Article
Biology
Daniel Min, Andrew C. Doxey, Josh D. Neufeld
Summary: AXIOME3 is a completely redeveloped pipeline for small subunit ribosomal RNA data analysis, with an interactive web interface that simplifies configuration processes and task status tracking. It uses an automated pipeline wrapped around QIIME2 to generate various outputs, including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations.
Article
Environmental Sciences
Christian X. Hiller, Christoph Schwaller, Christian Wurzbacher, Joerg E. Drewes
Summary: This study investigated the removal of antimicrobial resistance genes (ARGs) in wastewater using low-pressure membrane filtration. The size of the membrane pores was found to be the main factor affecting ARG removal, and the fouling layer on the membrane also had an impact on the removal efficiency.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Christian X. Hiller, Christoph Schwaller, Christian Wurzbacher, Joerg E. Drewes
Summary: Low-pressure membrane filtration was studied for its removal of antimicrobial resistance genes in conventional secondary treated wastewater plant effluents. The pore size of the membrane was found to be the key factor influencing ARG removal, while the formation of fouling layer had significant effects on the removal of mobile ARGs. Different ARG abundances in feeds directly impacted the abundance of ARGs in the filtrate.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Zhibo Zeng, Wen Yue, Cermon Kined, PengPeng Wang, Ran Liu, Jing Liu, Xinzhu Chen
Summary: This study found that Bacillus licheniformis could effectively restore gut microbial dysbiosis and inflammation levels induced by ceftriaxone sodium treatment, which is important for maintaining intestinal health.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Review
Microbiology
Iiana Lauren Brito
Summary: The Review discusses the impact of horizontal gene transfer on natural microbial communities and explores the application of new technologies in studying the ecology of HGT, as well as deepening our understanding of gene transfer.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Microbiology
Jason A. Rothman, Jenna L. Riis, Katrina R. Hamilton, Clancy Blair, Douglas A. Granger, Katrine L. Whiteson
Summary: Human oral microbial communities have significant implications for oral and systemic health due to their diversity. Understanding the differences between healthy and dysbiotic oral microbiomes is important, especially within and between families. This study investigates the changes in oral microbiome composition within individuals and the impact of factors such as environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. The findings reveal differences in oral microbiomes between children and caregivers, with shared diversity but distinct differences, and highlight the associations between the oral microbiome and various salivary markers.
Article
Environmental Sciences
Ademir Sergio Ferreira Araujo, Ana Roberta Lima Miranda, Arthur Prudencio de Araujo Pereira, Wanderley Jose de Melo, Vania Maria Maciel Melo, Sabrina Hermelindo Ventura, Eudemio Sousa Brito Jr, Erika Valente de Medeiros, Fabio Fernando Araujo, Lucas William Mendes
Summary: This study assessed the microbial community in the rhizosphere of maize and cowpea grown in Cr-contaminated soils using amplicon sequencing. The results showed that the microbial community in the maize rhizosphere clustered together, while the microbial community in the cowpea rhizosphere did not present clear clustering. Furthermore, Cr contamination had different effects on specific bacterial groups in the rhizospheres of maize and cowpea.
Article
Environmental Sciences
Marcela Franca Dias, Deborah Leroy-Freitas, Elayne Cristina Machado, Leticia da Silva Santos, Cintia Dutra Leal, Gabriel da Rocha Fernandes, Juliana Calabria de Araujo
Summary: Wastewater tertiary treatment is an effective method to reduce the concentration of antibiotic resistant bacteria and genes. Activated sludge and UV irradiation can significantly decrease the abundance of antibiotic resistance determinants. However, some genes, including intI1, remain in the treated effluents, suggesting the need for further investigation on ways to mitigate their release into the environment.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
D. D. Silveira, A. J. Farooq, S. J. Wallace, F. R. Lapolli, J. Nivala, K. P. Weber
Summary: A multiphasic study was conducted to investigate the spatial dynamics of microbial community within different designs of horizontal subsurface flow treatment wetlands (TWs) in Germany. The study found that the microbial community structure and function varied among different TW configurations, and the spatial positioning along the flow path was the main driver of microbial community dynamics and differences.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
Amaury Gerard, Soundous El-Hajjaji, Sophie Burteau, Papa Abdoulaye Fall, Barbara Pirard, Bernard Taminiau, Georges Daube, Marianne Sindic
Summary: This study is the first to investigate the microbial composition of artisanal cheeses from Belgium using metagenomics, revealing significant differences in bacterial richness and diversity among different cheese types. The dominant populations of bacteria were identified, with Lactococcus being dominant across all types and Streptococcus being co-dominant in smear-ripened and Saint-Paulin-type cheeses.
