Article
Microbiology
Juliana R. Almeida, Joana C. Fradinho, Gilda Carvalho, Adrian Oehmen, Maria A. M. Reis
Summary: This work evaluates the influence of different operational conditions on the bacterial communities reported in phototrophic mixed culture (PMC) systems with polyhydroxyalkanoates (PHA) production capabilities. Chromatiaceae members were identified as the main phototrophic PHA producers, favored under high carbon concentrations and the permanent feast regime. Increasing the organic loading rate in systems fed with fermented wastewater enriched for other bacteria responsible for PHA storage. High-sugar feedstock impaired PHA production under the permanent feast conditions, but not under feast and famine conditions.
Article
Soil Science
Jessica L. Sarauer, Mark D. Coleman
Summary: Biochar is an environmental soil application tool that can be used in forest soils to mitigate climate change and sequester carbon. This study investigated the effects of biochar amendment to soil in three managed forest sites in the western USA. The results showed that biochar did not have a detrimental effect on soil microbial community composition in the northwestern USA forests.
APPLIED SOIL ECOLOGY
(2023)
Article
Environmental Sciences
Qunxing Ding, Haiyan Zhu
Summary: Indoor air quality varies and is related to respiratory diseases. This study used metagenomic analysis to investigate microbial communities in indoor water cultures. Three water samples were collected: sterilized laboratory tap water (Al02), non-sterilized laboratory tap water (Al03), and water from the Ohio River near the campus (Al04). The genomic DNA of the samples was sequenced and analyzed, identifying a total of 1,123,463 open reading frames (ORFs). The ORFs were mainly associated with metabolism, environmental information processing, and genetic information processing. The most abundant phylum identified was Proteobacteria, with Chlorophyta also being significant in all three samples.
WATER AIR AND SOIL POLLUTION
(2023)
Article
Soil Science
Lenka Nemcova, Lukas Bystriansky, Martina Hujslova, Hana Auer Malinska, Hana Hrselova, Milan Gryndler
Summary: The microbial community of soil can be divided into planktonic organisms and biofilm communities. Biofilm communities are crucial for decomposition of plant litter and soil organic matter. However, the composition of soil biofilm communities is not well studied due to methodological challenges.
APPLIED SOIL ECOLOGY
(2022)
Article
Environmental Sciences
Maelle Deshoux, Sophie Sadet-Bourgeteau, Solene Gentil, Nicolas Chemidlin Prevosr-Boure
Summary: Changes in soil microbial communities may have significant implications for soil fertility and stability. Studies on the effects of biochar on soil microbial communities have shown a high degree of variability, highlighting the need for further research on the production and application conditions of biochar.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Daniela Peneda Pacheco, Federico Bertoglio, Cosmin Butnarasu, Natalia Suarez Vargas, Giuseppe Guagliano, Anna Ziccarelli, Francesco Briatico-Vangosa, Vincenzo Ruzzi, Stefano Buzzaccaro, Roberto Piazza, Sebastiao van Uden, Elena Crotti, Sonja Visentin, Livia Visai, Paola Petrini
Summary: The intrinsic heterogeneity of bacterial niches needs to be preserved in in vitro cultures to accurately represent the complex microbial ecology. This study focuses on generating mucin-containing hydrogels - CF-Mu(3)Gel, which mimic the cystic fibrosis (CF) mucus and serve as a challenging microbial niche for current therapeutic strategies. CF-Mu(3)Gel exhibits structural gradients, with a gradual decrease in oxygen tension across its thickness, which closely resembles the CF airway mucus. These distinctive features significantly influence bacterial organization and antimicrobial tolerance, resulting in a more accurate representation of bacterial behavior in patients and providing new insights for improved microbiology studies and drug testing.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Engineering, Environmental
Martin Hjorth Andersen, Lisette Thomsen, Mikkel Stokholm-Bjerregaard, Susan Hove Hansen, Mads Albertsen, Per Halkjaer Nielsen, Soren Eriksen
Summary: The partial nitritation/anammox process is a popular approach for removing nitrogen from sidestreams, but it requires extensive surveillance and monitoring due to its sensitivity to disturbances. In this study, we utilized online sensor data and Nanopore DNA sequencing to monitor the microbial community and detect system disturbances in two full-scale deammonification reactors over a year. DNA surveillance revealed unexpected variations in anammox bacteria, and the composition and dynamics of the surrounding community indicated causes for occasional process disturbances. Monitoring the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) could potentially optimize reactor operation. The use of frequent DNA sequencing was found to be an important supplement to online sensor data for process surveillance and control.
