Article
Engineering, Environmental
Xuemei Zhu, Chengmei Liao, Dongbao Song, Xuejun Yan, Yuxuan Wan, Hongwen Sun, Xin Wang
Summary: Organohalide respiring bacteria (OHRB) play a crucial role in the bioremediation of organohalide contaminated sites. Different domestication strategies affect the enrichment of OHRB, with nutrients having a greater impact on dehalogenation than inocula. The combination of glucose and anaerobic sludge (Glu-AS) showed faster degradation and more complete dechlorination efficacy. The microbial community structure provides insights into resource competition and nutrient dynamics, contributing to the development of efficient dehalogenating bacterial agents.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Danielle L. Sexton, Gao Chen, Fadime Kara Murdoch, Ameena Hashimi, Frank E. Loffler, Elitza Tocheva
Summary: In this study, the morphological and ultrastructural features of Dehalococcoides mccartyi (Dhc) and Dehalogenimonas spp. (Dhgm) bacteria, which respire organohalogen compounds, were revealed using cryo-electron tomography. The results provided insights into the overall cellular shape, cell envelope architecture, cytoskeletal filaments, enzymatic complexes involved in reductive dehalogenation, and the structure of extracellular vesicles.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Rifeng Wu, Rui Shen, Zhiwei Liang, Shengzhi Zheng, Yong Yang, Qihong Lu, Lorenz Adrian, Shanquan Wang
Summary: Strategies based on ecological principles can enhance the colonization of OHRB in niches, thereby improving the bioremediation efficiency of chloroethene-contaminated sites.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Microbiology
Yi Yang, Torsten Schubert, Yan Lv, Xiuying Li, Jun Yan
Summary: This study conducted phylogenetic and pangenome analyses of Sulfurospirillum genomes to understand their evolutionary and metabolic potentials. The results revealed conserved regions in the genomes of organohalide-respiring Sulfurospirillum strains that are involved in the organohalide respiration process. Additionally, various Sulfurospirillum species strains were found to have conserved metabolisms and biosynthesis capabilities. This study contributes to the understanding and potential applications of Sulfurospirillum in bioremediation of organohalide pollutants in low-pH environments.
Article
Ecology
Siyan Zhao, Chang Ding, Guofang Xu, Matthew J. Rogers, Rajaganesan Ramaswamy, Jianzhong He
Summary: Anaerobic PBDE debromination was observed in microcosms established from e-waste recycling sites. Bacterial genera Dehalococcoides, Dehalogenimonas, and Dehalobacter were implicated in PBDE debromination. Complete debromination of penta-BDE mixture was also observed in axenic cultures of Dehalococcoides mccartyi strains. Four reductive dehalogenases were identified as potential markers for PBDE debromination in microbial communities.
Article
Polymer Science
Patricia Concordio-Reis, Joao R. Pereira, Vitor D. Alves, Ana R. Nabais, Luisa A. Neves, Ana C. Marques, Elvira Fortunato, Xavier Moppert, Jean Guezennec, Maria A. M. Reis, Filomena Freitas
Summary: This study assessed the film-forming capacity of exopolysaccharides (EPS) produced by six Alteromonas strains isolated from marine environments in French Polynesia. The films showed transparency and had minimal color alterations when applied over colored surfaces. Scanning electron microscopy revealed that the EPS films were dense, compact, and had smooth surfaces. The films also had high water vapor permeabilities, characteristic of hydrophilic polysaccharide films, and demonstrated different mechanical properties under tensile tests.
Article
Biochemistry & Molecular Biology
Reiji Tanaka, Yu Kurishiba, Hideo Miyake, Toshiyuki Shibata
Summary: This study successfully isolated and identified 13 bacteria capable of degrading ulvan from marine environments. Four genera that can degrade ulvan were isolated for the first time from marine environments. One isolate showed the ability to produce ulvan lyase and to be located externally or on the cell surface.
