Article
Immunology
Wei-Jie Song, Jun Gao, Ji-Wei Huang, Yuan Liu, Zhi Long, Le-Ye He
Summary: By detecting the composition and function of microorganisms in expressed prostatic secretion (EPS) of patients with chronic prostatitis (CP) and healthy people, this study explored whether type III prostatitis is related to bacterial infection. The results showed that there were many microorganisms in EPS in both CP patients and healthy populations, but the relative abundance of specific bacteria in CP patients, including Pseudomonas, Haemophilus, Sneathia, Allobaculum, and Enterococcus, was significantly different. Metagenomics sequencing also revealed that different bacteria in the type III prostatitis group had certain biological functions.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Ecology
Vijaya Raghavan Rangamaran, Sai H. Sankara Subramanian, Karpaga Raja Sundari Balachandran, Dharani Gopal
Summary: This study investigated the bacterial communities at different depths of the Arabian Sea OMZ using high-throughput sequencing. The results showed high bacterial diversity in deep waters and sediment samples, with less richness at the core OMZ depths. Bacterial community composition varied with depth and dissolved oxygen levels, and predictive functional annotation suggested the presence of active nitrogen, sulphur, carbon, and methane metabolic cycles. The study also revealed the presence of nitrogen reduction bacterial group below the core OMZ depths, which may provide insights into the expansion of OMZ region in Arabian Sea.
Article
Microbiology
Jia Li, Ru Zhang, Jinxia Ma, Shuai Tang, Yuan Li, Yi Li, Jun Wan
Summary: This study thoroughly investigated the gut microbial profile of patients with SIBO, finding significant differences in bacterial compositions between fecal and mucosal samples, as well as potential microbial biomarkers in the mucosa-associated gut microbiome. Further research is needed to explore the mechanisms and roles of these mucosa-associated taxa in SIBO.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yang You, Meixiang Yin, Xiao Zheng, Qiuying Liang, Hui Zhang, Bu-Ling Wu, Wenan Xu
Summary: By analyzing samples from different ages and sexes of children, we found that Acinetobacter and Clostridiales were associated with caries in plaque and saliva, respectively. We also found the presence of Firmicutes and Clostridia in plaque from children of different ages. However, these bacterial markers varied greatly between different populations, with only Saccharibacteria being a consistent signal for childhood caries.
Article
Microbiology
Christian O'Dea, Roger Huerlimann, Nicole Masters, Anna Kuballa, Cameron Veal, Paul Fisher, Helen Stratton, Mohammad Katouli
Summary: The study revealed rich and diverse gut microbiota in Australian Eastern Grey Kangaroos, with variations in microbial diversity profiles among kangaroos from different regions, suggesting environmental factors may impact their microbial composition.
Article
Microbiology
Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski, Ulrich Stingl
Summary: Planktonic microbial communities in wetland ecosystems play a vital role, yet they are relatively underexplored compared to other aquatic ecosystems. This study conducted a high-resolution analysis of bacterial and eukaryotic microbial communities in the Florida Everglades, revealing significant variations along the salinity gradient.
Article
Biotechnology & Applied Microbiology
Yan-Feng Wei, Lu Wang, Zi-Yuan Xia, Min Gou, Zhao-Yong Sun, Wei-Feng Lv, Yue-Qin Tang
Summary: This study characterized indigenous microorganisms in oil reservoirs after polymer flooding (RAPF). The results showed that both crude oil and Aqu0.1 contained different functional microorganisms related to hydrocarbon degradation. This is significant for investment and exploration of indigenous microorganisms for microbial enhanced oil recovery (MEOR).
