Article
Ecology
Olivia E. Mosley, Emilie Gios, Murray Close, Louise Weaver, Chris Daughney, Kim M. Handley
Summary: The nitrogen cycle plays a crucial role in aquatic ecosystems, including the subsurface. However, the diversity of nitrogen transformations in these environments is not well understood. This study investigated how nitrogen cycling microorganisms respond to different groundwater chemistries. The results showed that regardless of site-specific conditions, nitrogen cycling mechanisms were prevalent and highly redundant in groundwater communities. The study also revealed the presence of oxic-anoxic interfaces and potential synergistic interactions between microorganisms at these interfaces. The findings provide insights into cooperative relationships in groundwater communities and the complexity of metabolic mechanisms leading to nitrogen loss.
Article
Engineering, Environmental
Xiaomin Wang, Bangrui Lan, Hexin Fei, Shanyun Wang, Guibing Zhu
Summary: This study found abundant and diverse ARGs in subsurface soils, with significant spatial heterogeneity among sampling sites. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, potentially triggering antibiotic resistance by increasing mobile genetic elements abundance or influencing bacterial communities.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Oluwadara Alegbeleye, Anderson S. Sant'Ana
Summary: Some serotypes of Escherichia coli are important human pathogens, causing diarrhea or life-threatening diseases. E. coli is commonly used as an indicator microorganism to assess water quality, especially for fecal contamination. This study investigated the survival of six E. coli strains in sandy and loam soil, as well as the impact of biochar amendment on their survival. The results showed that the survival of E. coli strains varied according to soil type and biochar amendment, with better survival in loam soil.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Qianxian He, Jingyu Li, Yongkai Ma, Qi Chen, Gu Chen
Summary: The study is the first report on probiotic screening and characterization of bacteria from PCR-Chachiensis, revealing some bacteria with cholesterol-lowering potential and carbohydrate utilization capability.
Article
Microbiology
Jennifer L. Goff, Elizabeth G. Szink, Michael P. Thorgersen, Andrew D. Putt, Yupeng Fan, Lauren M. Lui, Torben N. Nielsen, Kristopher A. Hunt, Jonathan P. Michael, Yajiao Wang, Daliang Ning, Ying Fu, Joy D. Van Nostrand, Farris L. Poole, John-Marc Chandonia, Terry C. Hazen, David A. Stahl, Jizhong Zhou, Adam P. Arkin, Michael W. W. Adams
Summary: Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from a highly contaminated area in the Oak Ridge Reservation (ORR) subsurface. The 16S rRNA gene sequencing revealed a variant with 100% identity to the CPTF sequence, which had the highest relative abundance in the community survey. Pangenomic analysis showed that CPTF has expanded genomic content due to plasmid acquisition and expansion of transposable elements, suggesting their importance in adapting to environmental stressors.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Sciences
Xiang Ning, Shengli Wang, Baojin Zhao, Song Long, Yuqing Wang, Zhongren Nan
Summary: This study aimed to remediate As pollution in arid soils by selecting native bacterial strains and adding Fe(II). Results showed that FeOB strains effectively removed As(III) through the oxidation of Fe(II) process, forming adsorption and co-precipitation of Fe(OH)(3), and potentially fixing NH4+.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Jeffrey D. Palumbo, Teresa L. O'Keeffe, Steven Huynh, Bertram Lee, Craig T. Parker
Summary: The complete genome sequences of Bacillus velezensis strains JP3042 and JP3144, isolated from California raisin vineyard soils, are presented to aid in the understanding of their antifungal activity and diversity within the species.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Plant Sciences
Aitana Ares, Marta Tacao, Daniela Figueira, Eva Garcia, Joana Costa
Summary: This study reported the draft genome of six strains of Pseudomonas syringae pv. actinidiae isolated from kiwifruit symptomatic leaves in Portugal, revealing genetic diversity within the population. The data suggests that there was genomic diversification following the clonal expansion of P. syringae pv. actinidiae in Europe.
Article
Microbiology
Angelina A. Kislichkina, Mikhail E. Platonov, Yury P. Skryabin, Angelika A. Sizova, Lidia A. Shishkina, Elena Galkina, Alexandr G. Bogun, Svetlana Dentovskaya
Summary: In this study, we reported the draft genome sequences of six Yersinia kristensenii strains, which will contribute to a better understanding of the genomic characteristics of this species.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Ahmed Adel Hamza, Ozlem Abaci Gunyar
Summary: In this study, different Rhizopus strains were isolated and tested for their probiotic potential and fermentative capacity. Three strains were found to have good probiotic properties and fermentative capacities, which could be beneficial for the poultry industry.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Zhijing Xue, Yuanhai You, Lihua He, Yanan Gong, Lu Sun, Xiurui Han, Ruyue Fan, Kangle Zhai, Yaming Yang, Maojun Zhang, Xiaomei Yan, Jianzhong Zhang
Summary: In this study, 503 CagA sequences were analyzed, revealing that most H. pylori strains in the Chinese population were of the CagA-ABD subtype, which was associated with gastroduodenal diseases. Amino acid polymorphisms at residues 893 and 894 flanking the EPIYA motifs were found to have a statistically significant association with gastric cancer.
