Review
Microbiology
Khandkar Shaharina Hossain, Sathya Amarasena, Shyamchand Mayengbam
Summary: B vitamins play crucial roles as coenzymes in various cellular reactions, such as energy production and neurotransmitter synthesis. Recent studies have revealed novel functions of B vitamins in gut microbial ecology and intestinal health. This review highlights the functional roles, biosynthesis, and effects of B vitamins on gut microbiota growth and proliferation, as well as their impact on intestinal morphology, inflammation, and disorders.
Review
Endocrinology & Metabolism
Lise Voland, Tiphaine Le Roy, Jean Debedat, Karine Clement
Summary: Vitamins play a crucial role in obesity and related metabolic disorders, with some being synthesized and absorbed by the gut bacteria. Vitamin deficiency can lead to serious health issues, highlighting the importance of monitoring the vitamin status of obese patients and examining alterations in gut microbiota.
Article
Gastroenterology & Hepatology
Juan P. Molina Ortiz, Mark Norman Read, Dale David McClure, Andrew Holmes, Fariba Dehghani, Erin Rose Shanahan
Summary: This study used genomic reconstruction modeling to infer the metabolic attributes and nutritional requirements of 816 gut strains, focusing on vitamin exchanges at different levels of community organization. The results showed that only 91 strains could satisfy their vitamin requirements, while the rest showed various degrees of dependence on external sources. The study also revealed marked metabolic differences in human gut microbial community enterotype indicators. Additionally, pre-defined interaction modules of gut species driven by, or independent of vitamin exchanges were identified.
Article
Nutrition & Dietetics
Jonguk Park, Koji Hosomi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Harumi Ohno, Kana Konishi, Kumpei Tanisawa, Masako Kifushi, Masato Kogawa, Haruko Takeyama, Haruka Murakami, Tetsuya Kubota, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Summary: This study reveals the significant effect of vitamin B1 on the survival and competition of gut bacteria, providing a solution for individual differences in the gut microbial community. Additionally, vitamin B1 is involved in the production of butyrate. Through animal experiments and pathway analysis, possible associations and mechanistic insights are obtained.
Article
Multidisciplinary Sciences
Anna S. Weiss, Lisa S. Niedermeier, Alexandra von Strempel, Anna G. Burrichter, Diana Ring, Chen Meng, Karin Kleigrewe, Chiara Lincetto, Johannes Huebner, Baerbel Stecher
Summary: By characterizing a synthetic gut bacterial community, the authors challenge the concept of universal keystone species in the gastrointestinal ecosystem, revealing a context dependency of keystone functions and bacterial interaction networks.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Ewelina Weglarz-Tomczak, Jakub M. Tomczak, Stanley Brul
Summary: M2R is a Python add-on that integrates information about gut microbiota metabolism models into human genome-scale metabolic models, facilitating research on the metabolic interaction between gut microbiota and human cells.
Article
Biotechnology & Applied Microbiology
Betuel Kaynar, Dilara Uzuner, Tunahan Cakir
Summary: In this study, a genome-scale metabolic network model, iPc610, was reconstructed for P. copri DSM 18205 through an intensive manual curation process. The model consists of 1737 metabolic reactions controlled by 610 genes. The prediction performance of iPc610 was validated with experimental data, showing reliable predictions of by-product secretions under anaerobic conditions. Gene essentiality simulations identified 70 essential genes, which can be used as candidate targets in future studies to restore dysregulated gut microbiota composition in various diseases.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Fisheries
Huiyu Shen, Xuechen Zhang, Dong Qian, Jiong Chen, Jinbo Xiong
Summary: The gut microbiota plays a crucial role in host health and fitness, and dysbiosis can lead to host disease. However, the effect of interkingdom infection, such as eukaryotic Enterocytozoon hepatopenaei (EHP), on the gut bacterial community remains unclear. This study found that EHP infection in shrimp resulted in decreased digestion activities but increased immune activities. EHP infection directly altered the gut bacterial community and enzyme activities, which in turn affected shrimp growth traits. In addition, EHP infection led to an unstable gut microbiota, making the shrimp more susceptible to bacterial pathogens and hindering their growth.