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Stephen Knobloch, Alexandra Maria Klonowski, Sigrun Tomasdottir, Bjarni Reyr Kristjansson, Sverrir Gudmundsson, Viggo Por Marteinsson
Summary: Groundwater is a vital resource for safe drinking water supply, but unconfined aquifers can be vulnerable to microbial contamination during extreme weather events. This study in South-West Iceland found that the microbial community in groundwater can change during surface runoff, highlighting the potential risk of contamination during such events.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Food Science & Technology
Niki Mougiou, Antiopi Tsoureki, Spyros Didos, Ioanna Bouzouka, Sofia Michailidou, Anagnostis Argiriou
Summary: The analysis of table olives microbiome using next-generation sequencing has provided valuable information about the microbial community composition of this popular fermented food. This study used 16S and 18S rRNA sequencing to evaluate the microbial communities of table olives from five Greek popular cultivars, fermented by Greek or Spanish style. The results showed that different curing and fermentation methods had an impact on the microbial composition and biochemical properties of the olives.
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
Microbiology
Susan Joseph, Joseph Aduse-Opoku, Ahmed Hashim, Eveliina Hanski, Ricarda Streich, Sarah C. L. Knowles, Amy B. Pedersen, William G. Wade, Michael A. Curtis
Summary: A curated murine oral microbiome database has been constructed, containing a collection of nearly full-length 16S rRNA gene sequences from cultured isolates and draft genomes from representative taxa. The database comprises 103 mouse oral taxa (MOT) spanning four phyla, including 12 novel undescribed species-level taxa. Key observations include the low diversity and predominantly culturable nature of the laboratory mouse oral microbiome, as well as the identification of three major murine-specific oral bacterial lineages.
Article
Microbiology
Fangchao Song, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin
Summary: In this study, a direct PCR method was evaluated as a cost-effective and time-saving alternative to traditional DNA extraction methods for analyzing microbial communities. The direct PCR method showed comparable efficiency to the conventional DNeasy PowerSoil protocol, with higher efficiency for extracting gDNA from Gram-negative strains. This method is significantly less expensive and faster, making it a potential solution for high-throughput large-scale bacterial community analysis.
Article
Biotechnology & Applied Microbiology
Maarten D. Verhoeven, Per H. Nielsen, Morten K. D. Dueholm
Summary: The researchers introduced an experimental setup, combining 16S rRNA gene amplicon sequencing with plating of dispersed activated sludge bacteria, to rapidly identify the growth conditions that allow for the isolation of key microbial species in activated sludge. They found that agarose plates supplemented with various carbon sources support the growth of many previously uncultivated activated sludge bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Aoyun Li, Yajing Wang, Yuanyuan He, Bingxian Liu, Mudassar Iqbal, Khalid Mehmood, Tariq Jamil, Yung-Fu Chang, Lianmei Hu, Ying Li, Jianying Guo, Jiaqiang Pan, Zhaoxin Tang, Hui Zhang
Summary: Fluorine and its compounds from industrial production and coal combustion can cause contamination of air, water, and soil, posing a threat to public health through accumulation in animals, plants, and humans via food chain. Exposure to fluoride resulted in damaged intestinal structure and altered gut microbial composition in ducks.
Article
Biotechnology & Applied Microbiology
Adeline Su Yien Ting, Muhammad Zarul Hanifah Md Zoqratt, Hock Siew Tan, Andreas Aditya Hermawan, Amin Talei, Soon Thiam Khu
Summary: This study profiled microbial communities in a lake and river within a highly urbanized township in Malaysia, revealing dominant prokaryotic phyla of Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, and predominant eukaryotic communities of SAR clade and Opisthokonta. The presence of pathogens such as Pseudomonas and Flavobacterium in urban water systems indicates possible health risks, as transient communities coexist with common indigenous aquatic communities. Urbanization influences the physicochemical properties and microbial dynamics in water systems, leading to variations in microbial abundances.
Article
Public, Environmental & Occupational Health
Casey W. Cooper, Kathleen A. N. Aithinne, Bradley S. Stevenson, Jon E. Black, David L. Johnson
AMERICAN JOURNAL OF INFECTION CONTROL
(2020)
Article
Biology
Victoria A. Petryshyn, Emily N. Junkins, Blake W. Stamps, Jake V. Bailey, Bradley S. Stevenson, John R. Spear, Frank A. Corsetti
Summary: This study examines the role of micro-organisms in modern stromatolite growth and finds that DNA sequences mainly originate from tenant or squatter communities, rather than the actual builders. It highlights the difficulty in interpreting the role of biology in stromatolite morphogenesis when removed from their environmental context.
