Article
Microbiology
Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young -Do Nam, Yoon-E Choi, Seong Woon Roh
Summary: A novel bacterial strain, CBA7301T, was isolated from human faeces and identified as a member of the genus Bacteroides. It showed 96.2% similarity in 16S rRNA gene sequence with its closest related species, Bacteroides faecichinchillae JCM 17102T. CBA7301T is a Gram-stain-negative, strictly anaerobic, rod-shaped bacterium that grows optimally at 30-35°C, pH 7.0, and 0.5% NaCl.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Yajun Ge, Gui Zhang, Jing Yang, Xin-He Lai, Dong Jin, Shan Lu, Ji Pu, Ying Huang, Xuelian Luo, Han Zheng, Xiaoyan Zhang, Jianguo Xu
Summary: Four unknown strains isolated from fresh feces of healthy humans in PR China have been identified as two novel species in the genus Bacteroides, named Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. The strains exhibited distinct phenotypic, biochemical, and genetic differences from their closest relatives, suggesting they represent unique taxa within the genus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Jeong Eun Bak, Byeong Seob Oh, Seoung Woo Ryu, Seung Yeob Yu, Won Jung Choi, Ji-Sun Kim, Jung-Sook Lee, Seung-Hwan Park, Se Won Kang, Jiyoung Lee, Mi-Kyung Lee, Chan Seok Yun, Won Yong Jung, Jo Eun Kim, Eun Seok Cho, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee
Summary: A Gram-negative, obligate anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain AGMB00274(T) was isolated from swine faeces. It belonged to the genus Parabacteroides, with the highest similarity to Parabacteroides johnsonii DSM 18315(T) (sequence similarity of 94.9%). The strain was proposed as a novel species named Parabacteroides faecalis sp. nov. with the type strain AGMB00274(T) (= KCTC 25286(T) = GDMCC 1.2742(T)).
CURRENT MICROBIOLOGY
(2023)
Article
Microbiology
Ji Young Choi, Seung-Hyeon Choi, Jam-Eon Park, Ji-Sun Kim, Jiyoung Lee, Mi-Kyung Lee, Jung-Sook Lee, Ju Huck Lee, Hyunjung Jung, Tai-Young Hur, Hyeun Bum Kim, Ju-Hoon Lee, Jae-Kyung Kim, Se Won Kang, Seung-Hwan Park
Summary: An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces. It belongs to the genus Phocaeicola and is closely related to Phocaeicola plebeius and Phocaeicola coprocola. The strain is able to grow at 30-45 degrees C and pH 6-9, producing acetate as the major end product of metabolism.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Han Sol Kim, Ji-Sun Kim, Min Kuk Suh, Mi Kyung Eom, Ju Huck Lee, Seung-Hwan Park, Se Won Kang, Dong Ho Lee, Hyuk Yoon, Je Hee Lee, Jung-Sook Lee
Summary: Two similar anaerobic bacteria were isolated from the feces of two Korean individuals. They belong to the genus Bacteroides and have the ability to utilize complex polysaccharides that cannot be digested by humans.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yuanqiang Zou, Xiaoqian Lin, Wenbin Xue, Li Tuo, Ming-Sheng Chen, Xiao-Hui Chen, Cheng-hang Sun, Feina Li, Shao-wei Liu, Ying Dai, Karsten Kristiansen, Liang Xiao
Summary: Two novel anaerobic strains, designated AF52-21(T) and CM04-06(T), were isolated from faeces of healthy Chinese donors using a pure culture strategy. Phylogenetic analysis revealed that these strains clustered with Faecalibacterium species, supporting their recognition as two new species within the genus. Genomic analysis showed differences below the proposed species threshold, confirming their uniqueness.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Yuyuan Huang, Jian Gong, Lingzhi Dong, Jing Yang, Shan Lu, Xin-He Lai, Ji Pu, Dong Jin, Jianguo Xu
Summary: Four mesophilic actinobacteria isolated from bat faeces in southern China were identified as two novel species of the genus Gordonia. They were named Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Rashidin Abdugheni, Yu-Jing Wang, Dan-Hua Li, Meng-Xuan Du, Chang Liu, Nan Zhou, Shuang-Jiang Liu
Summary: A new anaerobic and motile bacterium strain NSJ-9(T) was isolated from human faeces. It belongs to a new genus in the family Lachnospiraceae based on its cellular and genetic characteristics, showing high similarity to some known species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Lu Bai, Jayoung Paek, Hongik Kim, Si Hyun Kim, Jeong Hwan Shin, Joong-Ki Kook, Young Hyo Chang
