Article
Engineering, Environmental
Baogang Zhang, Jun Liu, Yizhi Sheng, Jiaxin Shi, Hailiang Dong
Summary: Research has shown that microbial communities in Cr(VI)-reducing groundwater bioreactors exhibit complex symbiotic relationships, coupling Cr(VI) reduction with other elemental cycles. The addition of iron significantly enhances Cr(VI) reduction rate and methane production, while sulfur is found to retard methane production by greatly slowing down acetoclastic methanogenesis.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Review
Biochemical Research Methods
Elie Desmond-Le Quemener, Roman Moscoviz, Nicolas Bernet, Andrew Marcus
Summary: The study of mathematical modeling of DIET and MIET in anaerobic ecosystems offers new strategies for improving biotechnologies. While the modeling of DIET kinetics is still in its early stages, recent concepts introduced for modeling electroactive biofilms should be further developed. DIET shows potential to increase IET rates compared to H 2 -MIET, but additional characterizations of biological components supporting IET are needed to enhance predictions.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Paula da Fonseca-Pereira, Rita de Cassia Monteiro-Batista, Wagner L. Araujo, Adriano Nunes-Nesi
Summary: Cofactors play a fundamental role in enzyme catalytic activity. Plants are a critical source of cofactors, including vitamin precursors, for human nutrition. Numerous studies have explored the metabolism of coenzymes and vitamins in plants, revealing their significant impact on plant development, metabolism, and stress responses.
Article
Environmental Sciences
Yingping Long, Yongwen Ma, Jinquan Wan, Yan Wang, Min Tang, Hao Fu, Jianye Cao
Summary: In this study, the denitrification efficacy of corn cob hydrolysate (CCH) was compared and analyzed with that of glucose and acetate. It was found that CCH had a high TN removal rate and low effluent COD during stable operation. The microbial community analysis showed a higher abundance of certain bacteria in the CCH stage, and the carbon metabolism of CCH was similar to that of acetate.
ENVIRONMENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Leilei Fan, Fulin Sun, Zhihao Yang
Summary: This study used metagenomic sequencing to investigate the effects of chromium(Cr)and copper(Cu)on microbial communities and function. The results showed that high concentrations of Cr(VI) and Cu(II) reduced the removal efficiency of total nitrogen and ammonium. Different concentrations of Cr(VI) and Cu(II) led to significant changes in microbial communities and triggered specific response strategies. Additionally, enzymes of nitrogen metabolism pathway were found to have significant associations with corresponding bacteria.
JOURNAL OF WATER PROCESS ENGINEERING
(2022)
Article
Engineering, Environmental
Shujun Yi, Nadia Morson, Elizabeth A. Edwards, Diwen Yang, Runzeng Liu, Lingyan Zhu, Scott A. Mabury
Summary: This study revealed the microbial transformation potential of 6:2 chlorinated polyfluorooctane ether sulfonate (6:2 Cl-PFESA) in anaerobic microbial systems. The compound was reductively dechlorinated to 6:2 hydrogen-substituted polyfluorooctane ether sulfonate (6:2 H-PFESA) as the sole metabolite. The results suggest that the mechanism for reductive dechlorination of 6:2 Cl-PFESA is likely co-metabolism rather than organohalide respiration. Additionally, the product 6:2 H-PFESA showed lower sorption affinity, indicating increased mobility in the environment.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zhao-Rong Li, Rui-Bo Jia, Donghui Luo, Lianzhu Lin, Qianwen Zheng, Mouming Zhao
Summary: The study revealed that UPP has anti-diabetic effects, improving blood sugar levels, insulin resistance, glucose tolerance, dyslipidemia, and organ damage in T2DM rats. The mechanisms of action include regulating intestinal microbiota composition, activating the IRS/PI3K/AKT signaling pathway, and affecting gene expression related to glucose and lipid metabolism.
Article
Environmental Sciences
Meng Zhang, Yaqi Luo, Yitao Zhu, Haiyun Zhang, Xilong Wang, Wei Li, Pingping Li, Jiangang Han
Summary: This study investigated the effects of wheat straw-derived biochars on the bioavailability of PAHs and microbial communities, and their comprehensive impact on PAH biodegradation. The results showed that biochar addition inhibited the mineralization of low-concentration phenanthrene, but enhanced the mineralization of high-concentration phenanthrene. These findings will guide the use of biochar in the remediation of soils with different PAH pollution levels.
Article
Engineering, Environmental
Depeng Wang, Qi Luo, Kailong Huang, Xu-Xiang Zhang
Summary: This study investigated the assembly processes and interactions of functional bacteria in anammox and denitrification coupling systems using lab-scale up-flow bioreactors. The results showed that the community composition of functional bacteria differed between the systems, and the community assembly was mainly governed by stochastic processes and homogeneous selection. Moreover, the network structures of anammox and denitrifying bacteria varied between the systems.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Environmental Sciences
Liping Huang, Jiangyu Ye, Kemei Jiang, Yichao Wang, Yunyi Li
Summary: The study revealed that oil pollution reduces correlations between co-existing bacteria and alters core genera related to oil metabolism. Under oil pollution pressure, indigenous bacteria Gammaproteobacteria was domesticated as biomarker and enzyme expression related to the metabolism of toxic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Environmental Sciences
J. M. S. Oliveira, J. S. Poulsen, E. Foresti, J. L. Nielsen
Summary: A multiple stage anaerobic system was proven effective for reductive decolorization of azo dyes in the presence of sulfate. The system achieved significant bulk color removal and organic matter and sulfate reduction in separate reactors. By utilizing amplicon sequencing and correlation analysis, the microbial communities and pathways involved in azo dye removal were identified, with reductive decolorization being mainly associated with hydrogen-producing pathways and the involvement of an azoreductase from Lactococcus lactis. The findings enhance our understanding of the role of different microbial communities in anaerobic treatment of azo dyes and can aid in the design of improved solutions for textile effluent treatment.
