Journal of Microbiology

Research Articles

Characteristics of skin microbiome associated with disease severity in systemic sclerosis: Kyung-Ann Lee, Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Sukyung Kim, Ho-Yeon Song, Hyun-Sook Kim; J. Microbiol. 2025;63(1):e.2409018. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409018

499 View
45 Download

Abstract PDF Supplementary Material: Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.

Lactic acid bacteria from Ethiopian traditional beverage, Tella: technological and metabolic profiles for industrial application: Gashaw Assefa Yehuala, Jaein Choe, Nurelegne Tefera Shibeshi, Kumsa Delessa, Asnake Desalegn, Mi-Kyung Park; J. Microbiol. 2025;63(1):e.2409008. Published online December 20, 2024; DOI: https://doi.org/10.71150/jm.2409008

158 View
48 Download

Abstract PDF: Tella is a traditional beverage widely accepted by consumers, despite the lack of product consistency owing to its reliance on natural fermentation. This study aimed to identify potential industrial lactic acid bacteria (LAB) starter cultures based on their technological properties. Seven LAB strains isolated from Tella were characterized for their carbohydrate utilization, salt content, temperature, and acid tolerances, growth and acidification rates, and metabolite profiles. Most strains efficiently utilized various carbohydrates, with Lactiplantibacillus plantarum TDM41 showing exceptional versatility. The strains exhibited similar growth characteristics. Principal component analysis of stress tolerance properties revealed that L. plantarum TDM41, Pediococcus pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 exhibited superior tolerance ability. Strong acidification properties were detected in the L. plantarum TDM41, P. pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 strains after 24 h incubation at 30°C. L. plantarum TDM41 displayed the fastest acidification rate throughout the analysis period. All LAB strains produced significant amounts of diverse organic acids, including lactic acid, citric acid, acetic acid, malic acid, and succinic acid, with lactic acid being the primary acid produced by each strain. Overall, strains L. plantarum TDM41 and P. pentosaceus TAA01 prove to be potential candidates for Tella industrial starter cultures and similar cereal products owing to their robust technological properties.

Journal Articles

Enhanced Poly-γ-Glutamic Acid Production by a Newly Isolated Bacillus halotolerans F29: Xiaorong Sun, Yaoyu Cai, Dexin Wang; J. Microbiol. 2024;62(8):695-707. Published online August 20, 2024; DOI: https://doi.org/10.1007/s12275-024-00153-w

68 View
0 Download
1 Web of Science
1 Crossref

Abstract

Poly-γ-glutamic acid (γ-PGA) is a promising biopolymer for various applications. In this study, we isolated a novel γ-PGA-producing strain, Bacillus halotolerans F29. The one-factor-at-a-time method was used to investigate the influence of carbon sources, nitrogen sources, and culture parameters on γ-PGA production. The optimal carbon and nitrogen sources were sucrose and (NH₄)₂SO₄, respectively. The optimal culture conditions for γ-PGA production were determined to be 37 °C and a pH of 5.5. Response surface methodology was used to determine the optimum medium components: 77.6 g/L sucrose, 43.0 g/L monosodium glutamate, and 2.2 g/L K₂HPO₄. The γ-PGA titer increased significantly from 8.5 ± 0.3 g/L to 20.7 ± 0.7 g/L when strain F29 was cultivated in the optimized medium. Furthermore, the γ-PGA titer reached 50.9 ± 1.5 g/L with a productivity of 1.33 g/L/h and a yield of 2.23 g of γ-PGA/g of L-glutamic acid with the optimized medium in fed-batch fermentation. The maximum γ-PGA titer reached 45.3 ± 1.1 g/L, with a productivity of 1.06 g/L/h when molasses was used as a carbon source. It should be noted that the γ-PGA yield in this study was the highest of all reported studies, indicating great potential for the industrial production of γ-PGA.

