- Sutterella faecalis sp. nov., isolated from human faeces
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Byeong Seob Oh , Ji-Sun Kim , Seung Yeob Yu , Seoung Woo Ryu , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Seung-Hyeon Choi , Kook-Il Han , Keun Chul Lee , Mi Kyung Eom , Min Kuk Suh , Han Sol Kim , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Jung-Sook Lee , Ju Huck Lee
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J. Microbiol. 2020;58(2):99-104. Published online January 29, 2020
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DOI: https://doi.org/10.1007/s12275-020-9396-9
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1,123
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An obligately anaerobic, Gram-stain-negative, non-motile,
non-spore-forming, and coccobacilli-shaped bacterial strain,
designated KGMB03119T, was isolated from human faeces
from a Korean. Phylogenetic analysis based on the 16S rRNA
gene sequence revealed that the isolate was a member of the
genus Sutterella and most closely related to Sutterlla wadsworthensis
KCTC 15691T (96.8% 16S rRNA gene sequence
similarity). The DNA G + C content of strain KGMB03119T
was 58.3 mol% as determined from its whole genome sequence.
Strain KGMB03119T was asaccharolytic, catalase-positive,
oxidase- and urease-negative. Furthermore, the isolate
was positive for alkaline phosphatase, leucine arylamidase,
acid phosphatase, arginine arylamidase, alanine arylamidase,
and glycine arylamidase. The major cellular fatty acids (> 10%)
of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5
(MMK-5, 100%) was the predominant isoprenoid quinone
in the isolate. Based on the phylogenetic, physiological, and
chemotaxonomic characteristics, strain KGMB03119T represents
a novel species, for which the name Sutterella faecalis
sp. nov. is proposed. The type strain is KGMB03119T (= KCTC
15823T = NBRC 114254T).
-
Citations
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Huilin Deng, Yaozhong Zheng, Qiongyao Wang, Jiaqi Peng, Weibin Bai, Lingmin Tian, Zouyan He, Rui Jiao
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International Journal of Molecular Sciences.2024; 25(23): 12600. CrossRef - Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023
Arianna Carella, Karen C. Carroll, Erik Munson, Romney M. Humphries
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Lauryn Langford, Dhara D. Shah
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Aharon Oren, Markus Göker
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- Anaerotignum faecicola sp. nov., isolated from human faeces
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Seung-Hyeon Choi , Ji-Sun Kim , Jam-Eon Park , Keun Chul Lee , Mi Kyung Eom , Byeong Seob Oh , Seung Yeob Yu , Se Won Kang , Kook-Il Han , Min Kuk Suh , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Ju Huck Lee , Jung-Sook Lee , Seung-Hwan Park
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J. Microbiol. 2019;57(12):1073-1078. Published online November 4, 2019
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DOI: https://doi.org/10.1007/s12275-019-9268-3
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1,431
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16
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Abstract
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A strictly anaerobic bacterium, designated as strain KGMB-
03357T, was isolated from the faeces of a healthy Korean selected
by Bundang Seoul National University based on health
status. Cells of strain KGMB03357T are Gram-stain-positive,
non-motile, non-spore-forming, and observed as straight or
curved rods. The isolate grew at 10–45°C (optimum temperature
of 40°C) and a pH range of 5.1–10.5 (optimum pH of
6.8). Analysis of phylogenetic trees based on the 16S rRNA
gene sequences revealed that strain KGMB03357T forms a
lineage within the genus Anaerotignum, and is most closely
related to Anaerotignum lactatifermentans G17T (= KCTC
15066T, 96.1%), Anaerotignum propionicum DSM 1682T (=
KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM
03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans
SH021T (= KCTC 15705T, 94.8%). The ANI values
between strain KGMB 03357T and members of the genus
Anaerotignum were 73.3–71.0%, which are below the ANI
criterion for interspecies identity. The DNA G + C content
based on the whole-genome sequence is 47.3 mol%. The major
cellular fatty acids of strain KGMB03357T are C16:0, C18:0,
C18:1 cis 9, and anteiso-C15:0. Strain KGMB03357T contains
meso-diaminopimelic acid as the diagnostic amino acid in
the cell wall peptidoglycan. Based on the phenotypic, phylogenetic,
and genomic properties, strain KGMB 03357T represents
a novel species of the genus Anaerotignum, for which
the name Anaerotignum faecicola sp. nov. is proposed. The
type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).
