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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.
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.
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.
Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease
Eom, Taekil,Kim, Yong Sung,Choi, Chang Hwan,Sadowsky, Michael J.,Unno, Tatsuya MICROBIOLOGICAL SOCIETY OF KOREA 2018 JOURNAL OF MICROBIOLOGY -SEOUL- 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.
Unno, Tatsuya,Han, Dukki,Jang, Jeonghwan,Widmer, Kenneth,Ko, GwangPyo,Sadowsky, Michael J.,Hur, Hor-Gil Japanese Society of Microbial Ecology · The Japane 2011 Microbes and environments Vol.26 No.3
<P>South Korea uses more antibiotics for animal production than any other member of the OECD. The excessive use could potentially lead to a greater incidence of antibiotic resistant microorganisms, some of which may be pathogenic. In this study, we examined potential diarrheagenic and extraintestinal pathogenic <I>E. coli</I> (ExPEC) isolates using virulence gene profiling (<I>eaeA</I>, <I>est</I>, <I>elt</I>, <I>ipaH</I>, <I>stx1</I> and <I>stx2</I> as diarrheagenic and <I>afa/dra</I>, <I>iutA</I>, <I>kpsMT II</I>, <I>papA/C</I>, and <I>sfa/foc</I> as extraintestinal pathogenic virulence genes). A cluster analysis of DNA fingerprint data indicated that certain genotypes of chicken <I>E. coli</I> isolates are likely ExPEC. Moreover, our results showed 38 of the 60 potential diarrheagenic and ExPEC isolates obtained from animals and humans were also resistant to antibiotics, mostly to tetracycline groups, penicillin groups, and folate pathway inhibitors. Our results suggest that the use of antibiotics in agriculture should be controlled due to potential impacts on human health.</P>
Unno, Tatsuya,Staley, Christopher,Brown, Clairessa M.,Han, Dukki,Sadowsky, Michael J.,Hur, Hor‐,Gil BLACKWELL SCIENCE 2018 ENVIRONMENTAL MICROBIOLOGY Vol.20 No.9
<P>In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.</P>