Article
Ecology
Josieli Lima da Silva, Lucas William Mendes, Sandra Mara Barbosa Rocha, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Vania Maria Maciel Melo, Francisca Andrea Silva Oliveira, Arthur Prudencio de Araujo Pereira, Gerson do Nascimento Costa, Veronica Brito da Silva, Regina Lucia Ferreira Gomes, Francisco de Alcantara Neto, Angela Celis de Almeida Lopes, Ademir Sergio Ferreira Araujo
Summary: Plant domestication has an impact on the assembly and diversity of microbial communities in the rhizosphere. The microbial community structure differs between wild, semi-domesticated, and domesticated genotypes of lima bean, with a decrease in community similarity and changes in the abundance of specific microbial groups. Domestication also affects the complexity of interactions among microbial communities in the rhizosphere.
Article
Immunology
Shakti Kumar, Naina Kumari, Daizee Talukdar, Akansha Kothidar, Mousumi Sarkar, Ojasvi Mehta, Pallavi Kshetrapal, Nitya Wadhwa, Ramachandran Thiruvengadam, Bapu Koundinya Desiraju, G. Balakrish Nair, Shinjini Bhatnagar, Souvik Mukherjee, Bhabatosh Das
Summary: The study found that specific species of Lactobacillus and other facultative anaerobes are associated with birth outcomes in Indian women, suggesting a protective role in reducing the risk of preterm birth.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Environmental Sciences
Liam D. H. Elbourne, Brodie Sutcliffe, William Humphreys, Amaranta Focardi, Mattia Sacco, Matthew A. Campbell, Ian T. Paulsen, Sasha G. Tetu
Summary: This study provides detailed analysis of microbial communities in Bundera sinkhole, revealing clear shifts in microbial abundance, diversity, structure and membership across different depths, which are related to changes in light, energy sources, pH, and salinity. The research highlights the potential for microbial novelty in anchialine systems, indicating adaptations to specific physicochemical environments. This work contributes new insights into the microbial residents of these important and sensitive environments.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Agricultural Engineering
Philip M. Roveto, Adwaith Gupta, Andrew J. Schuler
Summary: The study showed that surface skewness has significant impacts on biofilm development, with surfaces with negative skewness promoting nitrite oxidation and biomass growth. Analysis of 16s rRNA gene sequencing revealed differences in bacterial populations, and PCoA analysis indicated divergence between populations on skew and flat surfaces.
BIORESOURCE TECHNOLOGY
(2021)
Article
Environmental Sciences
B. Read-Daily, S. Ben Maamar, F. Sabba, S. Green, R. Nerenberg
Summary: This study found that N2O has a significant impact on mixed denitrifying communities. The presence of N2O alone selects for a low-diversity, fully denitrifying community, while the presence of N2O with NO2- or NO3- promotes more diverse microbial communities.
Article
Environmental Sciences
Hua Li, Arnaud Dechesne, Zhiming He, Marlene Mark Jensen, Hai Liang Song, Barth F. Smets
Summary: Current in the milliampere range can enhance conjugal plasmid transfer between bacteria, including antibiotic-resistant bacteria. The exposure to sublethal current intensities during electrochemical disinfection can lead to increased transconjugant frequency and expression of conjugation-related genes. It is crucial to carefully control the conditions of electrochemical disinfection to prevent the transmission of antibiotic resistance genes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Heidi Birch, Arnaud Dechesne, Karina Knudsmark Sjoholm, Philipp Mayer
Summary: This study investigated the effect of additional chemicals on the biodegradation kinetics and microbial composition in aquatic environments. It found that the impact of mixtures on degradation varied depending on the chemical, with longer lag-phases being more susceptible to mixture effects. Microbial composition was significantly affected by the presence of mixtures after 14 days of incubation, while individual chemicals had a lesser impact. Growth on chemical mixtures resulted in the proliferation of specific microorganisms, such as Pseudomonas and Malikia. These findings suggest that biodegradation kinetics should be determined in mixtures at environmentally relevant concentrations, and longer degradation times are associated with increased uncertainty.
