Journal Articles
- Probiotic supplements alleviate gestational diabetes mellitus by restoring the diversity of gut microbiota: a study based on 16S rRNA sequencing
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Qing-Xiang Zheng , Xiu-Min Jiang , Hai-Wei Wang , Li Ge , Yu-Ting Lai , Xin-Yong Jiang , Fan Chen , Ping-Ping Huang
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J. Microbiol. 2021;59(9):827-839. Published online August 12, 2021
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DOI: https://doi.org/10.1007/s12275-021-1094-8
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Abstract
- Probiotics effectively prevent and improve metabolic diseases
such as diabetes by regulating the intestinal microenvironment
and gut microbiota. However, the effects of probiotics
in gestational diabetes mellitus are not clear. Here, we
showed that probiotic supplements significantly improved
fasting blood glucose in a gestational diabetes mellitus rat
model. To further understand the mechanisms of probiotics
in gestational diabetes mellitus, the gut microbiota were analyzed
via 16S rRNA sequencing. We found that compared
with the normal pregnant group, the gestational diabetes mellitus
rats had decreased diversity of gut microbiota. Moreover,
probiotic supplementation restored the diversity of the
gut microbiota in gestational diabetes mellitus rats, and the
gut microbiota structure tended to be similar to that of normal
pregnant rats. In particular, compared with gestational
diabetes mellitus rats, the abundance of Firmicutes and Actinobacteria
was higher after probiotic supplementation. Furthermore,
activating carbohydrate metabolism and membrane
transport pathways may be involved in the potential mechanisms
by which probiotic supplements alleviate gestational
diabetes mellitus. Overall, our results suggested that probiotic
supplementation might be a novel approach to restore the gut
microbiota of gestational diabetes mellitus rats and provided
an experimental evidence for the use of probiotic supplements
to treat gestational diabetes melitus.
- STATR: A simple analysis pipeline of Ribo-Seq in bacteria
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Donghui Choe , Bernhard Palsson , Byung-Kwan Cho
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J. Microbiol. 2020;58(3):217-226. Published online January 28, 2020
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DOI: https://doi.org/10.1007/s12275-020-9536-2
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9
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Abstract
- Gene expression changes in response to diverse environmental
stimuli to regulate numerous cellular functions. Genes are expressed
into their functional products with the help of messenger
RNA (mRNA). Thus, measuring levels of mRNA in
cells is important to understand cellular functions. With advances
in next-generation sequencing (NGS), the abundance
of cellular mRNA has been elucidated via transcriptome sequencing.
However, several studies have found a discrepancy
between mRNA abundance and protein levels induced by
translational regulation, including different rates of ribosome
entry and translational pausing. As such, the levels of mRNA
are not necessarily a direct representation of the protein levels
found in a cell. To determine a more precise way to measure
protein expression in cells, the analysis of the levels of mRNA
associated with ribosomes is being adopted. With an aid of
NGS techniques, a single nucleotide resolution footprint of
the ribosome was determined using a method known as Ribo-
Seq or ribosome profiling. This method allows for the highthroughput
measurement of translation in vivo, which was
further analyzed to determine the protein synthesis rate, translational
pausing, and cellular responses toward a variety of
environmental changes. Here, we describe a simple analysis
pipeline for Ribo-Seq in bacteria, so-called simple translatome
analysis tool for Ribo-Seq (STATR). STATR can be
used to carry out the primary processing of Ribo-Seq data,
subsequently allowing for multiple levels of translatome study,
from experimental validation to in-depth analyses. A command-
by-command explanation is provided here to allow a
broad spectrum of biologists to easily reproduce the analysis.
- Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology
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Adriana Sturion Lorenzi , Mathias Ahii Chia , Fabyano Alvares Cardoso Lopes , Genivaldo Gueiros Z. Silva , Robert A. Edwards , Maria do Carmo Bittencourt-Oliveira
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J. Microbiol. 2019;57(6):450-460. Published online May 27, 2019
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DOI: https://doi.org/10.1007/s12275-019-8349-7
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Abstract
- Next-generation DNA sequencing technology was applied
to generate molecular data from semiarid reservoirs during
well-defined seasons. Target sequences of 16S-23S rRNA ITS
and cpcBA-IGS were used to reveal the taxonomic groups of
cyanobacteria present in the samples, and genes coding for
cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA),
and cylindrospermopsins (cyrJ) were investigated. The presence
of saxitoxins in the environmental samples was evaluated
using ELISA kit. Taxonomic analyses of high-throughput
DNA sequencing data showed the dominance of the genus
Microcystis in Mundaú reservoir. Furthermore, it was the
most abundant genus in the dry season in Ingazeira reservoir.
In the rainy season, 16S-23S rRNA ITS analysis revealed that
Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial
community in Ingazeira reservoir, while the cpcBAIGS
region revealed that C. raciborskii (31.8%) was the most
abundant taxon followed by Sphaerospermopsis aphanizomenoides
(17.3%) and Planktothrix zahidii (16.6%). Despite
the presence of other potential toxin-producing genera, the
detected sxtA gene belonged to C. raciborskii, while the mcyE
gene belonged to Microcystis in both reservoirs. The detected
mcyE gene had good correlation with MC content, while the
amplification of the sxtA gene was related to the presence of
STX. The cyrJ gene was not detected in these samples. Using
DNA analyses, our results showed that the cyanobacterial
composition of Mundaú reservoir was similar in successive
dry seasons, and it varied between seasons in Ingazeira reservoir.
In addition, our data suggest that some biases of analysis
influenced the cyanobacterial communities seen in
the NGS output of Ingazeira reservoir.
Review
- [MINIREVIEW] Progress of analytical tools and techniques for human gut microbiome research
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Eun-Ji Song , Eun-Sook Lee , Young-Do Nam
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J. Microbiol. 2018;56(10):693-705. Published online September 28, 2018
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DOI: https://doi.org/10.1007/s12275-018-8238-5
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52
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Abstract
- Massive DNA sequencing studies have expanded our insights
and understanding of the ecological and functional
characteristics of the gut microbiome. Advanced sequencing
technologies allow us to understand the close association of
the gut microbiome with human health and critical illnesses.
In the future, analyses of the gut microbiome will provide
key information associating with human individual health,
which will help provide personalized health care for diseases.
Numerous molecular biological analysis tools have been rapidly
developed and employed for the gut microbiome researches;
however, methodological differences among researchers
lead to inconsistent data, limiting extensive share of
data. It is therefore very essential to standardize the current
method
ologies and establish appropriate pipelines for human
gut microbiome research. Herein, we review the methods
and procedures currently available for studying the human
gut microbiome, including fecal sample collection, metagenomic
DNA extraction, massive DNA sequencing, and data
analyses with bioinformatics. We believe that this review will
contribute to the progress of gut microbiome research in
the clinical and practical aspects of human health.
Journal Article
- Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings
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Ui-Gi Min , So-Jeong Kim , Heeji Hong , Song-Gun Kim , Joo-Han Gwak , Man-Young Jung , Jong-Geol Kim , Jeong-Geol Na , Sung-Keun Rhee
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J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016
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DOI: https://doi.org/10.1007/s12275-016-6086-8
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Abstract
- A strictly anaerobic bacterium, strain B5T, was isolated from
sediment of an abandoned coal mine in Taebaek, Republic
of Korea. Cells of strain B5T were non-spore-forming, straight,
Gram-positive rods. The optimum pH and temperature for
growth were pH 7.0 and 30°C, respectively, while the strain
was able to grow within pH and temperature ranges of 5.5–
7.5 and 25–45°C, respectively. Growth of strain B5T was
observed at NaCl concentrations of 0 to 6.0% (w/v) with an
optimum at 3.0–4.0% (w/v). The polar lipids consisted of
phosphatidylethanolamine, phosphatidylglycerol, an unknown
phospholipid and three unknown polar lipids. Strain B5T
grew anaerobically by reducing nitrate, nitrite, ferric-citrate,
ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-
2-sulfonate in the presence of proteinaceous compounds,
organic acids, and carbohydrates as electron donors.