Article
Microbiology
Adrien Biessy, Marie Ciotola, Melanie Cadieux, Daphne Albert, Martin Filion
Summary: Two Chryseobacterium strains, B21-013 and B21-037, were isolated from agricultural soils in Quebec, Canada, as part of a screening for beneficial bacteria that can suppress lettuce bacterial pathogens. The genome sequences of these two strains are reported.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Infectious Diseases
Suganya Yongkiettrakul, Thidathip Wongsurawat, Piroon Jenjaroenpun, Daniel A. Acheampong, Potjanee Srimanote, Krissana Maneerat, Wonnop Visessanguan, Intawat Nookaew
Summary: Genomic analysis of antibiotic-resistant Streptococcus suis strains isolated in Thailand showed genetic relatedness to strains from other countries and revealed genes associated with aminoglycoside, macrolide, and fluoroquinolone resistance. This study provides further resources for future genomic epidemiological investigations of S. suis.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Microbiology
Tyson Bookout, Kira L. Goff, Jeff Gauthier, Roger C. Levesque, Shawn Lewenza
Summary: This study reports the draft genomes of six bacterial strains isolated from Cannabis rhizosphere soil samples, providing molecular-level insights into plant-microbe interactions in the Cannabis rhizosphere.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Susanna Sagerfors, Anja Poehlein, Bo Soderquist, Holger Bruggemann
Summary: Corynebacterium macginleyi is a slow-growing, lipid-requiring bacterium that can cause ocular infections. The complete genome sequences of two strains, T160811 and T180208, isolated from infectious keratitis, consist of circular chromosomes with high numbers of repetitive elements.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Ecology
Jan Hubert, Marta Nesvorna, Marie Bostlova, Bruno Sopko, Stefan J. Green, Thomas W. Phillips
Summary: Arthropods can host microbial communities that can degrade pesticides and confer tolerance to pests. This study compared two cultures of the stored-product mite Tyrophagus putrescentiae, one with a symbiotic microbiome containing Wolbachia and the other without Wolbachia, on pesticide residue-containing diets. Results showed that pesticide residues affected the composition of the mite microbiomes but did not show any significant trend for mite cultures with and without Wolbachia. The bacterial taxa Bartonella-like and Bacillus were most influenced in both cultures and Wolbachia was influenced in the culture containing this symbiont. However, there was no direct evidence of Wolbachia's effect on pesticide tolerance. The study suggests that pesticide residues affect the microbiomes of mites but do not have a systemic detoxification effect.
Article
Microbiology
Amruta Joglekar, Yogesh Nimonkar, Abhay Bajaj, Om Prakash
Summary: This study assessed the taxonomic resolution and variation among strains of W. confusa and W. cibaria using phenetic and molecular methods. The analysis revealed significant genomic variability and biochemical differences among the strains, highlighting the need for additional analysis methods to provide better taxonomic resolution in the Weissella group.
JOURNAL OF BASIC MICROBIOLOGY
(2023)
Article
Astronomy & Astrophysics
Stefan J. Green, Tamas Torok, Jonathan E. Allen, Emiley Eloe-Fadrosh, Scott A. Jackson, Sunny C. Jiang, Stuart S. Levine, Shawn Levy, Lynn M. Schriml, W. Kelley Thomas, Jason M. Wood, Scott W. Tighe
Summary: Molecular biology methods and technologies have advanced significantly, and NASA conducted a technology workshop to assess the feasibility of incorporating these methods into planetary protection. The workshop focused on modernizing and supplementing current assays and recommended metagenomics approaches as a revolutionary advance. Implementing metagenomics as an additional workflow will dramatically improve technology advancement for planetary protection.