Article
Multidisciplinary Sciences
Kazuki Nagashima, Aishan Zhao, Katayoon Atabakhsh, Minwoo Bae, Jamie E. Blum, Allison Weakley, Sunit Jain, Xiandong Meng, Alice G. Cheng, Min Wang, Steven Higginbottom, Alex Dimas, Pallavi Murugkar, Elizabeth S. Sattely, James J. Moon, Emily P. Balskus, Michael A. Fischbach
Summary: Certain bacterial strains from the microbiome induce a potent T cell response, and many T cells in the gut repertoire recognize multiple bacterial strains. 13 T cell clones show a one-to-many TCR-to-strain relationship, recognizing 18 Firmicutes strains.
Article
Ecology
Benoit Bechade, Christian S. Cabuslay, Yi Hu, Caroll M. Mendonca, Bahareh Hassanpour, Jonathan Y. Lin, Yangzhou Su, Valerie J. Fiers, Dharman Anandarajan, Richard Lu, Chandler J. Olson, Christophe Duplais, Gail L. Rosen, Corrie S. Moreau, Ludmilla Aristilde, John T. Wertz, Jacob A. Russell
Summary: Genome sequencing has revealed a new symbiont, Ischyrobacter davidsoniae, in the gut microbiome of turtle ants, which plays a crucial role in nitrogen recycling. The distribution of Ischyrobacter davidsoniae across the turtle ant genus Cephalotes suggests a long-term relationship of over 50 million years. Through genomic analysis and microscopy, it has been identified that Ischyrobacter davidsoniae occupies a specialized niche in the anterior ileum of the host and is involved in a symbiont-autonomous N-recycling pathway.
Article
Biochemistry & Molecular Biology
Anastasia A. Zabolotneva, Andrei M. Gaponov, Sergey A. Roumiantsev, Ilya Yu. Vasiliev, Tatiana V. Grigoryeva, Oleg I. Kit, Elena Yu. Zlatnik, Aleksey Yu. Maksimov, Anna S. Goncharova, Inna A. Novikova, Svetlana A. Appolonova, Pavel A. Markin, Aleksandr V. Shestopalov
Summary: Alkylresorcinols (ARs), polyphenolic compounds with diverse biological activities potentially involved in host metabolism regulation, were found to be produced by the human gut microbiota. Alterations in AR content and metabolic activity of the gut microbiota were observed in mice according to diet specifications and olivetol supplementation. The findings suggest that ARs may function as quorum-sensing molecules, influencing gut microbiota composition and host metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Food Science & Technology
Seung Yun Lee, Da Young Lee, Ji Hyeop Kang, Jae Hyeon Kim, Hyun Woo Kim, Dong Hoon Oh, Jae Won Jeong, Bum Keun Kim, Sun Jin Hur
Summary: The study aimed to investigate the impact of age (adults vs elderly) on antioxidant activity, digestibility, and stability of vitamins (vitamin C, vitamin B-6, and vitamin B-12) during in vitro human digestion. Results showed that the antioxidant activity and digestibility of vitamin C were not influenced by age, digestion phase, or the presence of gut microbiota, but its stability decreased in the presence of gut microbiota. The activities of vitamins B-6 and B-12 were affected by age, digestion phase, and the presence of gut microbiota. These findings could aid in developing strategies to enhance bioavailability of vitamin B-6 and B-12 in the human body by considering age and digestive conditions.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Guoqi Dang, Wenxing Wang, Ruqing Zhong, Weida Wu, Liang Chen, Hongfu Zhang
Summary: This study found that dietary pectin supplementation enhances the gut barrier and improves immunity to ameliorate LPS-induced injury by optimizing gut microbiota and their metabolites.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Multidisciplinary
Jia-Lu Hu, Zhi-Feng Yao, Min-Na Tang, Chun Tang, Xiao-Fan Zhao, Xi Su, Dan-Bo Lu, Qiu-Rong Li, Zhang-Sheng Wang, Yan Yan, Zeneng Wang
Summary: In this study, 78 human subjects were recruited and their gut microbiota compositions were analyzed. Specific microbial taxa associated with coronary artery disease (CAD) risks were identified, but the reproducibility of enriched taxa across different cohorts limited their use in early diagnosis and prevention of CAD. Only decreased Bacteroides abundance was found to be a reliable marker for indicating CAD progression.
