Article
Biochemistry & Molecular Biology
Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
Summary: Advances in sequencing technology have enabled in-depth profiling of microbial communities through pan-genome and metagenome analysis. The combination of pan-genome and metagenome approaches is seen as a promising method for tracking microbial sources and deciphering population-level evolution. Advanced analytical techniques, including big-data based artificial intelligence, are expected to further enhance our understanding of microbial community patterns.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Microbiology
Zhichao Zhou, Patricia Q. Tran, Adam M. Breister, Yang Liu, Kristopher Kieft, Elise S. Cowley, Ulas Karaoz, Karthik Anantharaman
Summary: Advances in microbiome science have been driven by the ability to study and infer microbial ecology from genomes. METABOLIC is a scalable software that allows for the study of microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. It provides annotation of microbial genomes, metabolic pathway analyses, and determination of microbial contributions to biogeochemical transformations and cycles. METABOLIC is a versatile tool that can be used with various metagenomic datasets, from diverse environments such as marine subsurface, terrestrial subsurface, and human gut.
Article
Multidisciplinary Sciences
Kie Kumaishi, Erika Usui, Kenta Suzuki, Shungo Kobori, Takumi Sato, Yusuke Toda, Hideki Takanashi, Satoshi Shinozaki, Munehiro Noda, Akiko Takakura, Kayoko Matsumoto, Yuji Yamasaki, Hisashi Tsujimoto, Hiroyoshi Iwata, Yasunori Ichihashi
Summary: Microbiota play a significant role in agroecosystems, especially the root microbiota in plant growth and health. We have improved the sample handling efficiency of 16S rRNA gene sequencing for plant root microbiota by optimizing DNA extraction and PCR purification steps. Our method enables the capture of microbial diversity comparable to manual methods and generates comparable microbiome profile data as commonly used DNA extraction kits. It provides a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Ilona den Hartog, Laura B. Zwep, Stefan M. T. Vestjens, Amy C. Harms, G. Paul Voorn, Dylan W. de Lange, Willem J. W. Bos, Thomas Hankemeier, Ewoudt M. W. van de Garde, J. G. Coen van Hasselt
Summary: Diagnosis of microbial disease etiology in hospitalized CAP patients can be supported by targeted metabolomic profiling, with the ability to differentiate between major pathogen groups such as S. pneumoniae, atypical bacteria, and respiratory viruses. Discrimination between atypical pathogens and other groups showed predictive capability, with an elastic net regression model achieving 61% sensitivity, 86% specificity, and an AUC of 0.81.
Article
Environmental Sciences
Naeun Kim, Yongtae Ahn, Jungman Jo, Heesoo Pyo, Jeongae Lee, Jaeyoung Choi
Summary: This study investigated the effects of accidental contamination of soils with various chemicals, and found that phytosphingosine and Sphingomonas could potentially serve as biomarkers to evaluate soil contamination. Rain played an important role in the recovery of microbial and metabolic profiles after chemical accidents.
Article
Agricultural Engineering
Geer An, Rong Yan, Zhimin Fu, Zepeng Chen, Yaru Guo, Jun Yang, Yongheng Zhou
Summary: The purpose of this study was to investigate the tolerance mechanism of anammox consortia in a microbial fuel cell (MFC) system at low temperature. The data showed that a total nitrogen removal of nearly 80% was achieved after the temperature dropped from 30°C to 15°C. The nitrogen removal rate of the system decreased by 26.3% at 15°C, indicating the impact of low temperature on the performance.
BIORESOURCE TECHNOLOGY
(2023)
Article
Oncology
Yi Wang, Dingding Qu, Yali Zhang, Yiping Jin, Yu Feng, He Zhang, Qingxin Xia
Summary: This study analyzed the microbial community composition in different subtypes of breast cancer and found that the microbe Turicibacter was more abundant in triple-negative breast cancer (TNBC). Furthermore, significant correlations were observed between the intra-tumoral microbiome, clinicopathological characteristics, and HER2 expression. This study provides insights into potential diagnostic biomarkers, therapeutic strategies, and early clinical diagnosis of TNBC.
