Article
Ecology
Walaa A. Eraqi, Marwa T. ElRakaiby, Salwa A. Megahed, Noha H. Yousef, Mostafa S. Elshahed, Aymen S. Yassin
Summary: Evaluation of the microbial identity, diversity, and community structure in the Nile River revealed that microbial communities were primarily influenced by sample type (sediment versus water) rather than seasonal or spatial factors. The presence of potential pathogens and toxin-producing cyanobacteria in low abundance was identified within the Nile microbiome. Functionally, antibiotic biosynthesis and aerobic xenobiotic degradation pathways were predicted in the river microbiome.
Article
Agriculture, Dairy & Animal Science
Fabio V. R. Portilho, Juliano Nobrega, Beatriz O. de Almeida, Andre R. Mota, Carolina L. de Paula, Fernando J. P. Listoni, Sandra M. G. Bosco, Alana L. Oliveira, Maria de Lourdes R. S. Cunha, Marcio G. Ribeiro
Summary: We investigated the oral microbiota of 100 healthy dogs and identified a complex community of bacteria and fungi, including potential pathogens to humans. We also observed multiple drug-resistant bacteria in the oral cavity of these dogs. This highlights the risk of transmission of microorganisms from dogs to humans and the challenges in treating infections caused by dog bites.
Article
Infectious Diseases
Dan Wang, Takayuki Nambu, Hiroaki Tanimoto, Naohiro Iwata, Kazushi Yoshikawa, Toshinori Okinaga, Kazuyo Yamamoto
Summary: The study reveals that violet LED irradiation significantly reduces the relative abundance of Fusobacterium species in the oral microbiome, while leading to a significant increase in species such as Veillonella and Campylobacter. This method shows potential for adjusting the balance of the oral microbiome without inducing antibiotic resistance.
Article
Virology
Wei Zhao, Mei Ling Yu, XiaoLi Tao, Mei Hui Cheng, Chang Cheng Liu, Yang Liu, Yong Gang Li
Summary: The study revealed significant differences in the gut microbiota composition between RV-infected and un-infected suckling mice, particularly evident in the composition and metabolic pathways of the intestinal flora. These findings shed light on the potential impact of bacterial genera changes during RV infection, which may be related to the replication and pathogenesis of RV.
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
Soil Science
Xiaolong Liang, Yusong Wang, Ying Zhang, Jie Zhuang, Mark Radosevich
Summary: The microbial abundance, diversity, and interactions in soil play a crucial role in ecosystem functions. Viruses can regulate microbial communities and processes, but the understanding of their relationships with environmental conditions is lacking. Soil properties like organic matter and nitrate content influence viral and bacterial abundance and reproduction strategies. Land management and physicochemical properties shape bacterial community composition, while viral community composition is closely related to cover plants. This study sheds light on how environmental factors influence virus-host interactions in soil ecosystems.
APPLIED SOIL ECOLOGY
(2021)
Article
Microbiology
Sini Skariah, Sara Abdul-Majid, Anthony G. Hay, Anushree Acharya, Noora Kano, Raghad Khalid Al-Ishaq, Paul de Figueiredo, Arum Han, Adrian Guzman, Soha Roger Dargham, Saad Sameer, Gi Eun Kim, Sabiha Khan, Priyamvada Pillai, Ali A. Sultan
Summary: This study provides the first detailed characterization of the microbiota and chemistry in different arid habitats of Qatar. The dominant microbial phyla were Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi, though their abundances varied across soils. The study also found correlations between microbial diversity and soil characteristics such as sand, clay, and silt.
MICROBIOLOGY SPECTRUM
(2023)
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
Biochemistry & Molecular Biology
Nan Zhong, Yongzheng Ma, Xinyue Meng, Alphonse Sowanou, Liaowei Wu, Wei Huang, Yanhui Gao, Junrui Pei
Summary: This study investigates the impact of fluoride on fecal microbes, revealing a biphasic effect on gut microbiota in rats. Certain bacteria show significant associations with fluoride exposure and dental fluorosis. The results suggest that gut microbiota may play a crucial role in fluorosis and could potentially serve as biomarkers for the condition.
BIOLOGICAL TRACE ELEMENT RESEARCH
(2022)
Article
Environmental Sciences
Baichun Wang, Sixi Zhu, Wujiang Li, Qian Tang, Hongyu Luo
Summary: Wetland plants play a significant role in phytoremediation, with the rhizosphere microbial community showing a certain response to chromium stress. The study found that there was no significant difference in community structure of rhizosphere microorganisms after being affected, and approximately 10.48% of microbial community variation was caused by chromium stress.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Agriculture, Dairy & Animal Science
Nyaradzo Stella Chaora, Khulekani Sedwell Khanyile, Kudakwashe Magwedere, Rian Pierneef, Frederick Tawi Tabit, Farai Catherine Muchadeyi
Summary: This study utilized gene sequencing and bioinformatics analysis to determine mislabeling of processed meat products using the mitochondrial 16S ribosomal RNA gene. The results showed that pork was the major contaminant in most meat samples. This method can be used to authenticate meat products and manage mislabeling.