Article
Microbiology
Mathilde Stephanie Willemin, Romain Hamelin, Florence Armand, Christof Holliger, Julien Maillard
Summary: In this study, proteomic analysis of Desulfitobacterium hafniense strain DCB-2 revealed key proteins involved in various energy metabolisms. The researchers identified proteins up-regulated in different growth conditions and analyzed their roles in metabolic pathways.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
D. Conte, J. K. Palmeiro, A. A. Bavaroski, L. S. Rodrigues, D. Cardozo, A. P. Tomaz, J. O. Camargo, L. M. Dalla-Costa
Summary: The study identified untreated healthcare effluents, presence of antimicrobials in the environment, and multidrug-resistant Aeromonas sp. as potential factors for the spread of resistance, posing a threat to public health.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Microbiology
Susma Bhattarai, Hanna Temme, Abhiney Jain, Jonathan P. Badalamenti, Jeffrey A. Gralnick, Paige J. Novak
Summary: This study analyzed genomes from three deep terrestrial subsurface sites and found that microorganisms in these environments are capable of reductive and hydrolytic dechlorination, potentially using chlorinated organic compounds for growth and competitive advantage.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Microbiology
Qian-Qian Cha, Xiu-Juan Wang, Xue-Bing Ren, Dong Li, Peng Wang, Ping-Yi Li, Hui-Hui Fu, Xi-Ying Zhang, Xiu-Lan Chen, Yu-Zhong Zhang, Fei Xu, Qi-Long Qin
Summary: This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria. The research found that alginate utilization genes cluster according to bacterial taxonomy rather than geographic location, indicating that these genes do not evolve independently in both polar regions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Medicinal
Thi Nhu Thuong Nguyen, Timothy Chataway, Ricardo Araujo, Munish Puri, Christopher Milton Mathew Franco
Summary: In this study, a novel alginate lyase, AlyDS44, was purified and characterized from a marine actinobacterium, Streptomyces luridiscabiei, isolated from decomposing seaweed. AlyDS44 is a bifunctional alginate lyase active on both polyguluronate and polymannuronate, with a preference for degrading polyguluronate. It has optimal activity at pH 8.5 and 45°C, and shows salt tolerance with optimal activity at 0.6 M NaCl. Metal ions Mn2+, Co2+, and Fe2+ increased its activity, while Zn2+ and Cu2+ inhibited it. The enzyme belongs to the polysaccharide lyase family 7 and mainly produces disaccharides, trisaccharides, and tetrasaccharides when degrading alginate, functioning as an endo-type alginate lyase with potential for efficient production of alginate oligosaccharides.
Article
Spectroscopy
Dana Cialla-May, Jennifer Gadkari, Andreea Winterfeld, Uwe Huebner, Karina Weber, Gabriele Diekert, Torsten Schubert, Tobias Goris, Juergen Popp
Summary: The study focused on using surface enhanced Raman spectroscopy (SERS) to quickly identify the cofactors involved in the respiration process of S. multivorans. Through SERS analysis of membrane proteins from the bacterium under different cultivation conditions, it was found that S. multivorans cultivated with tetrachloroethene mainly contained Vitamin B-12, while those cultivated with other electron acceptors did not.
JOURNAL OF RAMAN SPECTROSCOPY
(2021)
Article
Engineering, Environmental
Guofang Xu, Ning Zhang, Xuejie Zhao, Chen Chen, Chunfang Zhang, Jianzhong He
Summary: This study explores the potential for offshore marine microbiota to transform organohalide pollutants and finds that marine Dehalococcoidia have a versatile dehalogenation capacity. The study demonstrates dechlorination of diverse organohalides by offshore marine microbiota, including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), tetrabromobisphenol A (TBBPA), and 2,4,6-trichlorophenol (2,4,6-TCP). It also identifies the presence of Dehalococcoides and uncultivated Dehalococcoidia in initial sediment microcosms, with Dehalococcoides being dominant in all enrichment cultures.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Patricia Concordio-Reis, Vitor D. Alves, Xavier Moppert, Jean Guezennec, Filomena Freitas, Maria A. M. Reis
Summary: Marine environments make up a vast ecosystem on Earth's surface, with marine microorganisms showing potential as sources for novel biomolecules. Alteromonas strains from French Polynesia atolls were found to produce EPS with complex compositions, high degradation temperature, and the ability to form strong gels. These EPS could be versatile materials for various applications.
