Article
Environmental Sciences
Donlaporn Sripan, Alisa Wilantho, Khunnalack Khitmoh, Doonyapong Wongsawaeng, Jamal Ouazzani, Suchana Chavanich, Sissades Tongsima, Naraporn Somboonna
Summary: This study revealed microbiota and their metabolic potentials at an epipelagic depth in the southeast Andaman Sea of Thailand, showing significant differences between shallow and deep microbial communities.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Review
Dermatology
Samuel C. Williams, John W. Frew, James G. Krueger
Summary: Hidradenitis suppurativa is a chronic inflammatory skin disease with unknown pathogenesis. Recent studies using gene sequencing and culture have shed light on the microbial world of HS. Specific bacteria have been identified in HS lesions, but methodologies and analyses vary in current studies.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Biology
Modhi O. Alotaibi, Afrah E. Mohammed, Kamal H. Eltom
Summary: The current study aimed to assess possible changes in bacterial communities of the water at Wadi Namar Lake. The results showed variations in bacterial species and abundance between different locations, which were related to surrounding environmental factors. These findings are important for planning environmental protection and future restoration of affected ecosystems.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Immunology
Laure Flurin, Matthew J. Wolf, Melissa M. Mutchler, Matthew L. Daniels, Nancy L. Wengenack, Robin Patel
Summary: This study evaluated the addition of next-generation sequencing (NGS) to Sanger sequencing-based 16S rRNA gene PCR assay for diagnosing bacterial infection. The results showed that adding NGS substantially improved test positivity compared to Sanger sequencing alone. The assay incorporating NGS was more sensitive than culture, especially in patients who had received antibiotic therapy.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Immunology
Laure Flurin, Matthew J. Wolf, Melissa M. Mutchler, Matthew L. Daniels, Nancy L. Wengenack, Robin Patel
Summary: The addition of NGS to the Sanger sequencing-based 16S rRNA gene PCR assay significantly improved test positivity. The clinical sensitivity of the combined assay was higher than traditional culture, especially in patients who had received antibiotic therapy.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Philippe Bardou, Sandrine Laguerre, Sarah Maman Haddad, Sabrina Legoueix Rodriguez, Elisabeth Laville, Claire Dumon, Gabrielle Potocki-Veronese, Christophe Klopp
Summary: Functional metagenomics is a classical way to discover genes responsible for specific metabolic functions from uncultured bacteria, with hundreds of sequences already published in public databases. The MINTIA software package enables biologists to easily generate and analyze large metagenomic sequence sets retrieved after activity-based screening, improving research efficiency.
Article
Biodiversity Conservation
Paula Vico, Andres Iriarte, Sylvia Bonilla, Claudia Piccini
Summary: Raphidiopsis raciborskii, a toxic cyanobacteria, has defined biogeographic patterns attributed to ecotypes generated by local environmental filters and phenotypic plasticity. Different ecotypes of R. raciborskii exhibit distinct microbiomes, with varying dominant taxa and metabolic capabilities for nitrogen acquisition, suggesting ecotype-specific microbiomes play a role in cyanobacterial niche adaptation. Additionally, there is a hypothesis that saxitoxin-producing R. raciborskii benefits from external nitrogen sources provided by microbiome bacteria.