Article
Environmental Sciences
Masaaki Kitajima, Mercedes C. Cruz, Rohan B. H. Williams, Stefan Wuertz, Andrew J. Whittle
Summary: This study analyzed microbial communities in biofilm and water samples collected from a DWDS where monochloramine is used as a residual disinfectant. The study revealed differences in microbial species and abundance in different pipe sections representing different water ages, providing novel insights into the microbial ecology of DWDS.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
Vaidhegi Kugarajah, Sangeetha Dharmalingam
Summary: This study introduced silver as an effective additive in SPEEK membrane to reduce membrane biofouling in MFC. The incorporation of silver ions reduced biofilm formation, leading to the highest maximum power density from SPEEK + 7.5% Ag membrane after three months of MFC operation. Microbial community analysis identified microbes contributing to electron transfer.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Veterinary Sciences
Lee J. Pinnell, Arquimides A. Reyes, Cory A. Wolfe, Maggie D. Weinroth, Jessica L. Metcalf, Robert J. Delmore, Keith E. Belk, Paul S. Morley, Terry E. Engle
Summary: This study used 16S rRNA gene sequencing to investigate the composition and structure of microbial communities in the rumen of ruminants, and found significant differences in different regions of the rumen, which helps understand the influence of other environmental factors.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Annie Wing-Tung Lee, Chloe Toi-Mei Chan, Lily Lok-Yee Wong, Cheuk-Yi Yip, Wing-Tung Lui, Kai-Chun Cheng, Jake Siu-Lun Leung, Lam-Kwong Lee, Ivan Tak-Fai Wong, N. G. Timothy Ting-Leung, Hiu-Yin Lao, Gilman Kit-Hang Siu
Summary: Microbes in the built environment have been identified as a potential source of infectious diseases. The use of long-read taxonomic tools for microbial evaluations using nanopore sequencing has shown promising results. This study analyzed the performance of different taxonomic classifiers for microbial community analysis and provided recommendations for species-level classification and culturable species identification using 16S-nanopore dataset.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Cell Biology
Matthew C. Hibberd, Meng Wu, Dmitry A. Rodionov, Xiaoqing Li, Jiye Cheng, Nicholas W. Griffin, Michael J. Barratt, Richard J. Giannone, Robert L. Hettich, Andrei L. Osterman, Jeffrey I. Gordon
SCIENCE TRANSLATIONAL MEDICINE
(2017)
Article
Multidisciplinary Sciences
Carrie A. Cowardin, Philip P. Ahern, Vanderlene L. Kung, Matthew C. Hibberd, Jiye Cheng, Janaki L. Guruge, Vinaik Sundaresan, Richard D. Head, Daniela Barile, David A. Mills, Michael J. Barratt, Sayeeda Huq, Tahmeed Ahmed, Jeffrey I. Gordon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Jeanette L. Gehrig, Siddarth Venkatesh, Hao-Wei Chang, Matthew C. Hibberd, Vanderlene L. Kung, Jiye Cheng, Robert Y. Chen, Sathish Subramanian, Carrie A. Cowardin, Martin F. Meier, David O'Donnell, Michael Talcott, Larry D. Spears, Clay F. Semenkovich, Bernard Henrissat, Richard J. Giannone, Robert L. Hettich, Olga Ilkayeva, Michael Muehlbauer, Christopher B. Newgard, Christopher Sawyer, Richard D. Head, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Semen A. Leyn, Andrei L. Osterman, Md Iqbal Hossain, Munirul Islam, Nuzhat Choudhury, Shafiqul Alam Sarker, Sayeeda Huq, Inteaz Mahmud, Ishita Mostafa, Mustafa Mahfuz, Michael J. Barratt, Tahmeed Ahmed, Jeffrey I. Gordon
Article
Multidisciplinary Sciences
Arjun S. Raman, Jeanette L. Gehrig, Siddarth Venkatesh, Hao-Wei Chang, Matthew C. Hibberd, Sathish Subramanian, Gagandeep Kang, Pascal O. Bessong, Aldo A. M. Lima, Margaret N. Kosek, William A. Petri, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Semen A. Leyn, Andrei L. Osterman, Sayeeda Huq, Ishita Mostafa, Munirul Islam, Mustafa Mahfuz, Rashidul Haque, Tahmeed Ahmed, Michael J. Barratt, Jeffrey I. Gordon
Article
Microbiology
Ashley R. Wolf, Darryl A. Wesener, Jiye Cheng, Alexandra N. Houston-Ludlam, Zachary W. Beller, Matthew C. Hibberd, Richard J. Giannone, Samantha L. Peters, Robert L. Hettich, Semen A. Leyn, Dmitry A. Rodionov, Andrei L. Osterman, Jeffrey Gordon
CELL HOST & MICROBE
(2019)
Article
Multidisciplinary Sciences