Citations

Citations to this article as recorded by

Transcriptomics-guided rational engineering in Bacillus licheniformis for enhancing poly-γ-glutamic acid biosynthesis using untreated molasses
Rui Han, Qian Zhong, Yifan Yan, Juan Wang, Yifan Zhu, Sha Li, Peng Lei, Rui Wang, Yibin Qiu, Zhengshan Luo, Hong Xu
International Journal of Biological Macromolecules.2024; 282: 137514. CrossRef

Identification of avaC from Human Gut Microbial Isolates that Converts 5AVA to 2-Piperidone: Qiudi Zhou, Lihui Feng; J. Microbiol. 2024;62(5):367-379. Published online June 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00141-0

51 View
0 Download
1 Web of Science

Abstract: 2-piperidone is a crucial industrial raw material of high-value nylon-5 and nylon-6,5. Currently, a major bottleneck in the biosynthesis of 2-piperidone is the identification of highly efficient 2-piperidone synthases. In this study, we aimed to identify specific strains among 51 human gut bacterial strains capable of producing 2-piperidone and to elucidate its synthetic mechanism. Our findings revealed that four gut bacterial strains, namely Collinsella aerofaciens LFYP39, Collinsella intestinalis LFYP54, Clostridium bolteae LFYP116, and Clostridium hathewayi LFYP18, could produce 2-piperidone from 5-aminovaleric acid (5AVA). Additionally, we observed that 2-piperidone could be synthesized from proline through cross-feeding between Clostridium difficile LFYP43 and one of the four 2-piperidone producing strains, respectively. To identify the enzyme responsible for catalyzing the conversion of 5AVA to 2-piperidone, we utilized a gain-of-function library and identified avaC (5-aminovaleric acid cyclase) in C. intestinalis LFYP54. Moreover, homologous genes of avaC were validated in the other three bacterial strains. Notably, avaC were found to be widely distributed among environmental bacteria. Overall, our research delineated the gut bacterial strains and genes involved in 2-piperidone production, holding promise for enhancing the efficiency of industrial biosynthesis of this compound.

Reviews

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review: Chiranjib Chakraborty, Manojit Bhattacharya, Md Aminul Islam, Hatem Zayed, Elijah Ige Ohimain, Sang-Soo Lee, Prosun Bhattacharya, Kuldeep Dhama; J. Microbiol. 2024;62(5):337-354. Published online May 23, 2024; DOI: https://doi.org/10.1007/s12275-024-00138-9

67 View
0 Download
3 Web of Science
1 Crossref

Abstract

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

Citations

Citations to this article as recorded by

Development of a multiplex real-time PCR for the simultaneous detection of monkeypox virus clades I, II, and goatpox virus
Yongqiang Lin, Zijing Guo, Jinsong Chen, Xianwen Zhang, Long Zhou, Yanmin Li, Zhidong Zhang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

64 View
0 Download
1 Web of Science
1 Crossref

Abstract

Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

Citations

Citations to this article as recorded by

In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp: Kamin Ke, Yingjie Sun, Tingting He, Wenbo Liu, Yijiao Wen, Siyuan Liu, Qin Wang, Xiaowei Gao; J. Microbiol. 2024;62(6):473-487. Published online February 29, 2024; DOI: https://doi.org/10.1007/s12275-024-00118-z

51 View
0 Download
1 Web of Science

Abstract: Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein. Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.

Chemokine CCL6 Plays Key Role in the Inhibitory Effect of Vitamin A on Norovirus Infection: Heetae Lee , Giljae Lee , You-Hee Cho , Youngcheon Song , GwangPyo Ko; J. Microbiol. 2023;61(5):579-587. Published online May 26, 2023; DOI: https://doi.org/10.1007/s12275-023-00047-3

48 View
0 Download

Abstract: Norovirus (NoV) is the most common viral cause of acute gastroenteritis worldwide. Vitamin A has demonstrated the potential to protect against gastrointestinal infections. However, the effects of vitamin A on human norovirus (HuNoV) infections remain poorly understood. This study aimed to investigate how vitamin A administration affects NoV replication. We demonstrated that treatment with retinol or retinoic acid (RA) inhibited NoV replication in vitro based on their effects on HuNoV replicon-bearing cells and murine norovirus-1 (MNV-1) replication in murine cells. MNV replication in vitro showed significant transcriptomic changes, which were partially reversed by retinol treatment. RNAi knockdown of CCL6, a chemokine gene that was downregulated by MNV infection but upregulated by retinol administration, resulted in increased MNV replication in vitro. This suggested a role of CCL6 in the host response to MNV infections. Similar gene expression patterns were observed in the murine intestine after oral administration of RA and/or MNV-1.CW1. CCL6 directly decreased HuNoV replication in HG23 cells, and might indirectly regulate the immune response against NoV infection. Finally, relative replication levels of MNV-1.CW1 and MNV-1.CR6 were significantly increased in CCL6 knockout RAW 264.7 cells. This study is the first to comprehensively profile transcriptomes in response to NoV infection and vitamin A treatment in vitro, and thus may provide new insights into dietary prophylaxis and NoV infections.

Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes: Kang Xiao , Zhengyu Chen , Qin Long; J. Microbiol. 2023;61(5):571-578. Published online April 21, 2023; DOI: https://doi.org/10.1007/s12275-023-00045-5

53 View
0 Download
1 Web of Science
1 Crossref

Abstract

Microbial communities played a vital role in maintaining homeostasis of ocular surface. However, no studies explored the myopia-associated conjunctiva microbiota changes until now. In this study, conjunctival sac swab specimens were collected from 12 eyes of low myopia (LM), and 14 eyes of high myopia (HM) patients. The V3–V4 region of the 16S rRNA gene was amplified and then sequenced. Statistical analysis was performed to investigate differences in the taxonomy and diversity between two groups. Compared to LM, higher Ocular Surface Disease Index (OSDI) scores were observed in HM group. The Shannon index of the HM was lower than that of the LM group (P = 0.017). Principle coordinate analysis and Partial Least Squares Discrimination Analysis showed distinct microbiome composition between two groups. At the phylum level, there were higher relative abundances of Proteobacteria (68.27% vs 38.51%) and lower abundances of Actinobacteria (3.71% vs 9.19%) in HM, compared to LM group (P = 0.031, 0.010, respectively). At the genus level, the abundances of Acinetobacter in HM (18.16%) were significantly higher than the LM (6.52%) group (P = 0.011). Actinobacteria levels were negatively correlated with the myopic spherical equivalent and OSDI scores. Moreover, positive correlations were found between Proteobacteria levels and OSDI scores, Acinetobacter levels were positively correlated with myopic spherical equivalent and OSDI scores. In conclusion, HM Patients have bacterial microbiota imbalance in the conjunctival sac, compared with LM patients. Proteobacteria, Actinobacteria, Acinetobacter may play roles in the HM associated ocular surface irritation.

Citations

Citations to this article as recorded by

Gut Microbiota Profiles in Myopes and Nonmyopes
Wan E. W. Omar, Gurdeep Singh, Andrew J. McBain, Fiona Cruickshank, Hema Radhakrishnan
Investigative Ophthalmology & Visual Science.2024; 65(5): 2. CrossRef

Review

Recent Advances in CRISPR‑Cas Technologies for Synthetic Biology: Song Hee Jeong , Ho Joung Lee , Sang Jun Lee; J. Microbiol. 2023;61(1):13-36. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-022-00005-5

166 View
0 Download
21 Web of Science
24 Crossref

Abstract

With developments in synthetic biology, “engineering biology” has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.

