Journal of Microbiology

Review

Fecal Microbiota Transplantation: Indications, Methods, and Challenges.: Jee Young Lee, Yehwon Kim, Jiyoun Kim, Jiyeun Kate Kim; J. Microbiol. 2024;62(12):1057-1074. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00184-3

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Over the past two decades, as the importance of gut microbiota to human health has become widely known, attempts have been made to treat diseases by correcting dysbiosis of gut microbiota through fecal microbiota transplantation (FMT). Apart from current knowledge of gut microbiota, FMT to treat disease has a long history, from the treatment of food poisoning in the fourth century to the treatment of Clostridioides difficile infections in the twentieth century. In 2013, FMT was recognized as a standard treatment for recurrent C. difficile because it consistently showed high efficacy. Though recurrent C. difficile is the only disease internationally recognized for FMT efficacy, FMT has been tested for other diseases and shown some promising preliminary results. Different FMT methods have been developed using various formulations and administration routes. Despite advances in FMT, some issues remain to be resolved, such as donor screening, manufacturing protocols, and unknown components in the fecal microbiota. In this review, we discuss the mechanisms, clinical indications, methods, and challenges of current FMT. We also discuss the development of alternative therapies to overcome the challenges of FMT.

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Journal Articles

Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt: Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh; J. Microbiol. 2022;60(9):899-904. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2137-5

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Abstract PDF

Two novel halophilic archaeal strains, CBA1133T and CBA- 1134, were isolated from solar salt in South Korea. The 16S rRNA gene sequences of the isolates were identical to each other and were closely related to the genera Natronomonas (92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3– 92.0%), and Haloglomus (91.4%). The isolated strains were coccoid, Gram-stain-negative, aerobic, oxidase-positive, and catalase-negative. Growth occurred under temperatures of 25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum, 15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations of 0–500 mM (optimum, 100 mM). Digital DNADNA hybridization values between the strains and related genera ranged from 18.3% to 22.7%. The major polar lipids of the strains were phosphatidyl glycerol, phosphatidyl glycerol phosphate methyl ester, and phosphatidyl glycerol sulfate. Genomic, phenotypic, physiological, and biochemical analyses of the isolates revealed that they represent a novel genus and species in the family Halobacteriaceae. The type strain is CBA1133T (= KACC 22148T = JCM 34265T), for which the name Sala cibi gen. nov., sp. nov. is proposed.

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Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
International Journal of Food Science and Technology.2024; 59(12): 9490. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat
Yao Hu, Xue Ma, Shun Tan, Xin-Xin Li, Mu Cheng, Jing Hou, Heng-Lin Cui
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India
Chandra Veluchamy, Avinash Sharma, Kalaivani Thiagarajan
Environmental Monitoring and Assessment.2024;[Epub] CrossRef
Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
Frontiers in Marine Science.2023;[Epub] CrossRef
Naming new taxa of prokaryotes in the 21st century
Aharon Oren
Canadian Journal of Microbiology.2023; 69(4): 151. CrossRef

The transcription factor Cas5 suppresses hyphal morphogenesis during yeast-form growth in Candida albicans: Jong-Myeong Kim , Hye Yun Moon , Dong Wook Lee , Hyun Ah Kang , Jeong-Yoon Kim; J. Microbiol. 2021;59(10):911-919. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1326-y

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Abstract PDF

Candida albicans is an opportunistic human pathogen that exists as yeast, hyphal or pseudohyphal forms depending on pH, nutrients, and temperature. The morphological transition from yeast to hyphae, which is required for the complete virulence of C. albicans, is controlled by many transcription factors that activate or repress hypha-specific genes. The C. albicans transcriptional factor Cas5, a key regulator of genes involved in cell wall integrity, affects the susceptibility of C. albicans to fluconazole, an inhibitor of ergosterol synthesis. In this study, we found that deletion of CAS5 in C. albicans decreased the expression levels of a set of ergosterol biosynthesis genes, such as ERG2, ERG3, ERG5, ERG6, ERG11, and ERG24,
result
ing in the accumulation of lanosterol and zymosterol, which are intermediate metabolites in the ergosterol biosynthesis pathway. Interestingly, it was observed that the cas5Δ/Δ mutant could not maintain the yeast form under non-hyphainducing conditions, while the CAS5-overexpressing cells could not form hyphae under hypha-inducing conditions. Consistent with these observations, the cas5Δ/Δ mutant highly expressed hypha-specific genes, ALS3, ECE1, and HWP1, under non-hypha-inducing conditions. In addition, CAS5 transcription was significantly downregulated immediately after hyphal initiation in the wild-type strain. Furthermore, the cas5Δ/Δ mutant reduced the transcription of NRG1, which encodes a major repressor of hyphal morphogenesis, while Cas5 overexpression increased the transcription of NRG1 under hyphainducing conditions. Collectively, this study suggests the potential role of Cas5 as a repressor of hypha-specific genes during yeast-form growth of C. albicans.