BIODIVERSITY DATA JOURNAL
(2021)
Article
Immunology
Hyo Lim Hong, Laure Flurin, Matthew J. Thoendel, Matthew J. Wolf, Matthew P. Abdel, Kerryl E. Greenwood-Quaintance, Robin Patel
Summary: This study compared the performance of 16S rRNA gene-based targeted metagenomic sequencing (tNGS) and shotgun metagenomic sequencing (sNGS) in detecting and identifying pathogens in sonicate fluid from failed total hip arthroplasty (THA) and total knee arthroplasty (TKA). The study found that tNGS had a higher positive percent agreement with sonicate fluid culture compared to sNGS, and detected potential pathogens in culture-negative PJIs. The study concludes that tNGS is a potential diagnostic tool for identifying PJI pathogens in sonicate fluid, with similar performance characteristics to sNGS.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Microbiology
Laure Flurin, Matthew J. Wolf, Cody R. Fisher, Edison J. Cano Cevallos, James J. Vaillant, Bobbi S. Pritt, Daniel C. DeSimone, Robin Patel
Summary: This prospective pilot study evaluated the use of targeted metagenomic sequencing (tMGS) for early pathogen detection and identification in infective endocarditis (IE). The results indicate that blood-based tMGS may provide pathogen identification in subjects with IE, including culture-negative cases.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Hiroshi Mori, Tamotsu Kato, Hiroaki Ozawa, Mitsuo Sakamoto, Takumi Murakami, Todd D. Taylor, Atsushi Toyoda, Moriya Ohkuma, Ken Kurokawa, Hiroshi Ohno
Summary: To understand the biases in human gut microbiome studies, a reference microbiome composed of an artificial mock community is crucial. However, there is a lack of suitable mock communities that accurately represent the human gut microbiome. In this study, we created a novel mock community consisting of 18 major bacterial species found in the human gut and examined the impact of experimental and bioinformatics procedures on 16S rRNA gene and shotgun metagenomic sequencing. Our findings revealed that DNA extraction methods significantly influenced DNA yields and taxonomic composition of sequenced reads and certain commonly used primers for 16S rRNA genes led to underestimation of certain gut commensal taxa. Additionally, we demonstrated that the binning of shotgun metagenomic sequences using MetaBAT2 produced consistent, less-contaminated bins with varying completeness. The use of multiple binning tools with MetaWRAP improved completeness but sometimes increased contamination rate. This benchmark study provides a crucial foundation for interpreting human gut microbiome data, allowing for standardization among different methodologies, and facilitating the advancement of analytical methods.
Article
Biotechnology & Applied Microbiology
Todd Testerman, Lidia Beka, Emily Ann McClure, Stephen R. Reichley, Stacy King, Timothy J. Welch, Joerg Graf
Summary: In this study, two independent assays for detecting fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum in environmental samples were presented. Both methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. These methods can serve as useful tools for surveillance efforts in aquaculture facilities.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Horticulture
Hongfei Li, Fang Song, Xiaoxiao Wu, Chongling Deng, Qiang Xu, Shu'ang Peng, Zhiyong Pan
Summary: The study identified significant changes in rhizosphere and root bacterial genera in response to CLas infection, with particular impacts on carbohydrate metabolism and phosphoinositide signaling pathways.
Article
Multidisciplinary Sciences
Daisy Vanitha John, Meera Purushottam
Summary: A brain abscess is a collection of pus in the brain parenchyma surrounded by a capsule in response to an infection. The microbiome of brain abscesses is polymicrobial, consisting of uncultivable and anaerobic bacteria. This article provides bacterial 16S rRNA gene sequences from three culture-negative brain abscess samples, revealing the presence of different bacterial species. The data can be used for further research on comparative genomics and management of culture-negative brain abscesses.
Article
Microbiology
Laure Flurin, Joseph J. Hemenway, Cody R. Fisher, James J. Vaillant, Marisa Azad, Matthew J. Wolf, Kerryl E. Greenwood-Quaintance, Matthew P. Abdel, Robin Patel
Summary: Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. In this study, the accuracy of a 16S rRNA gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PM diagnosis was analyzed. The results showed that the sequencing-based approach did not have a significant advantage over conventional culture for diagnosing PJI, but yielded positive results in some culture-negative samples.