Citations

Citations to this article as recorded by

Sustainable Approaches for Managing Phthalate Pollution: Navigating Challenges, and Establishing the Future of Environmental Protection
Eswar Marcharla, Smarika Chauhan, Sneha Hariharan, Parthipan Punniyakotti, Thanigaivel Sundaram, Swamynathan Ganesan, Woong Kim, Muthusamy Govarthanan
Advanced Sustainable Systems.2025;[Epub] CrossRef
CRISPR applications in microbial World: Assessing the opportunities and challenges
Farhan Kursheed, Esha Naz, Sana Mateen, Ume Kulsoom
Gene.2025; 935: 149075. CrossRef
From Spores to Suffering: Understanding the Role of Anthrax in Bioterrorism
Ratnesh Singh Kanwar, Kirtida Gambhir, Tanishka Aggarwal, Akash Godiwal, Kuntal Bhadra
Military Medicine.2025; 190(3-4): e569. CrossRef
Unveiling the potential of gene editing techniques in revolutionizing Cancer treatment: A comprehensive overview
Pankaj Garg, Gargi Singhal, Siddhika Pareek, Prakash Kulkarni, David Horne, Aritro Nath, Ravi Salgia, Sharad S. Singhal
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(1): 189233. CrossRef
From nanotechnology to AI: The next generation of CRISPR-based smart biosensors for infectious disease detection
Irkham, Abdullahi Umar Ibrahim, Chidi Wilson Nwekwo, Pwadubashiyi Coston Pwavodi, Salma Nur Zakiyyah, Mehmet Ozsoz, Yeni Wahyuni Hartati
Microchemical Journal.2025; 208: 112577. CrossRef
Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy
Mohd Afaque Ansari, Damini Verma, Mohd-Akmal Hamizan, Maumita Das Mukherjee, Noor Faizah Mohd-Naim, Minhaz Uddin Ahmed
ACS Synthetic Biology.2025; 14(1): 21. CrossRef
Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations
Mehran khan, Mir Muhammad Nizamani, Muhammad Asif, Ali Kamran, Guandi He, Xiangyang Li, Sanwei Yang, Xin Xie
Journal of Environmental Management.2025; 374: 123969. CrossRef
Cell-free systems: A synthetic biology tool for rapid prototyping in metabolic engineering
Kumyoung Jeung, Minsun Kim, Eunsoo Jang, Yang Jun Shon, Gyoo Yeol Jung
Biotechnology Advances.2025; 79: 108522. CrossRef
Synthetic biology and parasite genomics: engineering parasite-resistant human microbiomes for sustainable disease prevention
Esam S. Al-Malki
Beni-Suef University Journal of Basic and Applied Sciences.2025;[Epub] CrossRef
Engineering Useful Microbial Species for Pharmaceutical Applications
Amankeldi K. Sadanov, Baiken B. Baimakhanova, Saltanat E. Orasymbet, Irina A. Ratnikova, Zere Z. Turlybaeva, Gul B. Baimakhanova, Aigul A. Amitova, Anel A. Omirbekova, Gulzat S. Aitkaliyeva, Bekzhan D. Kossalbayev, Ayaz M. Belkozhayev
Microorganisms.2025; 13(3): 599. CrossRef
AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach
Serena Rosignoli, Elisa Lustrino, Alessio Conci, Alessandra Fabrizi, Serena Rinaldo, Maria Carmela Latella, Elena Enzo, Gianni Prosseda, Laura De Rosa, Michele De Luca, Alessandro Paiardini
Nucleic Acids Research.2024; 52(W1): W29. CrossRef
Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing
Song Hee Jeong, Ho Joung Lee, Sang Jun Lee
Frontiers in Genome Editing.2024;[Epub] CrossRef
Developing pioneering pharmacological strategies with CRISPR/Cas9 library screening to overcome cancer drug resistance
Yu He, Huan Li, Xueming Ju, Bo Gong
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2024; 1879(6): 189212. CrossRef
Efficient CRISPR-Cas12f1-Mediated Multiplex Bacterial Genome Editing via Low-Temperature Recovery
Se Ra Lim, Hyun Ju Kim, Sang Jun Lee
Journal of Microbiology and Biotechnology.2024; 34(7): 1522. CrossRef
CRISPR-based biosensor for the detection of Marburg and Ebola virus
Irkham Irkham, Abdullahi Umar Ibrahim, Pwadubashiyi Coston Pwavodi, Chidi Wilson Nwekwo, Yeni Wahyuni Hartati
Sensing and Bio-Sensing Research.2024; 43: 100601. CrossRef
Advancements in Synthetic Biology for Enhancing Cyanobacterial Capabilities in Sustainable Plastic Production: A Green Horizon Perspective
Taufiq Nawaz, Liping Gu, Zhong Hu, Shah Fahad, Shah Saud, Ruanbao Zhou
Fuels.2024; 5(3): 394. CrossRef
Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR
Piao Yang, Abraham Condrich, Ling Lu, Sean Scranton, Camina Hebner, Mohsen Sheykhhasan, Muhammad Azam Ali
DNA.2024; 4(4): 427. CrossRef
Perspective Evaluation of Synthetic Biology Approaches for Effective Mitigation of Heavy Metal Pollution
Sandhya Mishra, Anju Patel, Pankaj Bhatt, Shaohua Chen, Pankaj Kumar Srivastava
Reviews of Environmental Contamination and Toxicology.2024;[Epub] CrossRef
Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine
Asiya Nazir, Fathima Hasnain Nadeem Hussain, Afsheen Raza
Frontiers in Bioengineering and Biotechnology.2024;[Epub] CrossRef
Multifaceted Applications of Synthetic Microbial Communities: Advances in Biomedicine, Bioremediation, and Industry
Edgar Adrian Contreras-Salgado, Ana Georgina Sánchez-Morán, Sergio Yair Rodríguez-Preciado, Sonia Sifuentes-Franco, Rogelio Rodríguez-Rodríguez, José Macías-Barragán, Mariana Díaz-Zaragoza
Microbiology Research.2024; 15(3): 1709. CrossRef
Prospects for synthetic biology in 21st Century agriculture
Xingyan Ye, Kezhen Qin, Alisdair R. Fernie, Youjun Zhang
Journal of Genetics and Genomics.2024;[Epub] CrossRef
Biotechnological production of omega-3 fatty acids: current status and future perspectives
Jiansong Qin, Elif Kurt, Tyler LBassi, Lucas Sa, Dongming Xie
Frontiers in Microbiology.2023;[Epub] CrossRef
Emerging Technologies in Industrial Microbiology: From Bioengineering to CRISPR-Cas Systems
Umar Farooq, Malathi Hanumanthayya, Izharul Haq
Salud, Ciencia y Tecnología.2023; 3: 406. CrossRef
Optimized Linear DNA Recombineering for CRISPR-Cpf1 System in Corynebacterium glutamicum
Ting Wang, Xiaowan Jiang, Shufang Lv, Linfeng Hu, Shuangcheng Gao, Qingyang Xu, Junhui Zhang, Dianyun Hou
Fermentation.2023; 10(1): 31. CrossRef