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Cas5 Regulates the Exposure of β-Glucan, the Cell Surface Hydrophobicity, and the Expression of Cell Wall Proteins to Remodel the Candida albicans Cell Wall and Participates in the Recruitment of Neutrophils
Qiyue Zhang, Guanglin Li, Yanmei Wang, Chen Yang, Wenhui Bai, Qingqing Li, Jiye Zhang, Peipei Zhang
Microorganisms.2025; 13(3): 683. CrossRef
The Role of Sfp1 in Candida albicans Cell Wall Maintenance
Che-Kang Chang, Min-Chi Yang, Hsueh-Fen Chen, Yi-Ling Liao, Chung-Yu Lan
Journal of Fungi.2022; 8(11): 1196. CrossRef

Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits: Brigita Nograsek , Tomaz Accetto , Lijana Fanedl , Gorazd Avgustin; J. Microbiol. 2015;53(8):503-510. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5142-0

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Abstract

Five strictly anaerobic Gram-negative bacterial strains, P4-65, P4-76T, P5-60, P5-119, and P5-125, presumably belonging to the genus Prevotella were isolated from pig fecal samples. Strains were tested for various phenotypic traits and nearcomplete genome sequences were obtained and analyzed. Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis based on five conserved genes confirmed that the strains belong to the genus Prevotella, revealing that they represent a novel and discrete lineage distinct from other known species of this genus. The size of the genome of the isolated strains is 3?.3 Mbp, and the DNA G+C content is 47.5?8.1 mol%. The isolates are strictly anaerobic, rod-shaped with rounded ends, non-motile and non-spore-forming. The main fermentation products are succinate and acetate, with minor concentrations of isovalerate, propionate and isobutyrate. Hydrogen is also produced. Major cellular fatty acids consist of anteiso-C15:0 and iso-C15:0, and a number of additional acids are present in lower concentrations. A substantial portion of genes involved in carbohydrate utilization is devoted to pectin degradation and utilization, while those supporting growth on xylan in ruminal Prevotella could not have been revealed. On the basis of the presented results, a novel species, Prevotella pectinovora sp. nov. is proposed. The type strain is P4-76T (=DSM 29996T =ZIM B1020T).

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Research Support, U.S. Gov't, Non-P.H.S.

Turkey Fecal Microbial Community Structure and Functional Gene Diversity Revealed by 16S rRNA Gene and Metagenomic Sequences: Jingrang Lu , Jorge Santo Domingo; J. Microbiol. 2008;46(5):469-477. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0117-z

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Abstract PDF

The primary goal of this study was to better understand the microbial composition and functional genetic diversity associated with turkey fecal communities. To achieve this, 16S rRNA gene and metagenomic clone libraries were sequenced from turkey fecal samples. The analysis of 382 16S rRNA gene sequences showed that the most abundant bacteria were closely related to Lactobacillales (47%), Bacillales (31%), and Clostridiales (11%). Actinomycetales, Enterobacteriales, and Bacteroidales sequences were also identified, but represented a smaller part of the community. The analysis of 379 metagenomic sequences showed that most clones were similar to bacterial protein sequences (58%). Bacteriophage (10%) and avian viruses (3%) sequences were also represented. Of all metagenomic clones potentially encoding for bacterial proteins, most were similar to low G+C Gram-positive bacterial proteins, particularly from Lactobacillales (50%), Bacillales (11%), and Clostridiales (8%). Bioinformatic analyses suggested the presence of genes encoding for membrane proteins, lipoproteins, hydrolases, and functional genes associated with the metabolism of nitrogen and sulfur containing compounds. The results from this study further confirmed the predominance of Firmicutes in the avian gut and highlight the value of coupling 16S rRNA gene and metagenomic sequencing data analysis to study the microbial composition of avian fecal microbial communities.

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Molecular cloning and expression of shiga-like toxin II gene (slt-II) from an isolated of healthy Korean native bovine feces, fscherichia coli KSC109: Cha, In Ho , Kim kyoung Sook , Kim, Sang Hyun , Kim, Young Hwan , Lee, Young Choon; J. Microbiol. 1996;34(2):151-157.

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Abstract PDF: By PCR amplification using the sequence of the previously cloned shiga-like toxin II DNA, a gene encoding it has been cloned from an isolate of healthy Korean native bovine feces, Escherichia coli KSC109. The nucleotide sequence s included tow open reading frames coding for 319 and 89 amino acids corresponding to A and B subunits, respectively. Comparison of the nucleotide and predicted amino acid sequences of newly cloned gene (slt-II) with those of others in the SLT-II family revealed completely identical homology with SLT-II cloned previously from bacteriophabe DNA of E. coli 933 derived from a patient with hemorrhagic colities. In addition, the sequence homology of SLT-II with SLT-II variant form bovine was more than 95% at both the nucleotide and protein levels. Overexpression of SLT-II recombinant gene by induction with IPTG using an E, coli host-vector, system was conducted and the correctly processed products with active mature form exhibited 1000-fold higher cytotoxycity for Vero cells than that form original strain.

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