Review
Nutrition & Dietetics
Kyoko Hasebe, Michael D. Kendig, Margaret J. Morris
Summary: The consumption of 'western'-style diets and sedentary lifestyles have led to a global epidemic of obesity, with maternal obesity, overnutrition, and unhealthy dietary patterns having lasting adverse effects on offspring's physical and mental health. Studies suggest that maternal overnutrition may disrupt offspring cognitive function, affective state, and psychosocial behavior through mechanisms such as neuroinflammation, disrupted neuronal circuities, dysregulated brain hormones, and changes in gut microbiota. Further research is needed to explore the specific pathways shaping abnormal behavior in offspring in the context of maternal obesogenic diet exposure.
Review
Microbiology
Le Chen, Wei Fang, Jianning Chang, Jinsong Liang, Panyue Zhang, Guangming Zhang
Summary: This article reviews the recent research progress on the mechanisms of direct interspecies electron transfer (DIET) mediated by conductive materials, and systematically explores the effects and underlying mechanisms of DIET on anaerobic digestion performance. It also discusses the challenges and future research directions for the practical application of DIET.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Soil Science
Chunfeng Chen, Ashutosh Kumar Singh, Bin Yang, Haofei Wang, Wenjie Liu
Summary: This study investigated the impact of termite nesting on soil microbial communities and their nutrient cycling functions in the humid tropical region of Southwest China. The results showed that termite mounds shaped microbial communities and influenced soil physicochemical properties. Furthermore, termites reduced microbial processes associated with nutrient cycling in the mounds.
Article
Environmental Sciences
Hengfang Wang, Honglin Liu, Tianhong Yang, Guanghui Lv, Wenjing Li, Yuncai Chen, Deyan Wu
Summary: This study elucidated the responses and potential functions of soil microbial communities during succession in alpine mining areas. The results showed that mining disturbance significantly reduced the relative abundance of archaea, while restoration increased bacterial network node connections and decreased archaeal network connections. The networks of microbial genes related to nitrogen and phosphorus cycle potential varied depending on the succession type.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
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
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
Ecology
Miriam N. Ojima, Lin Jiang, Aleksandr A. Arzamasov, Keisuke Yoshida, Toshitaka Odamaki, Jinzhong Xiao, Aruto Nakajima, Motomitsu Kitaoka, Junko Hirose, Tadasu Urashima, Toshihiko Katoh, Aina Gotoh, Douwe van Sinderen, Dmitry A. Rodionov, Andrei L. Osterman, Mikiyasu Sakanaka, Takane Katayama
Summary: This study applied assembly theory to investigate the formation of bifidobacterial communities in the infant gut. The results showed that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis dominated through inhibitory priority effects, while Bifidobacterium breve benefited from facilitative priority effects and utilized a specific degradant to dominate. This study highlights the importance of initial community assembly and its impact on the maturation trajectory of the infant gut microbiota.
Article
Biochemistry & Molecular Biology
Maria S. Frolova, Inna A. Suvorova, Stanislav N. Iablokov, Sergei N. Petrov, Dmitry A. Rodionov
Summary: This study reconstructed the synthesis pathways of short-chain fatty acids (SCFAs) in the human gut microbiota and evaluated the SCFA production potential in HGM samples through the analysis of genomic and phenotypic data. The findings contribute to the predictive metabolic phenotype profiling of HGM datasets and enhance the in vitro methodology for studying cross-feeding interactions in gut microbiomes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
James R. Crosby, Tunyaboon Laemthong, Ryan G. Bing, Ke Zhang, Tania N. N. Tanwee, Gina L. Lipscomb, Dmitry A. Rodionov, Ying Zhang, Michael W. W. Adams, Robert M. Kelly
Summary: This study characterizes the utilization of hemicellulose by the extreme thermophile Caldicellulosiruptor bescii by integrating genomic reconstruction, transcriptomic data, operon structures, and biochemical characteristics of key enzymes. The comparative genomics of the genus also reveals conserved and divergent mechanisms for hemicellulose utilization across the 15 sequenced species. These findings are essential for understanding lignocellulose degradation and can contribute to enhancing lignocellulose conversion for biofuel and chemical production through metabolic engineering efforts.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
German A. Ashniev, Natalia Sernova, Aleksei E. Shevkoplias, Ivan D. Rodionov, Irina A. Rodionova, Alexey G. Vitreschak, Mikhail S. Gelfand, Dmitry A. Rodionov
Summary: Using a comparative genomic approach, this study identified a novel DNA-binding transcription factor (HisR) and RNA regulatory elements (T-box riboswitches and RNA attenuators) involved in the regulation of histidine metabolism and transport genes in various bacterial taxa. The distribution of HisR and these regulatory mechanisms across over 600 species of Firmicutes were discussed from functional and evolutionary perspectives.
Article
Microbiology
Ryan McClure, Yuliya Farris, Robert Danczak, William Nelson, Hyun-Seob Song, Aimee Kessell, Joon-Yong Lee, Sneha Couvillion, Christopher Henry, Janet K. Jansson, Kirsten S. Hofmockel
Summary: This study investigates microbial interactions during chitin decomposition in a model soil consortium. The findings reveal emergent properties of species and the community, highlighting the importance of community context in species phenotypes. These conclusions provide critical insights into soil microbial interaction networks and central soil microbiome functions.
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
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.