Review
Biochemical Research Methods
Robbert Kleerebezem, Gerben Stouten, Jasper Koehorst, Alette Langenhoff, Peter Schaap, Hauke Smidt
Summary: Microbial ecology research aims to identify, understand, and explore the roles of various microorganisms in ecosystems, with a shift towards metagenomic studies due to advancements in DNA sequencing. However, the direct link between molecular properties and measurable changes in ecosystem performance is often inadequately documented.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Xiaoxue Yang, Zheng Peng, Qi Zhu, Chengcong Chen, Jiheng Liu, Songtao Fu, Juan Zhang
Summary: This study analyzed the compounds contributing to the aroma of aged Tieguanyin tea and explored the underlying aging mechanism. The results showed that certain volatile compounds were characteristic of the aged aroma, and bacteria and fungi had strong interactions with these compounds. The findings provide important insights into improving the quality of aged Tieguanyin tea.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Veterinary Sciences
Li Zhao, Yi-Min Ma, Bo Yang, Wen-Xiong Han, Wei-Hong Zhao, Hai-Liang Chai, Zhan-Sheng Zhang, Yong-Jie Zhan, Li-Feng Wang, Yu Xing, Lu-Fei Yu, Jin-Ling Wang, Yu-Lin Ding, Yong-Hong Liu
Summary: This study comprehensively analyzed the microbial community composition at different growth stages of Dermacentor nuttalli ticks, revealing their potential role as carriers of various pathogenic microorganisms, including Brucella melitensis, which poses a serious threat to humans and animals.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Sangeeta Chavan, Vishwas Sarangdhar, Nadanathangam Vigneshwaran
Summary: The use of nanotechnology products in crop improvement may have an impact on soil microorganisms that influence soil and plant health. A metagenomic study using nanopore-based technology showed shifts in the composition of soil microorganisms when treated with silver, titanium dioxide, and zinc oxide nanoparticles. Analysis revealed changes in the abundance of certain microbial groups at various taxonomic ranks, indicating potential effects on soil microbial communities.
Review
Biotechnology & Applied Microbiology
Jan-Niklas Hengsbach, Bjorn Sabel-Becker, Roland Ulber, Dirk Holtmann
Summary: The electrochemical process of microbial electrosynthesis (MES) is used to drive the metabolism of electroactive microorganisms for the production of valuable chemicals and fuels. Mixed cultures generally show better performance than pure cultures in MES, with a higher methane and acetate production rate. The focus of this review is on comparing the performance of pure and mixed cultures in MES.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Anna Townsend, Hendrik C. den Bakker, Amy Mann, Claire M. Murphy, Laura K. Strawn, Laurel L. Dunn
Summary: 16S amplicon sequencing was conducted on 317 environmental surface sponge swabs collected in 18 distribution centers (DCs) across the United States. The study found significant differences in microbial communities among different DCs and discovered the presence of pathogens related to foodborne diseases. It also identified a higher abundance of cold-tolerant bacteria in samples containing Listeria and significant variations in microbiome composition across different variables.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Seeu Si Ong, Jia Xu, Choon Kiat Sim, Alexis Jiaying Khng, Peh Joo Ho, Philip Kam Weng Kwan, Aarthi Ravikrishnan, Kiat-Tee Benita Tan, Qing Ting Tan, Ern Yu Tan, Su-Ming Tan, Thomas Choudary Putti, Swee Ho Lim, Ee Ling Serene Tang, Niranjan Nagarajan, Neerja Karnani, Jingmei Li, Mikael Hartman