Article
Microbiology
Om Prakash, Jeremy A. Dodsworth, Xiuzhu Dong, James G. Ferry, Stephane L'Haridon, Hiroyuki Imachi, Yoichi Kamagata, Sung-Keun Rhee, Isita Sagar, Viktoria Shcherbakova, Dirk Wagner, William B. Whitman
Summary: Methanogenic archaea are diverse prokaryotes capable of producing methane as their main product. With advancements in technology, taxonomy criteria for these archaea need to be revised. The previously recommended minimum standards for phenotypic characterization of pure cultures are mostly maintained. Obtaining whole genome sequences for type strains and comparing them with close relatives using genomic indices is now mandatory. Additionally, culture purity is not essential and alternative methods like single-cell or metagenomics can be used for taxonomic description.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew B. Conley, Lavanya Rishishwar, Maria Ahmad, Shivam Sharma, Emily T. Norris, I. King Jordan, Leonardo Marino-Ramirez
Summary: Biobank projects generate genomic data for thousands of individuals, requiring computational methods such as genetic ancestry inference tools. Current methods do not scale to biobank-sized datasets. The Rye algorithm was developed for scalable genetic ancestry inference, outperforming existing programs in accuracy and runtime performance on a dataset from the UK Biobank. Rye utilizes principal component analysis and optimization techniques to estimate genetic ancestry at both continental and subcontinental levels.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biotechnology & Applied Microbiology
Asmita Pramanic, Shreyansh Sharma, Manikprabhu Dhanorkar, Om Prakash, Pooja Singh
Summary: Microbial communities associated with aquatic plants, especially bacteria, play a crucial role in bioremediation and herbicidal effects. Further research is needed to explore the potential of these microorganisms for novel functions and to control aquatic weed problems effectively.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Medical Laboratory Technology
Bernard J. Wolff, Anna Gaines, Andrew B. Conley, Emily Norris, Lavanya Rishishwar, Aroon T. Chande, Eungi Yang, Maureen H. Diaz, Jonas M. Winchell
Summary: We developed a new multiplex real-time PCR assay for the detection and differentiation of Chlamydia species, including Chlamydia psittaci and Chlamydia pneumoniae, in human clinical specimens. The assay was validated using a panel of culture isolates and various clinical specimens, showing 100% specificity and a high limit of detection. This assay has the potential to improve the clinical diagnosis of Chlamydia infections and enhance our understanding of the burden of disease caused by these pathogens.
ANNALS OF LABORATORY MEDICINE
(2023)
Article
Multidisciplinary Sciences
Wieteke A. Holthuijzen, Elizabeth N. Flint, Stefan J. Green, Jonathan H. Plissner, Daniel Simberloff, Dagmar Sweeney, Coral A. Wolf, Holly P. Jones
Summary: The study used next-generation sequencing and stable isotope analysis to investigate the diet of house mice on Sand Island. The results showed that the mice mainly consumed arthropods and also fed on detrital-feeding arthropods in and around seabird carcasses. Most of the arthropods and plants consumed by the mice were non-native. The study also found that the mouse diet composition varied among habitat types but remained stable throughout the year.
Article
Engineering, Environmental
Young Gwang Kim, Sae Yun Kwon, Spencer J. Washburn, Scott C. Brooks, Ji Won Yoon, Lucien Besnard
Summary: The study uses Hg isotope ratios to identify the sources and exposure pathways of mercury in bivalves, finding that dissolved Hg phases in the water column are the primary source and exposure pathway to bivalves. This provides new insights into using bivalves as bioindicators for sediment quality monitoring.
Article
Genetics & Heredity
I. King Jordan, Shivam Sharma, Leonardo Marino-Ramirez
Summary: Health equity means ensuring equal opportunity for everyone to achieve optimal health. In the field of pharmacogenomics, genetic differences in how patients respond to medications can inform treatment decisions. Population pharmacogenomics studies the variations within and between human populations, and it can help promote fairness in patient treatments and outcomes. Racial and ethnic groups exhibit significant differences in the frequencies of pharmacogenomic variants, which have direct implications for clinical practice.
Article
Pharmacology & Pharmacy
Shivam Sharma, Leonardo Marino-Ramirez, I. King Jordan
Summary: The relevance of race and ethnicity to genetics and medicine is debated. This study evaluated the relationship between race, ethnicity, and clinically relevant pharmacogenomic variation. The results show that pharmacogenomic variation can predict race and ethnicity, indicating their importance in treatment decisions.
Article
Microbiology
Supriya D. Mehta, Walter Agingu, Garazi Zulaika, Elizabeth Nyothach, Runa Bhaumik, Stefan J. Green, Anna Maria van Eijk, Fredrick O. Otieno, Penelope A. Phillips-Howard, John Schneider
Summary: A non-optimal vaginal microbiome (VMB) is associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). This study compared the VMB of Kenyan girls with incident STIs to those who remained negative, and found that VMB networks of those with STI had less connectedness. Key taxa differed between those with and without STI and were not correlated with abundance. Sociodemographic and behavioral factors contribute to microbial network structure.
Article
Mathematical & Computational Biology
Shashwat Deepali Nagar, I. King Jordan, Leonardo Marino-Ramirez
Summary: The UK Biobank (UKB) is a large-scale biomedical database that holds demographic and electronic health record data for over 500,000 participants of diverse ethnic backgrounds, which could be a valuable resource for studying health disparities. However, there are no publicly accessible databases that catalog health disparities within the UKB. To address this, we developed the UKB Health Disparities Browser to facilitate exploration of health disparities in the UK and bring attention to areas of research with significant public health impact.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Letter
Multidisciplinary Sciences
Leonardo Marino-Ramirez, Eliseo J. Perez-Stable, I. King Jordan