Review
Biochemistry & Molecular Biology
Muhammad Shahid Riaz Rajoka, Rohit Thirumdas, Hafiza Mahreen Mehwish, Muhammad Umair, Mohsin Khurshid, Hafiz Fakhar Hayat, Yuthana Phimolsiripol, Noelia Pallares, Francisco J. Marti-Quijal, Francisco J. Barba
Summary: Dietary components play a crucial role in the structure and function of host gut microbial communities, and food-derived antioxidant compounds may protect the host from intestinal oxidative stress by modulating beneficial microbial species composition. Further research is needed to clarify the effects of food additives on metabolism and immune function through changes in certain microbial species.
Article
Microbiology
Christine Tara Peterson, Josue Perez Santiago, Stanislav N. Iablokov, Deepak Chopra, Dmitry A. Rodionov, Scott N. Peterson
Summary: This study evaluated the potential of short-chain fatty acids (SCFAs) to modulate the structure and function of the human gut microbiota. Each SCFA displayed unique modulatory potential, altering the fitness of specific bacterial strains through cross-feeding. These findings are important for the identification of prebiotics that can enhance the therapeutic effects of specific SCFAs.
CURRENT MICROBIOLOGY
(2022)
Article
Physics, Particles & Fields
S. N. Iablokov, A. Kuznetsov
Summary: This paper investigates the position-space propagators of charged scalar particles, fermions, and massive vector bosons in a constant external magnetic field. It proposes a unique representation that allows for a simultaneous study of the propagator from both spatial and energetic perspectives.
EUROPEAN PHYSICAL JOURNAL C
(2022)
Article
Cell Biology
Michael J. Barratt, Sharika Nuzhat, Kazi Ahsan, Steven A. Frese, Aleksandr A. Arzamasov, Shafiqul Alam Sarker, M. Munirul Islam, Parag Palit, Md Ridwan Islam, Matthew C. Hibberd, Swetha Nakshatri, Carrie A. Cowardin, Janaki L. Guruge, Alexandra E. Byrne, Siddarth Venkatesh, Vinaik Sundaresan, Bethany Henrick, Rebbeca M. Duar, Ryan D. Mitchell, Giorgio Casaburi, Johann Prambs, Robin Flannery, Mustafa Mahfuz, Dmitry A. Rodionov, Andrei L. Osterman, David Kyle, Tahmeed Ahmed, Jeffrey Gordon
Summary: Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. An experiment found that giving B. infantis combined with LNT can increase the abundance of B. infantis subspecies in infants with severe acute malnutrition and promote weight gain, but the effect is still much lower than in healthy controls. A B. infantis strain, Bg_2D9, with superior fitness may have potential in treating malnourished infants.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Irina A. Rodionova, Ye Gao, Jonathan Monk, Ying Hefner, Nicholas Wong, Richard Szubin, Hyun Gyu Lim, Dmitry A. Rodionov, Zhongge Zhang, Milton H. Saier, Bernhard O. Palsson
Summary: In this study, researchers elucidated the regulatory functions of seven out of the 19 LysR-type transcription factors in Escherichia coli K-12, establishing the functions for four LTFs and identifying the target genes for three LTFs.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
James S. Weagley, Mark Zaydman, Siddarth Venkatesh, Yo Sasaki, Neha Damaraju, Alex Yenkin, William Buchser, Dmitry A. Rodionov, Andrei Osterman, Tahmeed Ahmed, Michael J. Barratt, Aaron DiAntonio, Jeffrey Milbrandt, Jeffrey Gordon
Summary: This study characterized bacterial TIR protein domains and found that TIR NADases activity in bacterial strains resulted in a specific metabolite, v-cADPR-x. The research highlighted the correlation between acute malnutrition and decreased fecal levels of TIR genes encoding the generation of v-cADPR-x as well as decreased levels of the metabolite itself.
Article
Microbiology
German A. Ashniev, Sergey N. Petrov, Stanislav N. Iablokov, Dmitry A. Rodionov
Summary: The study focuses on the impact of human gut microbiota (HGM) on host health and disease. Through genome analysis of over 2800 genomes representing 823 cultured HGM species, the researchers reconstructed biosynthetic pathways for proteinogenic amino acids. The findings provide insights into the conservation of amino acid biosynthetic phenotypes and demonstrate the potential of metabolic phenotype profiling for predicting the overall metabolic properties of HGM microbiomes.