Article
Toxicology
Janneke Elzinga, Menno Grouls, Guido J. E. J. Hooiveld, Meike van der Zande, Hauke Smidt, Hans Bouwmeester
Summary: There is a need for standardized in vitro models of the human intestinal tract to study intestinal health without using animals. The Caco-2 cell line is a widely accepted and characterized model for studying intestinal drug transport, host-microbe interactions, and toxicity. We investigated the effect of different experimental variables on gene expression using transcriptome analysis of Caco-2 cells grown on permeable membranes. Our analysis revealed a weak association between experimental variables and gene expression, possibly due to heterogeneity in cell culture practice and inadequate reporting. This highlights the need for improved reporting protocols and serves as a template for future comparative studies.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Engineering, Environmental
Sara N. Jimenez-Volkerink, Joaquim Vila, Maria Jordan, Cristina Minguillon, Hauke Smidt, Magdalena Grifoll
Summary: Polar biotransformation products have been found to cause an increase in genotoxicity after the bioremediation of PAH-contaminated soils. The microorganisms and mechanisms underlying their further biodegradation have not been fully understood.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Medicinal
Ton That Huu Dat, Georg Steinert, Nguyen Thi Kim Cuc, Pham Viet Cuong, Hauke Smidt, Detmer Sipkema
Summary: Recent reviews have shown that sponge-associated bacteria are valuable sources of structurally diverse secondary metabolites with potent biological activities, making these microbial communities promising for new drug candidates. However, accessing the overall diversity of secondary metabolite biosynthetic potential in bacteria is challenging due to the difficulty in culturing the majority of bacteria in the laboratory. This study investigates the diversity of secondary metabolite biosynthetic gene clusters in metagenomes of bacterial communities associated with three different sponge species and identifies numerous potential gene clusters for the production of novel compounds.
Article
Gastroenterology & Hepatology
D. J. M. Barnett, M. F. Endika, C. E. Klostermann, F. Gu, C. Thijs, A. Nauta, H. A. Schols, H. Smidt, I. C. W. Arts, J. Penders
Summary: The infant gut microbiota is influenced by antibiotic exposures and prebiotic oligosaccharides found in breast milk. This study analyzed the stool microbiota of 1023 one-month-old infants and found that breastfeeding and antibiotic exposure both decrease gut microbial diversity, but have different effects on microbiota composition. Other factors such as C-section, homebirth, siblings, and exposure to animals also impact microbiota composition. Understanding these factors can help protect and promote a healthy infant gut microbiota.
Article
Microbiology
Martha F. Endika, David J. M. Barnett, Cynthia E. Klostermann, Henk A. Schols, Ilja C. W. Arts, John Penders, Arjen Nauta, Hauke Smidt, Koen Venema
Summary: Antibiotic exposure disrupts infant gut microbiota, but the ability to recover from this disruption depends on the type of antibiotic. This study investigated the effect of two common infant prebiotics, 2'-fucosyllactose (2'-FL) and galacto-oligosaccharides (GOS), on the resilience of the gut microbiota after exposure to amoxicillin/clavulanate. The results showed that the prebiotics supported the recovery of the microbiota and restored the production of beneficial fatty acids.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Andrea Aldas-Vargas, Jannigje G. G. Kers, Hauke Smidt, Huub H. M. Rijnaarts, Nora B. B. Sutton
Summary: Groundwater in The Netherlands is the main source of drinking water, but pesticide presence threatens its quality. Biodegradation is a natural process that can help remove pesticides. However, the oligotrophic groundwater conditions may limit biodegradation due to the lack of microbial communities capable of degrading pesticides. In this study, bioaugmentation with enriched mixed inocula was used to enhance pesticide biodegradation, and the effect of different redox conditions on biodegradation was observed.