Summary: This study investigated the microbial flora in patients with idiopathic granulomatous mastitis (IGM) and lactational mastitis (LM). The results showed differences between IGM pus samples and corresponding skin samples, while no significant differences were observed in LM samples. There was no characteristic dominant genus in IGM samples, but Corynebacterium kroppenstedtii showed higher levels in IGM pus samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Gregory S. Canfield, Anushila Chatterjee, Juliel Espinosa, Mihnea R. Mangalea, Emma K. Sheriff, Micah Keidan, Sara W. McBride, Bruce D. McCollister, Howard C. Hang, Breck A. Duerkop
Summary: Enterococcus faecium, a commensal of the human intestine, has evolved into a hospital-adapted, multidrug-resistant pathogen. Bacteriophages, natural predators of bacteria, show potential as therapeutics against MDR E. faecium infections, despite the unknown molecular events governing their interactions. While phage resistance may emerge, it is shown that lytic phages could effectively synergize with antibiotics to slow or inhibit E. faecium growth.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Microbiology
Mihnea R. Mangalea, David Paez-Espino, Kristopher Kieft, Anushila Chatterjee, Meagan E. Chriswell, Jennifer A. Seifert, Marie L. Feser, M. Kristen Demoruelle, Alexandra Sakatos, Karthik Anantharaman, Kevin D. Deane, Kristine A. Kuhn, V. Michael Holers, Breck A. Duerkop
Summary: Research shows that intestinal phage communities in individuals at risk for developing rheumatoid arthritis can vary based on the presence of anti-CCP antibodies, with these phages potentially influencing the metabolic and immunomodulatory capability of the microbiota.
CELL HOST & MICROBE
(2021)
Article
Microbiology
Taylor Morrisette, Katherine L. Lev, Gregory S. Canfield, Breck A. Duerkop, Razieh Kebriaei, Kyle C. Stamper, Dana Holger, Susan M. Lehman, Smaranda Willcox, Cesar A. Arias, Michael J. Rybak
Summary: Enterococcus faecium is an important multidrug-resistant pathogen. The use of bacteriophage cocktails as a complement to antibiotic therapy has been proposed. This study selected two phages (113 and 9184) with the broadest host ranges for further experiments and found that the combination of Daptomycin and the phage cocktail showed bactericidal activity and prevented phage resistance against daptomycin-nonsusceptible E. faecium.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
J. Alfredo Blakeley-Ruiz, Manuel Kleiner
Summary: Mass spectrometry-based metaproteomics is a prominent technique for studying specific organism functions in microbial communities. The construction of protein sequence databases plays a crucial role in identifying proteins and inferring taxonomic and functional information in metaproteomics studies. This review provides an overview of database construction strategies, relevant studies, and best practices.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Microbiology
Cydney N. Johnson, Dennise Palacios Araya, Viviane Schink, Moutusee Islam, Mihnea R. Mangalea, Emily K. Decurtis, Tuong-Vi C. Ngo, Kelli L. Palmer, Breck A. Duerkop
Summary: This study investigates the genome evolution of Enterococcus faecalis under phage infection, revealing that phage pressure leads to genetic mutations in E. faecalis and selects for diverse variants. This research is important for understanding E. faecalis genome evolution and informing the design of future therapeutic approaches.
Article
Infectious Diseases
Katherine Lev, Ashlan J. Kunz Coyne, Razieh Kebriaei, Taylor Morrisette, Kyle Stamper, Dana J. Holger, Gregory S. Canfield, Breck A. Duerkop, Cesar A. Arias, Michael J. Rybak
Summary: This study examined the synergy between lytic bacteriophages and antibiotics in treating multidrug-resistant Enterococcus faecium. The results showed that combinations of bacteriophages with daptomycin and other antibiotics had synergistic and bactericidal effects, while also preventing the emergence of resistance.