Summary: A rod-shaped, aerotolerant, Gram-stain-positive bacterium strain YH-lim2214T isolated from pig faeces showed the highest similarity to Limosilactobacillus pontis KCTC 25258T with 98.0% similarity based on 16S rRNA gene sequence analysis. The average nucleotide identity and average amino acid identity values between YH-lim2214T and the most closely related strain Lm. pontis KCTC 25258T were 81.4 and 81.3%, respectively. The chemotaxonomic, phenotypic and phylogenetic properties suggest that strain YH-lim2214T represents a novel taxon, proposed as Limosilactobacillus kribbianus sp. nov. (YH-lim2214T = KCTC 25572T = JCM 35701T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Ji Young Choi, Jam-Eon Park, Seung-Hyeon Choi, Ji-Sun Kim, Jung-Sook Lee, Ju Huck Lee, Hyeun Bum Kim, Ju-Hoon Lee, Jae-Kyung Kim, Se Won Kang, Seung-Hwan Park
Summary: A new bacterium belonging to the genus Succinivibrio, named Succinivibrio feacicola sp. nov., was isolated from feces of a cow. It is an obligately anaerobic, Gram-stain-negative helical rod-shaped bacterium with a genomic DNA G+C content of 35.9 mol%. It can grow at temperatures of 30-40 degrees C and pH 6-7, and in the presence of 0.5-1.0% (w/v) NaCl.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Boram Seo, Kyungchan Jeon, Inwoo Baek, Yung Mi Lee, Kiwoon Baek, GwangPyo Ko
Summary: Strain SNUG30386(T) is an obligately anaerobic, Gram-stain-positive and spore-forming bacterium belonging to the family Lachnospiraceae. Phylogenetic analysis based on 16S rRNA gene sequences suggests that it represents a novel species within the genus Clostridium, which has been proposed as Clostridium fessum sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Fuxiang Li, Wenhua Zhao, Qionghua Hong, Qingyong Shao, Jianling Song, Shibiao Yang
Summary: A novel Gram-negative, yellow-pigmented bacterium, designated Faecalibacter bovis sp. nov., was isolated from the faeces of a cow in Wenshan, Yunnan Province, southwest China. Through phenotypic, chemotaxonomic, and genotypic analysis, it was determined to belong to the genus Faecalibacter, with distinct characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Atsushi Hisatomi, Moriya Ohkuma, Mitsuo Sakamoto
Summary: Two strains of obligately anaerobic, Gram-stain-positive, small-chain coccobacilli were isolated from faecal samples of healthy Japanese humans and named Sellimonas catena sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Xin-Wei Sun, Rashidin Abdugheni, Hao-Jie Huang, Yu-Jing Wang, Min-Zhi Jiang, Chang Liu, Nan Zhou, He Jiang, Shuang-Jiang Liu
Summary: A novel species of the genus Bacteroides, named Bacteroides propionicigenes, was isolated from the feces of a healthy adult in China. The strain showed distinct phenotypic and genotypic characteristics, supporting its classification as a new species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Seoung Woo Ryu, Ji-Sun Kim, Byeong Seob Oh, Seung Yeob Yu, Jung-Sook Lee, Seung-Hwan Park, Se Won Kang, Jiyoung Lee, Mi-Kyung Lee, Moon-Soo Rhee, Hyunjung Jung, Tai-Young Hur, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee
Summary: AGMB00490(T) strain, isolated from swine faeces, belongs to the genus Peptoniphilus based on 16S rRNA gene sequence analysis. A new species, Peptoniphilus faecalis sp. nov., was proposed for this strain, which produces acetic acid as a major end product of metabolism.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Hiroki Tanno, Tadashi Fujii, Katsuaki Hirano, Shintaro Maeno, Takashi Tonozuka, Mitsuo Sakamoto, Moriya Ohkuma, Takumi Tochio, Akihito Endo
Summary: This study investigated the metabolic properties of gut butyrate producers in relation to fructooligosaccharides and other prebiotic oligosaccharides. The findings revealed that certain species of butyrate producers had the ability to metabolize all tested oligosaccharides, while others were only able to metabolize specific types.