Article
Biology
Fernando Medina Ferrer, Michael R. Rosen, Jayme Feyhl-Buska, Virginia V. Russell, Fredrik Sonderholm, Sean Loyd, Russell Shapiro, Blake W. Stamps, Victoria Petryshyn, Cansu Demirel-Floyd, Jake Bailey, Hope A. Johnson, John R. Spear, Frank A. Corsetti
Summary: Modern carbonate tufa towers in Big Soda Lake exhibit rapid precipitation rates exceeding 3 cm/year due to diverse microbial communities. Microorganisms promote fast carbonate precipitation through ureolysis, potentially forming biosignatures in the carbonate microfabric.
Article
Microbiology
Emily N. Junkins, Bradley S. Stevenson
Summary: Molecular techniques reveal the disparity between the diversity of microbial life and the small proportion in pure culture, guiding the search for novel antimicrobial drug targets. The use of molecular tools provides a more complete understanding of the microorganisms present during cultivation, emphasizing the importance of informing future cultivation efforts with these tools.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
James G. Floyd, Blake W. Stamps, Wendy J. Goodson, Bradley S. Stevenson
Summary: This study found that fungi in B20 biodiesel can increase acidity and accelerate the corrosion of carbon steel by degrading fatty acid methyl esters and alkanes. The fungi caused deeper corrosion pits, especially at the interface between the fuel and water.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Letter
Microbiology
Bradley Stevenson, Blake Stamps
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Environmental Sciences
Katrin Gaardbo Kuhn, Jane Jarshaw, Erin Jeffries, Kunle Adesigbin, Phil Maytubby, Nicole Dundas, A. Caitlin Miller, Emily Rhodes, Bradley Stevenson, Jason Vogel, Halley Reeves
Summary: This study demonstrates the effectiveness of wastewater surveillance in providing early warnings of COVID-19 outbreaks. The concentration of SARS-CoV-2 in wastewater can predict the number of cases with an accuracy of 81-92%. The study also highlights the importance of considering population structures when interpreting surveillance outputs and planning preventive measures.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Editorial Material
Biochemistry & Molecular Biology
Megan B. Diamond, Aparna Keshaviah, Ana Bento, Otakuye Conroy-Ben, Erin M. Driver, Katherine B. Ensor, Rolf U. Halden, Loren P. Hopkins, Katrin G. Kuhn, Christine L. Moe, Eric C. Rouchka, Ted Smith, Bradley S. Stevenson, Zachary Susswein, Jason R. Vogel, Marlene K. Wolfe, Lauren B. Stadler, Samuel Scarpino
Summary: Wastewater monitoring has proven effective in identifying outbreaks and variants, and should be expanded to enhance public health preparedness.
Article
Electrochemistry
Robert B. B. Miller, Hanieh Ghadimi, Sai Prasanna Chinthala, Anwar Sadek, Audra L. L. Crouch, James G. G. Floyd, Bradley S. S. Stevenson, Wendy Crookes-Goodson, John M. M. Senko, Chelsea N. N. Monty
Summary: Split-chamber zero resistance ammetry (SC-ZRA) was used to study microbiologically influenced corrosion by aerobic chemoorganotrophic microeukaryotes isolated from biodiesel storage tanks. The magnitude and direction of electric current were measured between two shorted carbon steel electrodes, which were deployed in separate chambers connected by a salt bridge (via a SC-ZRA assembly). This approach permitted rapid screening for the corrosive activity of these previously understudied microeukaryotes. During this study, two previously understudied microeukaryotes (Byssochlamys sp. SW2 and Yarrowia lipolytica) showed increased biomass, an increase in electrochemical signal (current), and a corresponding increase in corrosion rate (weight loss). However, other previously understudied microeukaryote (Wickerhammomyces sp. SE3) showed an increase in biomass without an increase in electrochemical signal and minimal corrosion rate, indicating that the SC-ZRA technique can screen for the corrosive activity of a microorganism, regardless of overall microbial activity. This technique could be used to quickly assess the corrosive potential for a range of previously understudied microorganisms.
