- Microbial source tracking using metagenomics and other new technologies
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Shahbaz Raza , Jungman Kim , Michael J. Sadowsky , Tatsuya Unno
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J. Microbiol. 2021;59(3):259-269. Published online February 10, 2021
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DOI: https://doi.org/10.1007/s12275-021-0668-9
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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.
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Citations
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Jang-Cheon Cho
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- Intervention with kimchi microbial community ameliorates obesity by regulating gut microbiota
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Seong-Eun Park , Sun Jae Kwon , Kwang-Moon Cho , Seung-Ho Seo , Eun-Ju Kim , Tatsuya Unno , So-Hyeon Bok , Dae-Hun Park , Hong-Seok Son
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J. Microbiol. 2020;58(10):859-867. Published online September 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-0266-2
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666
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21
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22
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Abstract
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The objective of this study was to evaluate anti-obesity effects
of kimchi microbial community (KMC) on obesity and
gut microbiota using a high fat diet-induced mouse model
compared to effects of a single strain. Administration of KMC
decreased body weight, adipose tissue, and liver weight gains.
Relative content of Muribaculaceae in the gut of the KMCtreated
group was higher than that in the high-fat diet (HFD)
group whereas relative contents of Akkermansiaceae, Coriobacteriaceae,
and Erysipelotrichaceae were lower in KMCtreated
group. Metabolic profile of blood was found to change
differently according to the administration of KMC and a
single strain of Lactobacillus plantarum. Serum metabolites
significantly increased in the HFD group but decreased in
the KMC-treated group included arachidic acid, stearic acid,
fumaric acid, and glucose, suggesting that the administration
of KMC could influence energy metabolism. The main genus
in KMC was not detected in guts of mice in KMC-treated
group. Since the use of KMC has advantages in terms of
safety, it has potential to improve gut microbial community
for obese people.
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Citations
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- Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant
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Sachin Kumar Gupta , Hanseob Shin , Dukki Han , Hor-Gil Hur , Tatsuya Unno
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J. Microbiol. 2018;56(6):408-415. Published online June 1, 2018
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DOI: https://doi.org/10.1007/s12275-018-8195-z
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555
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Abstract
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The increased antibiotic resistance among microorganisms
has resulted into growing interest for investigating the wastewater
treatment plants (WWTPs) as they are reported to be
the major source in the dissemination of antibiotic resistance
genes (ARGs) and heavy metal resistance genes (HMRGs)
in the environment. In this study, we investigated the prevalence
and persistence of ARGs and HMRGs as well as bacterial
diversity and mobile genetic elements (MGEs) in influent
and effluent at the WWTP in Gwangju, South Korea,
using high-throughput sequencing based metagenomic approach.
A good number of broad-spectrum of resistance
genes (both ARG and HMRG) were prevalent and likely
persistent, although large portion of them were successfully
removed at the wastewater treatment process. The relative
abundance of ARGs and MGEs was higher in effluent as compared
to that of influent. Our results suggest that the resistance
genes with high abundance and bacteria harbouring
ARGs and MGEs are likely to persist more through the treatment
process. On analyzing the microbial community, the
phylum Proteobacteria, especially potentially pathogenic species
belonging to the genus Acinetobacter, dominated in
WWTP. Overall, our study demonstrates that many ARGs
and HMRGs may persist the treatment processes in WWTPs
and their association to MGEs may contribute to the dissemination
of resistance genes among microorganisms in the
environment.
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Taekil Eom , Yong Sung Kim , Chang Hwan Choi , Michael J. Sadowsky , Tatsuya Unno
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J. Microbiol. 2018;56(3):189-198. Published online February 28, 2018
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DOI: https://doi.org/10.1007/s12275-018-8049-8
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Abstract
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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
result
ing 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.
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