Article
Microbiology
Nami Suzuki-Hashido, Sayaka Tsuchida, Takashi Hayakawa, Mitsuo Sakamoto, Akinori Azumano, Satoru Seino, Ikki Matsuda, Moriya Ohkuma, Kazunari Ushida
Summary: Three new strains of Lactobacillus were isolated from the stomach contents of a captive male proboscis monkey in Japan. Phylogenetic analysis indicated they formed a separate species within the genus Lactobacillus. The new species was named Lactobacillus nasalidis sp. nov. based on genetic and physiological evidence.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Immunology
Mitsuo Sakamoto, Nao Ikeyama, Atsushi Toyoda, Takumi Murakami, Hiroshi Mori, Sho Morohoshi, Tadao Kunihiro, Takao Iino, Moriya Ohkuma
Summary: Two novel bacterial strains were isolated from human feces in this study. Strain 2CBH44(T) was identified as a subspecies of Coprobacter secundus, named as Coprobacter secundus subsp. similis subsp. nov. Strain 12CBH8(T) belonged to a novel genus and species, named as Solibaculum mannosilyticum gen. nov., sp. nov.
MICROBIOLOGY AND IMMUNOLOGY
(2021)
Article
Microbiology
Masanori Tohno, Yasuhiro Tanizawa, Yoichiro Kojima, Mitsuo Sakamoto, Moriya Ohkuma, Hisami Kobayashi
Summary: A novel bacterium, Lentilactobacillus fungorum sp. nov., was isolated and identified from spent mushroom substrates in Japan. Strain YK48G(T) showed characteristics of being a member of the genus Lentilactobacillus and represented a new species within this genus._phylogenetic analyses supported the differentiation of strain YK48G(T) from previously described species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Yusuke Ogata, Mitsuo Sakamoto, Naveen Kumar, Moriya Ohkuma, Masahira Hattori, Wataru Suda
Summary: The complete genome sequence of Megamonas funiformis strain 1CBH44, isolated from the feces of a healthy Japanese person, consists of a circular chromosome with 2,170 putative protein-coding genes, 18 rRNA genes, and 54 tRNA genes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Takumi Shinkai, Nao Ikeyama, Masahiko Kumagai, Hideyuki Ohmori, Mitsuo Sakamoto, Moriya Ohkuma, Makoto Mitsumori
Summary: The bacterial strain R5019(T) isolated from the rumen of Holstein cows was classified as a novel species, Prevotella lacticifex sp. nov., within the genus Prevotella. This species plays an important role in polysaccharide degradation and fermentation in the rumen.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Mitsuo Sakamoto, Naomi Sakurai, Hiroki Tanno, Takao Iino, Moriya Ohkuma, Akihito Endo
Summary: In this study, the phenotypic, physiological, chemotaxonomic, and phylogenomic characteristics of six Faecalibacterium prausnitzii strains were examined. The results showed that three of the strains belong to the same species, while the other three are clearly separated. The cellular fatty acid patterns of these strains were also slightly different. Based on these findings, three new species of the genus Faecalibacterium are proposed.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Mitsuo Sakamoto, Nao Ikeyama, Takao Iino, Moriya Ohkuma
Summary: This study revealed an interaction between the gut commensal bacterium Bacteroides thetaiotaomicron JCM 5827T and asaccharolytic bacterium Dialister hominis JCM 33369T, indicating a syntrophic relationship mediated by succinate metabolism. The co-culture of these two bacteria resulted in enhanced growth of D. hominis, especially near B. thetaiotaomicron colonies. This study suggests that succinate plays a significant role in syntrophy within the human gut microbiota.