JOURNAL OF APPLIED ELECTROCHEMISTRY
(2023)
Article
Geochemistry & Geophysics
Jennifer McIntosh, Ji-Hyun Kim, Lydia Bailey, Magdalena Osburn, Henrik Drake, Anna Martini, Peter Reiners, Bradley Stevenson, Grant Ferguson
Summary: This study investigates the burial and exhumation, biodegradation, and fluid circulation history of hydrocarbon reservoirs across the Colorado Plateau to understand the response of subsurface microbial life to changing surface conditions over geologic time. The findings show that microbial communities were likely sterilized during deep burial but later reintroduced through upward migration of hydrocarbons. Recent erosion brought reservoirs closer to the surface and facilitated microbial activity and hydrocarbon biodegradation. This study provides insights into the evolution of the hypo-Critical Zone and microbial interactions with rocks and fluids in crustal environments.
GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS
(2023)
Article
Biochemical Research Methods
Samuel T. Shawn, Sean W. Harshman, Christina N. Davidson, Jae Hwan Lee, Anne E. Jung, Ariel Parker, M. Aaron Hawkins, Blake W. Stamps, Rhonda L. Pitsch, Jennifer A. Martin
Summary: Research on exhaled breath has been hindered by the lack of standardized collection and analysis methods. The Respiration Collector for In Vitro Analysis (ReCIVA) sampling device has shown potential as a consistent and convenient method for breath collection, but its high costs have limited its widespread use. To reduce expenses and logistical burdens, the possibility of sterilizing and reusing disposable masks and filters has been hypothesized.
JOURNAL OF BREATH RESEARCH
(2023)
Article
Microbiology
Katrin Gaardbo Kuhn, Rishabh Shukla, Mike Mannell, Grant M. Graves, A. Caitlin Miller, Jason Vogel, Kimberly Malloy, Gargi Deshpande, Gabriel Florea, Kristen Shelton, Erin Jeffries, Kara B. De Leon, Bradley Stevenson
Summary: During the COVID-19 pandemic, wastewater surveillance has been widely used to monitor infection trends. A statewide program for routine wastewater monitoring of gastrointestinal pathogens was established in Oklahoma. The results showed that wastewater concentrations of Salmonella, Campylobacter, and norovirus exhibited similar seasonal patterns to reported human cases, and wastewater can serve as an early warning tool for increases in cases. The use of wastewater surveillance surpasses traditional methods and improves our understanding of gastrointestinal infections.
Article
Genetics & Heredity
Ida G. Pantoja-Feliciano G. De Goodfellow, Richard Agans, Robyn Barbato, Sophie Colston, Michael S. Goodson, Rasha Hammamieh, Kristy Hentchel, Robert Jones, J. Philip Karl, Robert Kokoska, Dagmar H. Leary, Camilla Mauzy, Kenneth Racicot, Blake W. Stamps, Vanessa Varaljay, Jason W. Soares
Summary: The Tri-Service Microbiome Consortium (TSMC) was established to promote collaboration, coordination, and communication of microbiome research in the Department of Defense (DoD), as well as facilitate resource and information sharing between consortium members, including academic and industry collaborators. The 6th Annual TSMC Symposium, held in Fairlee, Vermont on 27-28 September 2022, focused on microbiome-related topics within seven thematic areas. The symposium provided updates on current DoD microbiome research efforts, showcased innovative research from academia and industry, and fostered collaboration opportunities.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Biotechnology & Applied Microbiology
Emily A. Kraus, Daniel Nothaft, Blake W. Stamps, Kaitlin R. Rempfert, Eric T. Ellison, Juerg M. Matter, Alexis S. Templeton, Eric S. Boyd, John R. Spear
Summary: The study explores the functional capability and activity of microbial methane cycling in serpentinization-impacted subsurface waters in the Samail Ophiolite of Oman. The results reveal active methanogenic and methanotrophic populations, particularly in waters with hyperalkaline pH. This highlights the potential for biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)