Journal Articles

Metformin Regulates Gut Microbiota Abundance to Suppress M2 Skewing of Macrophages and Colorectal Tumorigenesis in Mice: Linfeng Fan , Xiangfu Zeng , Guofeng Xu; J. Microbiol. 2023;61(1):109-120. Published online January 26, 2023; DOI: https://doi.org/10.1007/s12275-022-00010-8

63 View
0 Download
5 Web of Science
4 Crossref

Abstract

The correlation of imbalanced gut microbiota with the onset and progression of colorectal cancer (CRC) has become clear. This work investigates the effect of metformin on gut microbiota and genesis of CRC in mice. Human fecal samples were collected from healthy control (HC) donors and CRC patients. Compared to HC donors, CRC patients had reduced abundance of gut microbiota; however, they had increased abundance of detrimental Bacteroidetes. Mice were injected with azomethane (AOM) to induce colorectal tumorigenesis models. Treatment of CRC patients-sourced fecal microbiota promoted tumorigenesis, and it increased the expression of Ki67, β-catenin, COX-2, and Cyclin D1 in mouse colon tissues. Further treatment of metformin blocked the colorectal tumorigenesis in mice. Fecal microbiota from the metformin-treated mice was collected, which showed decreased Bacteroidetes abundance and suppressed AOM-induced colorectal tumorigenesis in mice as well. Moreover, the metformin- modified microbiota promoted the M1 macrophage-related markers IL-6 and iNOS but suppressed the M2 macrophage-related markers IL-4R and Arg1 in mouse colon tissues. In conclusion, this study suggests that metformin-mediated gut microbiota alteration suppresses macrophage M2 polarization to block colorectal tumorigenesis.

Citations

Citations to this article as recorded by

Metformin alleviates colitis-associated colorectal cancer via inhibition of the TLR4/MyD88/NFκB/MAPK pathway and macrophage M2 polarization
Xueying Lai, Bin Liu, Yu Wan, Ping Zhou, Wanjun Li, Wei Hu, Wei Gong
International Immunopharmacology.2025; 144: 113683. CrossRef
Metformin as an immunomodulatory agent in enhancing head and neck squamous cell carcinoma therapies
Wenting Li, Nanshu Liu, Mingwei Chen, Dongjuan Liu, Sai Liu
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(2): 189262. CrossRef
Clinical efficacy of metformin in familial adenomatous polyposis and the effect of intestinal flora
Linxin Zhou, Linfu Zheng, Binbin Xu, Zhou Ye, Dazhou Li, Wen Wang
Orphanet Journal of Rare Diseases.2024;[Epub] CrossRef
An AMPK agonist suppresses the progress of colorectal cancer by regulating the polarization of TAM to M1 through inhibition of HIF-1α and mTOR signal pathway
Yuanyuan Cao, Mingyi Wo, Chan Xu, Xianming Fei, Juan Jin, Zhiming Shan
Journal of Cancer Research and Therapeutics.2023; 19(6): 1560. CrossRef

Activation of the SigE-SigB signaling pathway by inhibition of the respiratory electron transport chain and its effect on rifampicin resistance in Mycobacterium smegmatis: Yuna Oh , Hye-In Lee , Ji-A Jeong , Seonghan Kim , Jeong-Il Oh; J. Microbiol. 2022;60(9):935-947. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2202-0