Lihui Feng, Arjun S. Raman, Matthew C. Hibberd, Jiye Cheng, Nicholas W. Griffin, Yangqing Peng, Semen A. Leyn, Dmitry A. Rodionov, Andrei L. Osterman, Jeffrey I. Gordon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Medicine, General & Internal
Robert Y. Chen, Vanderlene L. Kung, Subhasish Das, M. Shabab Hossain, Matthew C. Hibberd, Janaki Guruge, Mustafa Mahfuz, S. M. Khodeza Nahar Begum, M. Masudur Rahman, Shah Mohammad Fahim, M. Amran Gazi, Rashidul Haque, Shafiqul A. Sarker, Ramendra N. Mazumder, Blanda Di Luccia, Kazi Ahsan, Elizabeth Kennedy, Jesus Santiago-Borges, Dmitry A. Rodionov, Semen A. Leyn, Andrei L. Osterman, Michael J. Barratt, Tahmeed Ahmed, Jeffrey I. Gordon
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Article
Medicine, General & Internal
Robert Y. Chen, Ishita Mostafa, Matthew C. Hibberd, Subhasish Das, Mustafa Mahfuz, Nurun N. Naila, M. Munirul Islam, Sayeeda Huq, M. Ashraful Alam, Mahabub U. Zaman, Arjun S. Raman, Daniel Webber, Cyrus Zhou, Vinaik Sundaresan, Kazi Ahsan, Martin F. Meier, Michael J. Barratt, Tahmeed Ahmed, Jeffrey Gordon
Summary: The study found that providing a microbiota-directed complementary food prototype (MDCF-2) to children with moderate acute malnutrition in Bangladeshi slums showed positive effects on growth, particularly in weight-for-length and weight-for-age z scores, with changes in plasma proteins related to bone growth and neurodevelopment. These findings suggest that targeted manipulation of microbiota components may be linked to growth outcomes in children with moderate acute malnutrition.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Article
Multidisciplinary Sciences
Hao-Wei Chang, Nathan P. McNulty, Matthew C. Hibberd, David O'Donnell, Jiye Cheng, Vincent Lombard, Bernard Henrissat, Olga Ilkayeva, Michael J. Muehlbauer, Christopher B. Newgard, Michael J. Barratt, Xi Lin, Jack Odle, Jeffrey Gordon
Summary: The study found that microbiomes associated with diet restriction have specific features in amino acid metabolism, which affect ponderal growth and health. Experimental colonization of gnotobiotic mice further confirmed the impact of microbiomes on host energy metabolism and the selection of energy substrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Omar Delannoy-Bruno, Chandani Desai, Arjun S. Raman, Robert Y. Chen, Matthew C. Hibberd, Jiye Cheng, Nathan Han, Juan J. Castillo, Garret Couture, Carlito B. Lebrilla, Ruteja A. Barve, Vincent Lombard, Bernard Henrissat, Semen A. Leyn, Dmitry A. Rodionov, Andrei L. Osterman, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Kyleigh Kirbach, Tara Wilmot, Andrew C. Heath, Samuel Klein, Michael J. Barratt, Jeffrey Gordon
Summary: Westernization has led to changing food preferences which have negative health effects, along with increased food insecurity. Dietary fiber intake is beneficial in preventing cardiovascular disease and obesity, but the complex nature of the gut microbiome makes it difficult to define how food ingredients affect its properties. This study aimed to design snacks with different fiber preparations to target specific components of the microbiome in individuals with obesity.
Editorial Material
Biochemistry & Molecular Biology
Robert Y. Chen, Ishita Mostafa, Matthew C. Hibberd, Subhasish Das, Hannah M. Lynn, Daniel M. Webber, Mustafa Mahfuz, Michael J. Barratt, Tahmeed Ahmed, Jeffrey I. Gordon
Article
Cell Biology
Michael J. Barratt, Sharika Nuzhat, Kazi Ahsan, Steven A. Frese, Aleksandr A. Arzamasov, Shafiqul Alam Sarker, M. Munirul Islam, Parag Palit, Md Ridwan Islam, Matthew C. Hibberd, Swetha Nakshatri, Carrie A. Cowardin, Janaki L. Guruge, Alexandra E. Byrne, Siddarth Venkatesh, Vinaik Sundaresan, Bethany Henrick, Rebbeca M. Duar, Ryan D. Mitchell, Giorgio Casaburi, Johann Prambs, Robin Flannery, Mustafa Mahfuz, Dmitry A. Rodionov, Andrei L. Osterman, David Kyle, Tahmeed Ahmed, Jeffrey Gordon
Summary: Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. An experiment found that giving B. infantis combined with LNT can increase the abundance of B. infantis subspecies in infants with severe acute malnutrition and promote weight gain, but the effect is still much lower than in healthy controls. A B. infantis strain, Bg_2D9, with superior fitness may have potential in treating malnourished infants.
SCIENCE TRANSLATIONAL MEDICINE
(2022)