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
Ningning Xu, Wenlei Wang, Kai Xu, Yan Xu, Dehua Ji, Changsheng Chen, Chaotian Xie
Summary: This study investigated the effects of seasons and different seaweed species on microbial communities. The results showed that environmental factors in seaweed cultivation zones significantly influenced the variability of fungal and bacterial communities. Certain microbial groups responded positively to seaweed cultivation, and their enrichment was influenced by the composition of dissolved organic matter (DOM).
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Wang Qiongjie, Zhang Yong, Zhang Yangyang, Liu Zhouqi, Wang Jinxiaoxue, Chen Huijuan
Summary: This study found that biofilm can enhance the adsorption capacity of microplastics to copper and lead, while the influence of UV radiation is minimal. According to modeling analysis, adsorption on V-PS is dominated by intra-particle diffusion, while the adsorption rate on UV-PS and Bio-PS is mainly controlled by binding diffusion. Bio-PS has the strongest adsorption capacity and the adsorption mechanisms include physical adsorption, chemisorption, and biosorption.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
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
Agriculture, Dairy & Animal Science
Yukun Zhang, Xiaoxue Zhang, Fadi Li, Chong Li, Deyin Zhang, Xiaolong Li, Yuan Zhao, Weimin Wang
Summary: In modern sheep production systems, efforts are being made to reduce fat deposition costs by altering nutrient use to produce leaner carcasses. Limited research has been done on the effect of rumen microbiome on fat deposition, but this study identified variations in microbial populations in the rumen among sheep with different fat deposition phenotypes, which could help in developing strategies to manipulate rumen microbiota for improved production performance. Extensive study of sheep rumen microbiota has been conducted, but their role in regulating fat deposition remains unclear. This study aimed to identify correlations between fat deposition-related phenotypes and the impact of microbiota on changes in body fat accumulation, identifying 29 ruminal bacteria that may be key drivers of different fat deposition levels.
Article
Microbiology
Ya Wang, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Summary: This study comprehensively evaluates PMA-seq in synthetic and complex microbial communities, finding that the technique is effective for semi-quantitative purposes in simple synthetic communities but provides only qualitative assessments in realistically complex community samples.
Article
Environmental Sciences
Blaire M. Padayhag, Michael Angelou L. Nada, Jake Ivan P. Baquiran, Marilou P. Sison-Mangus, Maria Lourdes San Diego-McGlone, Patrick C. Cabaitan, Cecilia Conaco
Summary: This study found that the microbial biofilm communities near mariculture areas can affect the settlement of coral larvae. The biofilm farthest from the mariculture area had a higher effectiveness in inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae and gammaproteobacterial taxa, while biofilms closer to the mariculture zone had a higher proportion of cyanobacteria and no crustose coralline algae. These findings suggest that nutrient enrichment from mariculture activities can alter the composition of biofilm-associated microbiome and indirectly affect coral larval settlement.
MARINE POLLUTION BULLETIN
(2023)
Article
Environmental Sciences
Christen L. Grettenberger, Dawn Y. Sumner, Kate Wall, Ian Hawes, Tyler Mackey, Anne D. Jungblut
Summary: The McMurdo Dry Valleys are a cold and arid environment with low biomass. However, the ice-covered lakes in the valleys provide a refuge for diverse microbial communities. These communities form ornate structures and show differences in composition between lake depths and zones.
ARCTIC ANTARCTIC AND ALPINE RESEARCH
(2023)
Article
Environmental Sciences
Rehab K. Alhajjar, Ryan B. Ghannam, Jeremy R. Chen See, Olivia G. Wright, Maria Fernanda Campa, Terry C. Hazen, Regina Lamendella, Stephen M. Techtmann
Summary: The study investigated the impact of biocides and nanoparticles on microbial diversity in a hydraulic fracturing impacted stream. The results showed that different types of nanoparticles led to a decrease in bacterial abundance, while biocide-amended treatments saw an increase in microbial abundance. Differentially enriched taxa were observed in biocide and nanoparticle treatments compared to controls, indicating that nanoparticles slightly altered the microbial community composition. The study suggests the potential use of nanoparticles as an alternative to biocides in certain settings.