Article
Biochemical Research Methods
Danesh Moradigaravand, Liguan Li, Arnaud Dechesne, Joseph Nesme, Roberto de la Cruz, Huda Ahmad, Manuel Banzhaf, Soren J. Sorensen, Barth F. Smets, Jan-Ulrich Kreft
Summary: Wastewater treatment plants (WWTPs) contain diverse microbial communities that receive antimicrobial residues and resistant strains, allowing for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This study used machine learning models to predict plasmid permissiveness in water cycle microbial communities, which is the ability of cells to receive a plasmid through conjugation. The results showed a moderate-to-strong correlation between predicted and experimental permissiveness, indicating the potential for assessing the risk of AMR pollution in wastewater systems.
Article
Engineering, Environmental
Xiaole Yin, Xi Chen, Xiao-Tao Jiang, Ying Yang, Bing Li, Marcus Ho-Hin Shum, Tommy T. Y. Lam, Gabriel M. Leung, Joan Rose, Concepcion Sanchez-Cid, Timothy M. Vogel, Fiona Walsh, Thomas U. Berendonk, Janet Midega, Chibuzor Uchea, Dominic Frigon, Gerard D. Wright, Carlos Bezuidenhout, Renata C. Picao, Shaikh Z. Ahammad, Per Halkjaer Nielsen, Philip Hugenholtz, Nicholas J. Ashbolt, Gianluca Corno, Despo Fatta-Kassinos, Helmut Buergmann, Heike Schmitt, Chang-Jun Cha, Amy Pruden, Kornelia Smalla, Eddie Cytryn, Yu Zhang, Min Yang, Yong-Guan Zhu, Arnaud Dechesne, Barth F. Smets, David W. Graham, Michael R. Gillings, William H. Gaze, Celia M. Manaia, Mark C. M. van Loosdrecht, Pedro J. J. Alvarez, Martin J. Blaser, James M. Tiedje, Edward Topp, Tong Zhang
Summary: Surveillance of antibiotic resistance genes (ARGs) in environmental sectors is increasingly conducted to complement studies in human and animal sectors. However, comparing and synthesizing results from different studies using different test methods and bioinformatic analysis approaches pose substantial challenges. This article suggests a universal unit (ARG copy per cell) for reporting biological measurements of ARGs in order to improve comparability. By comparing commonly used quantification units, this study proposes a step towards standardization.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Microbiology
Shiraz A. Shah, Ling Deng, Jonathan Thorsen, Anders G. Pedersen, Moira B. Dion, Josue L. Castro-Mejia, Ronalds Silins, Fie O. Romme, Romain Sausset, Leon E. Jessen, Eric Olo Ndela, Mathis Hjelmso, Morten A. Rasmussen, Tamsin A. Redgwell, Cristina Leal Rodriguez, Gisle Vestergaard, Yichang Zhang, Bo Chawes, Klaus Bonnelykke, Soren J. Sorensen, Hans Bisgaard, Francois Enault, Jakob Stokholm, Sylvain Moineau, Marie-Agnes Petit, Dennis S. Nielsen
Summary: Deep sequencing of faecal viromes from 647 healthy infants identified over 230 previously unknown gut virus families, expanding our understanding of the diversity in the human infant gut virome. The findings highlight the importance of the gut microbiome in infancy for the development of the immune system and long-term protection against chronic diseases. This study provides valuable insights into the viral diversity in the infant gut virome and expands phage taxonomy, serving as a resource for future research.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Joachim Johansen, Koji Atarashi, Yasumichi Arai, Nobuyoshi Hirose, Soren J. Sorensen, Tommi Vatanen, Mikael Knip, Kenya Honda, Ramnik J. Xavier, Simon Rasmussen, Damian R. Plichta
Summary: Distinct gut virome composition in centenarians, with higher diversity and lytic activity compared to younger and older individuals, suggests a potential role in healthy aging. Furthermore, phage-encoded sulfate metabolism genes in the centenarian gut microbiome may contribute to mucosal integrity and resistance to pathogens.