Article
Biochemistry & Molecular Biology
Fernanda Salvato, Simina Vintila, Omri M. Finkel, Jeffery L. Dangl, Manuel Kleiner
Summary: Metaproteomics is a powerful tool for studying microbial communities, including plant-associated microbiota. This study optimized and evaluated protein extraction methods for metaproteomics of plant-associated microbiota in Arabidopsis and maize. The researchers identified two extraction methods that yield the highest number of identified microbial proteins in each plant species, providing valuable reference for future optimization in other plants.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Plant Sciences
Ashley E. Beck, Manuel Kleiner, Anna-Katharina Garrell
Summary: Understanding the complexity of plant-microbe interactions is a major challenge. Synthetic communities can help simplify these systems, but our understanding of plant-microbe interactions is still limited.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Yui Sato, Juliane Wippler, Cecilia Wentrup, Rebecca Ansorge, Miriam Sadowski, Harald Gruber-Vodicka, Nicole Dubilier, Manuel Kleiner
Summary: In this study, the relationship between the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its bacterial symbionts was investigated. The study found that partner fidelity varies among different symbiont species and can change over short periods of time. The fidelity was highest for the dominant chemoautotrophic, sulphur-oxidizing symbionts, while it was lower for sulphate-reducing and spirochaetal symbionts. This variation in fidelity is likely influenced by both selective and stochastic forces.
Article
Infectious Diseases
Ashlan J. Kunz Coyne, Kyle Stamper, Razieh Kebriaei, Dana J. Holger, Amer El Ghali, Taylor Morrisette, Biswajit Biswas, Melanie Wilson, Michael Deschenes, Gregory S. Canfield, Breck A. Duerkop, Cesar A. Arias, Michael J. Rybak
Summary: This study evaluated eight MDR E. faecium strains for biofilm production and phage susceptibility against nine phages. The use of DAP + AMP combined with 3- and 4-phage cocktails effectively eradicated biofilm-embedded MDR E. faecium clinical blood isolates.
Review
Multidisciplinary Sciences
Alexandria Bartlett, Manuel Kleiner
Summary: Dietary protein has a significant impact on the composition and function of the intestinal microbiota, and its interactions with the microbiota have critical implications for host health.
Article
Multidisciplinary Sciences
Dolma Michellod, Tanja Bien, Daniel Birgel, Marlene Violette, Manuel Kleiner, Sarah Fearn, Caroline Zeidler, Harald R. Gruber-Vodicka, Nicole Dubilier, Manuel Liebeke
Summary: Using various techniques, such as metabolite imaging and enzyme assays, we have discovered that gutless marine annelids synthesize the plant sterol sitosterol, which is commonly found in plants. This synthesis is facilitated by a noncanonical C-24 sterol methyltransferase, an enzyme that is essential for sitosterol synthesis in plants but not widely known in most animals. Our phylogenetic analyses also indicate that this enzyme is present in representatives of at least five animal phyla, suggesting that the synthesis of plant-like sterols is more common in animals than previously believed.
Article
Microbiology
Manuel Kleiner, Angela Kouris, Marlene Violette, Grace D'Angelo, Yihua Liu, Abigail Korenek, Nikola Tolic, Timo Sachsenberg, Janine McCalder, Mary S. S. Lipton, Marc Strous
Summary: In this study, a new protein-based stable isotope probing approach was developed, which allows for cost-effective analysis of associations between microbiome members and substrates. The approach also enables ultra-sensitive detection of stable isotopes and measurement of microbial activity under different diets.
Article
Ecology
Tal Zvi-Kedem, Simina Vintila, Manuel Kleiner, Dan Tchernov, Maxim Rubin-Blum
Summary: Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, and also have secondary symbionts whose role is unknown. In this study, the symbionts of Idas mussels were investigated using metagenomics, metatranscriptomics, and metaproteomics. The results revealed that the primary symbiont is a methylotrophic autotroph, while the secondary symbionts likely have roles in nitrogen metabolism and glycan degradation.
ISME COMMUNICATIONS
(2023)
Meeting Abstract
Critical Care Medicine
J. Colbert, J. Kirsch, C. Erzen, D. Frank, B. Duerkop, E. P. Schmidt
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)