Article
Environmental Sciences
R. G. Bulgarelli, M. F. A. Leite, M. De Hollander, P. Mazzafera, S. A. L. Andrade, E. E. Kuramae
Summary: The availability of soil phosphorus can affect plant growth, root-soil interactions, and rhizosphere microbial community composition. This study investigated the rhizosphere microbial communities of 24 species of eucalypts under low or sufficient soil phosphorus availability. It was found that eucalypt species identity was the main factor determining the composition of the rhizosphere microbial community, while the effect of phosphorus availability varied among species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
L. G. Schaerer, P. N. Webb, A. Corazzola, W. C. Christian, S. M. Techtmann
Summary: This study found that sources other than water can impact the microbial community of a boat, indicating that terrestrial micro-organisms may influence the boat microbial community.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Environmental Sciences
Zihao Li, Tantan Wang, Xu Yang, Xin Wen, Wenhao Chen, Yubo He, Zhigang Yu, Chang Zhang
Summary: This study compares the microbial communities and their functions in oxygen-depleted and oxygen-limited paddy soil. It finds that oxygen-limited soil has a higher concentration of methylmercury and enhances microbial activity, especially in metabolic pathways related to methylation. The research suggests that insufficient oxygen input in flooded paddy soil increases the risk of human exposure to methylmercury from rice consumption.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Immunology
Gisli G. Einarsson, Bart M. Vanaudenaerde, Christopher D. Spence, Andrew J. Lee, Mieke Boon, Geert M. Verleden, J. Stuart Elborn, Lieven J. Dupont, Dirk Van Raemdonck, Deirdre F. Gilpin, Robin Vos, Stijn E. Verleden, Michael M. Tunney
Summary: This study analyzed the microbiota in the lung tissue and airway luminal mucus of PWCF patients and compared them to disease characteristics and lung damage. The results showed significant differences in microbial communities between different groups, but also overlap. The luminal mucus of PWCF had lower microbial diversity and higher dominance. Variability in ecological parameters was observed both between and within patients, but no clear relationship was found between ecological parameters and disease characteristics.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Ecology
Maura Palacios Mejia, Connie A. Rojas, Emily Curd, Mark A. Renshaw, Kiumars Edalati, Beverly Shih, Nitin Vincent, Meixi Lin, Peggy H. Nguyen, Robert Wayne, Kelsey Jessup, Sophie S. Parker
Summary: This study investigates the impact of long-term contamination on the soil microbiome composition and diversity at an urban brownfield in Los Angeles. The findings suggest that the presence of heavy metals and organic pollutants shape the soil microbiome diversity, and certain bacteria and fungi show tolerance to these contaminants. The study recommends incorporating DNA-based multi-marker microbial community profiling in brownfield site assessment and restoration.
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.
Review
Ecology
Diane S. Srivastava, Laura Coristine, Amy L. Angert, Megan Bontrager, Sarah L. Amundrud, Jennifer L. Williams, Alex C. Y. Yeung, Devin R. de Zwaan, Patrick L. Thompson, Sally N. Aitken, Jennifer M. Sunday, Mary I. O'Connor, Jeannette Whitton, Norah E. M. Brown, Colin D. MacLeod, Laura Wegener Parfrey, Joey R. Bernhardt, Juli Carrillo, Christopher D. G. Harley, Patrick T. Martone, Benjamin G. Freeman, Michelle Tseng, Simon D. Donner
Summary: Forecasting the impact of climate change on biological systems is a major challenge for biologists, and there is a lack of effective framework in climate change biology to anticipate and resolve uncertainty. Attention should be paid to uncertainties in biological systems as well as predicting and addressing the effects of climate change on organisms.
ECOLOGICAL MONOGRAPHS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Stilianos Louca, Florent Mazel, Michael Doebeli, Laura Wegener Parfrey
Article
Substance Abuse
Tamara S. Bodnar, Christopher Lee, Athena Wong, Ilan Rubin, Laura Wegener Parfrey, Joanne Weinberg
Summary: This study provides the first evidence that prenatal alcohol exposure has a long-lasting and sex-specific impact on the fecal microbiota. This finding is of great significance for the development of new interventions in FASD.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Melissa Y. Chen, Alexandra Alexiev, Valerie J. McKenzie
Summary: Host-associated microbial biofilms play an important role in protecting against pathogen establishment. The diversity of bacteria, thickness of biofilms, and richness of inhibitory bacteria can collectively reduce the success of pathogen establishment.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Mary I. O'Connor, Gwendolyn Griffiths, Rhea Sanders-Smith, Margot Hessing-Lewis, Katherine M. Davis, Coreen Forbes, Angeleen M. Olson, Carolyn Prentice, Laura Wegener Parfrey
Summary: The composition and abundance of epibionts in aquatic foundation species can change significantly over small spatial distances. This study used visual and molecular surveys to investigate the spatial patterns in the abundance and distribution of a red macroalga in a seagrass meadow, and found that environmental factors play a role in its colonization and establishment.
Article
Biochemistry & Molecular Biology
Melissa Y. Chen, Jordan G. Kueneman, Antonio Gonzalez, Greg Humphrey, Rob Knight, Valerie J. McKenzie
Summary: Ecological community traits of host-associated microbiota can predict infection risk and intensity of pathogenic microbes, with richness and proportion being important predictors.