-
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- Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces
-
Ji-Sun Kim , Keun Chul Lee , Min Kuk Suh , Kook-Il Han , Mi Kyung Eom , Ju Huck Lee , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Byeong Seob Oh , Seung Yeob Yu , Seung-Hyeon Choi , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Seung-Jo Yang , Jung-Sook Lee
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J. Microbiol. 2019;57(1):38-44. Published online December 29, 2018
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DOI: https://doi.org/10.1007/s12275-019-8550-8
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1,457
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Abstract
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A Gram-stain-positive, obligately anaerobic, non-motile, nonspore-
forming, and rod-shaped bacterial strain, designated
KGMB01110T, was isolated from a faecal sample of a healthy
male in South Korea. Phylogenetic analysis based on 16S rRNA
gene showed that strain KGMB01110T belonged to Clostridium
cluster XIVa and was most closely related to Mediterraneibacter
glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA
gene sequence similarity). The DNA G + C content of strain
KGMB01110T based on its whole genome sequence was 44.1
mol%. The major cellular fatty acids (> 10%) of the isolate
were C14:0 and C16:0. The strain KGMB01110T was positive for
arginine dihydrolase, β-galactosidase-6-phosphatase, and
alkaline phosphatase. The strain KGMB01110T also produced
acid from D-glucose and D-rhamnose, and hydrolyzed gelatin
and aesculin. Furthermore, HPLC analysis and UV-tests
of culture supernatant revealed that the strain KGMB01110T
produced butyrate as the major end product of glucose fermentation.
Based on the phylogenetic and phenotypic characteristics,
strain KGMB01110T represent a novel species of
the genus Mediterraneibacter in the family Lachnospiraceae.
The type strain is KGMB01110T (= KCTC 15684T = CCUG
72830T).
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- Modulation of gut microbiome in nonalcoholic fatty liver disease: pro-, pre-, syn-, and antibiotics
-
Min Seok Cho , Sang Yeol Kim , Ki Tae Suk , Byung-Yong Kim
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J. Microbiol. 2018;56(12):855-867. Published online October 25, 2018
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DOI: https://doi.org/10.1007/s12275-018-8346-2
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981
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Abstract
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Nonalcoholic fatty liver disease (NAFLD) is one of the most
common types of liver diseases worldwide and its incidence
continues to increase. NAFLD occurs when the body can no
longer effectively store excess energy in the adipose tissue.
Despite the increasing prevalence of NAFLD, making lifestyle
changes, including increased exercise, is often an elusive
goal for patients with NAFLD. The liver directly connects to
the gut-gastrointestinal milieu via the portal vein, which are
all part of the gut-liver axis. Therefore, the gut-microbiome
and microbial products have been actively studied as likely
key factors in NAFLD pathophysiology. Hence, dysbiosis
of the gut microbiome and therapeutic manipulation of the
gut-liver axis are being investigated. Novel therapeutic approaches
for modulating gut microbiota through the administration
of probiotics, prebiotics, synbiotics, and antibiotics
have been proposed with numerous promising initial reports
on the effectiveness and clinical applications of these approaches.
This review delves into the current evidence on novel
therapies that modulate gut microbiota and discusses ongoing
clinical trials targeting the gut-liver axis for the management
and prevention of NAFLD.
