Review
	
	
				- Omics in gut microbiome analysis
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		Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh 		
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			J. Microbiol. 2021;59(3):292-297.   Published online February 23, 2021		
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							DOI: https://doi.org/10.1007/s12275-021-1004-0
					
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						 Abstract Abstract PDF PDF
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		Our understanding of the interactions between microbial communities
and their niche in the host gut has improved owing
to recent advances in environmental microbial genomics.
Integration of metagenomic and metataxonomic sequencing
data with other omics data to study the gut microbiome
has become increasingly common, but downstream analysis
after data integration and interpretation of complex omics
data remain challenging. Here, we review studies that have
explored the gut microbiome signature using omics approaches,
including metagenomics, metataxonomics, metatranscriptomics,
and metabolomics. We further discuss recent
analytics programs to analyze and integrate multi-omics datasets
and further utilization of omics data with other advanced
techniques, such as adaptive immune receptor repertoire sequencing,
microbial culturomics, and machine learning, to
evaluate important microbiome characteristics in the gut.	
		
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 Journal Articles
	
	
				- A murine colitis model developed using a combination of dextran sulfate sodium and Citrobacter rodentium
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		Jin-Il Park , Sun-Min Seo , Jong-Hyung Park , Hee-Yeon Jeon , Jun-Young Kim , Seung-Hyun Ryu , Yang-Kyu Choi 		
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			J. Microbiol. 2018;56(4):272-279.   Published online April 2, 2018		
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							DOI: https://doi.org/10.1007/s12275-018-7504-x
					
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						 Abstract Abstract PDF PDF
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		Adult mice were treated with dextran sulfate sodium (DSS)
and infected with Citrobacter rodentium for developing a
novel murine colitis model. C57BL/6N mice (7-week-old)
were divided into four groups. Each group composed of control,
dextran sodium sulfate-treated (DSS), C. rodentiuminfected
(CT), and DSS-treated and C. rodentium-infected
(DSS-CT) mice. The DSS group was administered 1% DSS
in drinking water for 7 days. The CT group was supplied
with normal drinking water for 7 days and subsequently infected
with C. rodentium via oral gavage. The DSS-CT group
was supplied with 1% DSS in drinking water for 7 days and
subsequently infected with C. rodentium via oral gavage. The
mice were sacrificed 10 days after the induction of C. rodentium
infection. The DSS-CT group displayed significantly
shorter colon length, higher spleen to body weight ratio, and
higher histopathological score compared to the other three
groups. The mRNA expression levels of tumor necrosis factor
(TNF)-α and interferon (INF)-γ were significantly upregulated;
however, those of interleukin (IL)-6 and IL-10 were
significantly downregulated in the DSS-CT group than in
the control group. These results demonstrated that a combination
of low DSS concentration (1%) and C. rodentium
infection could effectively induce inflammatory bowel disease
(IBD) in mice. This may potentially be used as a novel
IBD model, in which colitis is induced in mice by the combination
of a chemical and a pathogen.	
		
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			Citations Citations to this article as recorded by    
- Reduction of colitis in mice by chemically programmed supramolecular nanoassemblies of vitamin–lipid conjugates
 Shiyun Xian, Fanchao Meng, Xiaona Chen, Liqing Zhu, Hangxiang Wang
 Journal of Nanobiotechnology.2025;[Epub]     CrossRef
- 	Compound Xuejie Preparation Improved Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice by Mitigating Inflammation-Induced Damage and Downregulating TNF-α Expression
 M.M. Yajiao Zhao, M.D. Lin Jin, M.M. Xiaolong Yuan, M.D. Xiaochuan Liu, M.M. Guiming Zang
 International Journal of Pharmacology.2024; 20(4): 652.     CrossRef
- Development of a novel complex inflammatory bowel disease mouse model: Reproducing human inflammatory bowel disease etiologies in mice
 Sun-Min Seo, Na-Won Kim, Eun-Seon Yoo, Ji-Hun Lee, Ah-Reum Kang, Han-Bi Jeong, Won-Yong Shim, Dong-Hyun Kim, Young-Jun Park, Kieun Bae, Kyong-Ah Yoon, Yang-Kyu Choi, Pradeep Dudeja
 PLOS ONE.2024; 19(11): e0311310.     CrossRef
- Protective Role of the Toll-Like Receptor 5 Agonist KMRC011 against Murine Colitis Induced by Citrobacter rodentium and Dextran Sulfate Sodium
 Jun-Young Kim, Sun-Min Seo, Han-Woong Kim, Woo-Jong Lee, Yang-Kyu Choi
 Journal of Microbiology and Biotechnology.2023; 33(1): 35.     CrossRef
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 Ting QIU, Lu NIU, Yu ZHANG, Yifei LV
 Food Science and Technology.2023;[Epub]     CrossRef
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 Yunchang Zhang, Xuemeng Si, Ling Yang, Hui Wang, Ye Sun, Ning Liu
 Animal Models and Experimental Medicine.2022; 5(4): 311.     CrossRef
- Noni juice-fortified yogurt mitigates dextran sodium sulfate-induced colitis in mice through the modulation of inflammatory cytokines
 So-Hee Kwon, Damini Kothari, Hae-In Jung, Jeong-Min Lim, Woong-Lae Kim, Hyuk-Cheol Kwon, Sung-Gu Han, Sun-Min Seo, Yang-Kyu Choi, Soo-Ki Kim
 Journal of Functional Foods.2021; 86: 104652.     CrossRef
- Probiotic Bacillus cereus Alleviates Dextran Sulfate Sodium-Induced Colitis in Mice through Improvement of the Intestinal Barrier Function, Anti-Inflammation, and Gut Microbiota Modulation
 Kangliang Sheng, Yifan Xu, Xiaowei Kong, Jingmin Wang, Xiangdong Zha, Yongzhong Wang
 Journal of Agricultural and Food Chemistry.2021; 69(49): 14810.     CrossRef
 