NATURE MICROBIOLOGY
(2023)
Article
Plant Sciences
Yongming Duan, Min Han, Maja Grimm, Jasper Schierstaedt, Jafargholi Imani, Massimiliano Cardinale, Marie Le Jean, Joseph Nesme, Soren J. Sorensen, Adam Schikora
Summary: This study investigated the response of barley to three different beneficial bacteria, as well as the influence of soil-borne Ensifer meliloti on seed microbiome. The results showed distinct colonization patterns of the bacteria in the rhizosphere and induction of systemic resistance against foliar fungal pathogens. Transcriptome analysis revealed the regulation of ion- and stress-related genes in plants upon bacterial encounter. The study also found an effect of bacterial inoculation on the composition of seed endophytes. These findings contribute to the understanding of the interaction between ISR-triggering bacteria and crop plants, which is crucial for sustainable agriculture.
Article
Engineering, Environmental
Anders T. Mortensen, Estelle M. Goonesekera, Arnaud Dechesne, Tal Elad, Kai Tang, Henrik R. Andersen, Barth F. Smets, Borja Valverde-Perez
Summary: Pharmaceuticals and other organic micropollutants (OMPs) in wastewater are a growing concern due to their impact on the environment and human health. Conventional biological treatments have limited success in removing OMPs, but methanotrophic bacteria can degrade these pollutants. A novel bubble-free hybrid membrane biofilm bioreactor (hMBfR) was used to cultivate methanotrophic bacteria at varying CH4 loading rates, resulting in high biomass productivity and CH4 loading. The hMBfR also effectively removed OMPs, recovered nutrients, and promoted the growth of beneficial microorganisms, making it a promising technology for safer water reuse and resource recovery.
Article
Engineering, Environmental
Alejandro Palomo, Arnaud Dechesne, Barth F. Smets, Yan Zheng
Summary: Biofiltration is widely used for water treatment, and bacteriophages play a significant role in regulating bacterial populations within biofilters through interactions with key bacterial species. However, there is limited research on phages in biofiltration systems.
Article
Multidisciplinary Sciences
Yichao Wu, Chengxia Fu, Caroline L. Peacock, Soren J. Sorensen, Marc A. Redmile-Gordon, Ke-Qing Xiao, Chunhui Gao, Jun Liu, Qiaoyun Huang, Zixue Li, Peiyi Song, Yongguan Zhu, Jizhong Zhou, Peng Cai
Summary: Cooperative interactions between free-living and biofilm-forming bacteria are found to drive spatial segregation and enable species coexistence in a microfluidic chip environment, promoting their respective dominance in segregated microhabitats. This active spatial segregation is induced by cooperative interactions, improving the fitness of both biofilm and planktonic populations. The study also shows that free-living Arthrobacter induces surface colonization and receives benefits from public goods secreted by biofilm-forming strains.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Mojtaba Khani, Mads Frederik Hansen, Susanne Knochel, Behnam Rasekh, Karim Ghasemipanah, Seyed Morteza Zamir, Mohsen Nosrati, Mette Burmolle
Summary: Many food industry companies use reverse osmosis (RO) membranes to ensure high-quality water reuse, but biofouling is a common problem that decreases water recovery. This study identified bacteria that form biofilms on RO membranes and evaluated the potential of enzymes to disperse biofilms. Beta-Mannosidase was found to significantly reduce biofilm formation in a short time, and longer exposure to various enzymes resulted in significant biofilm reduction. The application of proteinase K and beta-Mannosidase showed promising results in reducing attached biomass on RO membranes.
Article
Microbiology
Boris Parra, Bastiaan Cockx, Veronika T. Lutz, Lone Brondsted, Barth F. Smets, Arnaud Dechesne
Summary: Two plasmid-dependent phages with broad host range have been discovered, which are capable of infecting bacteria carrying different conjugative plasmids and recognize plasmids carrying resistance genes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Lorrie Maccario, Ana F. Silva, Joseph Nesme, Cristina I. Amador, Soren J. Sorensen, Vaughn S. Cooper, Henriette L. Roder
Summary: We present the draft genomes of seven bacterial strains from two wastewater facilities in Denmark, two of which potentially belong to new groups within the Pseudomonas and Pseudochrobactrum genera. These genomes serve as valuable references for studying bacterial interactions and horizontal gene transfer in bacterial communities.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)