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- Paenibacillus cucumis sp. nov. Isolated from Greenhouse Soil
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Jae-Hyung Ahn , Byoung-chan Kim , Byung-Yong Kim , Soo-Jin Kim , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon
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J. Microbiol. 2014;52(6):460-464. Published online May 29, 2014
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DOI: https://doi.org/10.1007/s12275-014-4071-7
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1,057
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Abstract
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Strain CO 4-7T was isolated from greenhouse soil used for cultivation of cucumbers in Korea. The 16S rRNA gene sequence of strain CO 4-7T showed the highest sequence similarity with Paenibacillus contaminans CKOBP-6T (94.2%) among the type strains. Strain CO 4-7T was a strictly aerobic, Gram-staining-positive, endospore-forming, and motile rodshaped bacterium. Strain CO 4-7T grew at 10–45°C (optimum, 30°C), at pH 6.0–7.5 (optimum, pH 6.5) and in the presence of 0–5% NaCl (optimum, 0.5%). The DNA G+C content of strain CO 4-7T was 48.5 mol%. It contained MK-7 as the major isoprenoid quinone and anteiso-C15:0 (51.8%), C16:0 (12.7%), and iso-C16:0 (8.6%) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. Based on evidence from our polyphasic taxonomic study, it was concluded that strain CO 4-7T should be classified as a novel species of the genus Paenibacillus, for which, the name Paenibacillus cucumis sp. nov. is proposed. The type strain is CO 4-7T (=KACC 17444T=JCM 19515T).
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Citations
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Jae-Hyung Ahn , Eun-Hye Jo , Byung-Yong Kim , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon
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J. Microbiol. 2013;51(6):731-735. Published online December 19, 2013
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DOI: https://doi.org/10.1007/s12275-013-3507-9
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1,191
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An orange-colored bacterial strain, ICM 1-15T, was isolated
from greenhouse soil. The 16S rRNA gene sequence of this
strain showed the highest sequence similarity with Niabella
ginsengisoli GR10-1T (95.2%) and Niabella yanshanensis
CCBAU 05354T (95.0%) among the type strains. The strain
ICM 1-15T was a strictly aerobic, Gram-negative, non-sporeforming,
non-motile, flexirubin pigment-producing, short
rod-shaped bacterium. The strain grew at 15–35°C (optimum,
25°C), at a pH of 5.0–8.5 (optimum, pH 6.5), and in
the presence of 0–3% NaCl (optimum, 1%). The DNA G+C
content of strain ICM 1-15T was 43.6 mol%. It contained
MK-7 as the major isoprenoid quinone and iso-C15:0 (38.9%),
iso-C15:1 G (20.3%), and iso-C17:0 3-OH (12.9%) as the major
fatty acids. On the basis of evidence from our polyphasic
taxonomic study, we concluded that strain ICM 1-15T should
be classified within a novel species of the genus Niabella,
for which the name Niabella terrae sp. nov. is proposed.
The type strain is ICM 1-15T (=KACC 17443T =JCM 19502T).
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Jae-Hyung Ahn , Byung-Yong Kim , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2012;50(6):1071-1074. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2642-z
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634
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63
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Abstract
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The effects of PCR cycle number and DNA polymerase type on 16S rRNA gene pyrosequencing analysis were investigated using an artificially prepared bacterial community (mock community). The bacterial richness was overestimated at increased PCR cycle number mostly due to the occurence of chimeric sequences, and this was more serious with a DNA polymerase having proofreading activity than with Taq DNA polymerase. These results suggest that PCR cycle number must be kept as low as possible for accurate estimation of bacterial richness and that particular care must be taken when a DNA polymerase having proofreading activity is used.
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- Characterization of the Bacterial and Archaeal Communities in Rice Field Soils Subjected to Long-Term Fertilization Practices
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Jae-Hyung Ahn , Jaekyeong Song , Byung-Yong Kim , Myung-Sook Kim , Jae-Ho Joa , Hang-Yeon Weon
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J. Microbiol. 2012;50(5):754-765. Published online November 4, 2012
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DOI: https://doi.org/10.1007/s12275-012-2409-6
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The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.