FRONTIERS IN ONCOLOGY
(2023)
Article
Food Science & Technology
Paola Foti, Nunziatina Russo, Cinzia L. Randazzo, Altino Branco Choupina, Alessandra Pino, Cinzia Caggia, Flora V. Romeo
Summary: In this study, different microbial strains were used to ferment the pâte à olive cake (POC), a by-product of olive oil processing. The fermentation process was influenced by the strains used, which led to increased hydroxytyrosol content. Analysis of the microbial community revealed a decrease in acetic acid bacteria and an increase in Lactobacillaceae biodiversity at the end of fermentation. However, there was no significant effect on the fungal metagenomic profile.
Article
Biochemical Research Methods
Kristen D. Curry, Qi Wang, Michael G. Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, Tor Savidge, Sonia Villapol, Alexander Dilthey, Todd J. Treangen
Summary: 16S ribosomal RNA-based analysis is the standard method for studying microbial community composition. Full-length 16S rRNA gene sequences have the potential to provide species-level accuracy. Emu is an approach that can generate taxonomic abundance profiles from full-length 16S rRNA reads, accurately estimating microbial abundance.
Article
Microbiology
Pooja Sharma, Surendra Pratap Singh
Summary: This study aims to identify microbial communities in pulp and paper industry sludge and analyze their metagenomics profiling. The results show that the dominant phyla in the sludge include Anaerolinea, Pseudomonas, Clostridia, Bacteroidia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae, and some unknown microbial strains. Metagenomics is a useful tool for evaluating microbiota composition and function using gene sequencing. This research highlights the potential of using naturally adapted microorganisms for sludge treatment in the open environment.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Masahito Hosokawa, Taruho Endoh, Kazuma Kamata, Koji Arikawa, Yohei Nishikawa, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Haruko Takeyama
Summary: In this study, a method called PMA-SAG-gel was presented for viable bacteria-targeted single-cell genome sequencing. This method uses gel matrixes to selectively sequence the viable bacteria in microbial communities, removing interference from non-viable bacteria. The method was demonstrated to successfully recover near-complete genomes of oxygen-tolerant bacteria from human feces samples.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
J. L. Wood, W. C. Neil, S. A. Wade
Summary: The study found significant temporal and spatial variations in bacterial communities in ship bilges, mainly influenced by disturbance events such as cleaning and maintenance. Sessile and pelagic bacterial communities within the same bilge were notably distinct, with taxa associated with MIC functions prevalent in sessile communities. The research highlights the importance of developing standardized protocols for sampling and monitoring bilge biology to aid in the diagnosis and monitoring of MIC.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Food Science & Technology
Ting Mi, Yao Jin, Yulan Che, Jun Huang, Rongqing Zhou, Chongde Wu
Summary: Pellicle formation is a clear indicator of spoilage in fermented vegetables, leading to a loss of flavor. This study compared the microbial diversity and function between pellicle-forming and normal fermented radish paocai. The main microorganisms involved in pellicle formation were Yarrowia spp., Enterobacter spp., and Pichia spp., while certain components were responsible for the unpleasant flavor. The growth of Yarrowia lipolytica promoted an increase in pH and pellicle formation, creating a suitable environment for the growth of harmful bacteria and contributing to the changes in odor and texture of the fermented food.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Yu Miao, Monica B. Heintz, Caitlin H. Bell, Nicholas W. Johnson, Alexandra LaPat Polasko, David Favero, Shaily Mahendra
Summary: The study found that enhancing the degradation of 1,4-dioxane by adding nutrients resulted in increased expression of specific genes, leading to the degradation of organic pollutants and affecting the structure and function of microbial communities. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they continued to degrade 1,4-dioxane through indigenous propanotrophic and heterotrophic bacteria. Functional redundancy acted as a buffer capacity to ensure a stable microbiome and drove the restoration of microbial functions to original levels.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Xu Yang, Jin-long Lai, Yu Zhang, Xue-gang Luo, Meng-wei Han, San-ping Zhao
Summary: This experiment evaluated the ecotoxicity of typical explosives on soil microenvironment and their impact on soil enzyme activity, microbial community structure, and function. The results showed that explosives significantly inhibited soil microbial respiration, reduced microbial diversity, and richness, leading to the dominance of specific microorganisms able to degrade explosives. The non-targeted metabonomics analysis revealed that explosives residues in soil can inhibit soil metabolic processes and alter the soil microbial community structure.
ENVIRONMENTAL POLLUTION
(2021)
