Saadani, M.,Sadowsky, M.J.,An, C.S. Pergamon Press ; Elsevier Science Ltd 2009 Soil biology & biochemistry Vol.41 No.1
Twenty-eight Rhizobium strains were isolated from the root nodules of faba bean (Vicia faba L.) collected from 11 governorates in Egypt. A majority of these strains (57%) were identified as Rhizobium leguminosarum bv. viciae (Rlv) based on analysis of a nodC gene fragment amplified using specific primers for these faba bean symbionts. The strains were characterized using a polyphasic approach, including nodulation pattern, tolerance to environmental stresses, and genetic diversity based on amplified ribosomal DNA-restriction analysis (ARDRA) of both 16S and 23S rDNA. Analysis of tolerance to environmental stresses revealed that some of these strains can survive in the presence of 1% NaCl and a majority of them survived well at 37 <SUP>o</SUP>C. ARDRA indicated that the strains could be divided into six 16S rDNA genotypes and five 23S rDNA genotypes. Sequence analysis of 16S rDNA indicated that 57% were Rlv, two strains were Rhizobium etli, one strain was taxonomically related to Rhizobium rubi, and a group of strains were most closely related to Sinorhizobium meliloti. Results of these studies indicate that genetically diverse rhizobial strains are capable of forming N<SUB>2</SUB>-fixing symbiotic associations with faba bean and PCR done using nodC primers allows for the rapid identification of V. faba symbionts.
Jang, Jeonghwan,Suh, Yae-Seul,Di, Doris Y. W.,Unno, Tatsuya,Sadowsky, Michael J.,Hur, Hor-Gil American Chemical Society 2013 Environmental science & technology Vol.47 No.2
<P>A total of 3564 <I>E. coli</I> isolates obtained from Yeongsan River basin of South Korea were investigated for their production of extended-spectrum β-lactamases (ESBLs) and potential pathogenicity to better understand the linkage between antibiotic-resistant pathogens in the environment and their public health risks. Interestingly, 60% (53 of 89) of the screen-positive ESBL producers were determined to be potentially one or both of the diarrheagenic and extraintestinal pathogenic (ExPEC) pathotypes, suggesting that trade-off between resistance and virulence of <I>E. coli</I> may not apply to this study. In addition, 67% (60 of 89) of the screen-positive ESBL producers possessed more than one β-lactamase gene, and most (59 of 63) of the ESBL producers had the CTX-M-14 enzyme, which is the most dominant ESBL and seems to be related to urban anthropogenic activities. About 68% (36 of 53) of the potential pathogenic strains were resistant to more than 2 non-β-lactam antibiotics. Results from this study indicate that the Yeongsan River basin has been contaminated with antibiotic-resistant and potential pathogenic <I>E. coli</I> strains. While few studies have examined pathogenecity of ESBL-producing bacteria, this study reports the possible public health risk which could be caused by the fecal indicator bacterium itself containing both ESBL genes and virulence factors. This will likely impact the dissemination of potential pathogenic <I>E. coli</I> producing ESBLs in the environment and suggests the need for further investigations of antibiotic-resistant pathogens to prevent public health impacts in the Yeongsan River basin.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/esthag/2013/esthag.2013.47.issue-2/es303577u/production/images/medium/es-2012-03577u_0003.gif'></P>
Seo, Jiyoung,Ryu, Ji-Young,Han, Jaehong,Ahn, Joong-Hoon,Sadowsky, Michael J,Hur, Hor-Gil,Chong, Youhoon Springer International 2013 Applied microbiology and biotechnology Vol.97 No.2
<P>Wild-type naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 transforms relatively planar flavone and isoflavone to cis-dihydrodiols. However, this enzyme cannot catalyze the transformation of flavanone and isoflavanone in which a phenyl group bonds to the stereogenic C2 or C3 of the C-ring. Protein modeling suggested that Phe224 in the substrate binding site of NDO may play a key role in substrate specificity toward flavanone and isoflavanone. Site-directed mutants of NDO with substitution of Phe224 with Tyr biotransformed only the (S)-stereoisomers of flavanone and isoflavanone, producing an 8-OH group on the A-ring. In contrast, the Phe224Cys and Phe224Gln substitutions, which used (2S)-flavanone as a substrate, and Phe224Lys, which transformed (2S)-flavanone and (3S)-isoflavanone, each showed lower activity than the Phe224Tyr substitution. The remainder of the tested mutants had no activity with flavanone and isoflavanone. Protein docking studies of flavanone and isoflavanone to the modeled mutant enzyme structures revealed that an expanded substrate binding site, due to mutation at 224, as well as appropriate hydrophobic interaction with the residue at 224, are critical for successful binding of the substrates. Results of this study also suggested that in addition to the previously known Phe352, the Phe224 site of NDO appears to be important site for expanding the substrate range of NDO and bringing regiospecific and stereospecific hydroxylation reactions to C8 of the flavanone and isoflavanone A-rings.</P>