57 View
0 Download
4 Web of Science
4 Crossref

Abstract

Using a mutant of Mycobacterium smegmatis lacking the major aa3 cytochrome c oxidase of the electron transport chain (Δaa3), we demonstrated that inhibition of the respiratory electron transport chain led to an increase in antibiotic resistance of M. smegmatis to isoniazid, rifampicin, ethambutol, and tetracycline. The alternative sigma factors SigB and SigE were shown to be involved in an increase in rifampicin resistance of M. smegmatis induced under respiration-inhibitory conditions. As in Mycobacterium tuberculosis, SigE and SigB form a hierarchical regulatory pathway in M. smegmatis through SigE-dependent transcription of sigB. Expression of sigB and sigE was demonstrated to increase in the Δaa3 mutant, leading to upregulation of the SigB-dependent genes in the mutant. The phoU2 (MSMEG_1605) gene implicated in a phosphatesignaling pathway and the MSMEG_1097 gene encoding a putative glycosyltransferase were identified to be involved in the SigB-dependent enhancement of rifampicin resistance observed for the Δaa3 mutant of M. smegmatis. The significance of this study is that the direct link between the functionality of the respiratory electron transport chain and antibiotic resistance in mycobacteria was demonstrated for the first time using an electron transport chain mutant rather than inhibitors of electron transport chain.

Citations

Citations to this article as recorded by

Rel-dependent decrease in the expression of ribosomal protein genes by inhibition of the respiratory electron transport chain in Mycobacterium smegmatis
Na-Kyeong Kim, Jong-Eun Baek, Ye-Jin Lee, Yuna Oh, Jeong-Il Oh
Frontiers in Microbiology.2024;[Epub] CrossRef
MoaB2, a newly identified transcription factor, binds to σ A in Mycobacterium smegmatis
Barbora Brezovská, Subhash Narasimhan, Michaela Šiková, Hana Šanderová, Tomáš Kovaľ, Nabajyoti Borah, Mahmoud Shoman, Debora Pospíšilová, Viola Vaňková Hausnerová, Dávid Tužinčin, Martin Černý, Jan Komárek, Martina Janoušková, Milada Kambová, Petr Halada,
Journal of Bacteriology.2024;[Epub] CrossRef
Enhanced hypoxanthine utilization for cAMP salvage synthesis efficiently by Arthrobacter sp. CCTCC 2013431 via xanthine oxidase inhibition
Baofeng Chen, Hai Tan, Chang Li, Linbo Li, Zhonghua Zhang, Zhigang Li
Biotechnology Letters.2024; 46(6): 1095. CrossRef
Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions
Yuna Oh, Ha-Na Lee, Eon-Min Ko, Ji-A Jeong, Sae Woong Park, Jeong-Il Oh
Journal of Microbiology.2023; 61(3): 297. CrossRef

Cytophaga hutchinsonii chu_2177, encoding the O-antigen ligase, is essential for cellulose degradation: Yahong Tan , Wenxia Song , Lijuan Gao , Weican Zhang , Xuemei Lu; J. Microbiol. 2022;60(4):364-374. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1531-3

55 View
0 Download
1 Web of Science
2 Crossref

Abstract

Cytophaga hutchinsonii can efficiently degrade crystalline cellulose, in which the cell surface cellulases secreted by the type IX secretion system (T9SS) play important roles, but the degradation mechanism remains unclear, and the anchor mechanism of cellulases on the outer membrane in C. hutchinsonii has not been studied. Here, chu_2177 was identified by transposon mutagenesis and was proved to be indispensable for cellulose utilization in C. hutchinsonii. Disruption of chu_2177 resulted in O-antigen deficiency and chu_ 177 could confer O-antigen ligase activity upon an Escherichia coli waal mutant, indicating that chu_2177 encoded the Ontigen ligase. Moreover, deletion of chu_2177 caused defects in cellulose utilization, cell motility, biofilm formation, and stress resistance. Further study showed that the endoglucanase activity was markedly decreased in the outer membrane but was increased in the culture fluid without chu_2177. Western blot proved that endoglucanase CHU_1336 was not located on the outer membrane but was released in the culture fluid of the Δ2177 mutant. Further proteomics analysis showed that many cargo proteins of T9SS were missing in the outer membrane of the Δ2177 mutant. Our study revealed that the deletion of chu_2177 affected the localization of many T9SS cargo proteins including cellulases on the outer membrane of C. hutchinsonii.