 
	
	
				- Lactobacillus curvatus WiKim38 isolated from kimchi induces IL-10 production in dendritic cells and alleviates DSS-induced colitis in mice
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		Sung-Gang Jo , Eui-Jeong Noh , Jun-Young Lee , Green Kim , Joo-Hee Choi , Mo-Eun Lee , Jung-Hee Song , Ji-Yoon Chang , Jong-Hwan Park 		
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			J. Microbiol. 2016;54(7):503-509.   Published online June 28, 2016		
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							DOI: https://doi.org/10.1007/s12275-016-6160-2
					
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						 Abstract Abstract PDF PDF
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		Probiotics such as lactobacilli and bifidobacteria have healthpromoting
effects by immune modulation. In the present
study, we examined the immunomodulatory properties of
Lactobacillus curvatus WiKim38, which was newly isolated
from baechu (Chinese cabbage) kimchi. The ability of L.
curvatus WiKim38 to induce cytokine production in bone
marrow-derived dendritic cells (BMDCs) was determined by
enzyme-linked immunosorbent assay. To evaluate the molecular
mechanisms underlying L. curvatus Wikim38-mediated
IL-10 production, Western blot analyses and inhibitor
assays were performed. Moreover, the in vivo anti-inflammatory
effects of L. curvatus WiKim38 were examined in a dextran
sodium sulfate (DSS)-induced colitis mouse model. L.
curvatus WiKim38 induced significantly higher levels of IL-
10 in BMDCs compared with that induced by LPS. NF-κB
and ERK were activated by L. curvatus WiKim38, and an
inhibitor assay revealed that these pathways were required
for L. curvatus WiKim38-induced production of IL-10 in
BMDCs. An in vivo experiment showed that oral administration
of L. curvatus WiKim38 increased the survival rate
of mice with DSS-induced colitis and improved clinical signs
and histopathological severity in colon tissues. Taken together,
these results indicate that L. curvatus Wikim38 may
have health-promoting effects via immune modulation, and
may thus be applicable for therapy of various inflammatory
diseases.	
		
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 Research Support, Non-U.S. Gov't
	
	
				- Microbial Fingerprinting Detects Unique Bacterial Communities in the Faecal Microbiota of Rats with Experimentally-Induced Colitis
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		Ashis K. Samanta , Valeria A. Torok , Nigel J. Percy , Suzanne M. Abimosleh , Gordon S. Howarth 		
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			J. Microbiol. 2012;50(2):218-225.   Published online April 27, 2012		
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							DOI: https://doi.org/10.1007/s12275-012-1362-8
					
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						 Abstract Abstract PDF PDF
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		An abnormal composition of the gut microbiota is believed
to be associated with the pathogenesis of inflammatory
bowel disease (IBD). We utilized terminal restriction fragment
length polymorphism (T-RFLP) analysis to quantify
faecal bacterial communities from rats with experimental
colitis. Male Sprague Dawley rats (n=10/group) ingested
2% dextran sulfate sodium (DSS) or water for up to 7 days.
Rats were killed and colonic tissues collected for histological
analysis. Damage severity score in the distal colon was significantly
greater (P<0.001) following DSS consumption
compared to controls. T-RFLP faecal bacterial profiles generated
with either MspI or CfoI revealed a significant difference
(P<0.001) in community composition between healthy
and colitic rats, with bacterial composition in healthy rats
more variable than in rats with colitis. Operational taxonomic
units (OTU: taxonomically related groups of bacteria)
associated with either the healthy or colitic state were
identified. OTU (116, 226, 360, and 948; CfoI) and (118 and
188; MspI) were strongly associated with untreated healthy
rats, while OTU (94, 98, 174, and 384; CfoI) and (94 and
914; MspI) were predominantly associated with DSS-treated
colitic rats. Phylogenetic OTU assignment suggested that
Bacteroidales and Lactobacillus sp. were predominantly associated
with the colitic and healthy rats, respectively. These
 results
 show that faecal bacterial profiling is a rapid, sensitive
and non-invasive tool for detecting and identifying changes
in gut microbiota associated with colitis. Restoring microbial
homeostasis by targeting colitis-associated OTU through
specific microbiological interventions could form the basis
of novel therapeutic strategies for IBD.
- 
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