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- Pyrosequencing Analysis of the Bacterial Communities in the Guts of Honey Bees Apis cerana and Apis mellifera in Korea
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Jae-Hyung Ahn , In-Pyo Hong , Jeung-Im Bok , Byung-Yong Kim , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2012;50(5):735-745. Published online November 4, 2012
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DOI: https://doi.org/10.1007/s12275-012-2188-0
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The bacterial communities in the guts of the adults and larvae of the Asian honey bee Apis cerana and the European honey bee Apis mellifera were surveyed by pyrosequencing the 16S rRNA genes. Most of the gut bacterial 16S rRNA gene sequences were highly similar to the known honey bee-specific ones and affiliated with Pasteurellaceae or lactic acid bacteria (LAB). The numbers of operational taxonomic units (OTUs, defined at 97% similarity) were lower in the larval guts (6 or 9) than in the adult guts (18 or 20), and the frequencies of Pasteurellaceae-related OTUs were higher in the larval guts while those of LAB-related OTUs in the adult guts. The frequencies of Lactococcus, Bartonella, Spiroplasma, Enterobacteriaceae, and Flavobacteriaceae-related OTUs were much higher in A. cerana guts while Bifidobacterium and Lachnospiraceae-related OTUs were more abundant in A. mellfera guts. The bacterial community structures in the midguts and hindguts of the adult honey bees were not different for A. cerana, but significantly different for A. mellifera. The above results substantiated the previous observation that honey bee guts are dominated by several specific bacterial groups, and also showed that the relative abundances of OTUs could be markedly changed depending on the developmental stage, the location within the gut, and the honey bee species. The possibility of using the gut bacterial community as an indicator of honey bee health was discussed.
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DOI: https://doi.org/10.1007/s12275-011-1279-7
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Scab disease significantly damages potatoes and other root crops. Some Streptomyces species have been reported as potato-scab pathogens. Identification of the phytopathogenic Streptomyces is mainly done on the basis of the 16S rRNA gene, but use of this gene has some limitations for discriminating these strains because they share high similarities of 16S rRNA gene sequences. We tested the RNase P RNA (rnpB) gene as a taxonomic marker to clarify the relationship among closely related scab-causing Streptomyces strains. The rnpB genes were analyzed for 41 strains including 9 isolates from Jeju, Korea. There were 4 highly variable regions including nucleotide gaps in the rnpB genes. Interspecies similarity of the rnpB gene in tested Streptomyces strains was lower than about 97%, while the intraspecies similarity was higher than about 98%. Phylogenetic analysis demonstrated that the rnpB tree has similar topology to the 16S rRNA gene tree, but produces a more divergent phyletic lineage. These results revealed that the rnpB gene could be used as a powerful taxonomic tool for rapid differentiation of closely related Streptomyces species. In addition, it was also suggested that the variable regions marked as α, β, γ, and δ in the rnpB gene could be useful markers for the detection of specific Streptomyces species.
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Citations
Citations to this article as recorded by - Halotolerant Streptomyces albidoflavus INA 01478 as a Producer of Daidzein: Genome Annotation, purification and Antifungal Activity
O. N. Sineva, N. N. Markelova, K. V. Malysheva, O. A. Kolpakova, G. Kh. Kudryakova, I. A. Prokhorenko, O. V. Kisil, A. Yu. Simonov, V. I. Polshakov, I. B. Levshin, V. S. Sadykova
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J. Microbiol. 2010;48(1):36-39. Published online March 11, 2010
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DOI: https://doi.org/10.1007/s12275-009-0132-8
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A bacterial strain 5YN5-8T was isolated from peat layer on Yongneup in Korea. Cells of strain 5YN5-8T were strictly aerobic, Gram-negative, coccobacilli, non-spore forming, and non-motile. The isolate exhibited optimal growth at 28°C, pH 7.0, and 0-1% NaCl. Results of 16S rRNA gene sequence analyses indicated a close relationship of this isolate to Acinetobacter calcoaceticus (97.8% similarity for strain DSM 30006T). It also exhibited 94.4-97.8% 16S rRNA gene sequence similarities to the validly published Acinetobacter species. The value for DNA-DNA hybridization between strain 5YN5-8T and other members of the genus Acinetobacter ranged from 16 to 28%. Predominant cellular fatty acids were C18:1 ω9c, summed feature 4 containing C15:0 iso 2-OH and/or C16:1 ω7c, and C16:0. The DNA G+C content was 43.9 mol%. Phylogenetic, phenotypic, and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Acinetobacter. The name Acinetobacter brisouii sp. nov. is proposed for the novel species, with 5YN5-8T (=KACC 11602T =DSM 18516T) as the type strain.
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