Citations

Citations to this article as recorded by

Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil
Tianjiao Zhang, Shuli Wei, Yajie Liu, Chao Cheng, Jie Ma, Linfang Yue, Yanrong Gao, Yuchen Cheng, Yongfeng Ren, Shaofeng Su, Xiaoqing Zhao, Zhanyuan Lu
Frontiers in Microbiology.2023;[Epub] CrossRef
The type IX secretion system: Insights into its function and connection to glycosylation in Cytophaga hutchinsonii
Wenxia Song, Xueke Zhuang, Yahong Tan, Qingsheng Qi, Xuemei Lu
Engineering Microbiology.2022; 2(3): 100038. CrossRef

Review

MINIREVIEW]Phytochemicals for the treatment of COVID-19: Erica Españo , Jiyeon Kim , Kiho Lee , Jeong-Ki Kim; J. Microbiol. 2021;59(11):959-977. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1467-z

49 View
0 Download
17 Web of Science
18 Crossref

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has underscored the lack of approved drugs against acute viral diseases. Plants are considered inexhaustible sources of drugs for several diseases and clinical conditions, but plant-derived compounds have seen little success in the field of antivirals. Here, we present the case for the use of compounds from vascular plants, including alkaloids, flavonoids, polyphenols, and tannins, as antivirals, particularly for the treatment of COVID-19. We review current evidence for the use of these phytochemicals against SARS-CoV-2 infection and present their potential targets in the SARS-CoV-2 replication cycle.