Article
Microbiology
Masanori Tohno, Yasuhiro Tanizawa, Hiroyuki Sawada, Mitsuo Sakamoto, Moriya Ohkuma, Hisami Kobayashi
Summary: This study isolated a novel strain of lactic acid bacteria, AF129T, from alfalfa silage in Morioka, Iwate, Japan. Through polyphasic taxonomy, the strain was identified as a member of the genus Ligilactobacillus and represents a new species named Ligilactobacillus pabuli sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Hiroshi Mori, Tamotsu Kato, Hiroaki Ozawa, Mitsuo Sakamoto, Takumi Murakami, Todd D. Taylor, Atsushi Toyoda, Moriya Ohkuma, Ken Kurokawa, Hiroshi Ohno
Summary: To understand the biases in human gut microbiome studies, a reference microbiome composed of an artificial mock community is crucial. However, there is a lack of suitable mock communities that accurately represent the human gut microbiome. In this study, we created a novel mock community consisting of 18 major bacterial species found in the human gut and examined the impact of experimental and bioinformatics procedures on 16S rRNA gene and shotgun metagenomic sequencing. Our findings revealed that DNA extraction methods significantly influenced DNA yields and taxonomic composition of sequenced reads and certain commonly used primers for 16S rRNA genes led to underestimation of certain gut commensal taxa. Additionally, we demonstrated that the binning of shotgun metagenomic sequences using MetaBAT2 produced consistent, less-contaminated bins with varying completeness. The use of multiple binning tools with MetaWRAP improved completeness but sometimes increased contamination rate. This benchmark study provides a crucial foundation for interpreting human gut microbiome data, allowing for standardization among different methodologies, and facilitating the advancement of analytical methods.
Article
Microbiology
Atsushi Hisatomi, Moriya Ohkuma, Mitsuo Sakamoto
Summary: Two strains of obligately anaerobic, Gram-stain-positive, small-chain coccobacilli were isolated from faecal samples of healthy Japanese humans and named Sellimonas catena sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Shinji Kawasaki, Kaori Ozawa, Tatsunori Mori, Arisa Yamamoto, Midoriko Ito, Moriya Ohkuma, Mitsuo Sakamoto, Minenosuke Matsutani
Summary: This study analyzed the gut microbiomes of three Xylocopa species in Japan and found distinctive core gut microbiomes consisting of primarily lactic acid bacteria (LAB). The LAB species isolated from these bees were phylogenetically distant from known species and lacked genes for synthesizing the essential coenzyme NAD. The findings suggest the evolution and retention of Xylocopa-restricted bacteria through vertical transmission of microbes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Atsushi Hisatomi, Dieter M. Tourlousse, Mayu Hamajima, Moriya Ohkuma, Yuji Sekiguchi, Mitsuo Sakamoto
Summary: The complete genome sequences of two newly isolated Ruminococcus torques strains were reported, providing valuable information for understanding the characteristics and functions of this bacterium.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Hiroki Tanno, Jean-Marc Chatel, Rebeca Martin, Denis Mariat, Mitsuo Sakamoto, Masao Yamazaki, Seppo Salminen, Miguel Gueimonde, Akihito Endo
Summary: Faecalibacterium prausnitzii is a promising biomarker of a healthy human microbiota, but previous studies lacked specificity and failed to provide information on the heterogeneity within the species. In this study, a new gene marker rpoA was developed to quantify different groups of F. prausnitzii-related taxa, revealing marked differences in abundance and prevalence among the groups in stool samples from healthy adults.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Multidisciplinary Sciences
Mizue Anda, Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda, Wataru Iwasaki
Summary: It is generally assumed that all bacteria must have at least one rRNA operon on the chromosome, but some strains of Aureimonas and Oecophyllibacter have their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. In this study, the authors report the systematic search results for bacteria without chromosomal rrn operons, finding that at least four bacterial clades in different phyla lost their chromosomal rrn operons independently, with one clade maintaining this genome organization for hundreds of millions of years.
NATURE COMMUNICATIONS
(2023)