Article
Soil Science
C. Beraud, F. Piola, J. Gervaix, G. Meiffren, C. Creuze des Chatelliers, A. Delort, C. Boisselet, S. Poussineau, E. Lacroix, A. A. M. Cantarel
Summary: This study investigated the soil factors influencing the development of biological denitrification inhibition (BDI) and found that initial soil moisture, ammonium concentration, and the initial abundance of certain microbial genes play significant roles in BDI development. Additionally, the research highlighted the relevance of biotic factors in explaining BDI and proposed the use of procyanidin concentration from plant belowground system as a new proxy for measuring BDI intensity.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Yizhu Qiao, Tingting Wang, Qiwei Huang, Hanyue Guo, He Zhang, Qicheng Xu, Qirong Shen, Ning Ling
Summary: Soil microbial community coalescence, the mixing and interaction of microbial communities, has been found to enhance the stability and complexity of rhizobacterial networks, leading to improved plant health and biomass. This study investigated the effects of different degrees of bacterial community coalescence on plant disease resistance by mixing soils from healthy and diseased habitats for watermelon planting. The results showed that mixing in more healthy soil reduced the plant disease index and increased biomass by improving the stability and complexity of the rhizobacterial network. Core taxa Nitrospirillum and Singulisphaera were enriched in the rhizosphere from healthy soils and played important roles in disease suppression and regulating the positive cohesion and modularity of the networks. Overall, these findings provide insights into the potential mechanism of microbial community coalescence for improving plant microbial community function and suggest new tools for enhancing plant fitness via soil microbiota mixing.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Mengqiu He, Shending Chen, Lei Meng, Xiaoqian Dan, Wenjie Wang, Qinying Zhu, Zucong Cai, Jinbo Zhang, Pierfrancesco Nardi, Christoph Mueller
Summary: Maize genotypes directly affect gene expression and nitrogen uptake capacity. The feedback between maize genotypes and soil nitrogen transformations, as well as their regulations on nitrogen uptake capacity, have been studied. The findings suggest that maize genotypes play a central role in regulating these feedbacks, which are important for maize breeding and enhancing maize production.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Ke Shi, Jiahui Liao, Xiaoming Zou, Han Y. H. Chen, Manuel Delgado-Baquerizo, Zhengming Yan, Tingting Ren, Honghua Ruan
Summary: Through rewilding, microbial extracellular and cellular residues can continuously accumulate in soils and significantly contribute to soil organic carbon sequestration. Extracellular residues are mainly driven by fine root biomass, while cellular residues are mainly driven by soil nitrogen and organic carbon content.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Sensen Chen, Ying Teng, Yongming Luo, Eiko Kuramae, Wenjie Ren
Summary: This study comprehensively assesses the effects of NMs on the soil microbiome through a global meta-analysis. The results reveal significant negative impacts of NMs on soil microbial diversity, biomass, activity, and function. Metal NMs, especially Ag NMs, have the most pronounced negative effects on various soil microbial community metrics.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Shareen K. D. Sanders, Gerard Martinez-De Leon, Ludovico Formenti, Madhav P. Thakur
Summary: Collembolans, the diverse group of soil invertebrates, are affected by anthropogenic climate warming, which alters their diversity and density. In addition to abiotic stressors, changes in food availability, specifically the abundance of saprotrophic and mycorrhizal fungi, influence Collembola responses to climate warming. Collembolans prefer saprotrophic fungi but rely on mycorrhizal fungi when food sources are scarce. Understanding the mechanisms behind these dietary shifts in warm-dry and warm-wet soil conditions is crucial for predicting the impact of climate change on Collembola-fungal interactions.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Wimonsiri Pingthaisong, Sergey Blagodatsky, Patma Vityakon, Georg Cadisch
Summary: A study found that mixing high-C/N ratio rice straw with low-C/N ratio groundnut stover can improve the chemical composition of the input, stimulate microbial growth, decrease the loss of residue-derived carbon in the soil, and reduce native soil carbon and nitrogen consumption.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Jiachen Wang, Jie Zhao, Rong Yang, Xin Liu, Xuyuan Zhang, Wei Zhang, Xiaoyong Chen, Wende Yan, Kelin Wang
Summary: Nitrogen is vital for ecosystem productivity, restoration, and succession processes. This study found that legume intercropping was more effective than chemical nitrogen fertilizers in promoting the complexity and stability of the soil micro-food web, as it increased microbial and nematode communities and enhanced energy flow patterns.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)