Review
Microbiology
Angela Sessitsch, Steve Wakelin, Michael Schloter, Emmanuelle Maguin, Tomislav Cernava, Marie-Christine Champomier-Verges, Trevor C. Charles, Paul D. Cotter, Ilario Ferrocino, Aicha Kriaa, Pedro Lebre, Don Cowan, Lene Lange, Seghal Kiran, Lidia Markiewicz, Annelein Meisner, Marta Olivares, Inga Sarand, Bettina Schelkle, Joseph Selvin, Hauke Smidt, Leo van Overbeek, Gabriele Berg, Luca Cocolin, Yolanda Sanz, Wilson Lemos Fernandes, S. J. Liu, Matthew Ryan, Brajesh Singh, Tanja Kostic
Summary: Microbiomes play crucial roles in ecosystem functioning, supporting planetary health through nutrient cycling, climate regulation, and water filtration. They are closely associated with complex multicellular organisms and contribute to the health of their hosts. However, there is still limited understanding of microbiome transfer and connectivity.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Plant Sciences
Timothy J. Waller, Max M. Haggblom, Peter V. Oudemans
Summary: Aqueous extracts from flowers have a stimulating effect on the germination, secondary conidiation, and appressorial formation of fruit rotting fungi. Even raindrops passing over flowers can accumulate sufficient activity to influence the infectivity of these fungi. Nonpolar components of the cuticle were found to have high levels of bioactivity. Specific fatty acids and fatty acid methyl esters were identified as bioactive components, stimulating appressorial formation and secondary conidiation. This study emphasizes the importance of the bloom period for infection and suggests that the presence of specific fatty acids may affect the host susceptibility.
Article
Gastroenterology & Hepatology
Taojun Wang, Nils Leibrock, Caroline M. Plugge, Hauke Smidt, Erwin G. Zoetendal
Summary: Methanogens, reductive acetogens, and sulfate-reducing bacteria interact with each other in gut ecosystems, and their interactions may vary depending on environmental conditions.
Article
Environmental Sciences
James M. Tiedje, Yuhao Fu, Zhi Mei, Andreas Schaeffer, Qingyuan Dou, Wulf Amelung, Martin Elsner, Joseph Adu-Gyamfi, Lee Heng, Marko Virta, Xin Jiang, Hauke Smidt, Edward Topp, Fang Wang
Summary: The imprudent use of antibiotics in food production contributes to the spread of antibiotic resistance. This review emphasizes the need for collaborative efforts and preventive measures to mitigate the problem. Strategies such as heightened awareness, strengthened governance, and integrated surveillance systems are proposed to alleviate the burden of antibiotic resistance.
CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH
(2023)
Article
Biology
Bart Nijsse, Peter J. Schaap, Jasper J. Koehorst
Summary: The life sciences are a major source of scientific data. Reusing and connecting these data can lead to new concepts and insights. However, the availability of easy-to-adopt implementations that fulfill the needs of data producers is limited. In response, the FAIR Data Station, a lightweight application written in Java, has been developed to support researchers in managing research metadata according to the FAIR principles. It includes modules for generating metadata templates, validating recorded values, and converting metadata into RDF format.
Article
Microbiology
Caifang Wen, Mirelle Geervliet, Hugo de Vries, Lluis Faba, Petra J. Roubos-van den Hil, Kerstin Skovgaard, Huub F. J. Savelkoul, Henk A. Schols, Jerry M. Wells, Edwin Tijhaar, Hauke Smidt
Summary: The study found that adding a fermented feed additive - rye overgrown with mycelium of Agaricus subrufescens can modulate gut microbiota and immune system development in pigs. This supplementation may contribute to improving the health of piglets during the weaning transition period and reducing the use of antibiotics.
Article
Environmental Sciences
Sara N. Jimenez-Volkerink, Maria Jordan, Hauke Smidt, Cristina Minguillon, Joaquim Vila, Magdalena Grifoll
Summary: By studying a specific microbial consortium in PAH-contaminated soils, it was discovered that the degradation of the carcinogenic compound BaAQ may occur through the Baeyer-Villiger monooxygenase (BVMOs) pathway, and that horizontal gene transfer may play a significant role in this degradation process.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Correction
Biology
Andra Waagmeester, Egon L. Willighagen, Andrew I. Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernandez-Alvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
Article
Gastroenterology & Hepatology
Yangwenshan Ou, Eline Rots, Clara Belzer, Hauke Smidt, Carolina de Weerth
Summary: An increasing number of studies have shown the connection between gut microbiota and mental health. This study investigated the composition of gut microbiota in low-risk children during early puberty, and explored the behavioral associations with gut microbiota composition and metabolites. The study also explored the potential role of sex in these associations.