Correction
Biochemistry & Molecular Biology
Nathan D. Han, Jiye Cheng, Omar Delannoy-Bruno, Daniel Webber, Nicolas Terrapon, Bernard Henrissat, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Andrei L. Osterman, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Chandani Desai, Stacey Marion, Michael J. Barratt, Andrew C. Heath, Jeffrey I. Gordon
Article
Microbiology
Kendall Kling, Sonya A. Trinh, Semen A. Leyn, Dmitry A. Rodionov, Ivan D. Rodionov, Alfa Herrera, Kasey Cervantes, George Pankey, Deborah Ashcraft, Egon A. Ozer, Adam Godzik, Karla J. F. Satchell
Summary: Our study demonstrated that phylogenetic lineage and multifunctional autoprocessing repeats-in-toxin (MARTX) toxinotype do not predict severity of Vibrio vulnificus infection. Strains capable of causing severe human disease are genetically diverse and not concentrated in one specific lineage. Therefore, food surveillance based on lineage type or toxinotype may not be an appropriate intervention measure for controlling this rare but serious infection.
Article
Biotechnology & Applied Microbiology
Jason L. Vailionis, Weishu Zhao, Ke Zhang, Dmitry A. Rodionov, Gina L. Lipscomb, Tania N. N. Tanwee, Hailey C. O'Quinn, Ryan G. Bing, Robert M. Kelly, Michael W. W. Adams, Ying Zhang
Summary: A genome-scale metabolic model was developed for the growth of Pyrococcus furiosus, an archaeon that ferments carbohydrates and peptides at 100 degrees C. The model investigates the energy balance of P. furiosus and reveals the importance of acetate production and the coupling of ATP synthase and hydrogenase in generating a sodium gradient. The model is used to guide genetic engineering designs for ethanol production and provides valuable insights for bio-based chemical and fuel production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Medicine, General & Internal
Douglas M. Heithoff, Scott P. Mahan, V. Lucien Barnes, Semen A. Leyn, Cyril X. George, Jaime E. Zlamal, Jakkarin Limwongyut, Guillermo C. Bazan, Jeffrey C. Fried, Lynn N. Fitzgibbons, John K. House, Charles E. Samuel, Andrei L. Osterman, David A. Low, Michael J. Mahan
Summary: A compound called COE2-2hexyl has been identified as a synthetic antimicrobial with broad-spectrum antibacterial activity. It effectively cured mice infected with multi-drug resistant bacteria and did not induce bacterial resistance. The ease of molecular design, synthesis, and modular nature of COEs offer advantages over conventional antimicrobials, and these features enable the construction of a range of compounds with the potential to address a global health crisis.
Article
Microbiology
Christine Tara Peterson, Josue Perez-Santiago, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: This study examined the impact of prebiotics and medicinal herbs on gut microbiota composition and host physiology using in vitro cultivation and 16S rRNA sequencing. By analyzing the relationship between sugar composition and microbiota composition, the study found that restructuring microbial communities with glycan substrates can alter community metabolism and influence host physiological changes. The combination of genome-wide metabolic reconstruction and 16S rRNA sequence-based community profiles provides valuable insights into community metabolism.
Article
Microbiology
Christine Tara Peterson, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: Parkinson's disease is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Research indicates that initial dysregulation may occur in the gastrointestinal tract and gut barrier defects may accompany it. A study evaluated the effect of Ayurvedic herbs on fecal microbiota from Parkinson's disease patients and found that each participant showed unique changes, suggesting personalized response and potential for selecting individualized medicinal herbs.
Article
Biochemistry & Molecular Biology
Nathan D. Han, Jiye Cheng, Omar Delannoy-Bruno, Daniel Webber, Nicolas Terrapon, Bernard Henrissat, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Andrei L. Osterman, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Chandani Desai, Stacey Marion, Michael J. Barratt, Andrew C. Heath, Jeffrey Gordon
Summary: Plant fibers in byproduct streams produced by non-harsh food processing methods contain diverse and naturally occurring biomolecules with physiological activities. It has been found that human gut microbiota can release N-methylserotonin from orange fibers, and certain strains of Bacteroides ovatus have the ability to specifically liberate this compound. Orally administered N-methylserotonin has various effects on mice and its fecal accumulation in humans is positively correlated with microbial genes encoding enzymes that digest pectic glycans.