Citations

Citations to this article as recorded by

Role of dietary supplements in the continuous battle against COVID‐19
Rahela Zaman, Vignesh Ravichandran, Chung Keat Tan
Phytotherapy Research.2024; 38(2): 1071. CrossRef
The Potential of Anti-coronavirus Plant Secondary Metabolites in COVID-19 Drug Discovery as an Alternative to Repurposed Drugs: A Review
Zahra Alipour, Somayeh Zarezadeh, Ali Akbar Ghotbi-Ravandi
Planta Medica.2024; 90(03): 172. CrossRef
In Silico Screening of Some Active Phytochemicals to Identify Promising Inhibitors Against SARS-CoV-2 Targets
V. Alagarsamy, V. Raja Solomon, S. Murugesan, P. Shyam Sundar, MD. Muzaffar-Ur-Rehman, A. Chandu, A. Dharshini Aishwarya, B. Narendhar, M.T. Sulthana, V. Ravikumar
Current Drug Discovery Technologies.2024;[Epub] CrossRef
Screening Commercial Tea for Rapid Inactivation of Infectious SARS-CoV-2 in Saliva
Julianna N. Morris, Malak A. Esseili
Food and Environmental Virology.2024; 16(2): 159. CrossRef
Phytochemical-loaded Nanoparticles in COVID-19 Management
Suneetha Vuppu, Toshika Mishra, Shatakshi Mishra, Stany B, Anushka Das
Natural Resources for Human Health.2023; 4(1): 51. CrossRef
Nutritional deficiencies that may predispose to long COVID
John V. Schloss
Inflammopharmacology.2023; 31(2): 573. CrossRef
Curcumin-Based Nanomedicines in the Treatment of Inflammatory and Immunomodulated Diseases: An Evidence-Based Comprehensive Review
Lucas Fornari Laurindo, Gabriel Magno de Carvalho, Bárbara de Oliveira Zanuso, Maria Eduardo Figueira, Rosa Direito, Ricardo de Alvares Goulart, Daiene Santos Buglio, Sandra Maria Barbalho
Pharmaceutics.2023; 15(1): 229. CrossRef
Changes in phytochemical compositions and antioxidant activity of Schisandra sphenathera fruit during ripening
Bohan Ma, Xinghua Zhao, Bin Dai, Mengge Zhao, Xingbin Yang, Langjun Cui, Hongjun Shao
Industrial Crops and Products.2023; 199: 116773. CrossRef
Role of nutrition in minimizing mental and health-related issues during COVID-19: a systematic literature review
Luxita Sharma, Dhananjay Sharma
Nutrition & Food Science.2023; 53(4): 659. CrossRef
Current Update of Phytotherapeutic Agents in the Treatment of COVID-19: In-Silico Based Virtual Screening Approach for the Development of Antiviral Drug
Veena Ramesh, Seema A. Kulkarni, Palaniyandi Velusamy, Velmurugan Devadasan, Panneer Devaraju, Kandathil Narayanan Rajnish, Thirumurthy Madhavan, Periasamy Anbu, Palaniappan Ramasamy, Rajamanikandan Sundarraj
Frontiers in Bioscience-Landmark.2022;[Epub] CrossRef
Promising natural products against SARS‐CoV‐2: Structure, function, and clinical trials
Yan Zhao, Shanshan Deng, Yujiao Bai, Jinlin Guo, Guoyin Kai, Xinhe Huang, Xu Jia
Phytotherapy Research.2022; 36(10): 3833. CrossRef
Effective food hygiene principles and dietary intakes to reinforce the immune system for prevention of COVID-19: a systematic review
Jalaledin Mirzay-Razaz, Majid Hassanghomi, Marjan Ajami, Glareh Koochakpoor, Firoozeh Hosseini-Esfahani, Parvin Mirmiran
BMC Nutrition.2022;[Epub] CrossRef
Beneficial effect of polyphenols in COVID‐19 and the ectopic F1FO‐ATP synthase: Is there a link?
Isabella Panfoli, Alfonso Esposito
Journal of Cellular Biochemistry.2022; 123(8): 1281. CrossRef
In vitro inhibition of SARS-CoV-2 Infection by dry algae powders
Daniel Garcia-Ruiz, Erendira Villalobos-Sánchez, David Alam-Escamilla, Darwin Elizondo-Quiroga
Scientific Reports.2022;[Epub] CrossRef
Schizophyllum commune Reduces Expression of the SARS-CoV-2 Receptors ACE2 and TMPRSS2
Te-Kai Sun, Wen-Chin Huang, Yu-Wen Sun, Jeng-Shyan Deng, Liang-Hsuan Chien, Ya-Ni Chou, Wen-Ping Jiang, Jaung-Geng Lin, Guan-Jhong Huang
International Journal of Molecular Sciences.2022; 23(23): 14766. CrossRef
An exhaustive comprehension of the role of herbal medicines in Pre- and Post-COVID manifestations
Shiv Kumar Prajapati, Akanksha Malaiya, Gaurav Mishra, Dolly Jain, Payal Kesharwani, Nishi Mody, Amirhossein Ahmadi, Rishi Paliwal, Ankit Jain
Journal of Ethnopharmacology.2022; 296: 115420. CrossRef
Computational screening for investigating the synergistic regulatory potential of drugs and phytochemicals in combination with 2-deoxy-D-glucose against SARS-CoV-2
Anshika Gupta, Shweta Singh Chauhan, Anamika Singh Gaur, Ramakrishnan Parthasarathi
Structural Chemistry.2022; 33(6): 2179. CrossRef
BOTANICALS AS PROSPECTIVE AGENTS AGAINST SARS-COV-2 VIRUS
V. DUSHENKOV, A. DUSHENKOV
AVICENNA BULLETIN.2022; 24(1): 113. CrossRef

Journal Article

Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities: Edmond Kuete Yimagou , Jean-Pierre Baudoin , Rita Abou Abdallah , Fabrizio Di Pinto , Jacques Yaacoub Bou Khalil , Didier Raoult; J. Microbiol. 2020;58(5):377-386. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9365-3

56 View
0 Download
3 Web of Science
3 Crossref

Abstract

The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the “microscomics” approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our cultureindependent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect “minimicrobes” Candidate Phyla Radiation (CPR) for the first time in human stool samples. This “microscomics” approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

Citations

Citations to this article as recorded by

Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease
Sabrina Naud, Ahmad Ibrahim, Camille Valles, Mohamad Maatouk, Fadi Bittar, Maryam Tidjani Alou, Didier Raoult
Clinical Microbiology Reviews.2022;[Epub] CrossRef
Radiotherapy and the gut microbiome: facts and fiction
Jing Liu, Chao Liu, Jinbo Yue
Radiation Oncology.2021;[Epub] CrossRef
Host–microbiota maladaptation in colorectal cancer
Alina Janney, Fiona Powrie, Elizabeth H. Mann
Nature.2020; 585(7826): 509. CrossRef

First
Prev
Page of 6
Next
Last

Search