The isolate was not able to grow by fermentation. Strain B5T
did not grow under aerobic or microaerobic conditions. Phylogenetic
analysis based on 16S rRNA gene sequences showed
that strain B5T is most closely related to the genus Tepidibacillus
(T. fermentans STGHT; 96.3%) and Vulcanibacillus
(V. modesticaldus BRT; 94.6%). The genomic DNA G+C content
(36.9 mol%) of strain B5T was higher than those of T.
fermentans STGHT (34.8 mol%) and V. modesticaldus BRT
(34.5 mol%). Based on its phenotypic, chemotaxonomic, and
phylogenetic properties, we describe a new species of a novel
genus Calculibacillus, represented by strain B5T (=KCTC
15397T =JCM 19989T), for which we propose the name Calculibacillus
koreensis gen. nov., sp. nov.
Research Support, Non-U.S. Gov'ts
- Fungal Community Associated with Genetically Modified Poplar During Metal Phytoremediation
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Moonsuk Hur , Young Woon Lim , Jae Jeong Yu , Se Uk Cheon , Young Im Choi , Seok-Hwan Yoon , Sang-Cheol Park , Dong-Il Kim , Hana Yi
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J. Microbiol. 2012;50(6):910-915. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2491-9
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12
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Abstract
- Due to the increasing demand for phytoremediation, many transgenic poplars have been developed to enhance the bioremediation of heavy metals. However, structural changes to indigenous fungal communities by genetically modified organisms (GMO) presents a major ecological issue, due to the important role of fungi for plant growth in natural environments. To evaluate the effect of GM plant use on environmental fungal soil communities, extensive sequencing-based community analysis was conducted, while controlling the influence of plant clonality, plant age, soil condition, and harvesting season. The rhizosphere soils of GM and wild
type (WT) poplars at a range of growth stages were sampled together with unplanted, contaminated soil, and the fungal community structures were investigated by pyrosequencing the D1/D2 region of the 28S rRNA gene. The results show
that the overall structure of the rhizosphere fungal community was not significantly influenced by GM poplars. However, the presence of GM specific taxa, and faster rate of community change during poplar growth, appeared to be characteristic of the GM plant-induced effects on soil-born fungal communities. The results of this study provide additional information about the potential effects of GM poplar trees aged
1.5–3 years, on the soil fungal community.
- Scopulibacillus darangshiensis gen. nov., sp. nov., Isolated from Rock
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Soon Dong Lee , Dong Wan Lee
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J. Microbiol. 2009;47(6):710-715. Published online February 4, 2010
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DOI: https://doi.org/10.1007/s12275-009-0111-0
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12
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11
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Abstract
- A novel, Gram-positive bacterium, designated DLS-06T, was isolated from scoria (volcanic ash) under rock on the peak of small mountain (300 m above the sea level; known as Darangshi Oreum) in Jeju, Republic of Korea. The cells of the isolate were aerobic, oxidase-negative, catalase-positive, endospore- forming, non-motile rods. The organism grew at 25~30°C and initial pH 6.1~9.1. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family “Sporolactobacillaceae” and related taxa. The phylogenetic neighbours were Pullulanibacillus naganoensis (95.2% 16S rRNA gene sequence similarity), Tuberibacillus calidus (95.0%) and Sporolactobacillus (91.8~94.2%). Levels of 16S rRNA gene sequence similarity of the isolate to representatives of other genera were in the range of 87.2~93.7%. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, an unknown ninhydrin-positive phospholipid, three unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The G+C content of the DNA was 50.8 mol%. On the basis of the phenotypic and phylogenetic data presented in this study, this organism represents a novel genus and species in the order Bacillales, for which the name Scopulibacillus darangshiensis gen. nov., sp. nov. is proposed. The type strain is DLS-06T (=DSM 19377T =KCTC 13161T).