Review
Ecology
Genevieve Lajoie, Laura Wegener Parfrey
Summary: Our understanding of the influence of hosts on microbial evolution has mainly focused on symbiont specialization and genomic streamlining. However, there are many symbiotic lineages that facultatively interact with hosts or associate with multiple hosts, and the impact of host association on their niche and evolution is not well understood. This paper discusses the predicted effects of weak or variable selection, horizontal transmission, and low costs of adaptation on the expansion or maintenance of microbial niches in symbiotic associations. This broad perspective will contribute to the development of more accurate and general predictions for the evolution of microbial symbioses.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Biodiversity Conservation
Jordan Kueneman, Molly Bletz, Matthew Becker, Brian Gratwicke, Orlando A. Garces, Andreas Hertz, Whitney M. Holden, Roberto Ibanez, Andrew Loudon, Valerie McKenzie, Laura Parfrey, Brandon Sheafor, Louise A. Rollins-Smith, Corinne Richards-Zawacki, Jamie Voyles, Douglas C. Woodhams
Summary: Captive breeding plays an important role in safeguarding animal groups, but it can have significant effects on the microbial communities and health of captive-reared animals. This study conducted a meta-analysis on the skin microbiomes of 18 amphibian species and found substantial differences between captive and wild individuals. The impact of captivity on diversity metrics and antifungal function varied depending on the species, highlighting the need for individual species evaluations and a cohesive approach to mitigate the effects of captivity on amphibian skin microbes.
BIOLOGICAL CONSERVATION
(2022)
Article
Biochemistry & Molecular Biology
Emily M. Adamczyk, Mary O'Connor, Laura Wegener Parfrey
Summary: Seagrass leaf microbiota are influenced by both microbial selection and local environmental conditions, and they can flexibly assemble in response to different environmental conditions, contributing to their resilience in future climate change scenarios.
Article
Ecology
Daijiang Li, Sydne Record, Eric R. Sokol, Matthew E. Bitters, Melissa Y. Chen, Y. Anny Chung, Matthew R. Helmus, Ruvi Jaimes, Lara Jansen, Marta A. Jarzyna, Michael G. Just, Jalene M. LaMontagne, Brett A. Melbourne, Wynne Moss, Kari E. A. Noman, Stephanie M. Parker, Natalie Robinson, Bijan Seyednasroliah, Colin Smith, Sarah Spaulding, Thilina D. Surasinghe, Sarah K. Thomsen, Phoebe L. Zarnetske
Summary: Understanding patterns and drivers of species distribution and abundance is crucial for ecology research. However, the lack of standardized, high-quality data that cover large spatial scales and long time periods restricts current research. NEON provides freely available observational data generated from consistent sampling at 81 sites across the United States for at least 30 years. This data resource is valuable for advancing biodiversity research, but it is essential to ensure its accessibility and integration into researchers' workflows. To address this, a workflow and standardized data package have been developed, allowing for the use of NEON organismal data in biodiversity research.
Review
Plant Sciences
Zayda P. Morales Moreira, Melissa Y. Chen, Daniela L. Yanez Ortuno, Cara H. Haney
Summary: Engineering plant microbiomes has the potential to improve plant health rapidly and sustainably. However, successful lab approaches have not been widely implemented in the field. This article suggests an integrated approach to address knowledge gaps and facilitate translatability of plant microbiome engineering into real-world applications.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Microbiology
Alexandra Alexiev, Melissa Y. Chen, Timothy Korpita, Andrew M. Weier, Valerie J. McKenzie
Summary: Our research group studied the pathogen Bd and found that there are other bacterial strains besides J. lividum that can better inhibit its growth. We also discovered that in certain cases, using two strains in combination is more effective than using a single strain alone.
MICROBIOLOGY SPECTRUM
(2023)
Article
Genetics & Heredity
Jungsoo Park, Katherine Davis, Genevieve Lajoie, Laura Wegener Parfrey
Summary: This study compared different methods to identify core taxa in the microbiome of the widespread brown macroalga, Fucus distichus. The results showed that some core taxa were consistently identified by various approaches, with indicator species analysis being better at identifying host-specific microbes. Additionally, most of the core ASVs of F. distichus were found on multiple macroalgal hosts, indicating a macroalgal generalist niche.
ENVIRONMENTAL MICROBIOME
(2022)
Article
Biochemistry & Molecular Biology
Florent Mazel, Antoine Guisan, Laura Wegener Parfrey
Summary: Different gut microbes in mammals are associated with different host species, which is sometimes referred to as phylosymbiosis. The processes shaping this host specificity are not well understood. One model suggests that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. Our findings support this model and show that host specificity varies depending on transmission mode and dispersal ability of the microbes.
Meeting Abstract
Substance Abuse
T. S. Bodnar, V. Billy, A. Wong, C. Lee, G. Ainsworth-Cruickshank, L. Wegener Parfrey, J. Weinberg, C. Raineki
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2022)