- Bacterial Diversity at Different Depths in Lead-Zinc Mine Tailings as Revealed by 16S rRNA Gene Libraries
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Han-Bo Zhang , Wen Shi , Ming-Xia Yang , Tao Sha , Zhi-Wei Zhao
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J. Microbiol. 2007;45(6):479-484.
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DOI: https://doi.org/2648 [pii]
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Abstract
- Bacterial communities at 10 cm, 100 cm, and 200 cm depths in a 100-year-old lead-zinc tailing heap were evaluated by constructing 16S rRNA gene libraries. In total, 98 operational taxonomic units (OTUs) were identified from 193 clones at a 3% sequence difference level. The OTU number and species richness decreased with the depth. Species composition was significantly different between the three libraries. Fifty-seven percent of the examined clones were Acidobacteria and 27% belonged to Proteobacteria. Other sequences included Chloroflexi, Firmicutes, Chlamydiae, Actinobacteria, Gemmatimonadetes, Nitrospira, and three unclassified OTUs. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were mainly distributed in the rhizosphere of naturally colonizing plants; however, Deltaproteobacteria, Acidobacteria, and Chloroflexi tended to inhabit the deeper tailings (below the 100 cm-depth).
- Differential Response of Etiolated Pea Seedlings to Inoculation with Rhizobacteria Capable of Utilizing 1-Aminocyclopropane-1-Carboxylate or L-Methionine
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Baby Shaharoona , Muhammad Arshad , Azeem Khalid
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J. Microbiol. 2007;45(1):15-20.
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DOI: https://doi.org/2497 [pii]
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Abstract
- The majority of soil microorganisms can derive ethylene from L-methionine (L-MET), while some rhizobacteria can hydrolyze 1-aminocyclopropane-1-carboxylate (ACC) due to their ACC-deaminase activity. In this study, three strains having either ACC-deaminase activity (Pseudomonas putida biotype A, A7), or the ability to produce ethylene from L-MET (Acinetobacter calcoaceticus, M9) or both (Pseudomonas fluorescens, AM3) were used for inoculation. The highly ethylene specific bioassay of a classical “triple” response in pea seedlings was used to investigate the effect of the inoculation with the rhizobacteria in the presence of 10 mM ACC or L-MET. The exogenous application of ACC had a concentration-dependent effect on the etiolated pea seedlings in creating the classical “triple” response. The inoculation with P. putida diluted the effect of ACC, which was most likely due to its ACC-deaminase activity. Similarly, the application of Co2+ reduced the ACC-imposed effect on etiolated pea seedlings. In contrast, the inoculation of A. calcoaceticus or P. fluorescens in the presence of L-MET caused a stronger classical “triple” response in etiolated pea seedlings; most likely by producing ethylene from L-MET. This is the first study, to our knowledge, reporting on the comparative effect of rhizobacteria capable of utilizing ACC vs L-MET on etiolated pea seedlings.
Journal Article
- Isolation of Cryptococcus neoformans var. grubii (serotype A) from Pigeon Droppings in Seoul, Korea
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Hee Youn Chee , Kyung Bok Lee
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J. Microbiol. 2005;43(5):469-472.
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DOI: https://doi.org/2273 [pii]
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Abstract
- Seventy-two pigeon dropping samples were collected from 26 different localities in Seoul and investigated for the occurrence of Cryptococcus neoformans. Seventeen samples from 8 different localities were found to be positive for C. neoformans. All isolates were obtained from withered pigeon droppings. Identification and serotyping of the isolates were determined by means of serological testing and DNA fingerprinting. All isolates belonged to C. neoformans var. grubbi (serotype A).